Prophage-Dependent Neighbor Predation Fosters Horizontal Gene Transfer by Natural Transformation

ABSTRACT Natural transformation is a broadly conserved mechanism of horizontal gene transfer (HGT) in bacteria that can shape their evolution through the acquisition of genes that promote virulence, antibiotic resistance, and other traits. Recent work has established that neighbor predation via type VI secretion systems, bacteriocins, and virulent phages plays an important role in promoting HGT. Here, we demonstrate that in chitin estuary microcosms, Vibrio cholerae K139 lysogens exhibit prophage-dependent neighbor predation of nonlysogens to enhance HGT. Through predation of nonlysogens, K139 lysogens also have a fitness advantage under these microcosm conditions. The ecological strategy revealed by our work provides a better understanding of the evolutionary mechanisms used by bacteria to adapt in their natural setting and contributes to our understanding of the selective pressures that may drive prophage maintenance in bacterial genomes. IMPORTANCE Prophages are nearly ubiquitous in bacterial species. These integrated phage elements have previously been implicated in horizontal gene transfer (HGT) largely through their ability to carry out transduction (generalized or specialized). Here, we show that prophage-encoded viral particles promote neighbor predation leading to enhanced HGT by natural transformation in the waterborne pathogen Vibrio cholerae. Our findings contribute to a comprehensive understanding of the dynamic forces involved in prophage maintenance which ultimately drive the evolution of naturally competent bacteria in their natural environment.

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Prophage-dependent neighbor predation fosters horizontal gene transfer by natural transformation

10.1101/2020.09.19.304527 ◽

2020 ◽

Author(s):

Roberto C. Molina-Quiroz ◽

Triana N. Dalia ◽

Andrew Camilli ◽

Ankur B. Dalia ◽

Cecilia A. Silva-Valenzuela

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Vibrio Cholerae ◽

Natural Transformation ◽

Bacterial Species ◽

Natural Setting ◽

Secretion Systems ◽

Evolutionary Mechanisms ◽

Fitness Advantage ◽

Viral Particles

ABSTRACTNatural transformation is a broadly conserved mechanism of horizontal gene transfer (HGT) in bacteria (1) that can shape their evolution through the acquisition of genes that promote virulence, antibiotic resistance, and other traits (2). Recent work has established that neighbor predation via Type VI secretion systems (3), bacteriocins (4) and virulent phages (5), play an important role in promoting HGT. Here, we demonstrate that in chitin estuary microcosms, Vibrio cholerae K139 lysogens exhibit prophage-dependent neighbor predation of non-lysogens to enhance HGT. Through predation of non-lysogens, K139 lysogens also have a fitness advantage in these microcosm conditions. The ecological strategy revealed by our work provides a better understanding of the evolutionary mechanisms used by bacteria to adapt in their natural setting and contributes to our understanding of the selective pressures that may drive prophage maintenance in bacterial genomes.IMPORTANCEProphages are nearly ubiquitous in bacterial species. These integrated phage elements have previously been implicated in horizontal gene transfer (HGT) largely through their ability to carry out transduction (generalized or specialized). Here, we show that prophage-encoded viral particles promote neighbor predation leading to enhanced HGT by natural transformation in the water-borne pathogen Vibrio cholerae. Our findings contribute to a comprehensive understanding of the dynamic forces involved in prophage maintenance which ultimately drive the evolution of naturally competent bacteria in their natural environment.

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An Evolutionary Link between Natural Transformation and CRISPR Adaptive Immunity

mBio ◽

10.1128/mbio.00309-12 ◽

2012 ◽

Vol 3 (5) ◽

Cited By ~ 52

Author(s):

Peter Jorth ◽

Marvin Whiteley

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Bacterial Diversity ◽

Natural Transformation ◽

Bacterial Species ◽

Comparative Genomic ◽

Content Type ◽

Immune Systems ◽

Adaptive Immune ◽

Adaptive Immune Systems

ABSTRACTNatural transformation by competent bacteria is a primary means of horizontal gene transfer; however, evidence that competence drives bacterial diversity and evolution has remained elusive. To test this theory, we used a retrospective comparative genomic approach to analyze the evolutionary history ofAggregatibacter actinomycetemcomitans, a bacterial species with both competent and noncompetent sister strains. Through comparative genomic analyses, we reveal that competence is evolutionarily linked to genomic diversity and speciation. Competence loss occurs frequently during evolution and is followed by the loss of clustered regularly interspaced short palindromic repeats (CRISPRs), bacterial adaptive immune systems that protect against parasitic DNA. Relative to noncompetent strains, competent bacteria have larger genomes containing multiple rearrangements. In contrast, noncompetent bacterial genomes are extremely stable but paradoxically susceptible to infective DNA elements, which contribute to noncompetent strain genetic diversity. Moreover, incomplete noncompetent strain CRISPR immune systems are enriched for self-targeting elements, which suggests that the CRISPRs have been co-opted for bacterial gene regulation, similar to eukaryotic microRNAs derived from the antiviral RNA interference pathway.IMPORTANCEThe human microbiome is rich with thousands of diverse bacterial species. One mechanism driving this diversity is horizontal gene transfer by natural transformation, whereby naturally competent bacteria take up environmental DNA and incorporate new genes into their genomes. Competence is theorized to accelerate evolution; however, attempts to test this theory have proved difficult. Through genetic analyses of the human periodontal pathogenAggregatibacter actinomycetemcomitans, we have discovered an evolutionary connection between competence systems promoting gene acquisition and CRISPRs (clustered regularly interspaced short palindromic repeats), adaptive immune systems that protect bacteria against genetic parasites. We show that competentA. actinomycetemcomitansstrains have numerous redundant CRISPR immune systems, while noncompetent bacteria have lost their CRISPR immune systems because of inactivating mutations. Together, the evolutionary data linking the evolution of competence and CRISPRs reveals unique mechanisms promoting genetic heterogeneity and the rise of new bacterial species, providing insight into complex mechanisms underlying bacterial diversity in the human body.

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Acquisition of Beta-Lactamase by Neisseria meningitidis through Possible Horizontal Gene Transfer

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00831-18 ◽

2018 ◽

Vol 62 (9) ◽

Cited By ~ 7

Author(s):

Eva Hong ◽

Ala-Eddine Deghmane ◽

Muhamed-Kheir Taha

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Genome Sequencing ◽

Meningococcal Disease ◽

Bacterial Species ◽

Whole Genome ◽

Beta Lactamase ◽

Content Type ◽

Beta Lactamases ◽

Lactamase Gene

ABSTRACT We report the detection in France of a beta-lactamase-producing invasive meningococcal isolate. Whole-genome sequencing of the isolate revealed a ROB-1-type beta-lactamase gene that is frequently encountered in Haemophilus influenzae, suggesting horizontal transfer between isolates of these bacterial species. Beta-lactamases are exceptional in meningococci, with no reports for more than 2 decades. This report is worrying, as the expansion of such isolates may jeopardize the effective treatment against invasive meningococcal disease.

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Homologues of Genetic Transformation DNA Import Genes Are Required for Rhodobacter capsulatus Gene Transfer Agent Recipient Capability Regulated by the Response Regulator CtrA

Journal of Bacteriology ◽

10.1128/jb.00332-15 ◽

2015 ◽

Vol 197 (16) ◽

pp. 2653-2663 ◽

Cited By ~ 29

Author(s):

Cedric A. Brimacombe ◽

Hao Ding ◽

Jeanette A. Johnson ◽

J. Thomas Beatty

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Rhodobacter Capsulatus ◽

Natural Transformation ◽

Response Regulator ◽

Content Type ◽

Gene Acquisition ◽

Metabolic Properties ◽

Cell Genome ◽

Key Aspects

ABSTRACTGene transfer agents (GTAs) morphologically resemble small, double-stranded DNA (dsDNA) bacteriophages; however, their only known role is to package and transfer random pieces of the producing cell genome to recipient cells. The best understood GTA is that ofRhodobacter capsulatus, termed RcGTA. We discovered that homologues of three genes involved in natural transformation in other bacteria,comEC,comF, andcomM, are essential for RcGTA-mediated gene acquisition. This paper gives genetic and biochemical evidence that RcGTA-borne DNA entry into cells requires the ComEC and ComF putative DNA transport proteins and genetic evidence that putative cytoplasmic ComM protein of unknown function is required for recipient capability. Furthermore, the master regulator of RcGTA production in <1% of a cell population, CtrA, which is also required for gene acquisition in recipient cells, is expressed in the vast majority of the population. Our results indicate that RcGTA-mediated gene transfer combines key aspects of two bacterial horizontal gene transfer mechanisms, where donor DNA is packaged in transducing phage-like particles and recipient cells take up DNA using natural transformation-related machinery. Both of these differentiated subsets of a culture population, donors and recipients, are dependent on the same response regulator, CtrA.IMPORTANCEHorizontal gene transfer (HGT) is a major driver of bacterial evolution and adaptation to environmental stresses. Traits such as antibiotic resistance or metabolic properties can be transferred between bacteria via HGT; thus, HGT can have a tremendous effect on the fitness of a bacterial population. The three classically described HGT mechanisms are conjugation, transformation, and phage-mediated transduction. More recently, the HGT factor GTA was described, where random pieces of producing cell genome are packaged into phage-like particles that deliver DNA to recipient cells. In this report, we show that transport of DNA borne by theR. capsulatusRcGTA into recipient cells requires key genes previously thought to be specific to natural transformation pathways. These findings indicate that RcGTA combines central aspects of phage-mediated transduction and natural transformation in an efficient, regulated mode of HGT.

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Transposon Insertion Sequencing in a Clinical Isolate of Legionella pneumophila Identifies Essential Genes and Determinants of Natural Transformation

Journal of Bacteriology ◽

10.1128/jb.00548-20 ◽

2020 ◽

Vol 203 (3) ◽

Author(s):

Léo Hardy ◽

Pierre-Alexandre Juan ◽

Bénédicte Coupat-Goutaland ◽

Xavier Charpentier

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Legionella Pneumophila ◽

Genetic Basis ◽

Natural Transformation ◽

Essential Genes ◽

Content Type ◽

Transposon Insertion ◽

Life Traits ◽

Transposon Insertion Sequencing

ABSTRACT Legionella pneumophila is a Gram-negative bacterium ubiquitous in freshwater environments which, if inhaled, can cause a severe pneumonia in humans. The emergence of L. pneumophila is linked to several traits selected in the environment, the acquisition of some of which involved intra- and interkingdom horizontal gene transfer events. Transposon insertion sequencing (TIS) is a powerful method to identify the genetic basis of selectable traits as well as to identify fitness determinants and essential genes, which are possible antibiotic targets. TIS has not yet been used to its full power in L. pneumophila, possibly because of the difficulty of obtaining a high-saturation transposon insertion library. Indeed, we found that isolates of sequence type 1 (ST1), which includes the commonly used laboratory strains, are poorly permissive to saturating mutagenesis by conjugation-mediated transposon delivery. In contrast, we obtained high-saturation libraries in non-ST1 clinical isolates, offering the prospect of using TIS on unaltered L. pneumophila strains. Focusing on one of them, we then used TIS to identify essential genes in L. pneumophila. We also revealed that TIS could be used to identify genes controlling vertical transmission of mobile genetic elements. We then applied TIS to identify all the genes required for L. pneumophila to develop competence and undergo natural transformation, defining the set of major and minor type IV pilins that are engaged in DNA uptake. This work paves the way for the functional exploration of the L. pneumophila genome by TIS and the identification of the genetic basis of other life traits of this species. IMPORTANCE Legionella pneumophila is the etiologic agent of a severe form of nosocomial and community-acquired pneumonia in humans. The environmental life traits of L. pneumophila are essential to its ability to accidentally infect humans. A comprehensive identification of their genetic basis could be obtained through the use of transposon insertion sequencing. However, this powerful approach had not been fully implemented in L. pneumophila. Here, we describe the successful implementation of the transposon-sequencing approach in a clinical isolate of L. pneumophila. We identify essential genes, potential drug targets, and genes required for horizontal gene transfer by natural transformation. This work represents an important step toward identifying the genetic basis of the many life traits of this environmental and pathogenic species.

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CryoEM structure of the type IVa pilus secretin required for natural competence in Vibrio cholerae

Nature Communications ◽

10.1038/s41467-020-18866-y ◽

2020 ◽

Vol 11 (1) ◽

Author(s):

Sara J. Weaver ◽

Davi R. Ortega ◽

Matthew H. Sazinsky ◽

Triana N. Dalia ◽

Ankur B. Dalia ◽

...

Keyword(s):

Antibiotic Resistance ◽

Gene Transfer ◽

Horizontal Gene Transfer ◽

Vibrio Cholerae ◽

Natural Transformation ◽

Domain Architecture ◽

Genetic Material ◽

Surface Binding ◽

Exogenous Dna ◽

Insight Into

Abstract Natural transformation is the process by which bacteria take up genetic material from their environment and integrate it into their genome by homologous recombination. It represents one mode of horizontal gene transfer and contributes to the spread of traits like antibiotic resistance. In Vibrio cholerae, a type IVa pilus (T4aP) is thought to facilitate natural transformation by extending from the cell surface, binding to exogenous DNA, and retracting to thread this DNA through the outer membrane secretin, PilQ. Here, we use a functional tagged allele of VcPilQ purified from native V. cholerae cells to determine the cryoEM structure of the VcPilQ secretin in amphipol to ~2.7 Å. We use bioinformatics to examine the domain architecture and gene neighborhood of T4aP secretins in Proteobacteria in comparison with VcPilQ. This structure highlights differences in the architecture of the T4aP secretin from the type II and type III secretion system secretins. Based on our cryoEM structure, we design a series of mutants to reversibly regulate VcPilQ gate dynamics. These experiments support the idea of VcPilQ as a potential druggable target and provide insight into the channel that DNA likely traverses to promote the spread of antibiotic resistance via horizontal gene transfer by natural transformation.

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Lifestyle and Horizontal Gene Transfer-Mediated Evolution of Mucispirillum schaedleri, a Core Member of the Murine Gut Microbiota

mSystems ◽

10.1128/msystems.00171-16 ◽

2017 ◽

Vol 2 (1) ◽

Cited By ~ 51

Author(s):

Alexander Loy ◽

Carina Pfann ◽

Michaela Steinberger ◽

Buck Hanson ◽

Simone Herp ◽

...

Keyword(s):

Gene Expression ◽

Gene Transfer ◽

Horizontal Gene Transfer ◽

Gut Microbiota ◽

Intestinal Inflammation ◽

Effector Proteins ◽

Secretion Systems ◽

Associated Bacteria ◽

Content Type ◽

Gut Microbiota Composition

ABSTRACT Shifts in gut microbiota composition have been associated with intestinal inflammation, but it remains unclear whether inflammation-associated bacteria are commensal or detrimental to their host. Here, we studied the lifestyle of the gut bacterium Mucispirillum schaedleri, which is associated with inflammation in widely used mouse models. We found that M. schaedleri has specialized systems to handle oxidative stress during inflammation. Additionally, it expresses secretion systems and effector proteins and can modify the mucosal gene expression of its host. This suggests that M. schaedleri undergoes intimate interactions with its host and may play a role in inflammation. The insights presented here aid our understanding of how commensal gut bacteria may be involved in altering susceptibility to disease. Mucispirillum schaedleri is an abundant inhabitant of the intestinal mucus layer of rodents and other animals and has been suggested to be a pathobiont, a commensal that plays a role in disease. In order to gain insights into its lifestyle, we analyzed the genome and transcriptome of M. schaedleri ASF 457 and performed physiological experiments to test traits predicted by its genome. Although described as a mucus inhabitant, M. schaedleri has limited capacity for degrading host-derived mucosal glycans and other complex polysaccharides. Additionally, M. schaedleri reduces nitrate and expresses systems for scavenging oxygen and reactive oxygen species in vivo, which may account for its localization close to the mucosal tissue and expansion during inflammation. Also of note, M. schaedleri harbors a type VI secretion system and putative effector proteins and can modify gene expression in mucosal tissue, suggesting intimate interactions with its host and a possible role in inflammation. The M. schaedleri genome has been shaped by extensive horizontal gene transfer, primarily from intestinal Epsilon- and Deltaproteobacteria, indicating that horizontal gene transfer has played a key role in defining its niche in the gut ecosystem. IMPORTANCE Shifts in gut microbiota composition have been associated with intestinal inflammation, but it remains unclear whether inflammation-associated bacteria are commensal or detrimental to their host. Here, we studied the lifestyle of the gut bacterium Mucispirillum schaedleri, which is associated with inflammation in widely used mouse models. We found that M. schaedleri has specialized systems to handle oxidative stress during inflammation. Additionally, it expresses secretion systems and effector proteins and can modify the mucosal gene expression of its host. This suggests that M. schaedleri undergoes intimate interactions with its host and may play a role in inflammation. The insights presented here aid our understanding of how commensal gut bacteria may be involved in altering susceptibility to disease.

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CryoEM structure of the Vibrio cholerae Type IV competence pilus secretin PilQ

10.1101/2020.03.03.975896 ◽

2020 ◽

Cited By ~ 1

Author(s):

Sara J. Weaver ◽

Matthew H. Sazinsky ◽

Triana N. Dalia ◽

Ankur B. Dalia ◽

Grant J. Jensen

Keyword(s):

Antibiotic Resistance ◽

Gene Transfer ◽

Horizontal Gene Transfer ◽

Vibrio Cholerae ◽

Natural Transformation ◽

Structural Information ◽

Genetic Material ◽

Surface Binding ◽

Exogenous Dna ◽

Type Iv

AbstractNatural transformation is the process by which bacteria take up genetic material from their environment and integrate it into their genome by homologous recombination. It represents one mode of horizontal gene transfer and contributes to the spread of traits like antibiotic resistance. In Vibrio cholerae, the Type IV competence pilus is thought to facilitate natural transformation by extending from the cell surface, binding to exogenous DNA, and retracting to thread this DNA through the outer membrane secretin, PilQ. A lack of structural information has hindered our understanding of this process, however. Here, we solved the first ever high-resolution structure of a Type IV competence pilus secretin. A functional tagged allele of VcPilQ purified from native V. cholerae cells was used to determine the cryoEM structure of the PilQ secretin in amphipol to ∼2.7 Å. This structure highlights for the first time key differences in the architecture of the Type IV competence pilus secretin from the Type II and Type III Secretin System secretins. Based on our cryoEM structure, we designed a series of mutants to interrogate the mechanism of PilQ. These experiments provide insight into the channel that DNA likely traverses to promote the spread of antibiotic resistance via horizontal gene transfer by natural transformation. We prove that it is possible to reduce pilus biogenesis and natural transformation by sealing the gate, suggesting VcPilQ as a new drug target.

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Taking the Gonococcus-Human Relationship to a Whole New Level: Implications for the Coevolution of Microbes and Humans

mBio ◽

10.1128/mbio.00067-11 ◽

2011 ◽

Vol 2 (3) ◽

Cited By ~ 1

Author(s):

William M. Shafer ◽

Elizabeth A. Ohneck

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Neisseria Gonorrhoeae ◽

Bacterial Species ◽

Human Relationship ◽

Content Type ◽

Long Interspersed Nuclear Element

ABSTRACTWhile horizontal gene transfer occurs frequently among bacterial species, evidence for the transfer of DNA from host to microbe is exceptionally rare. However, the recent report by Anderson and Seifert [mBio 2(1):e00005-11, 2011] provides evidence for such an event with the finding that 11% ofNeisseria gonorrhoeaestrains harbor a 685-bp sequence that is 98 to 100% identical to the human long interspersed nuclear element L1. While the function of this element in gonococci remains unclear, this finding significantly impacts our consideration of the coevolution of hosts and microbes, particularly that of humans and pathogens.

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Fluorescence-Based Detection of Natural Transformation in Drug-ResistantAcinetobacter baumannii

Journal of Bacteriology ◽

10.1128/jb.00181-18 ◽

2018 ◽

Vol 200 (19) ◽

Cited By ~ 11

Author(s):

Anne-Sophie Godeux ◽

Agnese Lupo ◽

Marisa Haenni ◽

Simon Guette-Marquet ◽

Gottfried Wilharm ◽

...

Keyword(s):

Flow Cytometry ◽

Antibiotic Resistance ◽

Gene Transfer ◽

Horizontal Gene Transfer ◽

Natural Transformation ◽

Multidrug Resistant ◽

New Method ◽

Content Type ◽

Transfer Mechanisms ◽

Multiple Antibiotics

ABSTRACTAcinetobacter baumanniiis a nosocomial agent with a high propensity for developing resistance to antibiotics. This ability relies on horizontal gene transfer mechanisms occurring in theAcinetobactergenus, including natural transformation. To study natural transformation in bacteria, the most prevalent method uses selection for the acquisition of an antibiotic resistance marker in a target chromosomal locus by the recipient cell. Most clinical isolates ofA. baumanniiare resistant to multiple antibiotics, limiting the use of such selection-based methods. Here, we report the development of a phenotypic and selection-free method based on flow cytometry to detect transformation events in multidrug-resistant (MDR) clinicalA. baumanniiisolates. To this end, we engineered a translational fusion between the abundant and conservedA. baumanniinucleoprotein (HU) and the superfolder green fluorescent protein (sfGFP). The new method was benchmarked against the conventional antibiotic selection-based method. Using this new method, we investigated several parameters affecting transformation efficiencies and identified conditions of transformability one hundred times higher than those previously reported. Using optimized transformation conditions, we probed natural transformation in a set of MDR clinical and nonclinical animalA. baumanniiisolates. Regardless of their origin, the majority of the isolates displayed natural transformability, indicative of a conserved trait in the species. Overall, this new method and optimized protocol will greatly facilitate the study of natural transformation in the opportunistic pathogenA. baumannii.IMPORTANCEAntibiotic resistance is a pressing global health concern with the rise of multiple and panresistant pathogens. The rapid and unfailing resistance to multiple antibiotics of the nosocomial agentAcinetobacter baumannii, notably to carbapenems, prompt to understand the mechanisms behind acquisition of new antibiotic resistance genes. Natural transformation, one of the horizontal gene transfer mechanisms in bacteria, was only recently described inA. baumanniiand could explain its ability to acquire resistance genes. We developed a reliable method to probe and study natural transformation mechanism inA. baumannii. More broadly, this new method based on flow cytometry will allow experimental detection and quantification of horizontal gene transfer events in multidrug-resistantA. baumannii.

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