Journal of Bacteriology最新文献

{"title":"The CpxAR signaling system confers a fitness advantage for flea gut colonization by the plague bacillus.","authors":"Brandon Robin, Amélie Dewitte, Véronique Alaimo, Cecile Lecoeur, François Pierre, Gabriel Billon, Florent Sebbane, Sébastien Bontemps-Gallo","doi":"10.1128/jb.00173-24","DOIUrl":"10.1128/jb.00173-24","url":null,"abstract":"<p><p>The adaptation of <i>Yersinia pestis</i>, the flea-borne plague agent, to fluctuating environmental conditions is essential for the successful colonization of the flea vector. A previous comparative transcriptomic analysis showed that the Cpx pathway of <i>Y. pestis</i> is up-regulated in infected fleas. The CpxAR two-component system is a component of the envelope stress response and is critical for maintaining the integrity of the cell. Here, a phenotypic screening revealed a survival defect of the <i>cpxAR</i> mutant to oxidative stress and copper. The measured copper concentration in the digestive tract contents of fed fleas increased fourfold during the digestive process. By direct analysis of phosphorylation of CpxR by a Phos-Tag gel approach, we demonstrated that biologically relevant concentrations of copper triggered the system. Then, a competitive challenge highlighted the role of the CpxAR system in bacterial fitness during flea infection. Lastly, an <i>in vitro</i> sequential exposure to copper and then H₂O₂ to mimic the flea suggests a model in which, within the insect digestive tract, the CpxAR system would be triggered by copper, establishing an oxidative stress response.</p><p><strong>Importance: </strong>The bacterium <i>Yersinia pestis</i> is the agent of flea-borne plague. Our knowledge of the mechanisms used by the plague bacillus to infect the flea vector is limited. The up-regulation of the envelope stress response under the control of the Cpx signaling pathway was previously shown in a transcriptomic study. Here, our <i>in vivo</i> and <i>in vitro</i> approaches suggest a model in which <i>Y. pestis</i> uses the CpxAR phosphorelay system to sense and respond to the copper present in the flea gut, thereby optimizing the flea gut colonization. In other words, the system is essential for bacterial fitness in the flea.</p>","PeriodicalId":15107,"journal":{"name":"Journal of Bacteriology","volume":" ","pages":"e0017324"},"PeriodicalIF":2.7,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11411919/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141999929","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Hitchhiker's Guide to <i>Borrelia burgdorferi</i>.","authors":"Jeffrey S Bourgeois, Linden T Hu","doi":"10.1128/jb.00116-24","DOIUrl":"10.1128/jb.00116-24","url":null,"abstract":"<p><p>Don't Panic. In the nearly 50 years since the discovery of Lyme disease, <i>Borrelia burgdorferi</i> has emerged as an unlikely workhorse of microbiology. Interest in studying host-pathogen interactions fueled significant progress in making the fastidious microbe approachable in laboratory settings, including the development of culture methods, animal models, and genetic tools. By developing these systems, insight has been gained into how the microbe is able to survive its enzootic cycle and cause human disease. Here, we discuss the discovery of <i>B. burgdorferi</i> and its development as a model organism before diving into the critical lessons we have learned about <i>B. burgdorferi</i> biology at pivotal stages of its lifecycle: gene expression changes during the tick blood meal, colonization of a new vertebrate host, and developing a long-lasting infection in that vertebrate until a new tick feeds. Our goal is to highlight the advancements that have facilitated <i>B. burgdorferi</i> research and identify gaps in our current understanding of the microbe.</p>","PeriodicalId":15107,"journal":{"name":"Journal of Bacteriology","volume":" ","pages":"e0011624"},"PeriodicalIF":2.7,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11411949/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141975662","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Determinants of maturation of the <i>Staphylococcus aureus</i> autoinducing peptide.","authors":"Liwei Fang, Chance Cosgriff, Francis Alonzo","doi":"10.1128/jb.00195-24","DOIUrl":"10.1128/jb.00195-24","url":null,"abstract":"<p><p>The <u>a</u>ccessory <u>g</u>ene <u>r</u>egulatory (Agr) system is required for virulence factor gene expression and pathogenesis of <i>Staphylococcus aureus</i>. The Agr system is activated in response to the accumulation of a cyclic autoinducing peptide (AIP), which is matured and secreted by the bacterium. The precursor of AIP, AgrD, consists of the AIP flanked by an N-terminal [Formula: see text]-helical Leader and a charged C-terminal tail. AgrD is matured to AIP by the action of two proteases, AgrB and MroQ. AgrB cleaves the C-terminal tail and promotes the formation of a thiolactone ring, whereas MroQ cleaves the N-terminal Leader in a manner that depends on the four-amino acid linker immediately following a conserved IG helix breaker motif. However, the attributes of AgrD that dictate the sequence of events in peptide maturation are not fully defined. Here, we used engineered AgrD peptide intermediates to ascertain the sufficiency of MroQ for N-terminal peptide cleavage, peptide export, and generation of mature AIP. We found that MroQ promotes the removal of the N-terminal Leader peptide from both linear and cyclic peptide intermediates, while peptide cyclization remained essential for signaling. The expression of the Leader peptide in isolation was sufficient for MroQ-dependent cleavage proximal to the four-amino-acid linker. In addition, active site mutations within AgrB destabilized full-length AgrD and thiolactone-containing intermediates and prevented the release of the Leader peptide. Altogether, our data support a tandem peptide maturation event involving both MroQ and AgrB that appears to couple protease activity and export of bioactive AIP.IMPORTANCEThe <u>a</u>ccessory <u>g</u>ene <u>r</u>egulatory (Agr) system is important for <i>S. aureus</i> pathogenesis. Activation of the Agr system requires recognition of a cyclic peptide pheromone, which must be fully matured to exert its biological activity. The complete events in cyclic peptide maturation and export from the bacterial cell remain to be fully defined. We and others recently discovered that the membrane peptidase MroQ is required for pheromone maturation. This study builds off the identification of MroQ and considers the attributes of the pheromone pro-peptide that are required for MroQ-mediated processing as well as uncovers features important for peptide stability and export. Overall, the findings in this study have implications for understanding bacterial pheromone maturation and virulence.</p>","PeriodicalId":15107,"journal":{"name":"Journal of Bacteriology","volume":" ","pages":"e0019524"},"PeriodicalIF":2.7,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11412329/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142035929","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Response of <i>Staphylococcus aureus</i> physiology and Agr quorum sensing to low-shear modeled microgravity.","authors":"Matthew R Hauserman, Leia E Sullivan, Kimberly L James, Mariola J Ferraro, Kelly C Rice","doi":"10.1128/jb.00272-24","DOIUrl":"10.1128/jb.00272-24","url":null,"abstract":"<p><p><i>Staphylococcus aureus</i> is commonly isolated from astronauts returning from spaceflight. Previous analysis of omics data from <i>S. aureus</i> low Earth orbit cultures indicated significantly increased expression of the Agr quorum sensing system and its downstream targets in spaceflight samples compared to ground controls. In this current study, the rotary cell culture system (RCCS) was used to investigate the effect of low-shear modeled microgravity (LSMMG) on <i>S. aureus</i> physiology and Agr activity. When cultured in the same growth medium and temperature as the previous spaceflight experiment, <i>S. aureus</i> LSMMG cultures exhibited decreased <i>agr</i> expression and altered growth compared to normal gravity control cultures, which are typically oriented with oxygenation membrane on the bottom of the high aspect rotating vessel (HARV). When <i>S. aureus</i> was grown in an inverted gravity control orientation (oxygenation membrane on top of the HARV), reduced Agr activity was observed relative to both traditional control and LSMMG cultures, signifying that oxygen availability may affect the observed differences in Agr activity. Metabolite assays revealed increased lactate and decreased acetate excretion in both LSMMG and inverted control cultures. Secretomics analysis of LSMMG, control, and inverted control HARV culture supernatants corroborated these results, with inverted and LSMMG cultures exhibiting a decreased abundance of Agr-regulated virulence factors and an increased abundance of proteins expressed in low-oxygen conditions. Collectively, these studies suggest that the orientation of the HARV oxygenation membrane can affect <i>S. aureus</i> physiology and Agr quorum sensing in the RCCS, a variable that should be considered when interpreting data using this ground-based microgravity model.IMPORTANCE<i>S. aureus</i> is commonly isolated from astronauts returning from spaceflight and from surfaces within human-inhabited closed environments such as spacecraft. Astronaut health and immune function are significantly altered in spaceflight. Therefore, elucidating the effects of microgravity on <i>S. aureus</i> physiology is critical for assessing its pathogenic potential during long-term human space habitation. These results also highlight the necessity of eliminating potential confounding factors when comparing simulated microgravity model data with actual spaceflight experiments.</p>","PeriodicalId":15107,"journal":{"name":"Journal of Bacteriology","volume":" ","pages":"e0027224"},"PeriodicalIF":2.7,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11411946/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141906640","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"<i>Vibrio cholerae</i> pathogenicity island 2 encodes two distinct types of restriction systems.","authors":"Grazia Vizzarro, Alexandre Lemopoulos, David William Adams, Melanie Blokesch","doi":"10.1128/jb.00145-24","DOIUrl":"10.1128/jb.00145-24","url":null,"abstract":"<p><p>In response to predation by bacteriophages and invasion by other mobile genetic elements such as plasmids, bacteria have evolved specialized defense systems that are often clustered together on genomic islands. The O1 El Tor strains of <i>Vibrio cholerae</i> responsible for the ongoing seventh cholera pandemic (7PET) contain a characteristic set of genomic islands involved in host colonization and disease, many of which contain defense systems. Notably, <i>Vibrio</i> pathogenicity island 2 contains several characterized defense systems as well as a putative type I restriction-modification (T1RM) system, which, interestingly, is interrupted by two genes of unknown function. Here, we demonstrate that the T1RM system is active, methylates the host genomes of a representative set of 7PET strains, and identify a specific recognition sequence that targets non-methylated plasmids for restriction. We go on to show that the two genes embedded within the T1RM system encode a novel two-protein modification-dependent restriction system related to the GmrSD family of type IV restriction enzymes. Indeed, we show that this system has potent anti-phage activity against diverse members of the <i>Tevenvirinae</i>, a subfamily of bacteriophages with hypermodified genomes. Taken together, these results expand our understanding of how this highly conserved genomic island contributes to the defense of pandemic <i>V. cholerae</i> against foreign DNA.</p><p><strong>Importance: </strong>Defense systems are immunity systems that allow bacteria to counter the threat posed by bacteriophages and other mobile genetic elements. Although these systems are numerous and highly diverse, the most common types are restriction enzymes that can specifically recognize and degrade non-self DNA. Here, we show that the <i>Vibrio</i> pathogenicity island 2, present in the pathogen <i>Vibrio cholerae</i>, encodes two types of restriction systems that use distinct mechanisms to sense non-self DNA. The first system is a classical Type I restriction-modification system, and the second is a novel modification-dependent type IV restriction system that recognizes hypermodified cytosines. Interestingly, these systems are embedded within each other, suggesting that they are complementary to each other by targeting both modified and non-modified phages.</p>","PeriodicalId":15107,"journal":{"name":"Journal of Bacteriology","volume":" ","pages":"e0014524"},"PeriodicalIF":2.7,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11411939/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141916733","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"<i>N</i>-linked protein glycosylation in <i>Nanobdellati</i> (formerly DPANN) archaea and their hosts.","authors":"Satoshi Nakagawa, Hiroyuki D Sakai, Shigeru Shimamura, Yoshiki Takamatsu, Shingo Kato, Hirokazu Yagi, Saeko Yanaka, Maho Yagi-Utsumi, Norio Kurosawa, Moriya Ohkuma, Koichi Kato, Ken Takai","doi":"10.1128/jb.00205-24","DOIUrl":"10.1128/jb.00205-24","url":null,"abstract":"<p><p>Members of the kingdom <i>Nanobdellati</i>, previously known as DPANN archaea, are characterized by ultrasmall cell sizes and reduced genomes. They primarily thrive through ectosymbiotic interactions with specific hosts in diverse environments. Recent successful cultivations have emphasized the importance of adhesion to host cells for understanding the ecophysiology of <i>Nanobdellati</i>. Cell adhesion is often mediated by cell surface carbohydrates, and in archaea, this may be facilitated by the glycosylated S-layer protein that typically coats their cell surface. In this study, we conducted glycoproteomic analyses on two co-cultures of <i>Nanobdellati</i> with their host archaea, as well as on pure cultures of both host and non-host archaea. <i>Nanobdellati</i> exhibited various glycoproteins, including archaellins and hypothetical proteins, with glycans that were structurally distinct from those of their hosts. This indicated that <i>Nanobdellati</i> autonomously synthesize their glycans for protein modifications probably using host-derived substrates, despite the high energy cost. Glycan modifications on <i>Nanobdellati</i> proteins consistently occurred on asparagine residues within the N-X-S/T sequon, consistent with patterns observed across archaea, bacteria, and eukaryotes. In both host and non-host archaea, S-layer proteins were commonly modified with hexose, <i>N</i>-acetylhexosamine, and sulfonated deoxyhexose. However, the <i>N</i>-glycan structures of host archaea, characterized by distinct sugars such as deoxyhexose, nonulosonate sugar, and pentose at the nonreducing ends, were implicated in enabling <i>Nanobdellati</i> to differentiate between host and non-host cells. Interestingly, the specific sugar, xylose, was eliminated from the <i>N</i>-glycan in a host archaeon when co-cultured with <i>Nanobdella</i>. These findings enhance our understanding of the role of protein glycosylation in archaeal interactions.IMPORTANCE<i>Nanobdellati</i> archaea, formerly known as DPANN, are phylogenetically diverse, widely distributed, and obligately ectosymbiotic. The molecular mechanisms by which <i>Nanobdellati</i> recognize and adhere to their specific hosts remain largely unexplored. Protein glycosylation, a fundamental biological mechanism observed across all domains of life, is often crucial for various cell-cell interactions. This study provides the first insights into the glycoproteome of <i>Nanobdellati</i> and their host and non-host archaea. We discovered that <i>Nanobdellati</i> autonomously synthesize glycans for protein modifications, probably utilizing substrates derived from their hosts. Additionally, we identified distinctive glycosylation patterns that suggest mechanisms through which <i>Nanobdellati</i> differentiate between host and non-host cells. This research significantly advances our understanding of the molecular basis of microbial interactions in extreme environments.</p>","PeriodicalId":15107,"journal":{"name":"Journal of Bacteriology","volume":" ","pages":"e0020524"},"PeriodicalIF":2.7,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11411935/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142080391","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The regulatory functions of ESX-1 substrates, EspE and EspF, are separable from secretion.","authors":"Rebecca J Prest, Konstantin V Korotkov, Patricia A Champion","doi":"10.1128/jb.00271-24","DOIUrl":"10.1128/jb.00271-24","url":null,"abstract":"<p><p>Pathogenic mycobacteria are a significant global health burden. The ESX-1 secretion system is essential for mycobacterial pathogenesis. The secretion of ESX-1 substrates is required for phagosomal lysis, which allows the bacteria to enter the macrophage cytoplasm, induce a Type I IFN response, and spread to new host cells. EspE and EspF are dual-functioning ESX-1 substrates. Inside the mycobacterial cell, they regulate transcription of ESX-1-associated genes. Following secretion, EspE and EspF are essential for lytic activity. The link between EspE/F secretion and regulatory function has not been investigated. We investigated the relationship between EspE and EspF using molecular genetics in <i>Mycobacterium marinum</i>, a non-tuberculous mycobacterial species that serves as an established model for ESX-1 secretion and function in <i>Mycobacterium tuberculosis</i>. Our data support that EspE and EspF, which require each other for secretion, directly interact. The disruption of the predicted protein-protein interaction abrogates hemolytic activity and secretion but does not impact their gene regulatory activities in the mycobacterial cell. In addition, we predict a direct protein-protein interaction between the EsxA/EsxB heterodimer and EspF. Our data support that the EspF/EsxA interaction is also required for hemolytic activity and EspE secretion. Our study sheds light on the intricate molecular mechanisms governing the interactions between ESX-1 substrates, regulatory function, and ESX-1 secretion, moving the field forward.IMPORTANCETuberculosis (TB), caused by <i>Mycobacterium tuberculosis</i>, is a historical and pervasive disease responsible for millions of deaths annually. The rise of antibiotic and treatment-resistant TB, as well as the rise of infection by non-tuberculous mycobacterial species, calls for a better understanding of pathogenic mycobacteria. The ESX-1 secreted substrates, EspE and EspF, are required for mycobacterial virulence and may be responsible for phagosomal lysis. This study focuses on the mechanism of EspE and EspF secretion from the mycobacterial cell.</p>","PeriodicalId":15107,"journal":{"name":"Journal of Bacteriology","volume":" ","pages":"e0027124"},"PeriodicalIF":2.7,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11411940/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141971188","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Physiological significance of the two isoforms of initiator tRNAs in <i>Escherichia coli</i>.","authors":"Amit Kumar Sahu, Riyaz Ahmad Shah, Divya Nashier, Prafful Sharma, Rajagopal Varada, Kuldeep Lahry, Sudhir Singh, Sunil Shetty, Tanweer Hussain, Umesh Varshney","doi":"10.1128/jb.00251-24","DOIUrl":"10.1128/jb.00251-24","url":null,"abstract":"<p><p><i>Escherichia coli</i> possesses four initiator tRNA (i-tRNA) genes, three of which are present together as <i>metZWV</i> and the fourth one as <i>metY</i>. In <i>E. coli</i> B, all four genes (<i>metZWV</i> and <i>metY</i>) encode i-tRNA^fMet1, in which the G at position 46 is modified to m⁷G46 by TrmB (m⁷G methyltransferase). However, in <i>E. coli</i> K, because of a single-nucleotide polymorphism, <i>metY</i> encodes a variant, i-tRNA^fMet2, having an A in place of m⁷G46. We generated <i>E. coli</i> strains to explore the importance of this polymorphism in i-tRNAs. The strains were sustained either on <i>metY</i>_A46 (<i>metY</i> of <i>E. coli</i> K origin encoding i-tRNA^fMet2) or its derivative <i>metY</i>_G46 (encoding i-tRNA^fMet1) in single (chromosomal) or plasmid-borne copies. We show that the strains sustained on i-tRNA^fMet1 have a growth fitness advantage over those sustained on i-tRNA^fMet2. The growth fitness advantages are more pronounced for the strains sustained on i-tRNA^fMet1 in nutrient-rich media than in nutrient-poor media. The growth fitness of the strains correlates well with the relative stabilities of the i-tRNAs <i>in vivo</i>. Furthermore, the atomistic molecular dynamics simulations support the higher stability of i-tRNA^fMet1 than that of i-tRNA^fMet2. The stability of i-tRNA^fMet1 remains unaffected upon the deletion of TrmB. These studies highlight how <i>metY</i>_G46 and <i>metY</i>_A46 alleles might influence the growth fitness of <i>E. coli</i> under certain nutrient-limiting conditions.</p><p><strong>Importance: </strong><i>Escherichia coli</i> harbors four initiator tRNA (i-tRNA) genes: three of these at <i>metZWV</i> and the fourth one at <i>metY</i> loci. In <i>E. coli</i> B, all four genes encode i-tRNA^fMet1. In <i>E. coli</i> K, because of a single-nucleotide polymorphism, metY encodes a variant, i-tRNA^fMet2, having an A in place of G at position 46 of i-tRNA sequence in metY. We show that G46 confers stability to i-tRNA^fMet1. The strains sustained on i-tRNA^fMet1 have a growth fitness advantage over those sustained on i-tRNA^fMet2. Strains harboring <i>metY</i>_G46 (B mimic) or <i>metY</i>_A46 (K mimic) show that while in the nutrient-rich media, the K mimic is outcompeted rapidly; in the nutrient-poor medium, the K mimic is outcompeted less rapidly.</p>","PeriodicalId":15107,"journal":{"name":"Journal of Bacteriology","volume":" ","pages":"e0025124"},"PeriodicalIF":2.7,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11411947/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142017522","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Nature should be the model for microbial sciences.","authors":"Brett J Baker, Emily Hyde, Pedro Leão","doi":"10.1128/jb.00228-24","DOIUrl":"10.1128/jb.00228-24","url":null,"abstract":"<p><p>Until recently, microbiologists have relied on cultures to understand the microbial world. As a result, model organisms have been the focus of research into understanding Bacteria and Archaea at a molecular level. Diversity surveys and metagenomic sequencing have revealed that these model species are often present in low abundance in the environment; instead, there are microbial taxa that are cosmopolitan in nature. Due to the numerical dominance of these microorganisms and the size of their habitats, these lineages comprise mind-boggling population sizes upward of 10²⁸ cells on the planet. Many of these dominant groups have cultured representatives and have been shown to be involved in mediating key processes in nature. Given their importance and the increasing need to understand changes due to climate change, we propose that members of Nitrosophaerota (<i>Nitrosopumilus maritimus</i>), SAR11 (<i>Pelagibacter ubique</i>), Hadesarchaeia, Bathyarchaeia, and others become models in the future. Abundance should not be the only measure of a good model system; there are other organisms that are well suited to advance our understanding of ecology and evolution. For example, the most well-studied symbiotic bacteria, like <i>Buchnera</i>, <i>Aliivibrio</i>, and <i>Rhizobium</i>, should be models for understanding host-associations. Also, there are organisms that hold new insights into major transitions in the evolution of life on the planet like the Asgard Archaea (Heimdallarchaeia). Innovations in a variety of <i>in situ</i> techniques have enabled us to circumvent culturing when studying everything from genetics to physiology. Our deepest understanding of microbiology and its impact on the planet will come from studying these microbes in nature. Laboratory-based studies must be grounded in nature, not the other way around.</p>","PeriodicalId":15107,"journal":{"name":"Journal of Bacteriology","volume":" ","pages":"e0022824"},"PeriodicalIF":2.7,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11411942/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142001725","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A <i>Vibrio cholerae</i> Type IV restriction system targets glucosylated 5-hydroxymethylcytosine to protect against phage infection.","authors":"Jasper B Gomez, Christopher M Waters","doi":"10.1128/jb.00143-24","DOIUrl":"10.1128/jb.00143-24","url":null,"abstract":"<p><p>A major challenge faced by <i>Vibrio cholerae</i> is constant predation by bacteriophage (phage) in aquatic reservoirs and during infection of human hosts. To overcome phage predation, <i>V. cholerae</i> has acquired and/or evolved a myriad of phage defense systems. Although several novel defense systems have been discovered, we hypothesized that more were encoded in <i>V. cholerae</i> given the low diversity of phages that have been isolated, which infect this species. Using a <i>V. cholerae</i> genomic library, we identified a Type IV restriction system consisting of two genes within a 16-kB region of the <i>Vibrio</i> pathogenicity island-2, which we name TgvA and TgvB (<b><u>T</u></b>ype I-embedded <b><i><u>g</u></i></b><i>mrSD</i>-like system of <b><u>V</u></b>PI-2). We show that both TgvA and TgvB are required for defense against T2, T4, and T6 by targeting glucosylated 5-hydroxymethylcytosine (5hmC). T2 or T4 phages that lose the glucose modifications are resistant to TgvAB defense but exhibit a significant evolutionary tradeoff, becoming susceptible to other Type IV restriction systems that target unglucosylated 5hmC. We also show that the Type I restriction-modification system that embeds the <i>tgvAB</i> genes protects against phage T3, secΦ18, secΦ27, and λ, suggesting that this region is a phage defense island. Our study uncovers a novel Type IV restriction system in <i>V. cholerae</i>, increasing our understanding of the evolution and ecology of <i>V. cholerae,</i> while highlighting the evolutionary interplay between restriction systems and phage genome modification.IMPORTANCEBacteria are constantly being predated by bacteriophage (phage). To counteract this predation, bacteria have evolved a myriad of defense systems. Some of these systems specifically digest infecting phage by recognizing unique base modifications present on the phage DNA. In this study, we discover a Type IV restriction system encoded in <i>V. cholerae,</i> which we name TgvAB, and demonstrate it recognizes and restricts phage that have 5-hydroxymethylcytosine glucosylated DNA. Moreover, the evolution of resistance to TgvAB render phage susceptible to other Type IV restriction systems, demonstrating a significant evolutionary tradeoff. These results enhance our understanding of the evolution of <i>V. cholerae</i> and more broadly how bacteria evade phage predation.</p>","PeriodicalId":15107,"journal":{"name":"Journal of Bacteriology","volume":" ","pages":"e0014324"},"PeriodicalIF":2.7,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11411926/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142125805","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}