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Journal of Bacteriology
Journal Prestige (SJR): 1.885
Citation Impact (citeScore): 3
Number of Followers: 31  
 
  Hybrid Journal Hybrid journal (It can contain Open Access articles)
ISSN (Print) 0021-9193 - ISSN (Online) 1098-5530
Published by American Society for Microbiology Homepage  [17 journals]
  • Editorial Board [Masthead]

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      PubDate: 2021-05-20T08:00:27-07:00
      DOI: 10.1128/JB.masthead.203-12
      Issue No: Vol. 203, No. 12 (2021)
       
  • Nitrate-Responsive Suppression of Dimethyl Sulfoxide Respiration in a
           Facultative Anaerobic Haloarchaeon, Haloferax volcanii [Article]

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      Authors: Koyanagi, I; Dohra, H, Fujiwara, T.
      Abstract: Haloferax volcanii is a facultative anaerobic haloarchaeon that can grow using nitrate or dimethyl sulfoxide (DMSO) as a respiratory substrate under anaerobic conditions. Comparative transcriptome analysis of denitrifying and aerobic cells of H. volcanii indicated extensive changes in gene expression involving the activation of denitrification, suppression of DMSO respiration, and conversion of the heme biosynthetic pathway under denitrifying conditions. The anaerobic growth of H. volcanii by DMSO respiration was inhibited at nitrate concentrations of
      PubDate: 2021-05-20T08:00:27-07:00
      DOI: 10.1128/JB.00655-20
      Issue No: Vol. 203, No. 12 (2021)
       
  • Investigation of Burkholderia cepacia Complex Methylomes via
           Single-Molecule, Real-Time Sequencing and Mutant Analysis [Article]

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      Authors: Mannweiler, O; Pinto-Carbo, M, Lardi, M, Agnoli, K, Eberl, L.
      Abstract: Bacterial genomes can be methylated at particular motifs by methyltransferases (MTs). This DNA modification allows restriction endonucleases (REs) to discriminate between self and foreign DNA. While the accepted primary function of such restriction modification (RM) systems is to degrade incoming foreign DNA, other roles of RM systems and lone RE or MT components have been found in genome protection, stability, and the regulation of various phenotypes. The Burkholderia cepacia complex (Bcc) is a group of closely related opportunistic pathogens with biotechnological potential. Here, we constructed and analyzed mutants lacking various RM components in the clinical Bcc isolate Burkholderia cenocepacia H111 and used single-molecule, real-time (SMRT) sequencing of single mutants to assign the B. cenocepacia H111 MTs to their cognate motifs. DNA methylation is shown to affect biofilm formation, cell shape, motility, siderophore production, and membrane vesicle production. Moreover, DNA methylation had a large effect on the maintenance of the Bcc virulence megaplasmid pC3. Our data also suggest that the gp51 MT-encoding gene, which is essential in H111 and is located within a prophage, is required for maintaining the bacteriophage in a lysogenic state, thereby ensuring a constant, low level of phage production within the bacterial population.IMPORTANCE While the genome sequence determines an organism’s proteins, methylation of the nucleotides themselves can confer additional properties. In bacteria, MTs modify specific nucleotide motifs to allow discrimination of "self" from "nonself" DNA, e.g., from bacteriophages. Restriction enzymes detect "nonself" methylation patterns and cut foreign DNA. Furthermore, methylation of promoter regions can influence gene expression and hence affect various phenotypes. In this study, we determined the methylated motifs of four strains from the Burkholderia cepacia complex of opportunistic pathogens. We deleted all genes encoding the restriction and modification components in one of these strains, Burkholderia cenocepacia H111. It is shown that DNA methylation affects various phenotypic traits, the most noteworthy being lysogenicity of a bacteriophage and maintenance of a virulence megaplasmid.
      PubDate: 2021-05-20T08:00:27-07:00
      DOI: 10.1128/JB.00683-20
      Issue No: Vol. 203, No. 12 (2021)
       
  • The Selenophosphate Synthetase Gene, selD, Is Important for Clostridioides
           difficile Physiology [Article]

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      Authors: McAllister, K. N; Martinez Aguirre, A, Sorg, J. A.
      Abstract: The endospore-forming pathogen Clostridioides difficile is the leading cause of antibiotic-associated diarrhea and is a significant burden on the community and health care. C. difficile, like all forms of life, incorporates selenium into proteins through a selenocysteine synthesis pathway. The known selenoproteins in C. difficile are involved in a metabolic process that uses amino acids as the sole carbon and nitrogen source (Stickland metabolism). The Stickland metabolic pathway requires the use of two selenium-containing reductases. In this study, we built upon our initial characterization of the CRISPR-Cas9-generated selD mutant by creating a CRISPR-Cas9-mediated restoration of the selD gene at the native locus. Here, we use these CRISPR-generated strains to analyze the importance of selenium-containing proteins on C. difficile physiology. SelD is the first enzyme in the pathway for selenoprotein synthesis, and we found that multiple aspects of C. difficile physiology were affected (e.g., growth, sporulation, and outgrowth of a vegetative cell post-spore germination). Using transcriptome sequencing (RNA-seq), we identified multiple candidate genes which likely aid the cell in overcoming the global loss of selenoproteins to grow in medium which is favorable for using Stickland metabolism. Our results suggest that the absence of selenophosphate (i.e., selenoprotein synthesis) leads to alterations to C. difficile physiology so that NAD+ can be regenerated by other pathways.IMPORTANCE C. difficile is a Gram-positive, anaerobic gut pathogen which infects thousands of individuals each year. In order to stop the C. difficile life cycle, other nonantibiotic treatment options are in urgent need of development. Toward this goal, we find that a metabolic process used by only a small fraction of the microbiota is important for C. difficile physiology: Stickland metabolism. Here, we use our CRISPR-Cas9 system to "knock in" a copy of the selD gene into the deletion strain to restore selD at its native locus. Our findings support the hypothesis that selenium-containing proteins are important for several aspects of C. difficile physiology, from vegetative growth to spore formation and outgrowth postgermination.
      PubDate: 2021-05-20T08:00:26-07:00
      DOI: 10.1128/JB.00008-21
      Issue No: Vol. 203, No. 12 (2021)
       
  • Different Resource Allocation in a Bacillus subtilis Population Displaying
           Bimodal Motility [Article]

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      Authors: Syvertsson, S; Wang, B, Staal, J, Gao, Y, Kort, R, Hamoen, L. W.
      Abstract: To cope with sudden changes in their environment, bacteria can use a bet-hedging strategy by dividing the population into cells with different properties. This so-called bimodal or bistable cellular differentiation is generally controlled by positive feedback regulation of transcriptional activators. Due to the continuous increase in cell volume, it is difficult for these activators to reach an activation threshold concentration when cells are growing exponentially. This is one reason why bimodal differentiation is primarily observed from the onset of the stationary phase, when exponential growth ceases. An exception is the bimodal induction of motility in Bacillus subtilis, which occurs early during exponential growth. Several mechanisms have been put forward to explain this, including double-negative feedback regulation and the stability of the mRNA molecules involved. In this study, we used fluorescence-assisted cell sorting (FACS) to compare the transcriptomes of motile and nonmotile cells and noted that expression of ribosomal genes is lower in motile cells. This was confirmed using an unstable green fluorescent protein (GFP) reporter fused to the strong ribosomal rpsD promoter. We propose that the reduction in ribosomal gene expression in motile cells is the result of a diversion of cellular resources to the synthesis of the chemotaxis and motility systems. In agreement with this, single-cell microscopic analysis showed that motile cells are slightly shorter than nonmotile cells, an indication of slower growth. We speculate that this growth rate reduction can contribute to the bimodal induction of motility during exponential growth.IMPORTANCE To cope with sudden environmental changes, bacteria can use a bet-hedging strategy and generate different types of cells within a population—so-called bimodal differentiation. For example, a Bacillus subtilis culture can contain both motile and nonmotile cells. In this study, we compared the gene expression between motile and nonmotile cells. It appeared that motile cells express fewer ribosomes. To confirm this, we constructed a ribosomal promoter fusion that enabled us to measure expression of this promoter in individual cells. This reporter fusion confirmed our initial finding. The reallocation of cellular resources from ribosome synthesis toward synthesis of the motility apparatus results in a reduction in growth. Interestingly, this growth reduction has been shown to stimulate bimodal differentiation.
      PubDate: 2021-05-20T08:00:26-07:00
      DOI: 10.1128/JB.00037-21
      Issue No: Vol. 203, No. 12 (2021)
       
  • A-Type Carrier Proteins Are Involved in [4Fe-4S] Cluster Insertion into
           the Radical S-Adenosylmethionine Protein MoaA for the Synthesis of Active
           Molybdoenzymes [Article]

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      Authors: Hasnat, M. A; Zupok, A, Olas, J. J, Mueller-Roeber, B, Leimkühler, S.
      Abstract: Iron sulfur (Fe-S) clusters are important biological cofactors present in proteins with crucial biological functions, from photosynthesis to DNA repair, gene expression, and bioenergetic processes. For the insertion of Fe-S clusters into proteins, A-type carrier proteins have been identified. So far, three of them have been characterized in detail in Escherichia coli, namely, IscA, SufA, and ErpA, which were shown to partially replace each other in their roles in [4Fe-4S] cluster insertion into specific target proteins. To further expand the knowledge of [4Fe-4S] cluster insertion into proteins, we analyzed the complex Fe-S cluster-dependent network for the synthesis of the molybdenum cofactor (Moco) and the expression of genes encoding nitrate reductase in E. coli. Our studies include the identification of the A-type carrier proteins ErpA and IscA, involved in [4Fe-4S] cluster insertion into the radical S-adenosyl-methionine (SAM) enzyme MoaA. We show that ErpA and IscA can partially replace each other in their role to provide [4Fe-4S] clusters for MoaA. Since most genes expressing molybdoenzymes are regulated by the transcriptional regulator for fumarate and nitrate reduction (FNR) under anaerobic conditions, we also identified the proteins that are crucial to obtain an active FNR under conditions of nitrate respiration. We show that ErpA is essential for the FNR-dependent expression of the narGHJI operon, a role that cannot be compensated by IscA under the growth conditions tested. SufA does not appear to have a role in Fe-S cluster insertion into MoaA or FNR under anaerobic growth employing nitrate respiration, based on the low level of gene expression.IMPORTANCE Understanding the assembly of iron-sulfur (Fe-S) proteins is relevant to many fields, including nitrogen fixation, photosynthesis, bioenergetics, and gene regulation. Remaining critical gaps in our knowledge include how Fe-S clusters are transferred to their target proteins and how the specificity in this process is achieved, since different forms of Fe-S clusters need to be delivered to structurally highly diverse target proteins. Numerous Fe-S carrier proteins have been identified in prokaryotes like Escherichia coli, including ErpA, IscA, SufA, and NfuA. In addition, the diverse Fe-S cluster delivery proteins and their target proteins underlie a complex regulatory network of expression, to ensure that both proteins are synthesized under particular growth conditions.
      PubDate: 2021-05-20T08:00:26-07:00
      DOI: 10.1128/JB.00086-21
      Issue No: Vol. 203, No. 12 (2021)
       
  • An Extracytoplasmic Function Sigma/Anti-Sigma Factor System Regulates
           Hypochlorous Acid Resistance and Impacts Expression of the Type IV
           Secretion System in Brucella melitensis [Article]

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      Authors: Li, H; Hu, S, Yan, X, Yang, Y, Liu, W, Bu, Z, Li, G, Cai, W.
      Abstract: The intracellular bacterial pathogen Brucella causes persistent infections in various mammalian species. To survive and replicate within macrophages, these bacteria must be able to withstand oxidative stresses and express the type IV secretion system (T4SS) to evade host immune responses. The extracytoplasmic function (ECF) sigma factor system is a major signal transduction mechanism in bacteria that senses environmental cues and responds by regulating gene expression. In this study, we defined an ECF bcrS and its cognate anti- factor abcS in Brucella melitensis M28 by conserved domain analysis and a protein interaction assay. BcrS directly activates an adjacent operon, bcrXQP, that encodes a methionine-rich peptide and a putative methionine sulfoxide reductase system, whereas AbcS is a negative regulator of bcrS and bcrXQP. The bcrS-abcS and bcrXQP operons can be induced by hypochlorous acid and contribute to hypochlorous acid resistance in vitro. Next, RNA sequencing analysis and genome-wide recognition sequence search identified the regulons of BcrS and AbcS. Interestingly, we found that BcrS positively influences T4SS expression in an AbcS-dependent manner and that AbcS also affects T4SS expression independently of BcrS. Last, we demonstrate that abcS is required for the maintenance of persistent infection, while bcrS is dispensable in a mouse infection model. Collectively, we conclude that BcrS and AbcS influence expression of multiple genes responsible for Brucella virulence traits.IMPORTANCE Brucella is a notorious intracellular pathogen that induces chronic infections in animals and humans. To survive and replicate within macrophages, these bacteria require a capacity to withstand oxidative stresses and to express the type IV secretion system (T4SS) to combat host immune responses. In this study, we characterized an extracytoplasmic function sigma/anti-sigma factor system that regulates resistance to reactive chlorine species and T4SS expression, thereby establishing a potential link between two crucial virulence traits of Brucella. Furthermore, the anti-sigma factor AbcS contributes to Brucella persistent infection of mice. Thus, this work provides novel insights into Brucella virulence regulation as well as a potential drug target for fighting Brucella infections.
      PubDate: 2021-05-20T08:00:26-07:00
      DOI: 10.1128/JB.00127-21
      Issue No: Vol. 203, No. 12 (2021)
       
  • Articles of Significant Interest in This Issue [Spotlight]

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      PubDate: 2021-05-20T08:00:26-07:00
      DOI: 10.1128/JB.00186-21
      Issue No: Vol. 203, No. 12 (2021)
       
  • The Absence of Osmoregulated Periplasmic Glucan Confers Antimicrobial
           Resistance and Increases Virulence in Escherichia coli [Article]

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      Authors: Murakami, K; Nasu, H, Fujiwara, T, Takatsu, N, Yoshida, N, Furuta, K, Kaito, C.
      Abstract: Clarifying the molecular mechanisms by which bacteria acquire virulence traits is important for understanding the bacterial virulence system. In the present study, we utilized a bacterial evolution method in a silkworm infection model and revealed that deletion of the opgGH operon, encoding synthases for osmoregulated periplasmic glucan (OPG), increased the virulence of a nonpathogenic laboratory strain of Escherichia coli against silkworms. The opgGH knockout mutant exhibited resistance to host antimicrobial peptides and antibiotics. Compared with the parent strain, the opgGH knockout mutant produced greater amounts of colanic acid, which is involved in E. coli resistance to antibiotics. RNA sequence analysis revealed that the opgGH knockout altered the expression of various genes, including the evgS/evgA two-component system that functions in antibiotic resistance. In both a colanic acid-negative background and an evgS-null background, the opgGH knockout increased E. coli resistance to antibiotics and increased the silkworm-killing activity of E. coli. In the null background of the envZ/ompR two-component system, which genetically interacts with opgGH, the opgGH knockout increased antibiotic resistance and virulence in silkworms. These findings suggest that the absence of OPG confers antimicrobial resistance and virulence in E. coli in a colanic acid-, evgS/evgA-, and envZ/ompR-independent manner.IMPORTANCE The gene mutation types that increase the bacterial virulence of Escherichia coli remain unclear, in part due to the limited number of methods available for isolating bacterial mutants with increased virulence. We utilized a bacterial evolution method in the silkworm infection model, in which silkworms were infected with mutagenized bacteria and highly virulent bacterial mutants were isolated from dead silkworms. We revealed that knockout of OPG synthases increased E. coli virulence against silkworms. The OPG knockout mutants were resistant to host antimicrobial peptides as well as antibiotics. Our findings not only suggest a novel mechanism for virulence acquisition in E. coli but also support the usefulness of the bacterial experimental evolution method in the silkworm infection model.
      PubDate: 2021-05-20T08:00:26-07:00
      DOI: 10.1128/JB.00515-20
      Issue No: Vol. 203, No. 12 (2021)
       
  • How Rhizobia Adapt to the Nodule Environment [Minireviews]

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      Authors: Ledermann, R; Schulte, C. C. M, Poole, P. S.
      Abstract: Rhizobia are a phylogenetically diverse group of soil bacteria that engage in mutualistic interactions with legume plants. Although specifics of the symbioses differ between strains and plants, all symbioses ultimately result in the formation of specialized root nodule organs that host the nitrogen-fixing microsymbionts called bacteroids. Inside nodules, bacteroids encounter unique conditions that necessitate the global reprogramming of physiological processes and the rerouting of their metabolism. Decades of research have addressed these questions using genetics, omics approaches, and, more recently, computational modeling. Here, we discuss the common adaptations of rhizobia to the nodule environment that define the core principles of bacteroid functioning. All bacteroids are growth arrested and perform energy-intensive nitrogen fixation fueled by plant-provided C4-dicarboxylates at nanomolar oxygen levels. At the same time, bacteroids are subject to host control and sanctioning that ultimately determine their fitness and have fundamental importance for the evolution of a stable mutualistic relationship.
      PubDate: 2021-05-20T08:00:26-07:00
      DOI: 10.1128/JB.00539-20
      Issue No: Vol. 203, No. 12 (2021)
       
  • Essential Gene Analysis in Acinetobacter baumannii by High-Density
           Transposon Mutagenesis and CRISPR Interference [Article]

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      Authors: Bai, J; Dai, Y, Farinha, A, Tang, A. Y, Syal, S, Vargas-Cuebas, G, van Opijnen, T, Isberg, R. R, Geisinger, E.
      Abstract: Acinetobacter baumannii is a poorly understood bacterium capable of life-threatening infections in hospitals. Few antibiotics remain effective against this highly resistant pathogen. Development of rationally designed antimicrobials that can target A. baumannii requires improved knowledge of the proteins that carry out essential processes allowing growth of the organism. Unfortunately, studying essential genes has been challenging using traditional techniques, which usually require time-consuming recombination-based genetic manipulations. Here, we performed saturating mutagenesis with dual transposon systems to identify essential genes in A. baumannii, and we developed a CRISPR interference (CRISPRi) system for facile analysis of these genes. We show that the CRISPRi system enables efficient transcriptional silencing in A. baumannii. Using these tools, we confirmed the essentiality of the novel cell division protein AdvA and discovered a previously uncharacterized AraC family transcription factor (ACX60_RS03245) that is necessary for growth. In addition, we show that capsule biosynthesis is a conditionally essential process, with mutations in late-acting steps causing toxicity in strain ATCC 17978 that can be bypassed by blocking early-acting steps or activating the BfmRS stress response. These results open new avenues for analysis of essential pathways in A. baumannii.IMPORTANCE New approaches are urgently needed to control A. baumannii, one of the most drug-resistant pathogens known. To facilitate the development of novel targets that allow inhibition of the pathogen, we performed a large-scale identification of genes whose products the bacterium needs for growth. We also developed a CRISPR-based gene knockdown tool that operates efficiently in A. baumannii, allowing rapid analysis of these essential genes. We used these methods to define multiple processes vital to the bacterium, including a previously uncharacterized gene regulatory factor and export of a protective polymeric capsule. These tools will enhance our ability to investigate processes critical for the essential biology of this challenging hospital-acquired pathogen.
      PubDate: 2021-05-20T08:00:26-07:00
      DOI: 10.1128/JB.00565-20
      Issue No: Vol. 203, No. 12 (2021)
       
 
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