High DNA Uptake Capacity of International Clone II Acinetobacter baumannii Detected by a Novel Planktonic Natural Transformation Assay

ABSTRACTThe increasing frequency of bacteria showing antimicrobial resistance (AMR) raises the menace of entering into a postantibiotic era. Horizontal gene transfer (HGT) is one of the prime reasons for AMR acquisition.Acinetobacter baumanniiis a nosocomial pathogen with outstanding abilities to survive in the hospital environment and to acquire resistance determinants. Its capacity to incorporate exogenous DNA is a major source of AMR genes; however, few studies have addressed this subject. The transformation machinery as well as the factors that induce natural competence inA. baumanniiare unknown. In this study, we demonstrate that naturally competent strain A118 increases its natural transformation frequency upon the addition of Ca2+or albumin. We show thatcomEAandpilQare involved in this process since their expression levels are increased upon the addition of these compounds. An unspecific protein, like casein, does not reproduce this effect, showing that albumin's effect is specific. Our work describes the first specific inducers of natural competence inA. baumannii. Overall, our results suggest that the main protein in blood enhances HGT inA. baumannii, contributing to the increase of AMR in this threatening human pathogen.

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A DNase Encoded by Integrated Element CJIE1 Inhibits Natural Transformation of Campylobacter jejuni

Journal of Bacteriology ◽

10.1128/jb.01430-08 ◽

2009 ◽

Vol 191 (7) ◽

pp. 2296-2306 ◽

Cited By ~ 33

Author(s):

Esther J. Gaasbeek ◽

Jaap A. Wagenaar ◽

Magalie R. Guilhabert ◽

Marc M. S. M. Wösten ◽

Jos P. M. van Putten ◽

...

Keyword(s):

Genetic Diversity ◽

Molecular Mechanism ◽

Campylobacter Jejuni ◽

Natural Transformation ◽

Dnase Activity ◽

Comparative Genome Hybridization ◽

Dna Uptake ◽

Knockout Mutant ◽

Gene Encoding ◽

Plasmid Analysis

ABSTRACT The species Campylobacter jejuni is considered naturally competent for DNA uptake and displays strong genetic diversity. Nevertheless, nonnaturally transformable strains and several relatively stable clonal lineages exist. In the present study, the molecular mechanism responsible for the nonnatural transformability of a subset of C. jejuni strains was investigated. Comparative genome hybridization indicated that C. jejuni Mu-like prophage integrated element 1 (CJIE1) was more abundant in nonnaturally transformable C. jejuni strains than in naturally transformable strains. Analysis of CJIE1 indicated the presence of dns (CJE0256), which is annotated as a gene encoding an extracellular DNase. DNase assays using a defined dns mutant and a dns-negative strain expressing Dns from a plasmid indicated that Dns is an endogenous DNase. The DNA-hydrolyzing activity directly correlated with the natural transformability of the knockout mutant and the dns-negative strain expressing Dns from a plasmid. Analysis of a broader set of strains indicated that the majority of nonnaturally transformable strains expressed DNase activity, while all naturally competent strains lacked this activity. The inhibition of natural transformation in C. jejuni via endogenous DNase activity may contribute to the formation of stable lineages in the C. jejuni population.

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The major subunit of widespread competence pili exhibits a novel and conserved type IV pilin fold

Journal of Biological Chemistry ◽

10.1074/jbc.ra120.013316 ◽

2020 ◽

Vol 295 (19) ◽

pp. 6594-6604 ◽

Cited By ~ 1

Author(s):

Devon Sheppard ◽

Jamie-Lee Berry ◽

Rémi Denise ◽

Eduardo P. C. Rocha ◽

Steve Matthews ◽

...

Keyword(s):

Natural Transformation ◽

Dna Uptake ◽

Human Pathogens ◽

Unusual Structure ◽

Widespread Distribution ◽

Solution Structures ◽

Type Iv ◽

Filament Assembly ◽

Pilin Subunit ◽

Type Iv Pilin

Type IV filaments (T4F), which are helical assemblies of type IV pilins, constitute a superfamily of filamentous nanomachines virtually ubiquitous in prokaryotes that mediate a wide variety of functions. The competence (Com) pilus is a widespread T4F, mediating DNA uptake (the first step in natural transformation) in bacteria with one membrane (monoderms), an important mechanism of horizontal gene transfer. Here, we report the results of genomic, phylogenetic, and structural analyses of ComGC, the major pilin subunit of Com pili. By performing a global comparative analysis, we show that Com pili genes are virtually ubiquitous in Bacilli, a major monoderm class of Firmicutes. This also revealed that ComGC displays extensive sequence conservation, defining a monophyletic group among type IV pilins. We further report ComGC solution structures from two naturally competent human pathogens, Streptococcus sanguinis (ComGCSS) and Streptococcus pneumoniae (ComGCSP), revealing that this pilin displays extensive structural conservation. Strikingly, ComGCSS and ComGCSP exhibit a novel type IV pilin fold that is purely helical. Results from homology modeling analyses suggest that the unusual structure of ComGC is compatible with helical filament assembly. Because ComGC displays such a widespread distribution, these results have implications for hundreds of monoderm species.

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Methods for Natural Transformation in Acinetobacter baumannii

Methods in Molecular Biology - Acinetobacter baumannii ◽

10.1007/978-1-4939-9118-1_8 ◽

2019 ◽

pp. 75-85 ◽

Cited By ~ 2

Author(s):

Gottfried Wilharm ◽

Evelyn Skiebe

Keyword(s):

Acinetobacter Baumannii ◽

Natural Transformation

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Silencing of natural transformation by an RNA chaperone and a multitarget small RNA

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1601626113 ◽

2016 ◽

Vol 113 (31) ◽

pp. 8813-8818 ◽

Cited By ~ 60

Author(s):

Laetitia Attaiech ◽

Aïda Boughammoura ◽

Céline Brochier-Armanet ◽

Omran Allatif ◽

Flora Peillard-Fiorente ◽

...

Keyword(s):

Legionella Pneumophila ◽

Natural Transformation ◽

Bacterial Species ◽

Physiological State ◽

Uptake System ◽

Dna Uptake ◽

Exogenous Dna ◽

Major Mechanism ◽

Transcriptional Gene Regulation ◽

High Level

A highly conserved DNA uptake system allows many bacteria to actively import and integrate exogenous DNA. This process, called natural transformation, represents a major mechanism of horizontal gene transfer (HGT) involved in the acquisition of virulence and antibiotic resistance determinants. Despite evidence of HGT and the high level of conservation of the genes coding the DNA uptake system, most bacterial species appear non-transformable under laboratory conditions. In naturally transformable species, the DNA uptake system is only expressed when bacteria enter a physiological state called competence, which develops under specific conditions. Here, we investigated the mechanism that controls expression of the DNA uptake system in the human pathogenLegionella pneumophila. We found that a repressor of this system displays a conserved ProQ/FinO domain and interacts with a newly characterizedtrans-acting sRNA, RocR. Together, they target mRNAs of the genes coding the DNA uptake system to control natural transformation. This RNA-based silencing represents a previously unknown regulatory means to control this major mechanism of HGT. Importantly, these findings also show that chromosome-encoded ProQ/FinO domain-containing proteins can assisttrans-acting sRNAs and that this class of RNA chaperones could play key roles in post-transcriptional gene regulation throughout bacterial species.

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comH, a Novel Gene Essential for Natural Transformation of Helicobacter pylori

Journal of Bacteriology ◽

10.1128/jb.182.14.3948-3954.2000 ◽

2000 ◽

Vol 182 (14) ◽

pp. 3948-3954 ◽

Cited By ~ 54

Author(s):

Leonard C. Smeets ◽

Jetta J. E. Bijlsma ◽

Sacha Y. Boomkens ◽

Christina M. J. E. Vandenbroucke-Grauls ◽

Johannes G. Kusters

Keyword(s):

Helicobacter Pylori ◽

Natural Transformation ◽

Bacterial Genome ◽

Uptake System ◽

Dna Uptake ◽

Mutant Library ◽

Chromosomal Dna ◽

Orthologous Genes ◽

Helicobacter Felis ◽

H Pylori

ABSTRACT Helicobacter pylori is naturally competent for transformation, but the DNA uptake system of this bacterium is only partially characterized, and nothing is known about the regulation of competence in H. pylori. To identify other components involved in transformation or competence regulation in this species, we screened a mutant library for competence-deficient mutants. This resulted in the identification of a novel,Helicobacter-specific competence gene (comH) whose function is essential for transformation of H. pyloriwith chromosomal DNA fragments as well as with plasmids. Complementation of comH mutants in transcompletely restored competence. Unlike other transformation genes ofH. pylori, comH does not belong to a known family of orthologous genes. Moreover, no significant homologs ofcomH were identified in currently available databases of bacterial genome sequences. The comH gene codes for a protein with an N-terminal leader sequence and is present in both highly competent and less-efficient transforming H. pyloristrains. A comH homolog was found in Helicobacter acinonychis but not in Helicobacter felis andHelicobacter mustelae.

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Natural transformation in Gram-negative bacteria thriving in extreme environments: from genes and genomes to proteins, structures and regulation

Extremophiles ◽

10.1007/s00792-021-01242-z ◽

2021 ◽

Author(s):

Beate Averhoff ◽

Lennart Kirchner ◽

Katharina Pfefferle ◽

Deniz Yaman

Keyword(s):

Genetic Information ◽

Natural Transformation ◽

Thermus Thermophilus ◽

Extreme Environments ◽

Opportunistic Pathogen ◽

Dna Uptake ◽

Acinetobacter Baylyi ◽

And Function ◽

Transformation Systems ◽

Evolutionary Lineages

AbstractExtremophilic prokaryotes live under harsh environmental conditions which require far-reaching cellular adaptations. The acquisition of novel genetic information via natural transformation plays an important role in bacterial adaptation. This mode of DNA transfer permits the transfer of genetic information between microorganisms of distant evolutionary lineages and even between members of different domains. This phenomenon, known as horizontal gene transfer (HGT), significantly contributes to genome plasticity over evolutionary history and is a driving force for the spread of fitness-enhancing functions including virulence genes and antibiotic resistances. In particular, HGT has played an important role for adaptation of bacteria to extreme environments. Here, we present a survey of the natural transformation systems in bacteria that live under extreme conditions: the thermophile Thermus thermophilus and two desiccation-resistant members of the genus Acinetobacter such as Acinetobacter baylyi and Acinetobacter baumannii. The latter is an opportunistic pathogen and has become a world-wide threat in health-care institutions. We highlight conserved and unique features of the DNA transporter in Thermus and Acinetobacter and present tentative models of both systems. The structure and function of both DNA transporter are described and the mechanism of DNA uptake is discussed.

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Intra-species DNA exchange: Bacillus subtilis prefers sex with less related strains

10.1101/756569 ◽

2019 ◽

Author(s):

Polonca Stefanic ◽

Katarina Belcijan ◽

Barbara Kraigher ◽

Rok Kostanjšek ◽

Joseph Nesme ◽

...

Keyword(s):

Social Life ◽

Natural Transformation ◽

Bacterial Species ◽

Sexual Isolation ◽

Cell Contact ◽

Dna Uptake ◽

Kin Discrimination ◽

Dna Integration ◽

Profound Influence ◽

Adaptive Zone

B. subtilis is a soil dwelling bacterium with a diverse social life that includes quorum sensing-regulated interactions 1. These interactions result in bacterial equivalent of sex, and subsequently have a profound influence on bacterial evolution2. Sexual isolation in B. subtilis predicts for more frequent uptake of DNA isolated from closely related strains3–5, but DNA exchange between two interacting B. subtilis strains has never been addressed previously. Recently we discovered kin discrimination among highly related strains of B. subtilis, where less related strains showed antagonistic behaviour towards each other in the form of killing6. Here we show that antagonistic interactions between two less closely related B. subtilis strains result in increased recombination, which is in contrast to current dogma. We demonstrate that the induction of competence between non-kin strains is responsible for the observed elevated DNA uptake, which, through increased genetic variation, can increase the rate of adaptation as demonstrated here by the successful exploitation of a novel adaptive zone by a recombinant strain. Our results demonstrate an important evolutionary mechanism of ‘’promiscuous but safe sex’’: a type of bacterial cell-contact dependent DNA exchange that could promote diversification of conspecifics and exclude non-specific and potentially risky DNA of other species. Our findings could help understand the vast diversity of B. subtilis species at the genomic level despite existing mechanisms limiting less-related DNA integration during transformation. It is possible that this (or similar) mechanism could be accountable for the diversification of many other bacterial species capable of natural transformation.

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ZpdN, a Plasmid-Encoded Sigma Factor Homolog, Induces pBS32-Dependent Cell Death in Bacillus subtilis

Journal of Bacteriology ◽

10.1128/jb.00213-16 ◽

2016 ◽

Vol 198 (21) ◽

pp. 2975-2984 ◽

Cited By ~ 6

Author(s):

B.-E. Myagmarjav ◽

M. A. Konkol ◽

J. Ramsey ◽

S. Mukhopadhyay ◽

D. B. Kearns

Keyword(s):

Cell Death ◽

Bacillus Subtilis ◽

Mitomycin C ◽

Sigma Factor ◽

Natural Transformation ◽

Potent Inhibitor ◽

Dna Uptake ◽

Content Type ◽

Dependent Cell ◽

Necessary And Sufficient

ABSTRACTThe ancestralBacillus subtilisstrain 3610 contains an 84-kb plasmid called pBS32 that was lost during domestication of commonly used laboratory derivatives. Here we demonstrate that pBS32, normally present at 1 or 2 copies per cell, increases in copy number nearly 100-fold when cells are treated with the DNA-damaging agent mitomycin C. Mitomycin C treatment also caused cell lysis dependent on pBS32-borne prophage genes. ZpdN, a sigma factor homolog encoded by pBS32, was required for the plasmid response to DNA damage, and artificial expression of ZpdN was sufficient to induce pBS32 hyperreplication and cell death. Plasmid DNA released by cell death was protected by the capsid protein ZpbH, suggesting that the plasmid was packaged into a phagelike particle. The putative particles were further indicated by CsCl sedimentation but were not observed by electron microscopy and were incapable of killingB. subtiliscells extracellularly. We hypothesize that pBS32-mediated cell death releases a phagelike particle that is defective and unstable.IMPORTANCEProphages are phage genomes stably integrated into the host bacterium's chromosome and less frequently are maintained as extrachromosomal plasmids. Here we report that the extrachromosomal plasmid pBS32 ofBacillus subtilisencodes a prophage that, when activated, kills the host. pBS32 also encodes both the sigma factor homolog ZpdN that is necessary and sufficient for prophage induction and the protein ComI, which is a potent inhibitor of DNA uptake by natural transformation. We provide evidence that the entire pBS32 sequence may be part of the prophage and thus that competence inhibition may be linked to lysogeny.

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Unexpected connections between type VI-B CRISPR-Cas systems, bacterial natural competence, ubiquitin signaling network and DNA modification through a distinct family of membrane proteins

FEMS Microbiology Letters ◽

10.1093/femsle/fnz088 ◽

2019 ◽

Vol 366 (8) ◽

Cited By ~ 6

Author(s):

Kira S Makarova ◽

Linyi Gao ◽

Feng Zhang ◽

Eugene V Koonin

Keyword(s):

Natural Transformation ◽

Dna Modification ◽

Dna Uptake ◽

Transmembrane Helices ◽

Multidomain Proteins ◽

Signaling System ◽

The Core ◽

Foreign Dna ◽

Nascent Transcripts ◽

Cas Proteins

ABSTRACT In addition to core Cas proteins, CRISPR-Cas loci often encode ancillary proteins that modulate the activity of the respective effectors in interference. Subtype VI-B1 CRISPR-Cas systems encode the Csx27 protein that down-regulates the activity of Cas13b when the type VI-B locus is expressed in Escherichia coli. We show that Csx27 belongs to an expansive family of proteins that contain four predicted transmembrane helices and are typically encoded in predicted operons with components of the bacterial natural transformation machinery, multidomain proteins that consist of components of the ubiquitin signaling system and proteins containing the ligand-binding WYL domain and a helix-turn-helix domain. The Csx27 family proteins are predicted to form membrane channels for ssDNA that might comprise the core of a putative novel, Ub-regulated system for DNA uptake and, possibly, degradation. In addition to these associations, a distinct subfamily of the Csx27 family appears to be a part of a novel, membrane-associated system for DNA modification. In Bacteroidetes, subtype VI-B1 systems might degrade nascent transcripts of foreign DNA in conjunction with its uptake by the bacterial cell. These predictions suggest several experimental directions for the study of type VI CRISPR-Cas systems and distinct mechanisms of foreign DNA uptake and degradation in bacteria.

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