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  Subjects -> BIOLOGY (Total: 3310 journals)
    - BIOCHEMISTRY (255 journals)
    - BIOENGINEERING (130 journals)
    - BIOLOGY (1577 journals)
    - BIOPHYSICS (49 journals)
    - BIOTECHNOLOGY (259 journals)
    - BOTANY (245 journals)
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    - ENTOMOLOGY (73 journals)
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    - MICROBIOLOGY (270 journals)
    - MICROSCOPY (10 journals)
    - ORNITHOLOGY (28 journals)
    - PHYSIOLOGY (72 journals)
    - ZOOLOGY (143 journals)

BIOLOGY (1577 journals)                  1 2 3 4 5 6 7 8 | Last

Showing 1 - 200 of 1720 Journals sorted alphabetically
AAPS Journal     Hybrid Journal   (Followers: 29)
Achievements in the Life Sciences     Open Access   (Followers: 7)
ACS Pharmacology & Translational Science     Hybrid Journal   (Followers: 1)
ACS Synthetic Biology     Hybrid Journal   (Followers: 25)
Acta Biologica Colombiana     Open Access   (Followers: 7)
Acta Biologica Hungarica     Full-text available via subscription   (Followers: 4)
Acta Biologica Sibirica     Open Access   (Followers: 2)
Acta Biologica Turcica     Open Access  
Acta Biologica Venezuelica     Open Access  
Acta Biomaterialia     Hybrid Journal   (Followers: 30)
Acta Biotheoretica     Hybrid Journal   (Followers: 4)
Acta Chiropterologica     Full-text available via subscription   (Followers: 6)
acta ethologica     Hybrid Journal   (Followers: 4)
Acta Fytotechnica et Zootechnica     Open Access   (Followers: 1)
Acta Limnologica Brasiliensia     Open Access   (Followers: 4)
Acta Médica Costarricense     Open Access   (Followers: 2)
Acta Musei Silesiae, Scientiae Naturales     Open Access   (Followers: 1)
Acta Neurobiologiae Experimentalis     Open Access  
Acta Parasitologica     Hybrid Journal   (Followers: 11)
Acta Scientiarum. Biological Sciences     Open Access   (Followers: 2)
Acta Scientifica Naturalis     Open Access   (Followers: 2)
Acta Universitatis Agriculturae et Silviculturae Mendelianae Brunensis     Open Access   (Followers: 1)
Actualidades Biológicas     Open Access   (Followers: 1)
Advanced Health Care Technologies     Open Access   (Followers: 8)
Advanced Journal of Graduate Research     Open Access  
Advanced Nonlinear Studies     Hybrid Journal  
Advanced Studies in Biology     Open Access  
Advances in Antiviral Drug Design     Full-text available via subscription   (Followers: 2)
Advances in Bioinformatics     Open Access   (Followers: 20)
Advances in Biological Regulation     Hybrid Journal   (Followers: 4)
Advances in Biology     Open Access   (Followers: 12)
Advances in Cell Biology/ Medical Journal of Cell Biology     Open Access   (Followers: 30)
Advances in Cellular and Molecular Biology of Membranes and Organelles     Full-text available via subscription   (Followers: 14)
Advances in Developmental Biology     Full-text available via subscription   (Followers: 13)
Advances in DNA Sequence-Specific Agents     Full-text available via subscription   (Followers: 7)
Advances in Ecological Research     Full-text available via subscription   (Followers: 44)
Advances in Environmental Sciences - International Journal of the Bioflux Society     Open Access   (Followers: 17)
Advances in Enzyme Research     Open Access   (Followers: 11)
Advances in Experimental Biology     Full-text available via subscription   (Followers: 8)
Advances in Genome Biology     Full-text available via subscription   (Followers: 11)
Advances in High Energy Physics     Open Access   (Followers: 22)
Advances in Human Biology     Open Access   (Followers: 4)
Advances in Life Science and Technology     Open Access   (Followers: 18)
Advances in Life Sciences     Open Access   (Followers: 6)
Advances in Marine Biology     Full-text available via subscription   (Followers: 21)
Advances in Molecular and Cell Biology     Full-text available via subscription   (Followers: 25)
Advances in Organ Biology     Full-text available via subscription   (Followers: 2)
Advances in Planar Lipid Bilayers and Liposomes     Full-text available via subscription   (Followers: 3)
Advances in Space Biology and Medicine     Full-text available via subscription   (Followers: 6)
Advances in Structural Biology     Full-text available via subscription   (Followers: 5)
Advances in Tropical Biodiversity and Environmental Sciences     Open Access   (Followers: 1)
Advances in Virus Research     Full-text available via subscription   (Followers: 6)
African Journal of Range & Forage Science     Hybrid Journal   (Followers: 8)
AFRREV STECH : An International Journal of Science and Technology     Open Access   (Followers: 2)
Ageing Research Reviews     Hybrid Journal   (Followers: 12)
Aging Cell     Open Access   (Followers: 25)
Agrokémia és Talajtan     Full-text available via subscription   (Followers: 2)
Agrokreatif Jurnal Ilmiah Pengabdian kepada Masyarakat     Open Access  
AJP Cell Physiology     Hybrid Journal   (Followers: 18)
AJP Endocrinology and Metabolism     Hybrid Journal   (Followers: 24)
AJP Lung Cellular and Molecular Physiology     Hybrid Journal   (Followers: 3)
Al-Kauniyah : Jurnal Biologi     Open Access  
Alasbimn Journal     Open Access   (Followers: 2)
Alces : A Journal Devoted to the Biology and Management of Moose     Open Access  
AMB Express     Open Access   (Followers: 1)
Ambix     Hybrid Journal   (Followers: 3)
American Fern Journal     Full-text available via subscription   (Followers: 1)
American Journal of Agricultural and Biological Sciences     Open Access   (Followers: 9)
American Journal of Bioethics     Hybrid Journal   (Followers: 14)
American Journal of Human Biology     Hybrid Journal   (Followers: 16)
American Journal of Medical and Biological Research     Open Access   (Followers: 10)
American Journal of Plant Sciences     Open Access   (Followers: 20)
American Journal of Primatology     Hybrid Journal   (Followers: 17)
American Malacological Bulletin     Full-text available via subscription   (Followers: 3)
American Naturalist     Full-text available via subscription   (Followers: 80)
Amphibia-Reptilia     Hybrid Journal   (Followers: 6)
Anadol University Journal of Science and Technology B : Theoritical Sciences     Open Access  
Anadolu University Journal of Science and Technology : C Life Sciences and Biotechnology     Open Access   (Followers: 2)
Anaerobe     Hybrid Journal   (Followers: 4)
Analytical Methods     Full-text available via subscription   (Followers: 12)
Anatomical Science International     Hybrid Journal   (Followers: 3)
Animal Cells and Systems     Hybrid Journal   (Followers: 5)
Animal Models and Experimental Medicine     Open Access  
Annales de Limnologie - International Journal of Limnology     Hybrid Journal   (Followers: 1)
Annales françaises d'Oto-rhino-laryngologie et de Pathologie Cervico-faciale     Full-text available via subscription   (Followers: 3)
Annales Henri Poincaré     Hybrid Journal   (Followers: 3)
Annales Universitatis Mariae Curie-Sklodowska, sectio C – Biologia     Open Access   (Followers: 1)
Annals of Applied Biology     Hybrid Journal   (Followers: 7)
Annals of Biomedical Engineering     Hybrid Journal   (Followers: 19)
Annals of Human Biology     Hybrid Journal   (Followers: 5)
Annals of Science and Technology     Open Access  
Annual Review of Biomedical Engineering     Full-text available via subscription   (Followers: 14)
Annual Review of Biophysics     Full-text available via subscription   (Followers: 25)
Annual Review of Cancer Biology     Full-text available via subscription   (Followers: 3)
Annual Review of Cell and Developmental Biology     Full-text available via subscription   (Followers: 39)
Annual Review of Food Science and Technology     Full-text available via subscription   (Followers: 15)
Annual Review of Genomics and Human Genetics     Full-text available via subscription   (Followers: 25)
Annual Review of Phytopathology     Full-text available via subscription   (Followers: 13)
Anthropological Review     Open Access   (Followers: 24)
Antibiotics     Open Access   (Followers: 9)
Antioxidants     Open Access   (Followers: 5)
Antioxidants & Redox Signaling     Hybrid Journal   (Followers: 9)
Antonie van Leeuwenhoek     Hybrid Journal   (Followers: 5)
Anzeiger für Schädlingskunde     Hybrid Journal   (Followers: 1)
Apidologie     Hybrid Journal   (Followers: 4)
Apmis     Hybrid Journal   (Followers: 1)
APOPTOSIS     Hybrid Journal   (Followers: 9)
Applied Biology     Open Access   (Followers: 1)
Applied Bionics and Biomechanics     Open Access   (Followers: 7)
Applied Vegetation Science     Full-text available via subscription   (Followers: 10)
Aquaculture Environment Interactions     Open Access   (Followers: 4)
Aquaculture International     Hybrid Journal   (Followers: 26)
Aquaculture Reports     Open Access   (Followers: 3)
Aquaculture, Aquarium, Conservation & Legislation - International Journal of the Bioflux Society     Open Access   (Followers: 7)
Aquatic Biology     Open Access   (Followers: 6)
Aquatic Ecology     Hybrid Journal   (Followers: 37)
Aquatic Ecosystem Health & Management     Hybrid Journal   (Followers: 15)
Aquatic Science and Technology     Open Access   (Followers: 3)
Aquatic Toxicology     Hybrid Journal   (Followers: 23)
Archaea     Open Access   (Followers: 3)
Archiv für Molluskenkunde: International Journal of Malacology     Full-text available via subscription   (Followers: 3)
Archives of Biological Sciences     Open Access  
Archives of Microbiology     Hybrid Journal   (Followers: 9)
Archives of Natural History     Hybrid Journal   (Followers: 8)
Archives of Oral Biology     Hybrid Journal   (Followers: 3)
Archives of Virology     Hybrid Journal   (Followers: 5)
Archivum Immunologiae et Therapiae Experimentalis     Hybrid Journal   (Followers: 2)
Arid Ecosystems     Hybrid Journal   (Followers: 3)
Arquivos do Instituto Biológico     Open Access   (Followers: 1)
Arquivos do Museu Dinâmico Interdisciplinar     Open Access  
Arthropod Structure & Development     Hybrid Journal   (Followers: 2)
Arthropods     Open Access   (Followers: 1)
Artificial DNA: PNA & XNA     Hybrid Journal   (Followers: 3)
Asian Bioethics Review     Full-text available via subscription   (Followers: 3)
Asian Journal of Biodiversity     Open Access   (Followers: 5)
Asian Journal of Biological Sciences     Open Access   (Followers: 3)
Asian Journal of Cell Biology     Open Access   (Followers: 5)
Asian Journal of Developmental Biology     Open Access   (Followers: 2)
Asian Journal of Medical and Biological Research     Open Access   (Followers: 4)
Asian Journal of Nematology     Open Access   (Followers: 4)
Asian Journal of Poultry Science     Open Access   (Followers: 4)
Atti della Accademia Peloritana dei Pericolanti - Classe di Scienze Medico-Biologiche     Open Access  
Australian Life Scientist     Full-text available via subscription   (Followers: 2)
Australian Mammalogy     Hybrid Journal   (Followers: 7)
Autophagy     Hybrid Journal   (Followers: 4)
Avian Biology Research     Full-text available via subscription   (Followers: 5)
Avian Conservation and Ecology     Open Access   (Followers: 13)
Bacteriology Journal     Open Access   (Followers: 1)
Bacteriophage     Full-text available via subscription   (Followers: 3)
Bangladesh Journal of Bioethics     Open Access  
Bangladesh Journal of Plant Taxonomy     Open Access  
Bangladesh Journal of Scientific Research     Open Access   (Followers: 1)
Batman Üniversitesi Yaşam Bilimleri Dergisi     Open Access  
Berita Biologi     Open Access   (Followers: 1)
Between the Species     Open Access   (Followers: 1)
Bio Tribune Magazine     Hybrid Journal  
BIO Web of Conferences     Open Access  
BIO-Complexity     Open Access  
Bio-Grafía. Escritos sobre la Biología y su enseñanza     Open Access  
Bio-Lectura     Open Access  
Bioanalytical Reviews     Hybrid Journal   (Followers: 2)
Biocatalysis and Biotransformation     Hybrid Journal   (Followers: 6)
BioCentury Innovations     Full-text available via subscription   (Followers: 1)
Biochemistry and Cell Biology     Hybrid Journal   (Followers: 16)
Biochimie     Hybrid Journal   (Followers: 6)
BioControl     Hybrid Journal   (Followers: 6)
Biocontrol Science and Technology     Hybrid Journal   (Followers: 8)
Biodemography and Social Biology     Hybrid Journal  
BioDiscovery     Open Access   (Followers: 2)
Biodiversidade e Conservação Marinha : Revista CEPSUL     Open Access  
Biodiversitas : Journal of Biological Diversity     Open Access  
Biodiversity Data Journal     Open Access   (Followers: 4)
Biodiversity Informatics     Open Access   (Followers: 1)
Biodiversity Information Science and Standards     Open Access   (Followers: 2)
Biodiversity: Research and Conservation     Open Access   (Followers: 26)
Bioedukasi : Jurnal Pendidikan Biologi FKIP UM Metro     Open Access  
Bioeksperimen : Jurnal Penelitian Biologi     Open Access  
Bioelectrochemistry     Hybrid Journal   (Followers: 2)
Bioelectromagnetics     Hybrid Journal   (Followers: 2)
Bioenergy Research     Hybrid Journal   (Followers: 3)
Bioengineering and Bioscience     Open Access   (Followers: 3)
BioEssays     Hybrid Journal   (Followers: 11)
Bioethics     Hybrid Journal   (Followers: 17)
BioéthiqueOnline     Open Access  
Biofabrication     Hybrid Journal   (Followers: 5)
Biofilms     Full-text available via subscription   (Followers: 2)
Biogeosciences (BG)     Open Access   (Followers: 11)
Biogeosciences Discussions (BGD)     Open Access   (Followers: 3)
Bioinformatics     Hybrid Journal   (Followers: 380)
Bioinformatics and Biology Insights     Open Access   (Followers: 12)
Bioinspiration & Biomimetics     Hybrid Journal   (Followers: 7)
Biointerphases     Open Access   (Followers: 1)
Biojournal of Science and Technology     Open Access  
BioLink : Jurnal Biologi Lingkungan, Industri, Kesehatan     Open Access   (Followers: 1)
Biologia     Hybrid Journal  
Biologia on-line : Revista de divulgació de la Facultat de Biologia     Open Access  
Biological Bulletin     Partially Free   (Followers: 6)
Biological Control     Hybrid Journal   (Followers: 8)
Biological Invasions     Hybrid Journal   (Followers: 24)
Biological Journal of the Linnean Society     Hybrid Journal   (Followers: 18)

        1 2 3 4 5 6 7 8 | Last

Similar Journals
Journal Cover
Biochimie
Journal Prestige (SJR): 1.554
Citation Impact (citeScore): 3
Number of Followers: 6  
 
  Hybrid Journal Hybrid journal (It can contain Open Access articles)
ISSN (Print) 0300-9084
Published by Elsevier Homepage  [3181 journals]
  • Inside front cover-EDB
    • Abstract: Publication date: December 2019Source: Biochimie, Volume 167Author(s):
       
  • Metabolic shift in the production of corrinoid compounds by Lactobacillus
           coryniformis in the absence of purines
    • Abstract: Publication date: Available online 9 November 2019Source: BiochimieAuthor(s): Andrea Carolina Torres, Mariano Elean, Elvira María Hébert, Lucila Saavedra, María Pía Taranto Lactobacillus coryniformis CRL 1001 and L. reuteri CRL 1098 have the complete genes necessary to synthesize pseudo-cobalamin as final product in a vitamin B12 free commercial medium. Unlike vitamin-B12 (the most biologically active form), the pseudo-cobalamin contains adenine instead of 5,6-dimethlbenzimidazole (DMB) in the Coα-ligand. Considering the vitamin B12-gene clusters of these bacteria, the aim of this work was to analyze the production of corrinoids with DMB (vitamin B12) instead of adenine (pseudo-B12) as lower ligand base in a vitamin B12 free chemically defined medium (CDM) without purines. Genome-wide screening of genes related to purine metabolism showed that both strains possess all pur genes necessary for the synthesis of inositol monophosphate, the main precursor for purine biosynthesis. Accordingly, both strains were able to grow in B12 free CDM without purines, with the supplementation of different synthetic intermediaries. Isolated compounds with positive B12 activity were quantified and characterized by LC/MS-MS. Total corrinoids values were higher for both strains in comparison to those obtained in vitamin B12 free commercial medium. Interestingly, CRL 1001 strain synthesized cobalamin, suggesting that this strain is able to activate DMB as nitrogenous base instead adenine when it is in excess in a purine-free medium. The present paper represents the first demonstration of a partial metabolic shift to produce vitamin B12 in a Lactobacillus strain.Graphical abstractImage 1
       
  • Amelioration of diet-induced metabolic syndrome and fatty liver with
           Sitagliptin via regulation of adipose tissue inflammation and hepatic
           Adiponectin/AMPK levels in mice
    • Abstract: Publication date: Available online 9 November 2019Source: BiochimieAuthor(s): Swati Prakash, Uddipak Rai, Ramoji Kosuru, Vinod Tiwari, Sanjay Singh Chronic consumption of unhealthy diet and sedentary lifestyle induces fatty liver and metabolic complications. Adipocytes get overloaded with lipid succeeding low-grade inflammation and disrupting adipokine release. This research aims to investigate the effect of sitagliptin on white adipose tissue inflammation, adipokine level, metabolic syndrome, and fatty liver through 5’ adenosine monophosphate-activated protein kinase (AMPK) pathway. In sixteen weeks of the experimental protocol, Swiss albino mice were kept in a standard environment and were fed 60% high-fat diet and 20% fructose water (HFFW) where they developed metabolic syndrome features, adipose tissue inflammation, and altered adipokine profile. Sitagliptin was administered for the last eight weeks. They were allocated to following six groups, control diet with regular water (1), HFFW only (2), HFFW and metformin 100mg/kg (3), HFFW and sitagliptin 10mg/kg (4), HFFW and sitagliptin 20mg/kg (5), and HFFW and sitagliptin 30mg/kg (6). Fasting serum insulin (FSI), glucagon-like peptide-1 (GLP-1), adipokines (adiponectin and leptin), serum lipid profile, hepatic lipid content, and white adipose tissue inflammation were assessed. Protein expression of P-AMPK, P-Acetyl co-a carboxylase (ACC), and mRNA expression of fatty acid metabolism genes were also evaluated in the liver. Sitagliptin significantly and effectively reversed metabolic syndrome complexity. FSI and GLP-1 levels were improved. A significant reduction in hepatic lipid content and oxidative stress was also observed. Also, sitagliptin significantly ameliorated adipose tissue inflammation and adiponectin levels at 20mg/kg and 30mg/kg. P-AMPK and P-ACC expression increased significantly. Moreover, expression of fatty acid synthesis genes was down-regulated, and fatty acid oxidation genes were up-regulated. Sitagliptin significantly ameliorated obesity-induced adipose tissue inflammation, metabolic syndrome, and fatty liver via regulation of adiponectin and AMPK levels in obese mice. Also, increased GLP-1 levels would have induced insulin-independent effects on adipose tissue and liver.Graphical abstractImage 1
       
  • Sulfoxides of sulfur-containing amino acids are suicide substrates of
           Citrobacter freundii methionine γ-lyase. Structural bases of the enzyme
           inactivation
    • Abstract: Publication date: Available online 9 November 2019Source: BiochimieAuthor(s): Svetlana Revtovich, Elena Morozova, Vitalia Kulikova, Vasiliy Koval, Natalya Anufrieva, Alexei Nikulin, Tatyana Demidkina Interactions of Citrobacter freundii methionine γ-lyase (MGL) with sulfoxides of typical substrates were investigated. It was found that sulfoxides are suicide substrates of the enzyme. The products of the β- and γ-elimination reactions of sulfoxides, thiosulfinates, oxidize three cysteine residues of the enzyme. Three-dimensional structures of MGL inactivated by dimethyl thiosulfinate and diethyl thiosulfinate were determined at 1.46 Å and 1.59 Å resolution. Analysis of the structures identified SH groups oxidized by thiosulfinates and revealed the structural bases of MGL inactivation. The extent of inactivation of MGL in the catalysis of the β-elimination reaction depends on the length of the «tail» at oxidized Cys115. Oxidation of Cys115 results in MGL incapable to catalyze the stage of methyl mercaptan elimination of the physiological reaction.
       
  • Development of analytical methods GC-MS vs LC-UV for the serum monitoring
           of an inflammatory glycotoxin (methylglyoxal): a new biomarker of bovine
           hepatobiliary distomatosis
    • Abstract: Publication date: Available online 7 November 2019Source: BiochimieAuthor(s): Nadia. Taïbi, Amina. Taïbi, Rachid. Ameraoui, Mohamed. Abou-mustapha, Mohamed. Hadjadj, Zahra-Mouna. Boutaiba, Amel. Kaced, Souhila. Djema, Qosay-Ali. Al-balas, Ghazi-Ahmad. Al jabal, Miriem. Aissi, Khaled. Harhoura, Safia. Zenia, Farida. Khammar Two analytical methods; high performance liquid chromatography and gas chromatography were used to determine the content of 2-methylquinoxaline, a methylglyoxal-derived agent in sera from cattle with fascioliasis. Methylglyoxal is a highly mutagenic and cytotoxic reactive dicarbonyl compound formed by non-enzymatic fragmentation of triose phosphate GAP and DHAP during glycolysis which regularly contributes to repositioning the energetic balance between physiological and pathological situations. The aim of this study was to propose the MGO as a new biomarker in the bovine fasciolosis.Strongly infected animals showed a correlation between the relatively high levels of Fasciola hepatica anti-f2 antibody and methylglyoxal compared to unharmed animals. Also, an acute hyperglycemia was recorded and closely related to hepatic parenchyma hyperplasia, inflammation, bile ducts obstruction and scléro-fibrous foci formation.Unlike HPLC, which has shown analytical flaws and irregularities, GC-MS remains an excellent diagnostic tool for detecting and quantifying methylglyoxal in biological fluids. The developed method has been validated under FDA guidelines. A full scan-range was set from m/z 39 to 144/999 and the molecular weight of the 2-methylquinoxaline was identified according to NIST Database and ES. Methylglyoxal was the only analyte successfully quantified in a relatively short run time. It was linear over a concentration range of 0.057 to 5.7μg.ml-1with mean recoveries and RSD of 118% and 3.63% respectively. The intra and inter-day assays were satisfying and not exceed 3.00%. Results reflect the degree of precision of our method and indicate that MGO was an important contributor to understand the hepatic failure independently of other serum markers.
       
  • Dietary choline is related to increased risk of acute myocardial
           infarction in patients with stable angina pectoris
    • Abstract: Publication date: Available online 7 November 2019Source: BiochimieAuthor(s): Anthea Van Parys, Vegard Lysne, Gard Frodahl Tveitevåg Svingen, Per Magne Ueland, Indu Dhar, Jannike Øyen, Jutta Dierkes, Ottar K. Nygård High plasma choline has been associated with the metabolic syndrome and risk of chronic diseases, including cardiovascular disease. However, dietary choline is not correlated with choline plasma concentrations, and there are few studies and contradictory evidence regarding dietary choline and cardiovascular events. In addition, a recommended dietary allowance for choline has not been established and remains a point of contention.This study assessed the association between dietary choline, including choline forms, and risk of incident acute myocardial infarction (AMI) in patients with suspected stable angina pectoris (SAP).In total 1981 patients (80% men, median age 62) from the Western Norway B Vitamin Intervention Trial were included in this analysis. Information on dietary choline was obtained using a 169-item food frequency questionnaire. The Cardiovascular Disease in Norway project provided data on AMI. Risk associations were estimated using Cox-regression analysis using energy-adjusted choline intake.Median (25th, 75th percentile) total energy-adjusted choline intake was 288 (255, 326) mg/d. During a median (25th, 75th percentile) follow-up of 7.5 (6.3, 8.8) years, 312 (15.7%) patients experienced at least one AMI. Increased intakes of energy-adjusted choline (HR [95% CI] per 50 mg increase 1.11 [1.03, 1.20]), phosphatidylcholine (HR per 50 mg increase 1.24 [1.08, 1.42]) and sphingomyelin (HR per 5 mg increase 1.16 [1.02, 1.31]) were associated with higher AMI risk.Higher dietary intakes of total choline, phosphatidylcholine and sphingomyelin were associated with increased risk of AMI in patients with SAP. Future studies are necessary to explore underlying mechanisms for this observation.Graphical abstractImage 1
       
  • Epigenetically modified N 6-methyladenine inhibits DNA replication by
           human DNA Polymerase iota
    • Abstract: Publication date: Available online 5 November 2019Source: BiochimieAuthor(s): Shuming Zhang, Bianbian Li, Ke Du, Tingting Liang, Mengyuan Dai, Wenxin Huang, Huizhi Zhang, Yihui Ling, Huidong ZhangABSTRACTAmong human four Y-family DNA polymerases, hPol ι is exceptionally error-prone in DNA synthesis. 6mA plays significant roles in epigenetic regulation of numerous biological processes. Nonetheless, its effects on DNA replication by hPol ι is still unclear. In this work, we found that 6mA and Hyp, the intermediate of 6mA, inhibited the replication of DNA by hPol ι. 6mA lost priority in extension beyond 6mA:T pair, partially reducing dTTP incorporation efficiency and inhibiting next-base extension. Hyp was prone to dCTP incorporation and extension beyond Hyp:C instead of Hyp:T pair. Statistically, 6mA primarily reduced the burst incorporation rate (kpol) and slightly increased the dissociation constant (Kd,dTTP). However, Hyp mainly increased the Kd,dCTP yet did not affect the kpol, both reducing the burst incorporation efficiency (kpol/Kd,dCTP). 6mA together with Hyp weakened the binding affinity of hPol ι to DNA in binary or ternary complex. The misincorporation opposite 6mA or Hyp further weakened this binding affinity. The methyl group in 6mA doesn’t almost affect the H-bond formation with dTTP, therefore mildly inhibiting dTTP incorporation. As an analogue of G, Hyp can form only two H-bonds with dCTP, thus reducing dCTP incorporation. This work provides a new insight in how the epigenetically modified 6mA and its intermediate Hyp affect replication of DNA by human DNA polymerase ι.Graphical abstractImage 1
       
  • Meeting report: Seventh International Meeting on Quadruplex Nucleic Acids
           (Changchun, P.R. China, September 6-9, 2019)
    • Abstract: Publication date: Available online 5 November 2019Source: BiochimieAuthor(s): Jean-Louis Mergny DNA is prone to structural polymorphism: beyond the iconic Watson-Crick double helix, nucleic acids can adopt a number of unusual motifs, at least in vitro. Scientists around the world gather every two years to discuss two of these oddities: G-quadruplexes and i-DNA. The seventh international meeting on G-quadruplex Nucleic Acids was held in Changchun, in Jilin province of the P.R. of China, approx. 1000 km North-east of Beijing. Nearly 320 participants gathered from Asia, Europe, North America and Oceania. More than 80 talks and as many posters summarized our current knowledge of these unusual DNA and RNA structures. During this meeting, the creation of the G4 society was announced, in order to coordinate efforts and share tools and knowledge in our field (https://www.g4-society.org).
       
  • Biochemical characterization of the cAMP-dependent protein kinase
           regulatory subunit-like protein from Trypanosoma equiperdum, detection of
           its inhibitory activity, and identification of potential interacting
           proteins
    • Abstract: Publication date: Available online 5 November 2019Source: BiochimieAuthor(s): Nelson A. Araujo, Mónica Rincón, Eva Vonasek, Maritza Calabokis, José Bubis An enriched fraction of an inhibitor of both the catalytic subunit of the cAMP-dependent protein kinase (PKA) from pig heart and a Trypanosoma equiperdum PKA catalytic subunit-like protein (TeqC-like) was obtained from the soluble fraction of T. equiperdum parasites after three consecutive purification steps: sedimentation through a linear 5-20% sucrose gradient, diethylaminoethyl-Sepharose anion-exchange chromatography, and Bio-Sil Sec-400-S size-exclusion high-performance liquid chromatography. The inhibitor was identified as the T. equiperdum PKA regulatory subunit-like protein (TeqR-like) on the basis of western blot and mass spectrometry analyses, and behaved as an uncompetitive or anti-competitive inhibitor of the parasite TeqC-like protein, with respect to a fluorescently labeled substrate (kemptide, sequence: LRRASLG), showing a Ki of 1.17 μM. The isolated protein possesses a molecular mass of 57.54 kDa, a Stokes radius of 3.64 nm, and a slightly asymmetric shape with a frictional ratio f/fo = 1.43. As revealed during the purification steps and by immunoprecipitation experiments, the TeqR-like and TeqC-like proteins were not associated forming a heterooligomeric complex, differing from traditional PKA subunits. Co-immunoprecipitation results followed by mass spectrometry sequencing identified two isoforms of the parasite heat-shock protein 70, α-tubulin, and β-tubulin as candidates that interact with the TeqR-like protein in T. equiperdum.
       
  • Leucine increases mitochondrial metabolism and lipid content without
           altering insulin signaling in myotubes
    • Abstract: Publication date: Available online 2 November 2019Source: BiochimieAuthor(s): Madison E. Rivera, Emily S. Lyon, Michele A. Johnson, Roger A. Vaughan Elevated circulating branched-chain amino acids (BCAA) such as leucine have been consistently correlated with increasing severity of insulin resistance across numerous populations. BCAA may promote insulin resistance through either mTOR-mediated suppression of insulin receptor substrate-1 or through the accumulation of toxic BCAA catabolites. Although the link between circulating BCAA and insulin resistance has been consistent, it has yet to be concluded if BCAA causally contribute to the development or worsening of insulin resistance. This work investigated the effect of leucine both with and without varying levels of insulin resistance on metabolism, metabolic gene expression, and insulin signaling. C2C12 myotubes were treated with and without varied concentrations of leucine up to 2mM for 24 hours both with and without varied levels of insulin resistance. Gene and protein expression were measured via qRT-PCR and western blot, respectively. Mitochondrial metabolism was measured via O2 consumption. Leucine at 2mM increased oxidative metabolism as well as gene expression of mitochondrial biogenesis, which was associated with increased cellular lipid content. Despite increased lipid content of leucine-treated cells, neither acute nor chronic leucine treatment at 2mM affected insulin signaling in insulin sensitive, mildly insulin resistant, or severely insulin resistant cells. Similarly, leucine at lower concentrations (0.25mM, 0.5mM, and 1mM) did not alter insulin signaling either, regardless of insulin resistance. Leucine appears to improve myotube oxidative metabolism and related metabolic gene expression. And despite increased lipid content of leucine-treated cells, leucine does not appear to alter insulin sensitivity either acutely or chronically, regardless of level of insulin resistance.
       
  • Heat shock response to exercise in pancreatic islets of obese mice
    • Abstract: Publication date: Available online 31 October 2019Source: BiochimieAuthor(s): Aline Bittencourt, Helena Trevisan Schroeder, Rossana Rosa Porto, Carlos Henrique de Lemos Muller, Mauricio Krause, Paulo Ivo Homem de Bittencourt Chronic obesity imposes an organismal state of low-grade inflammation because the physiological resolution of inflammation is progressively repressed giving rise to cellular senescence and its accompanying Senescence-Associated Secretory Phenotype (SASP), which avoids apoptosis but perpetuates the relay of inflammatory signals from adipose tissue toward the rest the body. Conversely, resolution of inflammation depends on the integrity of heat shock response (HSR) pathway that leads to the expression of cytoprotective and anti-inflammatory protein chaperones of the 70 kDa family (HSP70). However, chronic exposure to the aforementioned injuring factors leads to SASP, which, in turn, suppress the HSR. A main metabolic tissue severely jeopardized by obesity-related dysfunctions is the endocrine pancreas, particularly β-cells of the islets of Langerhans. Because exercise is a powerful inducer of HSR and predicted to alleviate negative health outcomes of obesity, we sought whether obesity influence HSP70 expression in pancreatic islets and other metabolic tissues (adipose tissue and skeletal muscle) of adult B6.129SF2/J mice fed on a high-fat diet (HFD) for 13 weeks since the weaning and whether acute exercise as well as moderate-intensity exercise training (8 weeks) could interfere with this scenario. We showed that acute exercise of moderate intensity protects pancreatic islets against cytokine-induced cell death. In addition, acute exercise challenge time-dependently increased islet HSP70 that peaked at 12 h post-exercise in both trained and untrained mice fed on a control diet, suggesting an adequate HSR to exercise training. Unexpectedly, however, neither exercise training nor acute exercise challenges were able to increase islet HSP70 contents in trained mice submitted to HFD, but only in untrained HFD animals. In parallel, HFD disrupted glycemic status which is accompanied by loss of muscular mass resembling sarcopenic obesity that could not be rescued by exercise training. These results suggest that exercise influences HSR in pancreatic islets but obesity undermines islet, muscle and adipose tissue HSR, which is associated with metabolic abnormalities observed in such tissues.Graphical abstractImage 1
       
  • Fibroblast-secreted trophic factors contribute with ECM remodeling
           stimulus and upmodulate osteocyte gene markers in osteoblasts
    • Abstract: Publication date: Available online 30 October 2019Source: BiochimieAuthor(s): Célio Jr. da Costa Fernandes, Willian Fernando Zambuzzi As osteogenesis is a multifactorial mechanism, we wonder whether osteoblast-induced extracellular matrix (ECM) remodeling might be modulated by trophic factors released by fibroblasts in a paracrine signaling manner. To address this issue, fibroblasts were cultured for 72 hours under conventional conditions when their conditioned medium was harvested and used to challenge pre-osteoblasts (MC3T3-E1 cells) for 14 days. Preliminarily, we validated the potential effect of fibroblasts in contributing to osteocyte phenotype, which specifically requires significant expression of Dentin Matrix Protein 1 (DMP1; about 10-fold changes) and Sclerostin (SOST; about 7-fold changes), both biomarkers of osteocyte. Fibroblasts also seem contributing to ECM remodeling in osteoblasts, because we detected a high level of both mRNA and enzyme activities of matrix metalloproteinase -9 (MMP-9) as well as a high level of reversion inducing cysteine rich protein with kazal motifs (RECK) transcripts (about 13-fold changes), an membrane-anchored MMP inhibitor, which seems to be a constitutive pathway in osteoblasts. Considering inflammatory panorama and using RTqPCR technology, both IL-13 (about 13-fold changes) and IL-33 (about 5-fold changes) genes were up-expressed in response to the fibroblast-secreted trophic factors, as were the receptor activator of NF-κB ligand (RANKL; about 8-fold changes) and osteoprotegerin (OPG; about 3-fold changes). Although preliminary, these data suggest a stimulus to finely control osteoclastogenesis, and this mechanism reinforces the role of fibroblasts in bone remodeling and homeostasis. Moreover, these results suggest an important crosstalk between fibroblast and osteoblast, when fibroblast-secreted trophic factors upmodulate osteocyte gene markers and contribute to ECM remodeling stimulus in osteoblast.Graphical abstractImage 1
       
  • Protective role of adiponectin against testicular impairment in high-fat
           diet/streptozotocin-induced type 2 diabetic mice
    • Abstract: Publication date: Available online 30 October 2019Source: BiochimieAuthor(s): Mayank Choubey, Ashutosh Ranjan, Puran S. Bora, Amitabh Krishna Type 2 diabetes (T2D) is the most common endocrine and metabolic disorder, leading to reproductive impairments and infertility in male. Our recent study showed crucial role of adiponectin in the regulation of testicular functions, and the circulating level of adiponectin declines in diabetes. The current study thus aimed to examine the efficacy of adiponectin in improving testicular dysfunction in high-fat diet/streptozotocin-induced T2D mice. T2D was induced in pre-pubertal mice fed with high-fat diet for ∼10 weeks followed by single treatment of streptozotocin. T2D mice showed presence of increased body mass, hyperglycemia, hyperinsulinemia, insulin resistance, increased oxidative stress, and declined serum testosterone compared to vehicle-treated control mice. The spermatogenic, steroidogenic, metabolic, and antioxidative parameters were evaluated in T2D mice treated with adiponectin for both two and four weeks. The exogenous administration of adiponectin to T2D mice showed enhanced serum testosterone and expression of testicular steroidogenic markers proteins, insulin receptor and GLUT8 proteins, increase in intra-testicular concentrations of glucose and lactate and activity of LDH and antioxidant enzymes compared to the levels in untreated T2D mice. This suggests that treatment of adiponectin effectively improves testicular functions by increasing expression of insulin receptor-mediated increased transport of energy substrate (glucose and lactate) and a marked reduction in oxidative stress are the possible mechanism by which adiponectin effectively improves testicular function in T2D mice.
       
  • Impact of hepatitis C virus and alcohol, alone and combined, on the
           unfolded protein response in primary human hepatocytes
    • Abstract: Publication date: Available online 28 October 2019Source: BiochimieAuthor(s): Céline Hernandez, Etienne B. Blanc, Véronique Pène, Béatrice Le-Grand, Maxime Villaret, Lynda Aoudjehane, Arnaud Carpentier, Filomena Conti, Yvon Calmus, Philippe Podevin, Michèle Garlatti, Hélène Rouach, Arielle R. Rosenberg Hepatitis C virus (HCV) infection and alcohol abuse are leading causes of chronic liver disease and frequently coexist in patients. The unfolded protein response (UPR), a cellular stress response ranging along a spectrum from cytoprotection to apoptosis commitment, has emerged as a major contributor to human diseases including liver injuries. However, the literature contains conflicting reports as to whether HCV and ethanol activate the UPR and which UPR genes are involved. Here we have used primary human hepatocytes (PHH) to reassess this issue and address combined impacts. In this physiologically relevant model, either stressor activated a chronic complete UPR. However, the levels of UPR gene induction were only modest in the case of HCV infection. Moreover, when combined to the strong stressor thapsigargin, ethanol exacerbated the activation of pro-apoptotic genes whereas HCV tended to limit the induction of key UPR genes. The UPR resulting from HCV plus ethanol was comparable to that induced by ethanol alone with the notable exception of three pro-survival genes the expressions of which were selectively enhanced by HCV. Interestingly, HCV genome replication was maintained at similar levels in PHH exposed to ethanol. In conclusion, while both HCV and alcohol activate the hepatocellular UPR, only HCV manipulates UPR signalling in the direction of a cytoprotective response, which appears as a viral strategy to spare its own replication.
       
  • Pelargonidin ameliorates acetaminophen-induced hepatotoxicity in mice by
           inhibiting the ROS-induced inflammatory apoptotic response
    • Abstract: Publication date: Available online 25 October 2019Source: BiochimieAuthor(s): Minseok Seo, Hyunjin Kim, Jin Hyup Lee, Jeen-Woo ParkABSTRACTThe common analgesic acetaminophen (N-acetyl-p-aminophenol, APAP) is non-toxic to the liver at therapeutic doses. However, an overdose of APAP can lead to APAP-induced liver failure, which has emerged as a serious issue in the US and Europe. Pelargonidin is an anthocyanidin found in pomegranates, plums, and various berries. Pelargonidin has strong antioxidant effects, directly scavenging superoxide radicals and inhibiting H₂O₂-induced lipid peroxidation. Focusing on these effects, we studied the preventative effect of pelargonidin on APAP-induced hepatotoxicity and its underlying mechanisms in vivo. We observed that pelargonidin mitigates serum alanine aminotransferase and aspartate aminotransferase activity, which are strongly associated with APAP-induced hepatotoxicity. We also found that pelargonidin reduced APAP-induced hepatic necrosis by removing excessive ROS. Hepatic necrosis stimulates the release of molecular pathogens that induce inflammation, which increases cell stress and can lead to apoptosis. Therefore, pelargonidin was able to reduce levels of necrosis, inflammation, and hepatocyte apoptosis. These results indicate that the administration of pelargonidin protects against APAP-induced hepatotoxicity and that it could be a novel protective strategy against APAP-induced liver failure.Graphical abstractImage 1
       
  • Human apurinic/apyrimidinic endonuclease 1 is modified in vitro by
           poly(ADP-ribose) polymerase 1 under control of the structure of damaged
           DNA
    • Abstract: Publication date: Available online 24 October 2019Source: BiochimieAuthor(s): Nina A. Moor, Inna A. Vasil’eva, Nikita A. Kuznetsov, Olga I. LavrikApurinic/apyrimidinic endonuclease 1 (APE1) is an essential multifunctional protein in mammals involved in base excision DNA repair (BER), regulation of gene expression and RNA metabolism. Its major enzymatic function is incision of AP sites. Poly(ADP-ribose) polymerase 1 (PARP1) modifies itself and target proteins with poly(ADP-ribose) (PAR), contributing to regulation of many processes. To understand molecular basis of functional cooperation between APE1 and PARP1 in BER, we examined PAR-binding activity and ADP-ribosylation of human APE1 in comparison with known targets of PARP1, using the full-length, N-terminally truncated and catalytically inactive forms of APE1. The protein binds preferentially large ADP-ribose polymers, being very similar to DNA polymerase β (Polβ) but contrasting with the scaffold XRCC1 protein. The interaction with PAR involves the universally conserved catalytic portion and the eukaryote-specific extension of APE1. The ADP-ribosylation of APE1 depends on the structure of PARP1-activating DNA, contrasting APE1 with Polβ and XRCC1. Relative levels of APE1 modification in the presence of different DNA substrates were found to correlate with affinities of the DNAs for APE1 and substrate activities in the enzymatic incision, suggesting the ADP-ribosylation to occur within the DNA-mediated ternary complex. This conclusion was confirmed by importance of the length of DNA region 3’ to the AP site for the modification. Deletion of the N-terminal extension of APE1 produced no significant influence on both the ADP-ribosylation efficiency and hydrolytic stability of the modified protein, suggesting localization of target amino acids in the conserved catalytic portion. The most efficient ADP-ribosylation of the catalytically inactive APE1 mutant was shown to reduce the level of PARP1 automodification, suggesting possible role of APE1 in modulating PARP1 activity. Our data on primary role of DNA in controlling the PARP-catalysed modification provide new insights into mechanisms of protein targeting for ADP-ribosylation.
       
  • MLCK and ROCK Mutualism in Endothelial Barrier Dysfunction
    • Abstract: Publication date: Available online 24 October 2019Source: BiochimieAuthor(s): Olga A. Kazakova, Asker Y. Khapchaev, Vladimir P. ShirinskyABSTRACTMyosin activation contributes to the contractile forces that induce disturbances in the vascular endothelial integrity and promote protein-rich edema of the underlying tissues. Myosin light chain kinase (MLCK) and Rho-associated protein kinase (ROCK) have been reported to phosphorylate myosin regulatory light chains (RLC) for myosin activation. However, the relative contribution and roles of these kinases are debatable and not understood in very detail. In this study, using a combinational inhibitory analysis of MLCK, ROCK, and their antagonist, myosin light chain phosphatase (MLCP), we show that the MLCK-dependent RLC mono-(Ser19)phosphorylation (P-RLC) is sufficient to induce the FITC-dextran hyperpermeability in EA.hy926 endothelial cells (EC) in response to thrombin. However, MLCK relies on the ROCK assistance that attenuates MLCP activity. On the other hand, MLCK supplies P-RLC myosin as an intermediate substrate to ROCK thus adding to a faster accumulation of di-(Thr18/Ser19)phosphorylated RLC (PP-RLC) by the latter kinase. ROCK also produces P-RLC but is solely responsible for the thrombin-induced PP-RLC generation in EA.hy926 EC and other cell types. Still, as a direct myosin activator, ROCK contributes less to endothelial hyperpermeability than MLCK. Our findings are consistent with a concerted complementary mutual interplay between ROCK and MLCK to activate endothelial myosin and elicit the thrombin-mediated EC barrier dysfunction.
       
  • Autophagy mediated by JNK1 resists apoptosis through TRAF3 degradation in
           osteoclastogenesis
    • Abstract: Publication date: Available online 23 October 2019Source: BiochimieAuthor(s): Dianshan Ke, Yunrong Zhu, Wang Zheng, Xiaomin Fu, Jinyan Chen, Junyong Han RANKL induces osteoclastogenesis via JNK1 signal that exerts an anti-apoptotic effect during osteoclastogenesis. However, the classic downstream c-Jun/AP-1 pathway is not included in anti-apoptosis of JNK1. Thus, the detail mechanism underlying JNK1-resisted apoptosis remains unknown during RANKL-induced osteoclastogenesis. RANKL-induced autophagy results in the degradation of the osteoclastogenesis-inhibitor TRAF3, and TRAF3 is thought as a regulator of apoptosis. Given the key effect of JNK1 in mediating autophagy, our study aims to investigate the significance of TRAF3 in bridging JNK1-mediated autophagy and apoptotic resistance during osteoclastogenesis. In this study, by using Bone Marrow-derived macrophages (BMMs) as osteoclast precursors (OCPs), we found that RANKL-induced TRAF3 degradation was significantly suppressed by JNK inhibitor (SP600125), which was restored by overexpression of Beclin1 (key autophagic protein). Nevertheless, TRAF3 silencing partially reversed the reduced osteoclastogenesis under SP600125 intervention. Besides, OCP apoptosis was positively regulated by TRAF3 overexpression, regardless of the application of autophagy inhibitor or SP600125. Remarkably, the enhanced apoptosis caused by the pharmacological inhibition of Beclin1 was reversed by TRAF3 silencing. Together, these results suggest that JNK1-mediated autophagy could promote RANKL-induced osteoclastogenesis via enhancing TRAF3 degradation. Importantly, JNK1 could prevent OCP apoptosis through autophagy-TRAF3 signaling, which provides more potential targets for clinical treatment of pathological bone loss.
       
  • Conformational analysis and in vitro immunomodulatory and insulinotropic
           properties of the frog skin host-defense peptide rhinophrynin-27 and
           selected analogs
    • Abstract: Publication date: Available online 19 October 2019Source: BiochimieAuthor(s): Mariano A. Scorciapino, Paola Carta, Jelena Pantic, Miodrag L. Lukic, Aleksandra Lukic, Vishal Musale, Yasser H.A. Abdel-Wahab, J. Michael Conlon The study investigates conformational analysis and the in vitro cytokine-mediated immunomodulatory and insulin-releasing activities of rhinophrynin-27 (ELRLPEIARPVPEVLPARLPLPALPRN; RP-27), a proline-arginine-rich peptide first isolated from skin secretions of the Mexican burrowing toad Rhinophrynus dorsalis (Rhinophrynidae). In both water and 50% trifluoroethanol-water, the peptide adopts a polyproline type II helical conformation with a high degree of deviation from the canonical collagen-like folding and a pronounced bend in the molecule at the Glu13 residue. Incubation of mouse peritoneal cells with RP-27 significantly (P < 0.05) inhibited production of the pro-inflammatory cytokines TNF-α and IL-1β and stimulated production of the anti-inflammatory cytokine IL-10. The peptide significantly (P < 0.01) stimulated release of insulin from BRIN-BD11 rat clonal β-cells at concentrations ≥ 1 nM while maintaining the integrity of the plasma membrane and also stimulated insulin release from isolated mouse islets at a concentration of 10-6 M. Increasing the cationicity of RP-27 by substituting glutamic acid residues in the peptide by arginine and increasing hydrophobicity by substituting alanine residues by tryptophan did not result in analogues with increased activity with respect to cytokine production and insulin release. The combination of immunosuppressive and insulinotropic activities together with very low cytotoxicity suggests that RP-27 may represent a template for the development of an agent for use in anti-inflammatory and Type 2 diabetes therapies.Graphical abstractImage 1
       
  • Oligopeptidase B, a missing enzyme in mammals and a potential drug target
           for trypanosomatid diseases
    • Abstract: Publication date: Available online 16 October 2019Source: BiochimieAuthor(s): Flávia Nader Motta, Clênia dos Santos Azevedo, Beatriz Pereira Neves, Carla Nunes de Araújo, Philippe Grellier, Jaime Martins de Santana, Izabela Marques Dourado Bastos Oligopeptidases B (OPB) belong to the S9 prolyl oligopeptidase family and are expressed in prokaryotes, some eukaryotes and in some higher plants. OPB is not found in any of the mammalian genomes available to date. Evidences indicate that OPB participates in the infections caused by trypanosomatids Trypanosoma cruzi, Leishmania spp. and Trypanosoma brucei spp and therefore it is considered an important virulence factor. Trypanosomatids from the genera Leishmania and Trypanosoma also present other OPB, named OPB2. A more accurate investigation of trypanosomatid OPB sequences brought attention to what could be a third OPB sequence (OPB3). This review aims to discuss biochemical, structural, phylogenetic and functional properties of OPB and its potential as target for the development of drugs against Chagas disease, leishmaniasis and African trypanosomiasis.
       
  • Fli-1 promotes proliferation and upregulates NANOGP8 expression in
           T-lymphocyte leukemia cells
    • Abstract: Publication date: Available online 15 October 2019Source: BiochimieAuthor(s): Sung-Won Park, Hyun-Jin Do, Wonbin Choi, Jae-Hwan Kim Friend leukemia integration 1 (Fli-1) is a member of the E26 transformation-specific (ETS) transcription factor family. Fli-1 regulates normal hematopoiesis and vasculogenesis, and its aberrant expression underlies virus-induced leukemias and various types of human cancers. NANOGP8, a retro-pseudogene of stem cell mediator NANOG, is expressed predominantly in cancer cells and plays a role in tumorigenesis. In this study, we demonstrate that Fli-1 expression enhances human acute T-cell leukemia Jurkat cell proliferation and that Fli-1 acts as a transcriptional activator of NANOGP8 expression in these cells. NANOGP8 and Fli-1 are highly expressed in Jurkat cells, whereas NANOG was undetectable at both the RNA and protein levels. Moreover, the expression of endogenous NANOGP8 was significantly influenced by gain of function and loss of function of Fli-1. Promoter-reporter assays showed that NANOGP8 transcription was significantly upregulated by dose-dependent Fli-1 overexpression. A series of deletion mutagenesis of NANOGP8 promoter sequence revealed that NANOGP8 promoter activity was tightly regulated and found the minimal promoter region sufficient to activate NANOGP8 transcription mediated by Fli-1. Moreover, site-directed mutagenesis of the putative binding site abolished both NANOGP8 full-length and minimal promoter activities. Binding assays revealed that Fli-1 directly interacts with the potent binding site in NANOG promoter region. Taken together, our data demonstrate that Fli-1 is a novel upstream transcriptional activator of NANOGP8 and provide the molecular details of Fli-1-mediated NANOGP8 gene expression. Ultimately, these findings may contribute to understanding the expanded regulatory mechanisms of oncogenic NANOGP8 and ETS family transcription factors in leukemogenesis.
       
  • Mitochondrial dysfunction, AMPK activation and peroxisomal metabolism: a
           coherent scenario for non-canonical 3-methylglutaconic acidurias
    • Abstract: Publication date: Available online 15 October 2019Source: BiochimieAuthor(s): Joseph Vamecq, Bérengère Papegay, Vincent Nuyens, Jean Boogaerts, Oberdan Leo, Véronique Kruys The occurrence of 3-methylglutaconic aciduria (3-MGA) is a well understood phenomenon in leucine oxidation and ketogenesis disorders (primary 3-MGAs). In contrast, its genesis in non-canonical (secondary) 3-MGAs, a growing-up group of disorders encompassing more than a dozen of inherited metabolic diseases, is a mystery still remaining unresolved for three decades. To puzzle out this anthologic problem of metabolism, three clues were considered: (i) the variety of disorders suggests a common cellular target at the cross-road of metabolic and signaling pathways, (ii) the response to leucine loading test only discriminative for primary but not secondary 3-MGAs suggests these latter are disorders of extramitochondrial HMG-CoA metabolism as also attested by their failure to increase 3-hydroxyisovalerate, a mitochondrial metabolite accumulating only in primary 3-MGAs, (iii) the peroxisome is an extramitochondrial site possessing its own pool and displaying metabolism of HMG-CoA, suggesting its possible involvement in producing extramitochondrial 3-methylglutaconate (3-MG). Following these clues provides a unifying common basis to non-canonical 3-MGAs: constitutive mitochondrial dysfunction induces AMPK activation which, by inhibiting early steps in cholesterol and fatty acid syntheses, pipelines cytoplasmic acetyl-CoA to peroxisomes where a rise in HMG-CoA followed by local dehydration and hydrolysis may lead to 3-MGA yield. Additional contributors are considered, notably for 3-MGAs associated with hyperammonemia, and to a lesser extent in CLPB deficiency. Metabolic and signaling itineraries followed by the proposed scenario are essentially sketched, being provided with compelling evidence from the literature coming in their support.Graphical abstractImage 1
       
  • Alterations of endogenous sphingolipid metabolism in cardiometabolic
           diseases: towards novel therapeutic approaches
    • Abstract: Publication date: Available online 12 October 2019Source: BiochimieAuthor(s): Mélanie Le Barz, Marie-Michèle Boulet, Catherine Calzada, David Cheillan, Marie-Caroline MichalskiABSTRACTThe increasing prevalence of obesity and metabolic diseases is a worldwide public health concern, and the advent of new analytical technologies has made it possible to highlight the involvement of some molecules, such as sphingolipids (SL), in their pathophysiology. SL are constituents of cell membranes, lipoproteins and lipid droplets (LD), and are now considered as bioactive molecules. Indeed, growing evidence suggests that SL, characterized by diverse families and species, could represent one of the main regulators of lipid metabolism. There is an increasing amount of data reporting that plasma SL profile is altered in metabolic diseases. However, less is known about SL metabolism dysfunction in cells and tissues and how it may impact the lipoprotein metabolism, its functionality and composition. In cardiometabolic pathologies, the link between serum SL concentrations and alterations of their metabolism in various organs and LD is still unclear. Pharmacological approaches have been developed in order to activate or inhibit specific key enzymes of the SL metabolism, and to positively modulate SL profile or related metabolic pathways. Nevertheless, little is known about the long-term impact of such approaches in humans and the current literature still focuses on the decomposition of the different parts of this complex system rather than performing an integrated analysis of the whole SL metabolism. In addition, since SL can be provided from exogenous sources, it is also of interest to evaluate their impact on the homeostasis of endogenous SL metabolism, which could be beneficial in prevention or treatment of obesity and related metabolic disorders.
       
  • miR-21 deficiency contributes to the impaired protective effects of obese
           rat mesenchymal stem cell-derived exosomes against spinal cord injury
    • Abstract: Publication date: Available online 9 October 2019Source: BiochimieAuthor(s): Wenchen Ji, Wanting Jiang, Meng Li, Jia Li, Zhiqiang Li The therapeutic effect of stem cell transplantation in traumatic spinal cord injury (SCI) has been extensively studied these days, and evidence has shown that stem cell-derived exosomes and exosome-shuttled miRNA (e.g. miR-21) contribute to the protective effects of stem cell transplantation against SCI. It has been reported that obesity, a prevalent metabolic disorder, reshapes stem cells and their extracellular vesicles. However, the effects of exosomes derived from obese rat stem cells on SCI and its underlying mechanism remain unknown. Here, we examined the effects of exosomes derived from obese rat mesenchymal stem cells (MSCs) on SCI, and tested the role of miR-21 in their effects. We found that exosomes derived from obese rat MSCs showed decreased miR-21 levels and did not exert protective effects against SCI. Overexpression of miR-21 in obese rat MSCs restored the protective effects of exosomes purified from obese rat MSCs against SCI. In addition, obese rat MSCs showed insulin resistance, and MSC insulin resistance decreased miR-21 levels in its secreted exosomes. These results suggested that miR-21 deficiency in obese rat MSCs contributes to the impaired protective effects of obese rat MSCs-derived exosomes against SCI, and further reinforced the notion that miR-21 is a potential molecule for treatment of SCI.
       
  • Allosteric regulation of the ribosomal A site revealed by molecular
           dynamics simulations
    • Abstract: Publication date: Available online 9 October 2019Source: BiochimieAuthor(s): T.M. Makarova, A.A. Bogdanov The A site of the ribosome, which determines binding and orientation of a new aminoacid residue for the peptidyl transferase reaction, was found to occupy two different conformational states upon the molecular dynamics (MD) simulations study of the 70S E. coli ribosome. One of the states, defined as ”inactive”, appeared in trajectories with E–tRNA, mutations A2531U and UU2492-3C, which are known to decrease the A site affinity to the tRNA. This conformational transition was found to be allosterically connected with conformational alterations in different sites of the macromolecular complex, including the E site of the ribosome and intersubunit bridge B7a located near the E site.The MD simulations of the ribosomes with the A2531U and UU2492-3C mutations known to decrease the A–tRNA retention in the ribosome, demonstrated partial switching of the 16S and 23S rRNA conformation towards its characteristic one in the P/P, E/E state.
       
  • Phospholipid packing defects and oxysterols in atherosclerosis: dietary
           prevention and the French paradox
    • Abstract: Publication date: Available online 3 October 2019Source: BiochimieAuthor(s): Ronald B. Brown The research literature on atherosclerosis includes findings investigating the atherosclerotic effect of oxysterols, which are the oxidation products of cholesterol; and the literature on oxysterols refers to mechanisms by which oxysterols cause phospholipid packing defects in cell membranes. This review synthesizes these two bodies of research findings to describe how oxysterols cause phospholipid packing defects within the membranes of vascular endothelial cells, potentially increasing cell permeability of low-density lipoprotein cholesterol which may lead to atheroma formation. Exogenous sources of oxysterols are provided by dietary intake of animal-based foods that contain cholesterol oxidation products. This review proposes an explanation for the anti-atherosclerotic effect of plant-based dietary patterns, which is attributed to restriction or avoidance of dietary oxysterol intake from animal-based foods. Furthermore, raw-milk cheeses play an important role in the traditional French diet—low oxysterol content in these unheated foods may contribute to the French paradox, in which reduced coronary heart disease is associated with a diet high in saturated fat and cholesterol.
       
  • Babesia divergens glycosylphosphatidylinositols modulate blood coagulation
           and induce Th2-biased cytokine profiles in antigen presenting cells
    • Abstract: Publication date: Available online 1 October 2019Source: BiochimieAuthor(s): Françoise Debierre-Grockiego, Terry K. Smith, Stéphane Delbecq, Céline Ducournau, Louis Lantier, Jörg Schmidt, Virginie Brès, Isabelle Dimier-Poisson, Ralph T. Schwarz, Emmanuel Cornillot Glycosylphosphatidylinositols (GPIs) are glycolipids described as toxins of protozoan parasites due to their inflammatory properties in mammalian hosts characterized by the production of interleukin (IL)-1, IL-12 and tumor necrosis factor (TNF)-α. In the present work, we studied the cytokines produced by antigen presenting cells in response to ten different GPI species extracted from Babesia divergens, responsible for babesiosis. Interestingly, B. divergens GPIs induced the production of anti-inflammatory cytokines (IL-2, IL-5) and of the regulatory cytokine IL-10 by macrophages and dendritic cells. In contrast to all protozoan GPIs studied until now, GPIs from B. divergens did not stimulate the production of TNF-α and IL-12, leading to a unique Th1/Th2 profile. Analysis of the carbohydrate composition of the B. divergens GPIs indicated that the di-mannose structure was different from the evolutionary conserved tri-mannose structure, which might explain the particular cytokine profile they induce. Expression of major histocompatibility complex (MHC) molecules on dendritic cells and apoptosis of mouse peritoneal cells were also analysed. B. divergens GPIs did not change expression of MHC class I, but decreased expression of MHC class II at the cell surface, while GPIs slightly increased the percentages of apoptotic cells. During pathogenesis of babesiosis, the inflammation-coagulation auto-amplification loop can lead to thrombosis and the effect of GPIs on coagulation parameters was investigated. Incubation of B. divergens GPIs with rat plasma ex vivo led to increase of fibrinogen levels and to prolonged activated partial thromboplastin time, suggesting a direct modulation of the extrinsic coagulation pathway by GPIs.
       
  • Arabidopsis LDIP protein locates at a confined area within the lipid
           droplet surface and favors lipid droplet formation
    • Abstract: Publication date: Available online 27 September 2019Source: BiochimieAuthor(s): Denis Coulon, Lysiane Brocard, Karine Tuphile, Claire Bréhélin Lipid droplets (LDs) are cell organelles specialized in neutral lipid storage. Extendedly studied in seeds, LDs also accumulate in leaves during senescence or in response to abiotic stresses. However the mechanisms underlying their biogenesis remain relatively unknown. Here, we deciphered the distinct roles of two proteins during LD biogenesis: LD-associated protein 1 (AtLDAP1) and LDAP-interacting protein (AtLDIP). We demonstrated that AtLDIP overexpression favors the neo-formation of small LDs under growing conditions where LD accumulation is usually not observed. In addition, atldip knock-out mutant displayed fewer but larger LDs, confirming a role of AtLDIP in LD biogenesis. Interestingly, a synergistic effect of the overexpression of both AtLDIP and AtLDAP1 was observed, resulting in an increase of LD cluster occurrence and LD abundance within the clusters and the cells. AtLDIP overexpression has no significant impact on triacylglycerol and steryl ester accumulation but AtLDIP inactivation is associated with an increase of neutral lipid content, that is probably a consequence of the enlarged but less abundant LDs present in this line. Our localization study demonstrated that AtLDIP is localized at specific dotted sites within the LD in contrast to AtLDAP1 that covers the whole LD. In addition, AtLDIP sometimes localized away from the LD marker, but always associated with the ER network, suggesting a location at LD nascent sites within the ER. Taken together, our results suggested that AtLDIP promotes the formation of new LDs from ER localized TAG lenses.
       
  • RcsB-dependent effects on nar operon regulation during the aerobic growth
           of Salmonella Typhimurium
    • Abstract: Publication date: Available online 27 September 2019Source: BiochimieAuthor(s): Mónica F. Torrez Lamberti, María Florencia Ballesteros, Fabián E. López, María de las Mercedes Pescaretti, Mónica A. Delgado The intracellular pathogen Salmonella is an important cause of human foodborne diseases worldwide. Salmonella takes advantage of the phosphorelay regulatory systems to survive in the hostile environment of the host´s gastrointestinal tract. It has been reported that the nitrate reductase Z (NR-Z), encoded by the narUZYV operon, is required during Salmonella transition to anaerobic environments and is constitutively produced at low levels, but little is known about the regulatory mechanism involved in the operon gene expression. In this work, we found that the RcsCDB system is activated by high concentrations of specific sugars as a carbon source. In this activation state, the RcsCDB system participates in the negative control of narUZYWV expression. This control strategy occurs during exponential growth when the carbon source is high, allowing for normal aerobic respiration. The RcsCDB system’s participation in aerobic respiration is necessary to ensure efficient metabolism and optimal energy consumption when the bacteria are growing exponentially.
       
  • Chlamydomonas cell cycle mutant crcdc5 over-accumulates
           starch and oil
    • Abstract: Publication date: Available online 26 September 2019Source: BiochimieAuthor(s): Ismael Torres-Romero, Fantao Kong, Bertrand Légeret, Fred Beisson, Gilles Peltier, Yonghua Li-Beisson The use of algal biomass for biofuel production requires improvements in both biomass productivity and its energy density. Green microalgae store starch and oil as two major forms of carbon reserves. Current strategies to increase the amount of carbon reserves often compromise algal growth. To better understand the cellular mechanisms connecting cell division to carbon storage, we examined starch and oil accumulation in two Chlamydomonas mutants deficient in a gene encoding a homolog of the Arabidopsis Cell Division Cycle 5 (CDC5), a MYB DNA binding protein known to be involved in cell cycle in higher plants. The two crcdc5 mutants (crcdc5-1 and crcdc5-2) were found to accumulate significantly higher amount of starch and oil than their corresponding parental lines. Flow cytometry analysis on synchronized cultures cultivated in a diurnal light/dark cycle revealed an abnormal division of the two mutants, characterized by a prolonged S/M phase, therefore demonstrating its implication in cell cycle in Chlamydomonas. Taken together, these results suggest that the energy saved by a slowdown in cell division is used for the synthesis of reserve compounds. This work highlights the importance in understanding the interplay between cell cycle and starch/oil homeostasis, which should have a critical impact on improving lipid/starch productivity.
       
  • Interactions of the Rad51 Inhibitor DIDS with Human and Bovine Serum
           Albumins: Optical Spectroscopy and IsoThermal Calorimetry Approaches
    • Abstract: Publication date: Available online 25 September 2019Source: BiochimieAuthor(s): Denis Velic, Cathy Charlier, Milena Popova, Titouan Jaunet-Lahary, Zakaria Bouchouireb, Sébastien Henry, Pierre Weigel, Jean-Yves Masson, Adele Laurent, Igor Nabiev, Fabrice Fleury Rad51 is a key protein in DNA repair by homologous recombination and an important target for development of drugs in cancer therapy. 4'-diisothiocyanostilbene-2,2'-disulfonic acid (DIDS) has been used in clinic during the past 30 years as an inhibitor of anion transporters and channels. Recently DIDS has been demonstrated to affect Rad51-mediated homologous pairing and strand exchange, key processes in homologous recombination. Consequently, DIDS has been considered as a potential revertant of radio- and chemo-resistance of cancer cells, the major causes of therapy failure.Here, we have investigated the behavior of DIDS towards serum albumins. The effects of environmental factors, primarily, solvent polarity, on DIDS stability were evaluated, and the mechanisms of interaction of DIDS with human or bovine serum albumin were analyzed using isothermal calorimetry, circular dichroism and fluorescence spectroscopies. DIDS interaction with both serum albumins have been demonstrated, and the interaction characteristics have been determined. By comparing these characteristics for several DIDS derivatives, we have identified the DIDS moiety essential for the interaction. Furthermore, site competition data indicate that human albumin has two DIDS-binding sites: a high-affinity site in the IIIA subdomain and a low-affinity one in the IB subdomain. Molecular docking has revealed the key molecular moieties of DIDS responsible for its interactions in each site and shown that the IB site can bind two ligands. These findings show that binding of DIDS to serum albumin may change the balance between the free and bound DIDS forms, thereby affecting its bioavailability and efficacy against Rad51.
       
  • Heterodimerizing helices as tools for nanoscale control of the
           organization of protein-protein and protein-quantum dots
    • Abstract: Publication date: Available online 24 September 2019Source: BiochimieAuthor(s): Olga Sztatelman, Katarzyna Kopeć, Marta Pędziwiatr, Martyna Trojnar, Remigiusz Worch, Beata Wielgus-Kutrowska, Małgorzata Jemioła-Rzemińska, Agnieszka Bzowska, Joanna Grzyb In this study, we tested the possibility of creating complexes of two proteins by fusing them with heterodimerizing helices. We used the fluorescent proteins GFP and mCHERRY expressed with a His-tag as our model system. We added heterodimer-forming sequences at the C- or N- termini of the proteins, opposite to the His-tag position. Heterodimerization was tested for both helices at the C-terminus or at the N- terminus and C-terminus. We observed complex formation with a nanomolar dissociation constant in both cases that was higher by one order of magnitude than the Kds measured for helices alone. The binding of two C-terminal helices was accompanied by an increased enthalpy change. The binding between helices could be stabilized by introducing an additional turn of the helix with cysteine, which was capable of forming disulphide bridges. Covalently linked proteins were obtained using this strategy and observed using fluorescence cross-correlation spectroscopy. Finally, we demonstrated the formation of complexes of protein dimers and quantum dots.Graphical abstractImage 1
       
  • Structural variations within proteins can be as large as variations
           observed across their homologues
    • Abstract: Publication date: Available online 24 September 2019Source: BiochimieAuthor(s): Iyanar Vetrivel, Alexandre G. de Brevern, Frédéric Cadet, Narayanaswamy Srinivasan, Bernard Offmann Understanding the structural plasticity of proteins is key to understanding the intricacies of their functions and mechanistic basis. In the current study, we analyzed the available multiple crystal structures of the same protein for the structural differences. For this purpose we used an abstraction of protein structures referred as Protein Blocks (PBs) that was previously established. We also characterized the nature of the structural variations for a few proteins using molecular dynamics simulations. In both the cases, the structural variations were summarized in the form of substitution matrices of PBs. We show that certain conformational states are preferably replaced by other specific conformational states. Interestingly, these structural variations are highly similar to those previously observed across structures of homologous proteins (r2=0.923) or across the ensemble of conformations from NMR data (r2=0.919). Thus our study quantitatively shows that overall trends of structural changes in a given protein are nearly identical to the trends of structural differences that occur in the topologically equivalent positions in homologous proteins. Specific case studies are used to illustrate the nature of these structural variations.Graphical abstractImage 1
       
  • Protocatechuic acid exhibits hepatoprotective, vasculoprotective,
           antioxidant and insulin-like effects in dexamethasone-induced
           insulin-resistant rats
    • Abstract: Publication date: Available online 23 September 2019Source: BiochimieAuthor(s): Yomna A. El-Sonbaty, Ghada M. Suddek, Nirmeen Megahed, Nariman M. Gameil Protocatechuic acid (PCA), the natural phenolic antioxidant, reportedly exhibited hypoglycemic and insulin-like effects. Recent studies have reported its cardioprotective effect in glucocorticoid (GC)-induced hypertensive rats. Nevertheless, its beneficial role has not been investigated in the setting of GCs excess-induced insulin resistance. This study aimed to investigate the possible protective potential and the plausible mechanisms of pretreatment with PCA against GCs-induced insulin resistance, liver steatosis and vascular dysfunction. Insulin resistance was induced in male Wistar rats by a 7-day treatment with dexamethasone (DEX) (1 mg/kg/day, i.p.). PCA (50, 100 mg/kg/day, orally) was started 7 days before DEX administration and continued during the test period. PCA significantly and dose-dependently attenuated DEX-induced a) glucose intolerance (↓ AUCOGTT), b) hyperglycemia (↓ fasting blood glucose), c) impaired insulin sensitivity [↓fasting plasma insulin and homeostasis model assessment of insulin resistance (HOMA-IR) index)] and d) dyslipidemia (↓total cholesterol, triglycerides, low-density lipoprotein-cholesterol and very low-density lipoprotein-cholesterol). PCA mitigated DEX-induced liver steatosis with associated reduction in serum alanine aminotransferase (ALT) and aspartate aminotransferase (AST) activity. Moreover, PCA ameliorated DEX-induced vascular dysfunction and enhanced ACh-induced relaxation in aortic rings. The metabolic ameliorating effects of PCA might be attributed to the enhanced insulin signaling in soleus muscles (↑AKT phosphorylation) and mitigating gluconeogenesis (↓ hepatic mRNA expression of phosphoenolpyruvate carboxykinase (PEPCK) and glucose-6-phosphatase (G6Pase). The vasculoprotective effect of PCA might be related to its ability to restore normal mRNA expression of [endothelial nitric oxide synthase (eNOS) and NADPH Oxidase 4 (NOX4)]. PCA restored normal oxidative balance [↓ oxidant species, malondialdehyde (MDA) and (↑ antioxidant superoxide dismutase (SOD)]. The findings herein reveal for the first time that PCA may be taken as a supplement with GCs to limit their metabolic and vascular side effects through its hypoglycemic, insulin-sensitizing, hypolipidemic and antioxidant effects.Graphical abstractImage 1
       
  • Microalgal carotenoids and phytosterols regulate biochemical mechanisms
           involved in human health and disease prevention
    • Abstract: Publication date: Available online 20 September 2019Source: BiochimieAuthor(s): Manon Le Goff, Eric Le Ferrec, Claire Mayer, Virginie Mimouni, Dominique Lagadic-Gossmann, Benoît Schoefs, Lionel Ulmann Microalgae are photosynthetic microorganisms that produce numerous bioactive molecules that can be used as food supplement to prevent chronic disease installation. Indeed, they produce phycobiliproteins, polysaccharides, lipids, carotenoids and sterolic compounds. The use of microalgae in human nutrition provide a mixture of these molecules with synergistic effect.The aim of this review is to present the specific roles played by the xanthophylls, and specifically astaxanthin and fucoxanthin, two high added value carotenoids, and by microalgal phytosterols such as β-sitosterol, campesterol and stigmasterol on several cell mechanisms involved in the prevention of cardiometabolic diseases and cancers.This review explains how these microalgal molecules modulate cell signaling pathways involved in carbohydrate and lipid metabolisms, inflammation, apoptosis, invasion and metastasis. Xanthophylls and phytosterols are involved in the reduction of inflammatory markers in relation with the regulation of the c-Jun N-terminal kinases and nuclear factor-kappa B signaling pathways, and suppression of production of pro-inflammatory mediators. Xanthophylls act on glucose and lipid metabolisms via both the upregulation of peroxisome proliferator-activated receptors (PPARs) and glucose transporters and its effects on the expression of enzymes involved in fatty acid synthesis and cholesterol metabolism. Their anti-cancer effects are related to the induction of intrinsic apoptosis due to down-regulation of key regulatory kinases. The anti-angiogenesis, anti-proliferative and anti-invasive effects are correlated with decreased production of endothelial growth factors and of matrix metalloproteinases.Phytosterols have a major role on cholesterol absorption via modification of the activities of Niemann-Pick C1 like 1 and ATP-binding cassette transporters and on cholesterol esterification. Their action are also related with the modulation of PPARs and sterol regulatory element-binding protein-1 activities.Graphical abstractImage 1
       
  • A topology-based investigation of protein interaction sites using
           Hydrophobic Cluster Analysis
    • Abstract: Publication date: Available online 13 September 2019Source: BiochimieAuthor(s): Alexis Lamiable, Tristan Bitard-Feildel, Joseph Rebehmed, Flavien Quintus, Françoise Schoentgen, Jean-Paul Mornon, Isabelle Callebaut Hydrophobic clusters, as defined by Hydrophobic Cluster Analysis (HCA), are conditioned binary patterns, made of hydrophobic and non-hydrophobic positions, whose limits fit well those of regular secondary structures. They were proved to be useful for predicting secondary structures in proteins from the only information of a single amino acid sequence and have permitted to assess, in a comprehensive way, the leading role of binary patterns in RSS preference towards a particular state. Here, we considered the available experimental 3D structures of protein globular domains to enlarge our previously reported hydrophobic cluster database (HCDB), almost doubling the number of hydrophobic cluster species (each species being defined by a unique binary pattern) that represent the most frequent structural bricks encountered within protein globular domains. We then used this updated HCDB to show that the hydrophobic amino acids of discordant clusters, i.e. those less abundant clusters for which the observed secondary structure is in disagreement with the binary pattern preference of the species to which they belong, are more exposed to solvent and are more involved in protein interfaces than the hydrophobic amino acids of concordant clusters. As amino acid composition differs between concordant/discordant clusters, considering binary patterns may be used to gain novel insights into key features of protein globular domain cores and surfaces. It can also provide useful information on possible conformational plasticity, including disorder to order transitions.Graphical abstractImage 1
       
  • Oligoglutamylation of E. coli ribosomal protein S6 is under
           growth phase control
    • Abstract: Publication date: Available online 11 September 2019Source: BiochimieAuthor(s): Philipp I. Pletnev, Mikhail V. Nesterchuk, Maria P. Rubtsova, Marina V. Serebryakova, Ksenia Dmitrieva, Ilya A. Osterman, Alexey A. Bogdanov, Petr V. Sergiev Ribosomal protein S6 in Escherichia coli is modified by ATP-dependent glutamate ligase RimK. Up to four glutamate residues are added to the C-terminus of S6 protein. In this work we demonstrated that unlike the majority of ribosome modifications in E. coli, oligoglutamylation of S6 protein is regulated and happens only in the stationary phase of bacterial culture. Only S6 protein incorporated into assembled small ribosomal subunits, but not newly made free S6 protein is a substrate for RimK protein. Overexpression of the rimK gene leads to the modification of S6 protein even in the exponential phase of bacterial culture. Thus, it is unlikely that any stationary phase specific factor is needed for the modification. We propose a model that S6 modification is regulated solely via the rate of ribosome biosynthesis at limiting concentration of RimK enzyme.
       
  • GKN1 expression in gastric cancer cells is negatively regulated by
           miR-544a
    • Abstract: Publication date: Available online 8 September 2019Source: BiochimieAuthor(s): Chiara Stella di Stadio, Raffaella Faraonio, Antonella Federico, Filomena Altieri, Emilia Rippa, Paolo ArcariABSTRACTGastrokine1 (GKN1), important for maintaining the physiological function of the gastric mucosa, is highly expressed in the stomach of healthy individuals but is down-regulated or absent in gastric tumor tissues and derived cell lines. The mechanisms underlying GKN1 gene inactivation are still unknown. We previously showed that GKN1 downregulation in gastric tumors is likely associated with an epigenetic transcriptional complex that negatively regulates GKN1 expression. In addition, TSA-mediated inhibition of HDACs leads to GKN1 restoration at the transcriptional level, but no at the translational level. These findings led to hypothesize the activation of a second regulatory mechanism microRNAs-mediated, thus resulting in translational repression and gene silencing. Bioinformatic analyses performed with 5 different algorithms highlighted that 4 miRNAs contained a seed sequence for the 3’UTR of GKN1 mRNA. Among these, only two miRNAs, hsa-miR-544a and miR-1245b-3p directly target the GKN1-3’UTR as evaluated by luciferase reporter assays. TaqMan miRNA assay performed on gastric cancer cell lines after TSA treatment showed a stronger increase of miR-544a expression than that of miR-1245b-3p. Finally, co-transfection of AGS cells with GKN1-3’UTR and premiR-544a showed compared to controls, a strong reduction of GKN1 expression both at translational and transcriptional levels. The up-regulation of miR-544a could be crucially involved in the GKN1 translational repression, thus suggesting its potential role as a biomarker and therapeutic target in GC patients. These findings indicate that epigenetic mechanisms leading to the inactivation of GKN1 play a key role in the multi-step process of gastric carcinogenesis and would provide an essential starting point for the development of new therapeutic strategies based on epigenetic targets for alternatives gene.
       
  • Guide RNA modification as a way to improve CRISPR/Cas9-based
           genome-editing systems
    • Abstract: Publication date: Available online 4 September 2019Source: BiochimieAuthor(s): Julia Filippova, Anastasiya Matveeva, Evgenii Zhuravlev, Grigory Stepanov Genome-editing technologies, in particular, CRISPR systems, are widely used for targeted regulation of gene expression and obtaining modified human and animal cell lines, plants, fungi, and animals with preassigned features. Despite being well described and easy to perform, the most common methods for construction and delivery of CRISPR/Cas9-containing plasmid systems possess significant disadvantages, mostly associated with effects of the presence of exogenous DNA within the cell. Transfection with active ribonucleoprotein complexes of Cas9 with single-guide RNAs (sgRNAs) represents one of the most promising options because of faster production of sgRNAs, the ability of a researcher to control the amount of sgRNA delivered into the cell, and consequently, fewer off-target mutations. Artificial-RNA synthesis strategies allow for the introduction of various modified components, such as backbone alterations, native structural motifs, and labels for visualization. Modifications of RNA can increase its resistance to hydrolysis, alter the thermodynamic stability of RNA–protein and RNA–DNA complexes, and reduce the immunogenic and cytotoxic effects. This review describes various approaches to improving synthetic guide RNA function through nucleotide modification.Graphical abstractImage 1
       
  • MicroRNA biogenesis, gene silencing mechanisms and role in breast, ovarian
           and prostate cancer
    • Abstract: Publication date: Available online 4 September 2019Source: BiochimieAuthor(s): Sanna Khan, Humaira Ayub, Taous Khan, Fazli Wahid Micro-ribonucleic acids (miRNAs) are important class of short regulatory RNA molecules involved in regulation of several essential biological processes. In addition to Dicer and Drosha, over the past few years several other gene products are discovered that regulates miRNA biogenesis pathways. Similarly, various models of molecular mechanisms underlying miRNA mediated gene silencing have been uncovered through which miRNA contribute in diverse physiological and pathological processes. Dysregulated miRNA expression has been reported in many cancers manifesting tumor suppressive or oncogenic role. In this review, critical overview of recent findings in miRNA biogenesis, silencing mechanisms and specifically the role of miRNA in breast, ovarian and prostate cancer will be described. Recent advancements in miRNA research summarized in this review will enhance the molecular understanding of miRNA biogenesis and mechanism of action. Also, role of miRNAs in pathogenesis of breast, ovarian and prostate cancer will provide the insights for the use of miRNAs as biomarker or therapeutic agents for the cancers.
       
  • Ribonucleoside Triphosphates Promote T7 DNA Replication and the Lysis of
           T7-Infected Escherichia coli
    • Abstract: Publication date: Available online 4 September 2019Source: BiochimieAuthor(s): Zhenyu Zou, Wendi Xu, Chenyang Mi, Ying Xu, Ke Du, Bianbian Li, Yang Ye, Yihui Ling, Huidong Zhang rNTPs are structurally similar to dNTPs, but their concentrations are much higher than those of dNTPs in cells. rNTPs in solutions or rNMP at the primer terminus or embedded in template always inhibit or block DNA replication, due to the reduced Mg2+ apparent concentration, competition of rNTPs with dNTPs, and the extra repulsive interaction of rNTP or rNMP with polymerase active site. In this work, unexpectedly, we found rNTPs can promote T7 DNA replication with the maximal promotion at rNTPs/dNTPs concentration ratio of 20. This promotion was not due to the optimized Mg2+ apparent concentration or the direct incorporation of extra rNMPs into DNA. This promotion was dependent on the concentrations and types of rNTPs. Kinetic analysis showed that this promotion was originated from the increased fraction of polymerase-DNA productive complex and the accelerated DNA polymerization. Further evidence showed that more polymerase-DNA complex was formed and their binding affinity was also enhanced in the presence of extra rNTPs. Moreover, this promotion in T7 DNA replication also accelerated the lysis of T7-infected host Escherichia coli. This work discovered that rNTPs could promote DNA replication, completely different from the traditional concept that rNTPs always inhibit DNA replication.
       
  • ArgR directly inhibits lipA transcription in Pseudomonas
           protegens
    Pf-5
    • Abstract: Publication date: Available online 3 September 2019Source: BiochimieAuthor(s): Wei Ying, Xing-lian Wang, Hong-qiu Shi, Li-wei Yan, Bing-huo Zhang, Han-quan Li, Jian-yuan Yang, Dai-ming Zha ArgR, a transcriptional regulator belonging to the AraC/XylS family, plays a key role in arginine metabolism regulation. ArgR has also been found to repress the transcription of a lipase gene, but its molecular mechanism is still unknown. In this study, we investigated the molecular mechanism acting on the expression of intracellular lipase gene lipA regulated by ArgR in Pseudomonas protegens Pf-5 through knockout and overexpression of argR, detection of DNA-protein interaction in vivo, determining whole-cell lipase activities of various strains derived from Pf-5, and examining β-galactosidase activities of various lacZ fusions. The results demonstrated that ArgR inhibits lipA expression at the transcriptional level. Further results showed that the inhibition of lipA transcription by ArgR is mediated by binding to the ArgR binding site of lipA promoter to produce steric hindrance, in which the common sequence, TGTCGC is crucial for the ArgR binding. Besides, arginine inhibits lipA expression in both wild-type and argR mutant, and shows a synergistic inhibition on lipA expression when combined with ArgR. To the best of our knowledge, this is the first report on ArgR directly repressing the transcription of lipase gene.
       
  • Diversity of astacin-like metalloproteases identified by transcriptomic
           analysis in Peruvian Loxosceles laeta spider venom and in vitro activity
           characterization
    • Abstract: Publication date: Available online 30 August 2019Source: BiochimieAuthor(s): Raíssa Medina Santos, Clara Guerra-Duarte, Sabrina de Almeida Lima, Fernanda Costal-Oliveira, Priscilla Alves de Aquino, Anderson Oliveira do Carmo, César Bonilla Ferreyra, Edgar E. Gonzalez-Kozlova, Evanguedes Kalapothakis, Carlos Chavez-Olortegui Loxosceles spiders are found in almost all countries of South America. In Peru, Loxosceles laeta species is the main responsible for the accidents caused by poisonous animals, being known as "killer spiders", due to the large number of fatal accidents observed. Astacin-like metalloproteases, named LALPs (Loxosceles astacin-like metalloproteases) are highly expressed in Loxosceles spiders venom gland. These proteases may be involved in hemorrhage and venom spreading, being relevant to the envenoming proccess. Thus, the aim of this work was to analyze Peruvian L. laeta venom gland transcripts using bioinformatics tools, focusing on LALPs. A cDNA library from Peruvian L. laeta venom glands was constructed and sequenced by MiSeq (Illumina) sequencer. After assembly, the resulting sequences were annotated, seeking out for similarity with previously described LALPs. Nine possible LALPs isoforms from Peruvian L. laeta venom were identified and the results were validated by in silico and in vitro experiments. This study contributes to a better understanding of the molecular diversity of Loxosceles venom and provide insights about the action of LALPs.
       
  • Modulating DNA by polyamides to regulate transcription factor PU.1-DNA
           binding interactions
    • Abstract: Publication date: Available online 21 August 2019Source: BiochimieAuthor(s): Beibei Liu, James K. Bashkin, Gregory M.K. Poon, Shuo Wang, Siming Wang, W. David Wilson Hairpin polyamides are synthetic small molecules that bind DNA minor groove sequence-selectively and, in many sequences, induce widening of the minor groove and compression of the major groove. The structural distortion of DNA caused by polyamides has enhanced our understanding of the regulation of DNA-binding proteins via polyamides. Polyamides have DNA binding affinities that are comparable to those proteins, therefore, can potentially be used as therapeutic agents to treat diseases caused by aberrant gene expression. In fact, many diseases are characterized by over- or under-expressed genes. PU.1 is a transcription factor that regulates many immune system genes. Aberrant expression of PU.1 has been associated with the development of acute myeloid leukemia (AML). We have, therefore, designed and synthesized ten hairpin polyamides to investigate their capacity in controlling the PU.1-DNA interaction. Our results showed that nine of the polyamides disrupt PU.1-DNA binding and the inhibition capacity strongly correlates with binding affinity. One molecule, FH1024, was observed forming a FH1024-PU.1-DNA ternary complex instead of inhibiting PU.1-DNA binding. This is the first report of a small molecule that is potentially a weak agonist that recruits PU.1 to DNA. This finding sheds light on the design of polyamides that exhibit novel regulatory mechanisms on protein-DNA binding.Graphical abstractImage 1
       
  • Protein-protein interactions regulate the activity of Adipose Triglyceride
           Lipase in intracellular lipolysis
    • Abstract: Publication date: Available online 9 August 2019Source: BiochimieAuthor(s): Natalia Kulminskaya, Monika Oberer Carefully regulated lipid homeostastis generates an optimal physiological, non-toxic environment. Imbalances in lipid metabolism lead to obesity and are associated with type-2 diabetes, hepatic steatosis, hypertension and cardiovascular disease. Mammals store energy in lipid droplets predominantly in white adipose tissue. This energy reservoir builds up during periods of energy excess and is mobilized during energy deprivation. Triacylglycerols (TAGs) are unable to cross cell membranes for cell nutrition; they have to be cleaved before further transportation within the body. Lipolysis describes the cleavage of TAG and is carried out with the help of lipases. Adipose triglyceride lipase (ATGL) catalyzes the first step of intracellular lipolysis to mobilize TAG stores. In this minireview, we set the focus on molecular mechanism and interfaces behind co-activation and inhibition of ATGL, namely via its regulation by the co-activating protein CGI-58, the inhibitory proteins G0S2 and HILPDA, as well as the regulatory effect of fatty acid binding proteins and the perilipin protein family.
       
  • Mouse Fat-Specific Protein 27 (FSP27) expressed in plant cells localizes
           to lipid droplets and promotes lipid droplet accumulation and fusion
    • Abstract: Publication date: Available online 7 August 2019Source: BiochimieAuthor(s): Ann M. Price, Nathan M. Doner, Satinder K. Gidda, Srikarthika Jambunathan, Christopher N. James, Alyssa Schami, Olga Yurchenko, Robert T. Mullen, John M. Dyer, Vishwajeet Puri, Kent D. Chapman Fat-Specific Protein 27 (FSP27) belongs to a small group of vertebrate proteins containing a Cell-death Inducing DNA fragmentation factor-α-like Effector (CIDE)-C domain and is involved in lipid droplet (LD) accumulation and energy homeostasis. FSP27 is predominantly expressed in white and brown adipose tissues, as well as liver, and plays a key role in mediating LD-LD fusion. No orthologs have been identified in invertebrates or plants. In this study, we tested the function of mouse FSP27 in stably-transformed Arabidopsis thaliana leaves and seeds, as well as through transient expression in Nicotiana tabacum suspension-cultured cells and N. benthamiana leaves. Confocal microscopic analysis of plant cells revealed that, similar to ectopic expression in mammalian cells, FSP27 produced in plants 1) correctly localized to LDs, 2) accumulated at LD-LD contact sites, and 3) induced an increase in the number and size of LDs and also promoted LD clustering and fusion. Furthermore, FSP27 increased oil content in transgenic A. thaliana seeds. Given that plant oils have uses in human and animal nutrition as well as industrial uses such as biofuels and bioplastics, our results suggest that ectopic expression of FSP27 in plants represents a potential strategy for increasing oil content and energy density in bioenergy or oilseed crops.Graphical abstractImage 1
       
  • Relationship between acyl-lipid and sterol metabolisms in diatoms
    • Abstract: Publication date: Available online 7 July 2019Source: BiochimieAuthor(s): Eric Maréchal, Josselin Lupette Diatoms are a phylum of unicellular photosynthetic eukaryotes living in oceans and fresh waters, characterized by the complexity of their plastid, resulting from a secondary endosymbiosis event. In the model diatom Phaeodactylum tricornutum, fatty acids (FAs) are synthesized from acetyl-CoA in the stroma of the plastid, producing palmitic acid. FAs are elongated and desaturated to form very-long chain polyunsaturated fatty acids (VLC-PUFAs) in domains of the endomembrane system that need to be identified. Synthesis of VLC-PUFAs is coupled with their import to the core of the plastid via the so-called “omega” pathway. The biosynthesis of sterols in diatoms is likely to be localized in the endoplasmic reticulum as well as using precursors deriving from the mevalonate pathway, using acetyl-CoA as initial substrate. These metabolic modules can be characterized functionally by genetic analyzes or chemical treatments with appropriate inhibitors. Some ‘metabolic modules’ are characterized by a very low level of metabolic intermediates. Since some chemical treatments or genetic perturbation of lipid metabolism induce the accumulation of these intermediates, channeling processes are possibly involved, suggesting that protein-protein interactions might occur between enzymes within large size complexes or metabolons. At the junction of these modules, metabolic intermediates might therefore play dramatic roles in directing carbon fluxes from one direction to another. Here, acetyl-CoA seems determinant in the balance between TAGs and sterols. Future lines of research and potential utilization for biotechnological applications are discussed.
       
  • Characterization of all the lipolytic activities in pancreatin and
           comparison with porcine and human pancreatic juices
    • Abstract: Publication date: Available online 6 July 2019Source: BiochimieAuthor(s): Amal Salhi, Sawsan Amara, Pascal Mansuelle, Rémy Puppo, Régine Lebrun, Brigitte Gontero, Ahmed Aloulou, Frédéric Carrière Porcine pancreatic extracts (PPE), also named pancreatin, are commonly used as a global source of pancreatic enzymes for enzyme replacement therapy in patients with exocrine pancreatic insufficiency. They are considered as a good substitute of human pancreatic enzymes and they have become a material of choice for in vitro models of digestion. Nevertheless, while the global PPE contents in lipase, protease and amylase activities are well characterized, little is known about individual enzymes. Here we characterized the lipase, phospholipase, cholesterol esterase and galactolipase activities of PPE and compared them with those of porcine (PPJ) and human (HPJ) pancreatic juices. The phospholipase to lipase activity ratio was similar in PPJ and HPJ, but was 4-fold lower in PPE. The galactolipase and cholesterol esterase activities were found at lower levels in PPJ compared to HPJ, and they were further reduced in PPE. The enzymes known to display these activities in HPJ, pancreatic lipase-related protein 2 (PLRP2) and carboxylester hydrolase/bile salt-stimulated lipase (CEH/BSSL), were identified in PPJ using gel filtration experiments, SDS-PAGE and LC-MS/MS analysis. The galactolipase and cholesterol esterase activities of PPE indicated that PLRP2 and CEH/BSSL are still present at low levels in this enzyme preparation, but they were not detected by mass spectrometry. Besides differences between porcine and human enzymes, the lower levels of phospholipase, galactolipase and cholesterol esterase activities in PPE are probably due to some proteolysis occurring during the production process. In conclusion, PPE do not provide a full substitution of the lipolytic enzymes present in HPJ.
       
  • Targeting TOR signaling for enhanced lipid productivity in algae
    • Abstract: Publication date: Available online 29 June 2019Source: BiochimieAuthor(s): Laura Prioretti, Frédéric Carriere, Ben Field, Luisana Avilan, Marie-Hélène Montané, Benoît Menand, Brigitte Gontero Microalgae can produce large quantities of triacylglycerols (TAGs) and other neutral lipids that are suitable for making biofuels and as feedstocks for green chemistry. However, TAGs accumulate under stress conditions that also stop growth, leading to a trade-off between biomass production and TAG yield. Recently, in the model marine diatom Phaeodactylum tricornutum it was shown that inhibition of the target of rapamycin (TOR) kinase boosts lipid productivity by promoting TAG production without stopping growth. We believe that basic knowledge in this emerging field is required to develop innovative strategies to improve neutral lipid accumulation in oleaginous microalgae. In this minireview, we discuss current research on the TOR signaling pathway with a focus on its control on lipid homeostasis. We first provide an overview of the well characterized roles of TOR in mammalian lipogenesis, adipogenesis and lipolysis. We then present evidence of a role for TOR in controlling TAG accumulation in microalgae, and draw parallels between the situation in animals, plants and microalgae to propose a model of TOR signaling for TAG accumulation in microalgae.
       
 
 
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