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Durrant MG, Perry NT, Pai JJ, Jangid AR, Athukoralage JS, Hiraizumi M, McSpedon JP, Pawluk A, Nishimasu H, Konermann S, Hsu PD. Bridge RNAs direct modular and programmable recombination of target and donor DNA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.24.577089. [PMID: 38328150 PMCID: PMC10849738 DOI: 10.1101/2024.01.24.577089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Genomic rearrangements, encompassing mutational changes in the genome such as insertions, deletions, or inversions, are essential for genetic diversity. These rearrangements are typically orchestrated by enzymes involved in fundamental DNA repair processes such as homologous recombination or in the transposition of foreign genetic material by viruses and mobile genetic elements (MGEs). We report that IS110 insertion sequences, a family of minimal and autonomous MGEs, express a structured non-coding RNA that binds specifically to their encoded recombinase. This bridge RNA contains two internal loops encoding nucleotide stretches that base-pair with the target DNA and donor DNA, which is the IS110 element itself. We demonstrate that the target-binding and donor-binding loops can be independently reprogrammed to direct sequence-specific recombination between two DNA molecules. This modularity enables DNA insertion into genomic target sites as well as programmable DNA excision and inversion. The IS110 bridge system expands the diversity of nucleic acid-guided systems beyond CRISPR and RNA interference, offering a unified mechanism for the three fundamental DNA rearrangements required for genome design.
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Affiliation(s)
- Matthew G. Durrant
- Arc Institute, 3181 Porter Drive, Palo Alto, CA 94304, USA
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Nicholas T. Perry
- Arc Institute, 3181 Porter Drive, Palo Alto, CA 94304, USA
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- University of California, Berkeley - University of California, San Francisco Graduate Program in Bioengineering, Berkeley, CA, USA
| | - James J. Pai
- Arc Institute, 3181 Porter Drive, Palo Alto, CA 94304, USA
| | - Aditya R. Jangid
- Arc Institute, 3181 Porter Drive, Palo Alto, CA 94304, USA
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | | | - Masahiro Hiraizumi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | | | - April Pawluk
- Arc Institute, 3181 Porter Drive, Palo Alto, CA 94304, USA
| | - Hiroshi Nishimasu
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
- Structural Biology Division, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Inamori Research Institute for Science, 620 Suiginya-cho, Shimogyo-ku, Kyoto 600-8411, Japan
- Japan Science and Technology Agency, Core Research for Evolutional Science and Technology, 4-1-8, Honcho, Kawaguchi-shi, Saitama 332-0012, Japan
| | - Silvana Konermann
- Arc Institute, 3181 Porter Drive, Palo Alto, CA 94304, USA
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Patrick D. Hsu
- Arc Institute, 3181 Porter Drive, Palo Alto, CA 94304, USA
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
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Chandler M, Ross K, Varani AM. The insertion sequence excision enhancer: A PrimPol-based primer invasion system for immobilizing transposon-transmitted antibiotic resistance genes. Mol Microbiol 2023; 120:658-669. [PMID: 37574851 DOI: 10.1111/mmi.15140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 07/24/2023] [Accepted: 07/31/2023] [Indexed: 08/15/2023]
Abstract
Evolutionary studies often identify genes that have been exchanged between different organisms and the phrase Lateral or Horizontal Gene Transfer is often used in this context. However, they rarely provide any mechanistic information concerning how these gene transfers might have occurred. With the astonishing increase in the number of sequences in public databases over the past two or three decades, identical antibiotic resistance genes have been identified in many different sequence contexts. One explanation for this would be that genes are initially transmitted by transposons which have subsequently decayed and can no longer be detected. Here, we provide an overview of a protein, IEE (Insertion Sequence Excision Enhancer) observed to facilitate high-frequency excision of IS629 from clinically important Escherichia coli O157:H7 and subsequently shown to affect a large class of bacterial insertion sequences which all transpose using the copy-out-paste-in transposition mechanism. Excision depends on both IEE and transposase indicating association with the transposition process itself. We review genetic and biochemical data and propose that IEE immobilizes genes carried by compound transposons by removing the flanking insertion sequence (IS) copies. The biochemical activities of IEE as a primase with the capacity to recognize DNA microhomologies and the observation that its effect appears restricted to IS families which use copy-out-paste-in transposition, suggests IS deletion occurs by abortive transposition involving strand switching (primer invasion) during the copy-out step. This reinforces the proposal made for understanding the widespread phenomenon loss of ISApl1 flanking mcr-1 in the compound transposon Tn6330 which we illustrate with a detailed model. This model also provides a convincing way to explain the high levels of IEE-induced precise IS excision.
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Affiliation(s)
- Mick Chandler
- Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center, Washington, DC, USA
| | - Karen Ross
- Protein Information Resource, Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center, Washington, DC, USA
| | - Alessandro M Varani
- School of Agricultural and Veterinary Sciences, Universidade Estadual Paulista, Sao Paulo, Brazil
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Zhong ZP, Vik D, Rapp JZ, Zablocki O, Maughan H, Temperton B, Deming JW, Sullivan MB. Lower viral evolutionary pressure under stable versus fluctuating conditions in subzero Arctic brines. MICROBIOME 2023; 11:174. [PMID: 37550784 PMCID: PMC10405475 DOI: 10.1186/s40168-023-01619-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 07/12/2023] [Indexed: 08/09/2023]
Abstract
BACKGROUND Climate change threatens Earth's ice-based ecosystems which currently offer archives and eco-evolutionary experiments in the extreme. Arctic cryopeg brine (marine-derived, within permafrost) and sea ice brine, similar in subzero temperature and high salinity but different in temporal stability, are inhabited by microbes adapted to these extreme conditions. However, little is known about their viruses (community composition, diversity, interaction with hosts, or evolution) or how they might respond to geologically stable cryopeg versus fluctuating sea ice conditions. RESULTS We used long- and short-read viromics and metatranscriptomics to study viruses in Arctic cryopeg brine, sea ice brine, and underlying seawater, recovering 11,088 vOTUs (~species-level taxonomic unit), a 4.4-fold increase of known viruses in these brines. More specifically, the long-read-powered viromes doubled the number of longer (≥25 kb) vOTUs generated and recovered more hypervariable regions by >5-fold compared to short-read viromes. Distribution assessment, by comparing to known viruses in public databases, supported that cryopeg brine viruses were of marine origin yet distinct from either sea ice brine or seawater viruses, while 94% of sea ice brine viruses were also present in seawater. A virus-encoded, ecologically important exopolysaccharide biosynthesis gene was identified, and many viruses (~half of metatranscriptome-inferred "active" vOTUs) were predicted as actively infecting the dominant microbial genera Marinobacter and Polaribacter in cryopeg and sea ice brines, respectively. Evolutionarily, microdiversity (intra-species genetic variations) analyses suggested that viruses within the stable cryopeg brine were under significantly lower evolutionary pressures than those in the fluctuating sea ice environment, while many sea ice brine virus-tail genes were under positive selection, indicating virus-host co-evolutionary arms races. CONCLUSIONS Our results confirmed the benefits of long-read-powered viromics in understanding the environmental virosphere through significantly improved genomic recovery, expanding viral discovery and the potential for biological inference. Evidence of viruses actively infecting the dominant microbes in subzero brines and modulating host metabolism underscored the potential impact of viruses on these remote and underexplored extreme ecosystems. Microdiversity results shed light on different strategies viruses use to evolve and adapt when extreme conditions are stable versus fluctuating. Together, these findings verify the value of long-read-powered viromics and provide foundational data on viral evolution and virus-microbe interactions in Earth's destabilized and rapidly disappearing cryosphere. Video Abstract.
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Affiliation(s)
- Zhi-Ping Zhong
- Byrd Polar and Climate Research Center, Ohio State University, Columbus, OH, USA
- Department of Microbiology, Ohio State University, Columbus, OH, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH, USA
| | - Dean Vik
- Department of Microbiology, Ohio State University, Columbus, OH, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH, USA
| | - Josephine Z Rapp
- Department of Biology, Université Laval, Québec, QC, Canada
- Center for Northern Studies (CEN), Université Laval, Québec, QC, Canada
| | - Olivier Zablocki
- Department of Microbiology, Ohio State University, Columbus, OH, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH, USA
| | | | - Ben Temperton
- School of Biosciences, University of Exeter, Exeter, Devon, UK
| | - Jody W Deming
- School of Oceanography and Astrobiology Program, University of Washington, Seattle, WA, USA.
| | - Matthew B Sullivan
- Byrd Polar and Climate Research Center, Ohio State University, Columbus, OH, USA.
- Department of Microbiology, Ohio State University, Columbus, OH, USA.
- Center of Microbiome Science, Ohio State University, Columbus, OH, USA.
- Department of Civil, Environmental and Geodetic Engineering, Ohio State University, Columbus, OH, USA.
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Metagenomic methylation patterns resolve bacterial genomes of unusual size and structural complexity. THE ISME JOURNAL 2022; 16:1921-1931. [PMID: 35459792 PMCID: PMC9296519 DOI: 10.1038/s41396-022-01242-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 04/05/2022] [Accepted: 04/08/2022] [Indexed: 01/01/2023]
Abstract
The plasticity of bacterial and archaeal genomes makes examining their ecological and evolutionary dynamics both exciting and challenging. The same mechanisms that enable rapid genomic change and adaptation confound current approaches for recovering complete genomes from metagenomes. Here, we use strain-specific patterns of DNA methylation to resolve complex bacterial genomes from long-read metagenomic data of a marine microbial consortium, the “pink berries” of the Sippewissett Marsh (USA). Unique combinations of restriction-modification (RM) systems encoded by the bacteria produced distinctive methylation profiles that were used to accurately bin and classify metagenomic sequences. Using this approach, we finished the largest and most complex circularized bacterial genome ever recovered from a metagenome (7.9 Mb with >600 transposons), the finished genome of Thiohalocapsa sp. PB-PSB1 the dominant bacteria in the consortia. From genomes binned by methylation patterns, we identified instances of horizontal gene transfer between sulfur-cycling symbionts (Thiohalocapsa sp. PB-PSB1 and Desulfofustis sp. PB-SRB1), phage infection, and strain-level structural variation. We also linked the methylation patterns of each metagenome-assembled genome with encoded DNA methyltransferases and discovered new RM defense systems, including novel associations of RM systems with RNase toxins.
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Siguier P, Gourbeyre E, Chandler M. Known knowns, known unknowns and unknown unknowns in prokaryotic transposition. Curr Opin Microbiol 2017; 38:171-180. [PMID: 28683354 DOI: 10.1016/j.mib.2017.06.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2017] [Revised: 06/15/2017] [Accepted: 06/19/2017] [Indexed: 02/06/2023]
Abstract
Although the phenomenon of transposition has been known for over 60 years, its overarching importance in modifying and streamlining genomes took some time to recognize. In spite of a robust understanding of transposition of some TE, there remain a number of important TE groups with potential high genome impact and unknown transposition mechanisms and yet others, only recently identified by bioinformatics, yet to be formally confirmed as mobile. Here, we point to some areas of limited understanding concerning well established important TE groups with DDE Tpases, to address central gaps in our knowledge of characterised Tn with other types of Tpases and finally, to highlight new potentially mobile DNA species. It is not exhaustive. Examples have been chosen to provide encouragement in the continued exploration of the considerable prokaryotic mobilome especially in light of the current threat to public health posed by the spread of multiple AbR.
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Affiliation(s)
- Patricia Siguier
- Centre National de la Recherche Scientifique (CNRS), Toulouse, France
| | - Edith Gourbeyre
- Centre National de la Recherche Scientifique (CNRS), Toulouse, France
| | - Michael Chandler
- Centre National de la Recherche Scientifique (CNRS), Toulouse, France; Department of Biochem., Mol. and Cell. Biol. Georgetown University Medical Center, 3900 Reservoir Rd., Washington, DC 20057-1455, USA.
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Abstract
ABSTRACT
The number and diversity of known prokaryotic insertion sequences (IS) have increased enormously since their discovery in the late 1960s. At present the sequences of more than 4000 different IS have been deposited in the specialized ISfinder database. Over time it has become increasingly apparent that they are important actors in the evolution of their host genomes and are involved in sequestering, transmitting, mutating and activating genes, and in the rearrangement of both plasmids and chromosomes. This review presents an overview of our current understanding of these transposable elements (TE), their organization and their transposition mechanism as well as their distribution and genomic impact. In spite of their diversity, they share only a very limited number of transposition mechanisms which we outline here. Prokaryotic IS are but one example of a variety of diverse TE which are being revealed due to the advent of extensive genome sequencing projects. A major conclusion from sequence comparisons of various TE is that frontiers between the different types are becoming less clear. We detail these receding frontiers between different IS-related TE. Several, more specialized chapters in this volume include additional detailed information concerning a number of these.
In a second section of the review, we provide a detailed description of the expanding variety of IS, which we have divided into families for convenience. Our perception of these families continues to evolve and families emerge regularly as more IS are identified. This section is designed as an aid and a source of information for consultation by interested specialist readers.
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Goldberg A, Fridman O, Ronin I, Balaban NQ. Systematic identification and quantification of phase variation in commensal and pathogenic Escherichia coli. Genome Med 2014; 6:112. [PMID: 25530806 PMCID: PMC4272514 DOI: 10.1186/s13073-014-0112-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Accepted: 11/14/2014] [Indexed: 11/10/2022] Open
Abstract
Bacteria have been shown to generate constant genetic variation in a process termed phase variation. We present a tool based on whole genome sequencing that allows detection and quantification of coexisting genotypes mediated by genomic inversions in bacterial cultures. We tested our method on widely used strains of Escherichia coli, and detected stable and reproducible phase variation in several invertible loci. These are shown here to be responsible for maintaining constant variation in populations grown from a single colony. Applying this tool on other bacterial strains can shed light on how pathogens adjust to hostile environments by diversifying their genomes.
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Affiliation(s)
- Amir Goldberg
- Racah Institute of Physics and the Sudarsky Center for Computational Biology, The Hebrew University, Edmond J. Safra Campus, Jerusalem, 91904 Israel
| | - Ofer Fridman
- Racah Institute of Physics and the Sudarsky Center for Computational Biology, The Hebrew University, Edmond J. Safra Campus, Jerusalem, 91904 Israel
| | - Irine Ronin
- Racah Institute of Physics and the Sudarsky Center for Computational Biology, The Hebrew University, Edmond J. Safra Campus, Jerusalem, 91904 Israel
| | - Nathalie Q Balaban
- Racah Institute of Physics and the Sudarsky Center for Computational Biology, The Hebrew University, Edmond J. Safra Campus, Jerusalem, 91904 Israel
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Abstract
Bacterial genomes are remarkably stable from one generation to the next but are plastic on an evolutionary time scale, substantially shaped by horizontal gene transfer, genome rearrangement, and the activities of mobile DNA elements. This implies the existence of a delicate balance between the maintenance of genome stability and the tolerance of genome instability. In this review, we describe the specialized genetic elements and the endogenous processes that contribute to genome instability. We then discuss the consequences of genome instability at the physiological level, where cells have harnessed instability to mediate phase and antigenic variation, and at the evolutionary level, where horizontal gene transfer has played an important role. Indeed, this ability to share DNA sequences has played a major part in the evolution of life on Earth. The evolutionary plasticity of bacterial genomes, coupled with the vast numbers of bacteria on the planet, substantially limits our ability to control disease.
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9
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Raff EC, Andrews ME, Turner FR, Toh E, Nelson DE, Raff RA. Contingent interactions among biofilm-forming bacteria determine preservation or decay in the first steps toward fossilization of marine embryos. Evol Dev 2013; 15:243-56. [PMID: 23809699 DOI: 10.1111/ede.12028] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Fossils of soft tissues provide important records of early animals and embryos, and there is substantial evidence for a role for microbes in soft tissue fossilization. We are investigating the initial events in interactions of bacteria with freshly dead tissue, using marine embryos as a model system. We previously found that microbial invasion can stabilize embryo tissue that would otherwise disintegrate in hours or days by generating a bacterial pseudomorph, a three dimensional biofilm that both replaces the tissue and replicates its morphology. In this study, we sampled seawater at different times and places near Sydney, Australia, and determined the range and frequency of different taphonomic outcomes. Although destruction was most common, bacteria in 35% of seawater samples yielded morphology‐preserving biofilms. We could replicate the taphonomic pathways seen with seawater bacterial communities using single cultured strains of marine gammaproteobacteria. Each given species reproducibly generated a consistent taphonomic outcome and we identified species that yielded each of the distinct pathways produced by seawater bacterial communities. Once formed,bacterial pseudomorphs are stable for over a year and resist attack by other bacteria and destruction by proteases and other lytic enzymes. Competition studies showed that the initial action of a pseudomorphing strain can be blocked by a strain that destroys tissues. Thus embryo preservation in nature may depend on contingent interactions among bacterial species that determine if pseudomorphing occurs.We used Artemia nauplius larvae to show that bacterial biofilm replacement of tissue is not restricted to embryos, but is relevant for preservation of small multicellular organisms. We present a model for bacterial self‐assembly of large‐scale three‐dimensional tissue pseudomorphs, based on smallscaleinteractions among individual bacterial cells to form local biofilms at structural boundaries within the tissue. Localbiofilms then conjoin to generate the pseudomorph.
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Affiliation(s)
- Elizabeth C Raff
- Department of Biology, Indiana University, Bloomington, IN 47405, USA.
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Coordinated phenotype switching with large-scale chromosome flip-flop inversion observed in bacteria. Proc Natl Acad Sci U S A 2012; 109:E1647-56. [PMID: 22645353 DOI: 10.1073/pnas.1204307109] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Genome inversions are ubiquitous in organisms ranging from prokaryotes to eukaryotes. Typical examples can be identified by comparing the genomes of two or more closely related organisms, where genome inversion footprints are clearly visible. Although the evolutionary implications of this phenomenon are huge, little is known about the function and biological meaning of this process. Here, we report our findings on a bacterium that generates a reversible, large-scale inversion of its chromosome (about half of its total genome) at high frequencies of up to once every four generations. This inversion switches on or off bacterial phenotypes, including colony morphology, antibiotic susceptibility, hemolytic activity, and expression of dozens of genes. Quantitative measurements and mathematical analyses indicate that this reversible switching is stochastic but self-organized so as to maintain two forms of stable cell populations (i.e., small colony variant, normal colony variant) as a bet-hedging strategy. Thus, this heritable and reversible genome fluctuation seems to govern the bacterial life cycle; it has a profound impact on the course and outcomes of bacterial infections.
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Gonzaga A, Martin-Cuadrado AB, López-Pérez M, Megumi Mizuno C, García-Heredia I, Kimes NE, Lopez-García P, Moreira D, Ussery D, Zaballos M, Ghai R, Rodriguez-Valera F. Polyclonality of concurrent natural populations of Alteromonas macleodii. Genome Biol Evol 2012; 4:1360-74. [PMID: 23212172 PMCID: PMC3542563 DOI: 10.1093/gbe/evs112] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/29/2012] [Indexed: 01/28/2023] Open
Abstract
We have analyzed a natural population of the marine bacterium, Alteromonas macleodii, from a single sample of seawater to evaluate the genomic diversity present. We performed full genome sequencing of four isolates and 161 metagenomic fosmid clones, all of which were assigned to A. macleodii by sequence similarity. Out of the four strain genomes, A. macleodii deep ecotype (AltDE1) represented a different genome, whereas AltDE2 and AltDE3 were identical to the previously described AltDE. Although the core genome (~80%) had an average nucleotide identity of 98.51%, both AltDE and AltDE1 contained flexible genomic islands (fGIs), that is, genomic islands present in both genomes in the same genomic context but having different gene content. Some of the fGIs encode cell surface receptors known to be phage recognition targets, such as the O-chain of the lipopolysaccharide, whereas others have genes involved in physiological traits (e.g., nutrient transport, degradation, and metal resistance) denoting microniche specialization. The presence in metagenomic fosmids of genomic fragments differing from the sequenced strain genomes, together with the presence of new fGIs, indicates that there are at least two more A. macleodii clones present. The availability of three or more sequences overlapping the same genomic region also allowed us to estimate the frequency and distribution of recombination events among these different clones, indicating that these clustered near the genomic islands. The results indicate that this natural A. macleodii population has multiple clones with a potential for different phage susceptibility and exploitation of resources, within a seemingly unstructured habitat.
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Affiliation(s)
- Aitor Gonzaga
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, Alicante, Spain
| | - Ana-Belen Martin-Cuadrado
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, Alicante, Spain
| | - Mario López-Pérez
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, Alicante, Spain
| | - Carolina Megumi Mizuno
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, Alicante, Spain
| | - Inmaculada García-Heredia
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, Alicante, Spain
| | - Nikole E. Kimes
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, Alicante, Spain
| | | | - David Moreira
- Unité d’Ecologie, Systématique et Evolution, CNRS UMR 8079, Université Paris-Sud, Orsay, France
| | - David Ussery
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, Alicante, Spain
- Present address: Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark
| | - Mila Zaballos
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, Alicante, Spain
| | - Rohit Ghai
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, Alicante, Spain
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Abstract
Reversible insertion of IS492 at a site within epsG on the Pseudoalteromonas atlantica chromosome controls peripheral extracellular polysaccharide production and biofilm formation by P. atlantica. High-frequency precise excision of IS492 from epsG requires 5 and 7 bp of flanking DNA, suggesting that IS492 transposition involves a site-specific recombination mechanism. The site specificity of IS492 insertion was examined in P. atlantica and shown to be specific for a 7-bp target, 5'-CTTGTTA-3'. Characterization of numerous insertion events at the target site in epsG indicated that insertion is also orientation specific. The frequency of IS492 insertion at the epsG target site (2.7 x 10(-7)/cell/generation), determined by quantitative PCR, is 4 to 5 orders of magnitude lower than the frequency of IS492 precise excision from the same site. Comparison of insertion sites for IS492 and the highly related ISPtu2 from Pseudoalteromonas tunicata suggests DNA sequence and/or structural features that may contribute to site recognition and recombination by the transposase of IS492.
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Thomas T, Evans FF, Schleheck D, Mai-Prochnow A, Burke C, Penesyan A, Dalisay DS, Stelzer-Braid S, Saunders N, Johnson J, Ferriera S, Kjelleberg S, Egan S. Analysis of the Pseudoalteromonas tunicata genome reveals properties of a surface-associated life style in the marine environment. PLoS One 2008; 3:e3252. [PMID: 18813346 PMCID: PMC2536512 DOI: 10.1371/journal.pone.0003252] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2008] [Accepted: 08/21/2008] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Colonisation of sessile eukaryotic host surfaces (e.g. invertebrates and seaweeds) by bacteria is common in the marine environment and is expected to create significant inter-species competition and other interactions. The bacterium Pseudoalteromonas tunicata is a successful competitor on marine surfaces owing primarily to its ability to produce a number of inhibitory molecules. As such P. tunicata has become a model organism for the studies into processes of surface colonisation and eukaryotic host-bacteria interactions. METHODOLOGY/PRINCIPAL FINDINGS To gain a broader understanding into the adaptation to a surface-associated life-style, we have sequenced and analysed the genome of P. tunicata and compared it to the genomes of closely related strains. We found that the P. tunicata genome contains several genes and gene clusters that are involved in the production of inhibitory compounds against surface competitors and secondary colonisers. Features of P. tunicata's oxidative stress response, iron scavenging and nutrient acquisition show that the organism is well adapted to high-density communities on surfaces. Variation of the P. tunicata genome is suggested by several landmarks of genetic rearrangements and mobile genetic elements (e.g. transposons, CRISPRs, phage). Surface attachment is likely to be mediated by curli, novel pili, a number of extracellular polymers and potentially other unexpected cell surface proteins. The P. tunicata genome also shows a utilisation pattern of extracellular polymers that would avoid a degradation of its recognised hosts, while potentially causing detrimental effects on other host types. In addition, the prevalence of recognised virulence genes suggests that P. tunicata has the potential for pathogenic interactions. CONCLUSIONS/SIGNIFICANCE The genome analysis has revealed several physiological features that would provide P. tunciata with competitive advantage against other members of the surface-associated community. We have also identified properties that could mediate interactions with surfaces other than its currently recognised hosts. This together with the detection of known virulence genes leads to the hypothesis that P. tunicata maintains a carefully regulated balance between beneficial and detrimental interactions with a range of host surfaces.
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Affiliation(s)
- Torsten Thomas
- Centre of Marine Bio-Innovation and School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, Australia.
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14
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Phase and antigenic variation mediated by genome modifications. Antonie van Leeuwenhoek 2008; 94:493-515. [DOI: 10.1007/s10482-008-9267-6] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2008] [Accepted: 07/09/2008] [Indexed: 11/26/2022]
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