1
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Torrance EL, Burton C, Diop A, Bobay LM. Evolution of homologous recombination rates across bacteria. Proc Natl Acad Sci U S A 2024; 121:e2316302121. [PMID: 38657048 PMCID: PMC11067023 DOI: 10.1073/pnas.2316302121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 03/08/2024] [Indexed: 04/26/2024] Open
Abstract
Bacteria are nonsexual organisms but are capable of exchanging DNA at diverse degrees through homologous recombination. Intriguingly, the rates of recombination vary immensely across lineages where some species have been described as purely clonal and others as "quasi-sexual." However, estimating recombination rates has proven a difficult endeavor and estimates often vary substantially across studies. It is unclear whether these variations reflect natural variations across populations or are due to differences in methodologies. Consequently, the impact of recombination on bacterial evolution has not been extensively evaluated and the evolution of recombination rate-as a trait-remains to be accurately described. Here, we developed an approach based on Approximate Bayesian Computation that integrates multiple signals of recombination to estimate recombination rates. We inferred the rate of recombination of 162 bacterial species and one archaeon and tested the robustness of our approach. Our results confirm that recombination rates vary drastically across bacteria; however, we found that recombination rate-as a trait-is conserved in several lineages but evolves rapidly in others. Although some traits are thought to be associated with recombination rate (e.g., GC-content), we found no clear association between genomic or phenotypic traits and recombination rate. Overall, our results provide an overview of recombination rate, its evolution, and its impact on bacterial evolution.
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Affiliation(s)
- Ellis L Torrance
- Department of Biology, University of North Carolina, Greensboro, NC 27412
| | - Corey Burton
- Department of Biology, University of North Carolina, Greensboro, NC 27412
| | - Awa Diop
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695
| | - Louis-Marie Bobay
- Department of Biology, University of North Carolina, Greensboro, NC 27412
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695
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2
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Sheinman M, Arndt PF, Massip F. Modeling the mosaic structure of bacterial genomes to infer their evolutionary history. Proc Natl Acad Sci U S A 2024; 121:e2313367121. [PMID: 38517978 PMCID: PMC10990148 DOI: 10.1073/pnas.2313367121] [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: 08/03/2023] [Accepted: 01/30/2024] [Indexed: 03/24/2024] Open
Abstract
The chronology and phylogeny of bacterial evolution are difficult to reconstruct due to a scarce fossil record. The analysis of bacterial genomes remains challenging because of large sequence divergence, the plasticity of bacterial genomes due to frequent gene loss, horizontal gene transfer, and differences in selective pressure from one locus to another. Therefore, taking advantage of the rich and rapidly accumulating genomic data requires accurate modeling of genome evolution. An important technical consideration is that loci with high effective mutation rates may diverge beyond the detection limit of the alignment algorithms used, biasing the genome-wide divergence estimates toward smaller divergences. In this article, we propose a novel method to gain insight into bacterial evolution based on statistical properties of genome comparisons. We find that the length distribution of sequence matches is shaped by the effective mutation rates of different loci, by the horizontal transfers, and by the aligner sensitivity. Based on these inputs, we build a model and show that it accounts for the empirically observed distributions, taking the Enterobacteriaceae family as an example. Our method allows to distinguish segments of vertical and horizontal origins and to estimate the time divergence and exchange rate between any pair of taxa from genome-wide alignments. Based on the estimated time divergences, we construct a time-calibrated phylogenetic tree to demonstrate the accuracy of the method.
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Affiliation(s)
- Michael Sheinman
- Institute for Advanced Studies, Sevastopol State University, Sevastopol299053, Crimea
| | - Peter F. Arndt
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin12163, Germany
| | - Florian Massip
- Department U900, Centre for Computational Biology, Mines Paris, PSL University, Paris75006, France
- Department U900, Institut Curie, Université Paris Sciences et Lettres, Paris75005, France
- INSERM, U900, Paris75005, France
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3
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Arizala D, Arif M. Impact of Homologous Recombination on Core Genome Evolution and Host Adaptation of Pectobacterium parmentieri. Genome Biol Evol 2024; 16:evae032. [PMID: 38385549 PMCID: PMC10946231 DOI: 10.1093/gbe/evae032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 02/02/2024] [Accepted: 02/11/2024] [Indexed: 02/23/2024] Open
Abstract
Homologous recombination is a major force mechanism driving bacterial evolution, host adaptability, and acquisition of novel virulence traits. Pectobacterium parmentieri is a plant bacterial pathogen distributed worldwide, primarily affecting potatoes, by causing soft rot and blackleg diseases. The goal of this investigation was to understand the impact of homologous recombination on the genomic evolution of P. parmentieri. Analysis of P. parmentieri genomes using Roary revealed a dynamic pan-genome with 3,742 core genes and over 55% accessory genome variability. Bayesian population structure analysis identified 7 lineages, indicating species heterogeneity. ClonalFrameML analysis displayed 5,125 recombination events, with the lineage 4 exhibiting the highest events. fastGEAR analysis identified 486 ancestral and 941 recent recombination events ranging from 43 bp to 119 kb and 36 bp to 13.96 kb, respectively, suggesting ongoing adaptation. Notably, 11% (412 genes) of the core genome underwent recent recombination, with lineage 1 as the main donor. The prevalence of recent recombination (double compared to ancient) events implies continuous adaptation, possibly driven by global potato trade. Recombination events were found in genes involved in vital cellular processes (DNA replication, DNA repair, RNA processing, homeostasis, and metabolism), pathogenicity determinants (type secretion systems, cell-wall degrading enzymes, iron scavengers, lipopolysaccharides (LPS), flagellum, etc.), antimicrobial compounds (phenazine and colicin) and even CRISPR-Cas genes. Overall, these results emphasize the potential role of homologous recombination in P. parmentieri's evolutionary dynamics, influencing host colonization, pathogenicity, adaptive immunity, and ecological fitness.
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Affiliation(s)
- Dario Arizala
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Mohammad Arif
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI, USA
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4
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Liu Z, Good BH. Dynamics of bacterial recombination in the human gut microbiome. PLoS Biol 2024; 22:e3002472. [PMID: 38329938 PMCID: PMC10852326 DOI: 10.1371/journal.pbio.3002472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 12/14/2023] [Indexed: 02/10/2024] Open
Abstract
Horizontal gene transfer (HGT) is a ubiquitous force in microbial evolution. Previous work has shown that the human gut is a hotspot for gene transfer between species, but the more subtle exchange of variation within species-also known as recombination-remains poorly characterized in this ecosystem. Here, we show that the genetic structure of the human gut microbiome provides an opportunity to measure recent recombination events from sequenced fecal samples, enabling quantitative comparisons across diverse commensal species that inhabit a common environment. By analyzing recent recombination events in the core genomes of 29 human gut bacteria, we observed widespread heterogeneities in the rates and lengths of transferred fragments, which are difficult to explain by existing models of ecological isolation or homology-dependent recombination rates. We also show that natural selection helps facilitate the spread of genetic variants across strain backgrounds, both within individual hosts and across the broader population. These results shed light on the dynamics of in situ recombination, which can strongly constrain the adaptability of gut microbial communities.
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Affiliation(s)
- Zhiru Liu
- Department of Applied Physics, Stanford University, Stanford, California, United States of America
| | - Benjamin H. Good
- Department of Applied Physics, Stanford University, Stanford, California, United States of America
- Department of Biology, Stanford University, Stanford, California, United States of America
- Chan Zuckerberg Biohub–San Francisco, San Francisco, California, United States of America
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5
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Zarras C, Karampatakis T, Pappa S, Iosifidis E, Vagdatli E, Roilides E, Papa A. Genetic Characterization of Carbapenem-Resistant Klebsiella pneumoniae Clinical Isolates in a Tertiary Hospital in Greece, 2018-2022. Antibiotics (Basel) 2023; 12:976. [PMID: 37370295 DOI: 10.3390/antibiotics12060976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 05/23/2023] [Accepted: 05/25/2023] [Indexed: 06/29/2023] Open
Abstract
BACKGROUND Carbapenem-resistant Klebsiella pneumoniae (CRKP) is a serious public health issue. The study aimed to identify the antimicrobial resistance and accessory genes, the clonal relatedness, and the evolutionary dynamics of selected CRKP isolates recovered in an adult and pediatric intensive care unit of a tertiary hospital in Greece. METHODS Twenty-four CRKP isolates recovered during 2018-2022 were included in the study. Next-generation sequencing was performed using the Ion Torrent PGM Platform. The identification of the plasmid content, MLST, and antimicrobial resistance genes, as well as the comparison of multiple genome alignments and the identification of core genome single-nucleotide polymorphism sites, were performed using various bioinformatics software. RESULTS The isolates belonged to eight sequence types: 11, 15, 30, 35, 39, 307, 323, and 512. A variety of carbapenemases (KPC, VIM, NDM, and OXA-48) and resistance genes were detected. CRKP strains shared visually common genomic regions with the reference strain (NTUH-K2044). ST15, ST323, ST39, and ST11 CRKP isolates presented on average 17, 6, 16, and 866 recombined SNPs, respectively. All isolates belonging to ST15, ST323, and ST39 were classified into distinct phylogenetic branches, while ST11 isolates were assigned to a two-subclade branch. For large CRKP sets, the phylogeny seems to change approximately every seven SNPs. CONCLUSIONS The current study provides insight into the genetic characterization of CRKP isolates in the ICUs of a tertiary hospital. Our results indicate clonal dispersion of ST15, ST323, and ST39 and highly diverged ST11 isolates.
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Affiliation(s)
- Charalampos Zarras
- Department of Microbiology, Medical Faculty, School of Health Sciences, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece
- Microbiology Department, Hippokration General Hospital, 546 42 Thessaloniki, Greece
| | - Theodoros Karampatakis
- Department of Microbiology, Medical Faculty, School of Health Sciences, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece
| | - Styliani Pappa
- Department of Microbiology, Medical Faculty, School of Health Sciences, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece
| | - Elias Iosifidis
- Infectious Disease Unit, 3rd Department of Pediatrics, Medical Faculty, School of Health Sciences, Hippokration General Hospital, 546 42 Thessaloniki, Greece
| | - Eleni Vagdatli
- Microbiology Department, Hippokration General Hospital, 546 42 Thessaloniki, Greece
| | - Emmanuel Roilides
- Infectious Disease Unit, 3rd Department of Pediatrics, Medical Faculty, School of Health Sciences, Hippokration General Hospital, 546 42 Thessaloniki, Greece
| | - Anna Papa
- Department of Microbiology, Medical Faculty, School of Health Sciences, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece
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6
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Kislichkina AA, Kartsev NN, Skryabin YP, Sizova AA, Kanashenko ME, Teymurazov MG, Kuzina ES, Bogun AG, Fursova NK, Svetoch EA, Dyatlov IA. Genomic Analysis of a Hybrid Enteroaggregative Hemorrhagic Escherichia coli O181:H4 Strain Causing Colitis with Hemolytic-Uremic Syndrome. Antibiotics (Basel) 2022; 11:antibiotics11101416. [PMID: 36290074 PMCID: PMC9598891 DOI: 10.3390/antibiotics11101416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/12/2022] [Accepted: 10/13/2022] [Indexed: 11/16/2022] Open
Abstract
Hybrid diarrheagenic E. coli strains combining genetic markers belonging to different pathotypes have emerged worldwide and have been reported as a public health concern. The most well-known hybrid strain of enteroaggregative hemorrhagic E. coli is E. coli O104:H4 strain, which was an agent of a serious outbreak of acute gastroenteritis and hemolytic uremic syndrome (HUS) in Germany in 2011. A case of intestinal infection with HUS in St. Petersburg (Russian Federation) occurred in July 2018. E. coli strain SCPM-O-B-9427 was obtained from the rectal swab of the patient with HUS. It was determined as O181:H4-, stx2-, and aggR-positive and belonged to the phylogenetic group B2. The complete genome assembly of the strain SCPM-O-B-9427 contained one chromosome and five plasmids, including the plasmid coding an aggregative adherence fimbriae I. MLST analysis showed that the strain SCPM-O-B-9427 belonged to ST678, and like E. coli O104:H4 strains, 2011C-3493 caused the German outbreak in 2011, and 2009EL-2050 was isolated in the Republic of Georgia in 2009. Comparison of three strains showed almost the same structure of their chromosomes: the plasmids pAA and the stx2a phages are very similar, but they have distinct sets of the plasmids and some unique regions in the chromosomes.
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Affiliation(s)
- Angelina A. Kislichkina
- Department of Culture Collection, State Research Center for Applied Microbiology and Biotechnology, Territory “Kvartal A”, 142279 Obolensk, Russia
- Correspondence:
| | - Nikolay N. Kartsev
- Department of Molecular Microbiology, State Research Center for Applied Microbiology and Biotechnology, Territory “Kvartal A”, 142279 Obolensk, Russia
| | - Yury P. Skryabin
- Department of Molecular Microbiology, State Research Center for Applied Microbiology and Biotechnology, Territory “Kvartal A”, 142279 Obolensk, Russia
| | - Angelika A. Sizova
- Department of Culture Collection, State Research Center for Applied Microbiology and Biotechnology, Territory “Kvartal A”, 142279 Obolensk, Russia
| | - Maria E. Kanashenko
- Department of Molecular Microbiology, State Research Center for Applied Microbiology and Biotechnology, Territory “Kvartal A”, 142279 Obolensk, Russia
| | - Marat G. Teymurazov
- Department of Molecular Microbiology, State Research Center for Applied Microbiology and Biotechnology, Territory “Kvartal A”, 142279 Obolensk, Russia
| | - Ekaterina S. Kuzina
- Department of Training and Improvement of Specialists, State Research Center for Applied Microbiology and Biotechnology, Territory “Kvartal A”, 142279 Obolensk, Russia
| | - Alexander G. Bogun
- Department of Culture Collection, State Research Center for Applied Microbiology and Biotechnology, Territory “Kvartal A”, 142279 Obolensk, Russia
| | - Nadezhda K. Fursova
- Department of Molecular Microbiology, State Research Center for Applied Microbiology and Biotechnology, Territory “Kvartal A”, 142279 Obolensk, Russia
| | - Edward A. Svetoch
- Department of Molecular Microbiology, State Research Center for Applied Microbiology and Biotechnology, Territory “Kvartal A”, 142279 Obolensk, Russia
| | - Ivan A. Dyatlov
- Department of Culture Collection, State Research Center for Applied Microbiology and Biotechnology, Territory “Kvartal A”, 142279 Obolensk, Russia
- Department of Molecular Microbiology, State Research Center for Applied Microbiology and Biotechnology, Territory “Kvartal A”, 142279 Obolensk, Russia
- Department of Training and Improvement of Specialists, State Research Center for Applied Microbiology and Biotechnology, Territory “Kvartal A”, 142279 Obolensk, Russia
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7
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Halaji M, Fayyazi A, Rajabnia M, Zare D, Pournajaf A, Ranjbar R. Phylogenetic Group Distribution of Uropathogenic Escherichia coli and Related Antimicrobial Resistance Pattern: A Meta-Analysis and Systematic Review. Front Cell Infect Microbiol 2022; 12:790184. [PMID: 35281449 PMCID: PMC8914322 DOI: 10.3389/fcimb.2022.790184] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 01/26/2022] [Indexed: 12/20/2022] Open
Abstract
The phylogenetic classification of Escherichia coli isolates is of great importance not only for understanding the populations of E. coli but also for clarifying the relationship between strains and diseases. The present study aimed to evaluate the prevalence of phylogenetic groups, antibiotic susceptibility pattern, and virulence genes among uropathogenic E. coli (UPEC) isolated from different parts of Iran through a systematic review and meta-analysis. Several international electronic sources, including Web of Science, PubMed, Scopus, and Embase, were searched (2000–2020) in order to identify the studies compatible with our inclusion criteria. The meta-analysis was performed using the metaprop program in the STATA (version 11) software. Based on our comprehensive search, 28 studies meeting the eligibility criteria were included in the meta-analysis. The pooled prevalence of phylogroups B2, D, B1, and A was 39%, 26%, 18%, and 8%, respectively. In addition, there was a significant heterogeneity among different phylogroups. However, according to the results of Begg’s and Egger’s tests, there were no significant publication bias in phylogroups B2, D, B1, and A. This research provided the first comprehensive study on phylogroups of UPEC isolated in Iran. Our findings indicated that phylogroup B2 and group D were the most predominant phylogenetic groups among UPEC isolates in various regions of Iran. In addition, we observed that certain phylogenetic groups are more antibiotic resistant than the others. It was also observed that the dissemination of virulent phylogroup B2 and D should be controlled via comprehensive infection control measures. Additionally, certain strategies should be developed for monitoring the antibiotic therapy.
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Affiliation(s)
- Mehrdad Halaji
- Infectious Diseases and Tropical Medicine Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
- Department of Microbiology, School of Medicine, Babol University of Medical Sciences, Babol, Iran
| | - Amirhossein Fayyazi
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mehdi Rajabnia
- Infectious Diseases and Tropical Medicine Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
- Department of Microbiology, School of Medicine, Babol University of Medical Sciences, Babol, Iran
| | - Donya Zare
- Department of Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Abazar Pournajaf
- Infectious Diseases and Tropical Medicine Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
- Department of Microbiology, School of Medicine, Babol University of Medical Sciences, Babol, Iran
| | - Reza Ranjbar
- Molecular Biology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
- *Correspondence: Reza Ranjbar,
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8
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Leclercq SO, Branger M, Smith DGE, Germon P. Lipopolysaccharide core type diversity in the Escherichia coli species in association with phylogeny, virulence gene repertoire and distribution of type VI secretion systems. Microb Genom 2021; 7. [PMID: 34586053 PMCID: PMC8715443 DOI: 10.1099/mgen.0.000652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Escherichia coli is a very versatile species for which diversity has been explored from various perspectives highlighting, for example, phylogenetic groupings and pathovars, as well as a wide range of O serotypes. The highly variable O-antigen, the most external part of the lipopolysaccharide (LPS) component of the outer membrane of E. coli, is linked to the innermost lipid A through the core region of LPS of which five different structures, denominated K-12, R1, R2, R3 and R4, have been characterized so far. The aim of the present study was to analyse the prevalence of these LPS core types in the E. coli species and explore their distribution in the different E. coli phylogenetic groups and in relationship with the virulence gene repertoire. Results indicated an uneven distribution of core types between the different phylogroups, with phylogroup A strains being the most diverse in terms of LPS core types, while phylogroups B1, D and E strains were dominated by the R3 type, and phylogroups B2 and C strains were dominated by the R1 type. Strains carrying the LEE virulence operon were mostly of the R3 type whatever the phylogroup while, within phylogroup B2, strains carrying a K-12 core all belonged to the complex STc131, one of the major clones of extraintestinal pathogenic E. coli (ExPEC) strains. The origin of this uneven distribution is discussed but remains to be fully explained, as well as the consequences of carrying a specific core type on the wider aspects of bacterial phenotype.
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Affiliation(s)
| | - Maxime Branger
- UMR ISP, INRAE, Université François Rabelais de Tours, F-37380 Nouzilly, France
| | - David G E Smith
- Institute for Biological Chemistry, Biophysics and Bioengineering (IB3), Riccarton Campus, Heriot-Watt University, Edinburgh EH14 4AS, UK
| | - Pierre Germon
- UMR ISP, INRAE, Université François Rabelais de Tours, F-37380 Nouzilly, France
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9
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Sheinman M, Arkhipova K, Arndt PF, Dutilh BE, Hermsen R, Massip F. Identical sequences found in distant genomes reveal frequent horizontal transfer across the bacterial domain. eLife 2021; 10:62719. [PMID: 34121661 PMCID: PMC8270642 DOI: 10.7554/elife.62719] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 06/13/2021] [Indexed: 12/19/2022] Open
Abstract
Horizontal gene transfer (HGT) is an essential force in microbial evolution. Despite detailed studies on a variety of systems, a global picture of HGT in the microbial world is still missing. Here, we exploit that HGT creates long identical DNA sequences in the genomes of distant species, which can be found efficiently using alignment-free methods. Our pairwise analysis of 93,481 bacterial genomes identified 138,273 HGT events. We developed a model to explain their statistical properties as well as estimate the transfer rate between pairs of taxa. This reveals that long-distance HGT is frequent: our results indicate that HGT between species from different phyla has occurred in at least 8% of the species. Finally, our results confirm that the function of sequences strongly impacts their transfer rate, which varies by more than three orders of magnitude between different functional categories. Overall, we provide a comprehensive view of HGT, illuminating a fundamental process driving bacterial evolution.
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Affiliation(s)
- Michael Sheinman
- Theoretical Biology and Bioinformatics, Biology Department, Utrecht University, Utrecht, Netherlands.,Division of Molecular Carcinogenesis, the Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Ksenia Arkhipova
- Theoretical Biology and Bioinformatics, Biology Department, Utrecht University, Utrecht, Netherlands
| | - Peter F Arndt
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Biology Department, Utrecht University, Utrecht, Netherlands
| | - Rutger Hermsen
- Theoretical Biology and Bioinformatics, Biology Department, Utrecht University, Utrecht, Netherlands
| | - Florian Massip
- Berlin Institute for Medical Systems Biology, Max Delbrück Center, Berlin, Germany.,Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, Villleurbanne, France
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10
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Ely B. Genomic GC content drifts downward in most bacterial genomes. PLoS One 2021; 16:e0244163. [PMID: 34038432 PMCID: PMC8153448 DOI: 10.1371/journal.pone.0244163] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 05/07/2021] [Indexed: 11/18/2022] Open
Abstract
In every kingdom of life, GC->AT transitions occur more frequently than any other type of mutation due to the spontaneous deamination of cytidine. In eukaryotic genomes, this slow loss of GC base pairs is counteracted by biased gene conversion which increases genomic GC content as part of the recombination process. However, this type of biased gene conversion has not been observed in bacterial genomes, so we hypothesized that GC->AT transitions cause a reduction of genomic GC content in prokaryotic genomes on an evolutionary time scale. To test this hypothesis, we used a phylogenetic approach to analyze triplets of closely related genomes representing a wide range of the bacterial kingdom. The resulting data indicate that genomic GC content is drifting downward in bacterial genomes where GC base pairs comprise 40% or more of the total genome. In contrast, genomes containing less than 40% GC base pairs have fewer opportunities for GC->AT transitions to occur so genomic GC content is relatively stable or actually increasing. It should be noted that this observed change in genomic GC content is the net change in shared parts of the genome and does not apply to parts of the genome that have been lost or acquired since the genomes being compared shared common ancestor. However, a more detailed analysis of two Caulobacter genomes revealed that the acquisition of mobile elements by the two genomes actually reduced the total genomic GC content as well.
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Affiliation(s)
- Bert Ely
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina, United States of America
- * E-mail:
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11
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Seferbekova Z, Zabelkin A, Yakovleva Y, Afasizhev R, Dranenko NO, Alexeev N, Gelfand MS, Bochkareva OO. High Rates of Genome Rearrangements and Pathogenicity of Shigella spp. Front Microbiol 2021; 12:628622. [PMID: 33912145 PMCID: PMC8072062 DOI: 10.3389/fmicb.2021.628622] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 03/22/2021] [Indexed: 02/01/2023] Open
Abstract
Shigella are pathogens originating within the Escherichia lineage but frequently classified as a separate genus. Shigella genomes contain numerous insertion sequences (ISs) that lead to pseudogenisation of affected genes and an increase of non-homologous recombination. Here, we study 414 genomes of E. coli and Shigella strains to assess the contribution of genomic rearrangements to Shigella evolution. We found that Shigella experienced exceptionally high rates of intragenomic rearrangements and had a decreased rate of homologous recombination compared to pathogenic and non-pathogenic E. coli. The high rearrangement rate resulted in independent disruption of syntenic regions and parallel rearrangements in different Shigella lineages. Specifically, we identified two types of chromosomally encoded E3 ubiquitin-protein ligases acquired independently by all Shigella strains that also showed a high level of sequence conservation in the promoter and further in the 5′-intergenic region. In the only available enteroinvasive E. coli (EIEC) strain, which is a pathogenic E. coli with a phenotype intermediate between Shigella and non-pathogenic E. coli, we found a rate of genome rearrangements comparable to those in other E. coli and no functional copies of the two Shigella-specific E3 ubiquitin ligases. These data indicate that the accumulation of ISs influenced many aspects of genome evolution and played an important role in the evolution of intracellular pathogens. Our research demonstrates the power of comparative genomics-based on synteny block composition and an important role of non-coding regions in the evolution of genomic islands.
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Affiliation(s)
- Zaira Seferbekova
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia.,Institute for Information Transmission Problems (The Kharkevich Institute, RAS), Moscow, Russia
| | - Alexey Zabelkin
- Computer Technologies Laboratory, ITMO University, Saint Petersburg, Russia.,JetBrains Research, Saint Petersburg, Russia.,Bioinformatics Institute, Saint Petersburg, Russia
| | - Yulia Yakovleva
- Bioinformatics Institute, Saint Petersburg, Russia.,Department of Cytology and Histology, Saint Petersburg State University, Saint Petersburg, Russia
| | - Robert Afasizhev
- Institute for Information Transmission Problems (The Kharkevich Institute, RAS), Moscow, Russia
| | - Natalia O Dranenko
- Institute for Information Transmission Problems (The Kharkevich Institute, RAS), Moscow, Russia
| | - Nikita Alexeev
- Computer Technologies Laboratory, ITMO University, Saint Petersburg, Russia
| | - Mikhail S Gelfand
- Institute for Information Transmission Problems (The Kharkevich Institute, RAS), Moscow, Russia.,Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Olga O Bochkareva
- Institute for Information Transmission Problems (The Kharkevich Institute, RAS), Moscow, Russia.,Institute of Science and Technology (IST Austria), Klosterneuburg, Austria
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12
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Sakoparnig T, Field C, van Nimwegen E. Whole genome phylogenies reflect the distributions of recombination rates for many bacterial species. eLife 2021; 10:e65366. [PMID: 33416498 PMCID: PMC7884076 DOI: 10.7554/elife.65366] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 01/07/2021] [Indexed: 12/26/2022] Open
Abstract
Although recombination is accepted to be common in bacteria, for many species robust phylogenies with well-resolved branches can be reconstructed from whole genome alignments of strains, and these are generally interpreted to reflect clonal relationships. Using new methods based on the statistics of single-nucleotide polymorphism (SNP) splits, we show that this interpretation is incorrect. For many species, each locus has recombined many times along its line of descent, and instead of many loci supporting a common phylogeny, the phylogeny changes many thousands of times along the genome alignment. Analysis of the patterns of allele sharing among strains shows that bacterial populations cannot be approximated as either clonal or freely recombining but are structured such that recombination rates between lineages vary over several orders of magnitude, with a unique pattern of rates for each lineage. Thus, rather than reflecting clonal ancestry, whole genome phylogenies reflect distributions of recombination rates.
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Affiliation(s)
- Thomas Sakoparnig
- Biozentrum, University of Basel, and Swiss Institute of BioinformaticsBaselSwitzerland
| | - Chris Field
- Biozentrum, University of Basel, and Swiss Institute of BioinformaticsBaselSwitzerland
| | - Erik van Nimwegen
- Biozentrum, University of Basel, and Swiss Institute of BioinformaticsBaselSwitzerland
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13
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Kang Y, Yuan L, Shi X, Chu Y, He Z, Jia X, Lin Q, Ma Q, Wang J, Xiao J, Hu S, Gao Z, Chen F, Yu J. A fine-scale map of genome-wide recombination in divergent Escherichia coli population. Brief Bioinform 2020; 22:6034796. [PMID: 33319232 DOI: 10.1093/bib/bbaa335] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/19/2020] [Accepted: 10/23/2020] [Indexed: 01/09/2023] Open
Abstract
Recombination is one of the most important molecular mechanisms of prokaryotic genome evolution, but its exact roles are still in debate. Here we try to infer genome-wide recombination within a species, utilizing a dataset of 149 complete genomes of Escherichia coli from diverse animal hosts and geographic origins, including 45 in-house sequenced with the single-molecular real-time platform. Two major clades identified based on physiological, clinical and ecological characteristics form distinct genetic lineages based on scarcity of interclade gene exchanges. By defining gene-based syntenies for genomic segments within and between the two clades, we build a fine-scale recombination map for this representative global E. coli population. The map suggests extensive within-clade recombination that often breaks physical linkages among individual genes but seldom interrupts the structure of genome organizational frameworks as well as primary metabolic portfolios supported by the framework integrity, possibly due to strong natural selection for both physiological compatibility and ecological fitness. In contrast, the between-clade recombination declines drastically when phylogenetic distance increases to the extent where a 10-fold reduction can be observed, establishing a firm genetic barrier between clades. Our empirical data suggest a critical role for such recombination events in the early stage of speciation where recombination rate is associated with phylogenetic distance in addition to sequence and gene variations. The extensive intraclade recombination binds sister strains into a quasisexual group and optimizes genes or alleles to streamline physiological activities, whereas the sharply declined interclade recombination split the population into clades adaptive to divergent ecological niches.
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Affiliation(s)
- Yu Kang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, 100101, Beijing, PR China.,China National Center for Bioinformation, Beijing 100101, PR China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lina Yuan
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, 100101, Beijing, PR China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xing Shi
- Department of Respiratory & Critical Care Medicine, Peking University People's Hospital, Beijing, 100044, PR China
| | - Yanan Chu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, 100101, Beijing, PR China.,China National Center for Bioinformation, Beijing 100101, PR China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zilong He
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Interdisciplinary Innovation Institute of Medicine and Engineering, Beihang University, Beijing, 100191, PR China
| | - Xinmiao Jia
- Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100730, PR China
| | - Qiang Lin
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Qin Ma
- Department of Agronomy, Horticulture, and Plant Science, South Dakota State University, Brookings, SD, 57007, USA
| | - Jian Wang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, 100101, Beijing, PR China.,China National Center for Bioinformation, Beijing 100101, PR China
| | - Jingfa Xiao
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, 100101, Beijing, PR China.,China National Center for Bioinformation, Beijing 100101, PR China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Songnian Hu
- University of Chinese Academy of Sciences, Beijing 100049, China.,State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, PR China
| | - Zhancheng Gao
- Department of Respiratory & Critical Care Medicine, Peking University People's Hospital, Beijing, 100044, PR China
| | - Fei Chen
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, 100101, Beijing, PR China.,China National Center for Bioinformation, Beijing 100101, PR China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jun Yu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, 100101, Beijing, PR China.,China National Center for Bioinformation, Beijing 100101, PR China.,University of Chinese Academy of Sciences, Beijing 100049, China
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14
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Jackson LK, Potter B, Schneider S, Fitzgibbon M, Blair K, Farah H, Krishna U, Bedford T, Peek RM, Salama NR. Helicobacter pylori diversification during chronic infection within a single host generates sub-populations with distinct phenotypes. PLoS Pathog 2020; 16:e1008686. [PMID: 33370399 PMCID: PMC7794030 DOI: 10.1371/journal.ppat.1008686] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 01/08/2021] [Accepted: 10/22/2020] [Indexed: 12/15/2022] Open
Abstract
Helicobacter pylori chronically infects the stomach of approximately half of the world's population. Manifestation of clinical diseases associated with H. pylori infection, including cancer, is driven by strain properties and host responses; and as chronic infection persists, both are subject to change. Previous studies have documented frequent and extensive within-host bacterial genetic variation. To define how within-host diversity contributes to phenotypes related to H. pylori pathogenesis, this project leverages a collection of 39 clinical isolates acquired prospectively from a single subject at two time points and from multiple gastric sites. During the six years separating collection of these isolates, this individual, initially harboring a duodenal ulcer, progressed to gastric atrophy and concomitant loss of acid secretion. Whole genome sequence analysis identified 1,767 unique single nucleotide polymorphisms (SNPs) across isolates and a nucleotide substitution rate of 1.3x10-4 substitutions/site/year. Gene ontology analysis identified cell envelope genes among the genes with excess accumulation of nonsynonymous SNPs (nSNPs). A maximum likelihood tree based on genetic similarity clusters isolates from each time point separately. Within time points, there is segregation of subgroups with phenotypic differences in bacterial morphology, ability to induce inflammatory cytokines, and mouse colonization. Higher inflammatory cytokine induction in recent isolates maps to shared polymorphisms in the Cag PAI protein, CagY, while rod morphology in a subgroup of recent isolates mapped to eight mutations in three distinct helical cell shape determining (csd) genes. The presence of subgroups with unique genetic and phenotypic properties suggest complex selective forces and multiple niches within the stomach during chronic infection.
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Affiliation(s)
- Laura K. Jackson
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA, United States of America
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
| | - Barney Potter
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
| | - Sean Schneider
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
| | - Matthew Fitzgibbon
- Genomics & Bioinformatics Shared Resource, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
| | - Kris Blair
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA, United States of America
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
| | - Hajirah Farah
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA, United States of America
| | - Uma Krishna
- Division of Gastroenterology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States of America
| | - Trevor Bedford
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
| | - Richard M. Peek
- Division of Gastroenterology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States of America
| | - Nina R. Salama
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA, United States of America
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA, United States of America
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15
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Decano AG, Tran N, Al-Foori H, Al-Awadi B, Campbell L, Ellison K, Mirabueno LP, Nelson M, Power S, Smith G, Smyth C, Vance Z, Woods C, Rahm A, Downing T. Plasmids shape the diverse accessory resistomes of Escherichia coli ST131. Access Microbiol 2020; 3:acmi000179. [PMID: 33997610 PMCID: PMC8115979 DOI: 10.1099/acmi.0.000179] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 10/27/2020] [Indexed: 12/22/2022] Open
Abstract
The human gut microbiome includes beneficial, commensal and pathogenic bacteria that possess antimicrobial resistance (AMR) genes and exchange these predominantly through conjugative plasmids. Escherichia coli is a significant component of the gastrointestinal microbiome and is typically non-pathogenic in this niche. In contrast, extra-intestinal pathogenic E. coli (ExPEC) including ST131 may occupy other environments like the urinary tract or bloodstream where they express genes enabling AMR and host cell adhesion like type 1 fimbriae. The extent to which commensal E. coli and uropathogenic ExPEC ST131 share AMR genes remains understudied at a genomic level, and we examined this here using a preterm infant resistome. We found that individual ST131 had small differences in AMR gene content relative to a larger shared resistome. Comparisons with a range of plasmids common in ST131 showed that AMR gene composition was driven by conjugation, recombination and mobile genetic elements. Plasmid pEK499 had extended regions in most ST131 Clade C isolates, and it had evidence of a co-evolutionary signal based on protein-level interactions with chromosomal gene products, as did pEK204 that had a type IV fimbrial pil operon. ST131 possessed extensive diversity of selective type 1, type IV, P and F17-like fimbriae genes that was highest in subclade C2. The structure and composition of AMR genes, plasmids and fimbriae vary widely in ST131 Clade C and this may mediate pathogenicity and infection outcomes.
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Affiliation(s)
- Arun Gonzales Decano
- School of Biotechnology, Dublin City University, Ireland.,Present address: School of Medicine, University of St., Andrews, UK
| | - Nghia Tran
- School of Maths, Applied Maths and Statistics, National University of Ireland Galway, Ireland
| | | | | | | | - Kevin Ellison
- School of Biotechnology, Dublin City University, Ireland
| | - Louisse Paolo Mirabueno
- School of Biotechnology, Dublin City University, Ireland.,Present address: National Institute of Agricultural Botany - East Malling Research, Kent, UK
| | - Maddy Nelson
- School of Biotechnology, Dublin City University, Ireland
| | - Shane Power
- School of Biotechnology, Dublin City University, Ireland
| | | | - Cian Smyth
- School of Biotechnology, Dublin City University, Ireland.,Present address: Dept of Biology, Maynooth University, Dublin, Ireland
| | - Zoe Vance
- School of Genetics & Microbiology, Trinity College Dublin, Ireland
| | | | - Alexander Rahm
- School of Maths, Applied Maths and Statistics, National University of Ireland Galway, Ireland.,Present address: GAATI Lab, Université de la Polynésie Française, Puna'auia, French Polynesia
| | - Tim Downing
- School of Biotechnology, Dublin City University, Ireland
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16
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Gurung D, Blumenthal RM. Distribution of RecBCD and AddAB recombination-associated genes among bacteria in 33 phyla. MICROBIOLOGY-SGM 2020; 166:1047-1064. [PMID: 33085588 DOI: 10.1099/mic.0.000980] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Homologous recombination plays key roles in fundamental processes such as recovery from DNA damage and in bacterial horizontal gene transfer, yet there are still open questions about the distribution of recognized components of recombination machinery among bacteria and archaea. RecBCD helicase-nuclease plays a central role in recombination among Gammaproteobacteria like Escherichia coli; while bacteria in other phyla, like the Firmicute Bacillus subtilis, use the related AddAB complex. The activity of at least some of these complexes is controlled by short DNA sequences called crossover hotspot instigator (Chi) sites. When RecBCD or AddAB complexes encounter an autologous Chi site during unwinding, they introduce a nick such that ssDNA with a free end is available to invade another duplex. If homologous DNA is present, RecA-dependent homologous recombination is promoted; if not (or if no autologous Chi site is present) the RecBCD/AddAB complex eventually degrades the DNA. We examined the distribution of recBCD and addAB genes among bacteria, and sought ways to distinguish them unambiguously. We examined bacterial species among 33 phyla, finding some unexpected distribution patterns. RecBCD and addAB are less conserved than recA, with the orthologous recB and addA genes more conserved than the recC or addB genes. We were able to classify RecB vs. AddA and RecC vs. AddB in some bacteria where this had not previously been done. We used logo analysis to identify sequence segments that are conserved, but differ between the RecBC and AddAB proteins, to help future differentiation between members of these two families.
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Affiliation(s)
- Deepti Gurung
- Present address: Department of Cancer Biology, College of Medicine & Life Sciences, The University of Toledo, Toledo OH 43614-1021, USA.,Department of Medical Microbiology & Immunology, and Program in Bioinformatics, College of Medicine & Life Sciences, The University of Toledo, Toledo OH 43614-1021, USA
| | - Robert M Blumenthal
- Department of Medical Microbiology & Immunology, and Program in Bioinformatics, College of Medicine & Life Sciences, The University of Toledo, Toledo OH 43614-1021, USA
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17
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Abstract
Escherichia coli is a commensal of the vertebrate gut that is increasingly involved in various intestinal and extra-intestinal infections as an opportunistic pathogen. Numerous pathotypes that represent groups of strains with specific pathogenic characteristics have been described based on heterogeneous and complex criteria. The democratization of whole-genome sequencing has led to an accumulation of genomic data that render possible a population phylogenomic approach to the emergence of virulence. Few lineages are responsible for the pathologies compared with the diversity of commensal strains. These lineages emerged multiple times during E. coli evolution, mainly by acquiring virulence genes located on mobile elements, but in a specific chromosomal phylogenetic background. This repeated emergence of stable and cosmopolitan lineages argues for an optimization of strain fitness through epistatic interactions between the virulence determinants and the remaining genome.
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18
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Touchon M, Perrin A, de Sousa JAM, Vangchhia B, Burn S, O’Brien CL, Denamur E, Gordon D, Rocha EPC. Phylogenetic background and habitat drive the genetic diversification of Escherichia coli. PLoS Genet 2020; 16:e1008866. [PMID: 32530914 PMCID: PMC7314097 DOI: 10.1371/journal.pgen.1008866] [Citation(s) in RCA: 99] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 06/24/2020] [Accepted: 05/18/2020] [Indexed: 12/15/2022] Open
Abstract
Escherichia coli is mostly a commensal of birds and mammals, including humans, where it can act as an opportunistic pathogen. It is also found in water and sediments. We investigated the phylogeny, genetic diversification, and habitat-association of 1,294 isolates representative of the phylogenetic diversity of more than 5,000 isolates from the Australian continent. Since many previous studies focused on clinical isolates, we investigated mostly other isolates originating from humans, poultry, wild animals and water. These strains represent the species genetic diversity and reveal widespread associations between phylogroups and isolation sources. The analysis of strains from the same sequence types revealed very rapid change of gene repertoires in the very early stages of divergence, driven by the acquisition of many different types of mobile genetic elements. These elements also lead to rapid variations in genome size, even if few of their genes rise to high frequency in the species. Variations in genome size are associated with phylogroup and isolation sources, but the latter determine the number of MGEs, a marker of recent transfer, suggesting that gene flow reinforces the association of certain genetic backgrounds with specific habitats. After a while, the divergence of gene repertoires becomes linear with phylogenetic distance, presumably reflecting the continuous turnover of mobile element and the occasional acquisition of adaptive genes. Surprisingly, the phylogroups with smallest genomes have the highest rates of gene repertoire diversification and fewer but more diverse mobile genetic elements. This suggests that smaller genomes are associated with higher, not lower, turnover of genetic information. Many of these genomes are from freshwater isolates and have peculiar traits, including a specific capsule, suggesting adaptation to this environment. Altogether, these data contribute to explain why epidemiological clones tend to emerge from specific phylogenetic groups in the presence of pervasive horizontal gene transfer across the species. Previous large scale studies on the evolution of E. coli focused on clinical isolates emphasizing virulence and antibiotic resistance in medically important lineages. Yet, most E. coli strains are either human commensals or not associated with humans at all. Here, we analyzed a large collection of non-clinical isolates of the species to assess the mechanisms of gene repertoire diversification in the light of isolation sources and phylogeny. We show that gene repertoires evolve so rapidly by the high turnover of mobile genetic elements that epidemiologically indistinguishable strains can be phenotypically extremely heterogeneous, illustrating the velocity of bacterial adaptation and the importance of accounting for the information on the whole genome at the epidemiological scale. Phylogeny and habitat shape the genetic diversification of E. coli to similar extents. Surprisingly, freshwater strains seem specifically adapted to this environment, breaking the paradigm that E. coli environmental isolates are systematically fecal contaminations. As a consequence, the evolution of this species is also shaped by environmental habitats, and it may diversify by acquiring genes and mobile elements from environmental bacteria (and not just from gut bacteria). This may facilitate the acquisition of virulence factors and antibiotic resistance in the strains that become pathogenic.
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Affiliation(s)
- Marie Touchon
- Microbial Evolutionary Genomics, Institut Pasteur, CNRS, UMR3525, 25-28 rue Dr Roux, Paris, 75015, France
- * E-mail:
| | - Amandine Perrin
- Microbial Evolutionary Genomics, Institut Pasteur, CNRS, UMR3525, 25-28 rue Dr Roux, Paris, 75015, France
- Sorbonne Université, Collège doctoral, F-75005 Paris, France
| | - Jorge André Moura de Sousa
- Microbial Evolutionary Genomics, Institut Pasteur, CNRS, UMR3525, 25-28 rue Dr Roux, Paris, 75015, France
| | - Belinda Vangchhia
- Ecology and Evolution, Research School of Biology, The Australian National University, Acton, ACT, Australia
- Department of Veterinary Microbiology, College of Veterinary Sciences & Animal Husbandry, Central Agricultural University, Selesih, Aizawl, Mizoram, India
| | - Samantha Burn
- Ecology and Evolution, Research School of Biology, The Australian National University, Acton, ACT, Australia
| | - Claire L. O’Brien
- School of Medicine, University of Wollongong, Northfields Ave Wollongong, Australia
| | - Erick Denamur
- Université de Paris, IAME, UMR 1137, INSERM, Paris, 75018, France
- AP-HP, Laboratoire de Génétique Moléculaire, Hôpital Bichat, 75018, Paris, France
| | - David Gordon
- Ecology and Evolution, Research School of Biology, The Australian National University, Acton, ACT, Australia
| | - Eduardo PC Rocha
- Microbial Evolutionary Genomics, Institut Pasteur, CNRS, UMR3525, 25-28 rue Dr Roux, Paris, 75015, France
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19
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Pang TY. A coarse-graining, ultrametric approach to resolve the phylogeny of prokaryotic strains with frequent homologous recombination. BMC Evol Biol 2020; 20:52. [PMID: 32381044 PMCID: PMC7204016 DOI: 10.1186/s12862-020-01616-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Accepted: 04/20/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND A frequent event in the evolution of prokaryotic genomes is homologous recombination, where a foreign DNA stretch replaces a genomic region similar in sequence. Recombination can affect the relative position of two genomes in a phylogenetic reconstruction in two different ways: (i) one genome can recombine with a DNA stretch that is similar to the other genome, thereby reducing their pairwise sequence divergence; (ii) one genome can recombine with a DNA stretch from an outgroup genome, increasing the pairwise divergence. While several recombination-aware phylogenetic algorithms exist, many of these cannot account for both types of recombination; some algorithms can, but do so inefficiently. Moreover, many of them reconstruct the ancestral recombination graph (ARG) to help infer the genome tree, and require that a substantial portion of each genome has not been affected by recombination, a sometimes unrealistic assumption. METHODS Here, we propose a Coarse-Graining approach for Phylogenetic reconstruction (CGP), which is recombination-aware but forgoes ARG reconstruction. It accounts for the tendency of a higher effective recombination rate between genomes with a lower phylogenetic distance. It is applicable even if all genomic regions have experienced substantial amounts of recombination, and can be used on both nucleotide and amino acid sequences. CGP considers the local density of substitutions along pairwise genome alignments, fitting a model to the empirical distribution of substitution density to infer the pairwise coalescent time. Given all pairwise coalescent times, CGP reconstructs an ultrametric tree representing vertical inheritance. RESULTS Based on simulations, we show that the proposed approach can reconstruct ultrametric trees with accurate topology, branch lengths, and root positioning. Applied to a set of E. coli strains, the reconstructed trees are most consistent with gene distributions when inferred from amino acid sequences, a data type that cannot be utilized by many alternative approaches. CONCLUSIONS The CGP algorithm is more accurate than alternative recombination-aware methods for ultrametric phylogenetic reconstructions.
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Affiliation(s)
- Tin Yau Pang
- Computational Cell Biology, Heinrich Heine University, 40225, Düsseldorf, Germany.
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20
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Hitchhiking, collapse, and contingency in phage infections of migrating bacterial populations. ISME JOURNAL 2020; 14:2007-2018. [PMID: 32358533 DOI: 10.1038/s41396-020-0664-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 04/05/2020] [Accepted: 04/15/2020] [Indexed: 01/17/2023]
Abstract
Natural bacterial populations are subjected to constant predation pressure by bacteriophages. Bacteria use a variety of molecular mechanisms to defend themselves from phage predation. However, since phages are nonmotile, perhaps the simplest defense against phage is for bacteria to move faster than phages. In particular, chemotaxis, the active migration of bacteria up attractant gradients, may help the bacteria escape slowly diffusing phages. Here we study phage infection dynamics in migrating bacterial populations driven by chemotaxis through low viscosity agar plates. We find that expanding phage-bacteria populations supports two moving fronts, an outermost bacterial front driven by nutrient uptake and chemotaxis and an inner phage front at which the bacterial population collapses due to phage predation. We show that with increasing adsorption rate and initial phage population, the speed of the moving phage front increases, eventually overtaking the bacterial front and driving the system across a transition from a regime where bacterial front speed exceeds that of the phage front to one where bacteria must evolve phage resistance to survive. Our data support the claim that this process requires phage to hitchhike with moving bacteria. A deterministic model recapitulates the transition under the assumption that phage virulence declines with host growth rate which we confirm experimentally. Finally, near the transition between regimes we observe macroscopic fluctuations in bacterial densities at the phage front. Our work opens a new, spatio-temporal, line of investigation into the eco-evolutionary struggle between bacteria and phage.
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21
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Ely B. Recombination and gene loss occur simultaneously during bacterial horizontal gene transfer. PLoS One 2020; 15:e0227987. [PMID: 31990919 PMCID: PMC6986707 DOI: 10.1371/journal.pone.0227987] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 01/03/2020] [Indexed: 11/19/2022] Open
Abstract
Bacteria can acquire new genes by incorporating environmental DNA into their genomes, yet genome sizes stay relatively constant. In nature, gene acquisition is a rare event so it is difficult to observe. However, the Caulobacter crescentus CB2A genome contains 114 insertions of genetic material from the closely-related NA1000 strain, providing a unique opportunity to analyze the horizontal transfer of genetic material. Analyses of these insertions led to a new model that involves preferential recombination at non-homologous regions that are flanked by regions of homology and does not involve any mutational processes. The net result is the replacement of segments of the recipient genome instead of the simple addition of genetic material during horizontal gene transfer. Analyses of the genomes of closely related strains of other bacterial and archaea genera, suggested that horizontal gene transfer occurs preferentially in non-homologous regions in these organisms as well. Thus, it appears to be a general phenomenon that prokaryotic horizontal gene transfer occurs preferentially at sites where the incoming DNA contains a non-homologous region that is flanked by regions of homology. Therefore, gene replacement is a common phenomenon during horizontal gene transfer.
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Affiliation(s)
- Bert Ely
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina, United States of America
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22
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Bacterial Microcompartment-Mediated Ethanolamine Metabolism in Escherichia coli Urinary Tract Infection. Infect Immun 2019; 87:IAI.00211-19. [PMID: 31138611 PMCID: PMC6652756 DOI: 10.1128/iai.00211-19] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 05/16/2019] [Indexed: 12/23/2022] Open
Abstract
Urinary tract infections (UTIs) are common and in general are caused by intestinal uropathogenic Escherichia coli (UPEC) ascending via the urethra. Microcompartment-mediated catabolism of ethanolamine, a host cell breakdown product, fuels the competitive overgrowth of intestinal E. coli, both pathogenic enterohemorrhagic E. coli and commensal strains. During a UTI, urease-negative E. coli bacteria thrive, despite the comparative nutrient limitation in urine. Urinary tract infections (UTIs) are common and in general are caused by intestinal uropathogenic Escherichia coli (UPEC) ascending via the urethra. Microcompartment-mediated catabolism of ethanolamine, a host cell breakdown product, fuels the competitive overgrowth of intestinal E. coli, both pathogenic enterohemorrhagic E. coli and commensal strains. During a UTI, urease-negative E. coli bacteria thrive, despite the comparative nutrient limitation in urine. The role of ethanolamine as a potential nutrient source during UTIs is understudied. We evaluated the role of the metabolism of ethanolamine as a potential nitrogen and carbon source for UPEC in the urinary tract. We analyzed infected urine samples by culture, high-performance liquid chromatography, reverse transcription-quantitative PCR, and genomic sequencing. The ethanolamine concentration in urine was comparable to the concentration of the most abundant reported urinary amino acid, d-serine. Transcription of the eut operon was detected in the majority of urine samples containing E. coli screened. All sequenced UPEC strains had conserved eut operons, while metabolic genotypes previously associated with UTI (dsdCXA, metE) were mainly limited to phylogroup B2. In vitro ethanolamine was found to be utilized as a sole source of nitrogen by UPEC strains. The metabolism of ethanolamine in artificial urine medium (AUM) induced metabolosome formation and provided a growth advantage at the physiological levels found in urine. Interestingly, eutE (which encodes acetaldehyde dehydrogenase) was required for UPEC strains to utilize ethanolamine to gain a growth advantage in AUM, suggesting that ethanolamine is also utilized as a carbon source. These data suggest that urinary ethanolamine is a significant additional carbon and nitrogen source for infecting E. coli strains.
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23
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Tchesnokova V, Radey M, Chattopadhyay S, Larson L, Weaver JL, Kisiela D, Sokurenko EV. Pandemic fluoroquinolone resistant Escherichia coli clone ST1193 emerged via simultaneous homologous recombinations in 11 gene loci. Proc Natl Acad Sci U S A 2019; 116:14740-14748. [PMID: 31262826 PMCID: PMC6642405 DOI: 10.1073/pnas.1903002116] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Global growth in antibiotic resistance is a major social problem. A high level of resistance to fluoroquinolones requires the concurrent presence of at least 3 mutations in the target proteins-2 in DNA gyrase (GyrA) and 1 in topoisomerase IV (ParC), which occur in a stepwise manner. In the Escherichia coli chromosome, the gyrA and parC loci are positioned about 1 Mb away from each other. Here we show that the 3 fluoroquinolone resistance mutations are tightly associated genetically in naturally occurring strains. In the latest pandemic uropathogenic and multidrug-resistant E. coli clonal group ST1193, the mutant variants of gyrA and parC were acquired not by a typical gradual, stepwise evolution but all at once. This happened as part of 11 simultaneous homologous recombination events involving 2 phylogenetically distant strains of E. coli, from an uropathogenic clonal complex ST14 and fluoroquinolone-resistant ST10. The gene exchanges swapped regions between 0.5 and 139 Kb in length (183 Kb total) spread along 976 Kb of chromosomal DNA around and between gyrA and parC loci. As a result, all 3 fluoroquinolone resistance mutations in GyrA and ParC have simultaneously appeared in ST1193. Based on molecular clock estimates, this potentially happened as recently as <12 y ago. Thus, naturally occurring homologous recombination events between 2 strains can involve numerous chromosomal gene locations simultaneously, resulting in the transfer of distant but tightly associated genetic mutations and emergence of a both highly pathogenic and antibiotic-resistant strain with a rapid global spread capability.
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Affiliation(s)
| | - Matthew Radey
- Department of Microbiology, University of Washington, Seattle, WA 98105
| | - Sujay Chattopadhyay
- Institute of Advanced Studies and Research, JIS University, Kolkata 700091, India
| | - Lydia Larson
- Department of Microbiology, University of Washington, Seattle, WA 98105
| | - Jamie Lee Weaver
- Department of Microbiology, University of Washington, Seattle, WA 98105
| | - Dagmara Kisiela
- Department of Microbiology, University of Washington, Seattle, WA 98105
| | - Evgeni V Sokurenko
- Department of Microbiology, University of Washington, Seattle, WA 98105;
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Reimer A, Weedmark K, Petkau A, Peterson CL, Walker M, Knox N, Kent H, Mabon P, Berry C, Tyler S, Tschetter L, Jerome M, Allen V, Hoang L, Bekal S, Clark C, Nadon C, Van Domselaar G, Pagotto F, Graham M, Farber J, Gilmour M. Shared genome analyses of notable listeriosis outbreaks, highlighting the critical importance of epidemiological evidence, input datasets and interpretation criteria. Microb Genom 2019; 5. [PMID: 30648944 PMCID: PMC6412057 DOI: 10.1099/mgen.0.000237] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The persuasiveness of genomic evidence has pressured scientific agencies to supplement or replace well-established methodologies to inform public health and food safety decision-making. This study of 52 epidemiologically defined Listeria monocytogenes isolates, collected between 1981 and 2011, including nine outbreaks, was undertaken (1) to characterize their phylogenetic relationship at finished genome-level resolution, (2) to elucidate the underlying genetic diversity within an endemic subtype, CC8, and (3) to re-evaluate the genetic relationship and epidemiology of a CC8-delimited outbreak in Canada in 2008. Genomes representing Canadian Listeria outbreaks between 1981 and 2010 were closed and manually annotated. Single nucleotide variants (SNVs) and horizontally acquired traits were used to generate phylogenomic models. Phylogenomic relationships were congruent with classical subtyping and epidemiology, except for CC8 outbreaks, wherein the distribution of SNV and prophages revealed multiple co-evolving lineages. Chronophyletic reconstruction of CC8 evolution indicates that prophage-related genetic changes among CC8 strains manifest as PFGE subtype reversions, obscuring the relationship between CC8 isolates, and complicating the public health interpretation of subtyping data, even at maximum genome resolution. The size of the shared genome interrogated did not change the genetic relationship measured between highly related isolates near the tips of the phylogenetic tree, illustrating the robustness of these approaches for routine public health applications where the focus is recent ancestry. The possibility exists for temporally and epidemiologically distinct events to appear related even at maximum genome resolution, highlighting the continued importance of epidemiological evidence.
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Affiliation(s)
- Aleisha Reimer
- 1Public Health Agency of Canada, Winnipeg, MB, R3E 3R2, Canada
| | - Kelly Weedmark
- 2Health Canada, Bureau of Microbial Hazards, Ottawa, ON, K1A 0K9, Canada
| | - Aaron Petkau
- 1Public Health Agency of Canada, Winnipeg, MB, R3E 3R2, Canada
| | | | - Matthew Walker
- 1Public Health Agency of Canada, Winnipeg, MB, R3E 3R2, Canada
| | - Natalie Knox
- 1Public Health Agency of Canada, Winnipeg, MB, R3E 3R2, Canada
| | - Heather Kent
- 1Public Health Agency of Canada, Winnipeg, MB, R3E 3R2, Canada
| | - Philip Mabon
- 1Public Health Agency of Canada, Winnipeg, MB, R3E 3R2, Canada
| | - Chrystal Berry
- 1Public Health Agency of Canada, Winnipeg, MB, R3E 3R2, Canada
| | - Shaun Tyler
- 1Public Health Agency of Canada, Winnipeg, MB, R3E 3R2, Canada
| | | | - Morganne Jerome
- 1Public Health Agency of Canada, Winnipeg, MB, R3E 3R2, Canada
| | - Vanessa Allen
- 3Public Health Ontario, Toronto, ON, M5G 1M1, Canada
| | - Linda Hoang
- 4British Columbia Centre for Disease Control, Public Health Microbiology and Reference Laboratory, Vancouver, BC V5Z 4R4, Canada
| | - Sadjia Bekal
- 5Laboratoire de Santé Publique du Québec, Sainte-Anne-de-Bellevue, Québec, H9X 3R5, Canada
| | - Clifford Clark
- 1Public Health Agency of Canada, Winnipeg, MB, R3E 3R2, Canada
| | - Celine Nadon
- 1Public Health Agency of Canada, Winnipeg, MB, R3E 3R2, Canada
| | | | - Franco Pagotto
- 2Health Canada, Bureau of Microbial Hazards, Ottawa, ON, K1A 0K9, Canada
| | - Morag Graham
- 1Public Health Agency of Canada, Winnipeg, MB, R3E 3R2, Canada
| | - Jeff Farber
- 6University of Guelph, Guelph, ON, N1G 2W, Canada
| | - Matthew Gilmour
- 1Public Health Agency of Canada, Winnipeg, MB, R3E 3R2, Canada
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25
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Garud NR, Good BH, Hallatschek O, Pollard KS. Evolutionary dynamics of bacteria in the gut microbiome within and across hosts. PLoS Biol 2019; 17:e3000102. [PMID: 30673701 PMCID: PMC6361464 DOI: 10.1371/journal.pbio.3000102] [Citation(s) in RCA: 186] [Impact Index Per Article: 37.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 02/04/2019] [Accepted: 12/19/2018] [Indexed: 12/16/2022] Open
Abstract
Gut microbiota are shaped by a combination of ecological and evolutionary forces. While the ecological dynamics have been extensively studied, much less is known about how species of gut bacteria evolve over time. Here, we introduce a model-based framework for quantifying evolutionary dynamics within and across hosts using a panel of metagenomic samples. We use this approach to study evolution in approximately 40 prevalent species in the human gut. Although the patterns of between-host diversity are consistent with quasi-sexual evolution and purifying selection on long timescales, we identify new genealogical signatures that challenge standard population genetic models of these processes. Within hosts, we find that genetic differences that accumulate over 6-month timescales are only rarely attributable to replacement by distantly related strains. Instead, the resident strains more commonly acquire a smaller number of putative evolutionary changes, in which nucleotide variants or gene gains or losses rapidly sweep to high frequency. By comparing these mutations with the typical between-host differences, we find evidence that some sweeps may be seeded by recombination, in addition to new mutations. However, comparisons of adult twins suggest that replacement eventually overwhelms evolution over multi-decade timescales, hinting at fundamental limits to the extent of local adaptation. Together, our results suggest that gut bacteria can evolve on human-relevant timescales, and they highlight the connections between these short-term evolutionary dynamics and longer-term evolution across hosts.
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Affiliation(s)
- Nandita R. Garud
- Gladstone Institutes, San Francisco, California, United States of America
| | - Benjamin H. Good
- Department of Physics, University of California, Berkeley, Berkeley, California, United States of America
- Department of Bioengineering, University of California, Berkeley, Berkeley, California, United States of America
- Kavli Institute for Theoretical Physics, University of California, Santa Barbara, Santa Barbara, California, United States of America
| | - Oskar Hallatschek
- Department of Physics, University of California, Berkeley, Berkeley, California, United States of America
- Kavli Institute for Theoretical Physics, University of California, Santa Barbara, Santa Barbara, California, United States of America
- Department of Integrative Biology, University of California, Berkeley, Berkeley, California, United States of America
| | - Katherine S. Pollard
- Gladstone Institutes, San Francisco, California, United States of America
- Department of Epidemiology and Biostatistics, Institute for Human Genetics, Quantitative Biology Institute, and Institute for Computational Health Sciences, University of California, San Francisco, San Francisco, California, United States of America
- Chan-Zuckerberg Biohub, San Francisco, California, United States of America
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26
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Each of 3,323 metabolic innovations in the evolution of E. coli arose through the horizontal transfer of a single DNA segment. Proc Natl Acad Sci U S A 2018; 116:187-192. [PMID: 30563853 DOI: 10.1073/pnas.1718997115] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Even closely related prokaryotes often show an astounding diversity in their ability to grow in different nutritional environments. It has been hypothesized that complex metabolic adaptations-those requiring the independent acquisition of multiple new genes-can evolve via selectively neutral intermediates. However, it is unclear whether this neutral exploration of phenotype space occurs in nature, or what fraction of metabolic adaptations is indeed complex. Here, we reconstruct metabolic models for the ancestors of a phylogeny of 53 Escherichia coli strains, linking genotypes to phenotypes on a genome-wide, macroevolutionary scale. Based on the ancestral and extant metabolic models, we identify 3,323 phenotypic innovations in the history of the E. coli clade that arose through changes in accessory genome content. Of these innovations, 1,998 allow growth in previously inaccessible environments, while 1,325 increase biomass yield. Strikingly, every observed innovation arose through the horizontal acquisition of a single DNA segment less than 30 kb long. Although we found no evidence for the contribution of selectively neutral processes, 10.6% of metabolic innovations were facilitated by horizontal gene transfers on earlier phylogenetic branches, consistent with a stepwise adaptation to successive environments. Ninety-eight percent of metabolic phenotypes accessible to the combined E. coli pangenome can be bestowed on any individual strain by transferring a single DNA segment from one of the extant strains. These results demonstrate an amazing ability of the E. coli lineage to adapt to novel environments through single horizontal gene transfers (followed by regulatory adaptations), an ability likely mirrored in other clades of generalist bacteria.
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27
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Alfsnes K, Frye SA, Eriksson J, Eldholm V, Brynildsrud OB, Bohlin J, Harrison OB, Hood DW, Maiden MCJ, Tønjum T, Ambur OH. A genomic view of experimental intraspecies and interspecies transformation of a rifampicin-resistance allele into Neisseria meningitidis. Microb Genom 2018; 4. [PMID: 30251949 PMCID: PMC6321871 DOI: 10.1099/mgen.0.000222] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The spread of antibiotic resistance within and between different bacterial populations is a major health problem on a global scale. The identification of genetic transformation in genomic data from Neisseria meningitidis, the meningococcus (Mc), and other bacteria is problematic, since similar or even identical alleles may be involved. A particular challenge in naturally transformable bacteria generally is to distinguish between common ancestry and true recombined sites in sampled genome sequences. Furthermore, the identification of recombination following experimental transformation of homologous alleles requires identifiable differences between donor and recipient, which in itself influences the propensity for homologous recombination (HR). This study identifies the distribution of HR events following intraspecies and interspecies Mc transformations of rpoB alleles encoding rifampicin resistance by whole-genome DNA sequencing and single nucleotide variant analysis. The HR events analysed were confined to the genomic region surrounding the single nucleotide genetic marker used for selection. An exponential length distribution of these recombined events was found, ranging from a few nucleotides to about 72 kb stretches. The lengths of imported sequences were on average found to be longer following experimental transformation of the recipient with genomic DNA from an intraspecies versus an interspecies donor (P<0.001). The recombination events were generally observed to be mosaic, with donor sequences interspersed with recipient sequence. Here, we present four models to explain these observations, by fragmentation of the transformed DNA, by interruptions of the recombination mechanism, by secondary recombination of endogenous self-DNA, or by repair/replication mechanisms.
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Affiliation(s)
| | - Stephan A Frye
- 2Department of Microbiology, Oslo University Hospital (Rikshospitalet), Oslo, Norway
| | - Jens Eriksson
- 2Department of Microbiology, Oslo University Hospital (Rikshospitalet), Oslo, Norway
| | - Vegard Eldholm
- 3Department of Molecular Biology, Domain of Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Ola Brønstad Brynildsrud
- 4Department of Methodology Research and Analysis, Domain of Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Jon Bohlin
- 4Department of Methodology Research and Analysis, Domain of Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Odile B Harrison
- 5The Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
| | - Derek W Hood
- 6Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, UK
| | - Martin C J Maiden
- 5The Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
| | - Tone Tønjum
- 2Department of Microbiology, Oslo University Hospital (Rikshospitalet), Oslo, Norway.,7Department of Microbiology, University of Oslo, Oslo, Norway
| | - Ole Herman Ambur
- 2Department of Microbiology, Oslo University Hospital (Rikshospitalet), Oslo, Norway.,8OsloMet - Oslo Metropolitan University, Oslo, Norway
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28
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Jibrin MO, Potnis N, Timilsina S, Minsavage GV, Vallad GE, Roberts PD, Jones JB, Goss EM. Genomic Inference of Recombination-Mediated Evolution in Xanthomonas euvesicatoria and X. perforans. Appl Environ Microbiol 2018; 84:e00136-18. [PMID: 29678917 PMCID: PMC6007113 DOI: 10.1128/aem.00136-18] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 04/06/2018] [Indexed: 01/23/2023] Open
Abstract
Recombination is a major driver of evolution in bacterial populations, because it can spread and combine independently evolved beneficial mutations. Recombinant lineages of bacterial pathogens of plants are typically associated with the colonization of novel hosts and the emergence of new diseases. Here we show that recombination between evolutionarily and phenotypically distinct plant-pathogenic lineages generated recombinant lineages with unique combinations of pathogenicity and virulence factors. Xanthomonas euvesicatoria and Xanthomonas perforans are two closely related lineages causing bacterial spot disease on tomato and pepper worldwide. We sequenced the genomes of atypical strains collected from tomato in Nigeria and observed recombination in the type III secretion system and effector genes, which showed alleles from both X. euvesicatoria and X. perforans Wider horizontal gene transfer was indicated by the fact that the lipopolysaccharide cluster of one strain was most similar to that of a distantly related Xanthomonas pathogen of barley. This strain and others have experienced extensive genomewide homologous recombination, and both species exhibited dynamic open pangenomes. Variation in effector gene repertoires within and between species must be taken into consideration when one is breeding tomatoes for disease resistance. Resistance breeding strategies that target specific effectors must consider possibly dramatic variation in bacterial spot populations across global production regions, as illustrated by the recombinant strains observed here.IMPORTANCE The pathogens that cause bacterial spot of tomato and pepper are extensively studied models of plant-microbe interactions and cause problematic disease worldwide. Atypical bacterial spot strains collected from tomato in Nigeria, and other strains from Italy, India, and Florida, showed evidence of genomewide recombination that generated genetically distinct pathogenic lineages. The strains from Nigeria and Italy were found to have a mix of type III secretion system genes from X. perforans and X. euvesicatoria, as well as effectors from Xanthomonas gardneri These genes and effectors are important in the establishment of disease, and effectors are common targets of resistance breeding. Our findings point to global diversity in the genomes of bacterial spot pathogens, which is likely to affect the host-pathogen interaction and influence management decisions.
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Affiliation(s)
- Mustafa O Jibrin
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
- Southwest Research and Education Center, University of Florida, Immokalee, Florida, USA
- Department of Crop Protection, Ahmadu Bello University, Zaria, Nigeria
| | - Neha Potnis
- Department of Entomology and Plant Pathology, Auburn University, Auburn, Alabama, USA
| | - Sujan Timilsina
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
| | - Gerald V Minsavage
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
| | - Gary E Vallad
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
- Gulf Coast Research and Education Center, University of Florida, Wimauma, Florida, USA
| | - Pamela D Roberts
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
- Southwest Research and Education Center, University of Florida, Immokalee, Florida, USA
| | - Jeffrey B Jones
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
| | - Erica M Goss
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
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29
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Chu HY, Sprouffske K, Wagner A. Assessing the benefits of horizontal gene transfer by laboratory evolution and genome sequencing. BMC Evol Biol 2018; 18:54. [PMID: 29673327 PMCID: PMC5909237 DOI: 10.1186/s12862-018-1164-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 03/22/2018] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Recombination is widespread across the tree of life, because it helps purge deleterious mutations and creates novel adaptive traits. In prokaryotes, it often takes the form of horizontal gene transfer from a donor to a recipient bacterium. While such transfer is widespread in natural communities, its immediate fitness benefits are usually unknown. We asked whether any such benefits depend on the environment, and on the identity of donor and recipient strains. To this end, we adapted Escherichia coli to two novel carbon sources over several hundred generations of laboratory evolution, exposing evolving populations to various DNA donors. RESULTS At the end of these experiments, we measured fitness and sequenced the genomes of 65 clones from 34 replicate populations to study the genetic changes associated with adaptive evolution. Furthermore, we identified candidate de novo beneficial mutations. During adaptive evolution on the first carbon source, 4-Hydroxyphenylacetic acid (HPA), recombining populations adapted better, which was likely mediated by acquiring the hpa operon from the donor. In contrast, recombining populations did not adapt better to the second carbon source, butyric acid, even though they suffered fewer extinctions than non-recombining populations. The amount of DNA transferred, but not its benefit, strongly depended on the donor-recipient strain combination. CONCLUSIONS To our knowledge, our study is the first to investigate the genomic consequences of prokaryotic recombination and horizontal gene transfer during laboratory evolution. It shows that the benefits of recombination strongly depend on the environment and the foreign DNA donor.
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Affiliation(s)
- Hoi Yee Chu
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Kathleen Sprouffske
- The Swiss Institute of Bioinformatics, Quartier Sorge – Batiment Genopode, 1015 Lausanne, Switzerland
| | - Andreas Wagner
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- The Swiss Institute of Bioinformatics, Quartier Sorge – Batiment Genopode, 1015 Lausanne, Switzerland
- Santa Fe Institute, Santa Fe, New Mexico USA
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30
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Carbon limitation drives GC content evolution of a marine bacterium in an individual-based genome-scale model. ISME JOURNAL 2018; 12:1180-1187. [PMID: 29330536 DOI: 10.1038/s41396-017-0023-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2017] [Revised: 11/14/2017] [Accepted: 11/21/2017] [Indexed: 01/13/2023]
Abstract
An important unanswered question in evolutionary genomics is the source of considerable variation of genomic base composition (GC content) even among organisms that share one habitat. Evolution toward GC-poor genomes has been considered a major adaptive pathway in the oligotrophic ocean, but GC-rich bacteria are also prevalent and highly successful in this environment. We quantify the contribution of multiple factors to the change of genomic GC content of Ruegeria pomeroyi DSS-3, a representative and GC-rich member in the globally abundant Roseobacter clade, using an agent-based model. The model simulates 2 × 108 cells, which allows random genetic drift to act in a realistic manner. Each cell has a whole genome subject to base-substitution mutation and recombination, which affect the carbon and nitrogen requirements of DNA and protein pools. Nonsynonymous changes can be functionally deleterious. Together, these factors affect the growth and fitness. Simulations show that experimentally determined mutation bias toward GC is not sufficient to build the GC-rich genome of DSS-3. While nitrogen availability has been repeatedly hypothesized to drive the evolution of GC content in marine bacterioplankton, our model instead predicts that DSS-3 and its ancestors have been evolving in environments primarily limited by carbon.
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31
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Maddamsetti R, Lenski RE. Analysis of bacterial genomes from an evolution experiment with horizontal gene transfer shows that recombination can sometimes overwhelm selection. PLoS Genet 2018; 14:e1007199. [PMID: 29385126 PMCID: PMC5809092 DOI: 10.1371/journal.pgen.1007199] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 02/12/2018] [Accepted: 01/15/2018] [Indexed: 12/23/2022] Open
Abstract
Few experimental studies have examined the role that sexual recombination plays in bacterial evolution, including the effects of horizontal gene transfer on genome structure. To address this limitation, we analyzed genomes from an experiment in which Escherichia coli K-12 Hfr (high frequency recombination) donors were periodically introduced into 12 evolving populations of E. coli B and allowed to conjugate repeatedly over the course of 1000 generations. Previous analyses of the evolved strains from this experiment showed that recombination did not accelerate adaptation, despite increasing genetic variation relative to asexual controls. However, the resolution in that previous work was limited to only a few genetic markers. We sought to clarify and understand these puzzling results by sequencing complete genomes from each population. The effects of recombination were highly variable: one lineage was mostly derived from the donors, while another acquired almost no donor DNA. In most lineages, some regions showed repeated introgression and others almost none. Regions with high introgression tended to be near the donors' origin of transfer sites. To determine whether introgressed alleles imposed a genetic load, we extended the experiment for 200 generations without recombination and sequenced whole-population samples. Beneficial alleles in the recipient populations were occasionally driven extinct by maladaptive donor-derived alleles. On balance, our analyses indicate that the plasmid-mediated recombination was sufficiently frequent to drive donor alleles to fixation without providing much, if any, selective advantage.
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Affiliation(s)
- Rohan Maddamsetti
- Ecology, Evolutionary Biology, and Behavior Program, Michigan State University, East Lansing, MI, United States of America
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI, United States of America
- Department of Systems Biology, Harvard Medical School, Boston, MA, United States of America
| | - Richard E. Lenski
- Ecology, Evolutionary Biology, and Behavior Program, Michigan State University, East Lansing, MI, United States of America
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI, United States of America
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States of America
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32
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Mutator genomes decay, despite sustained fitness gains, in a long-term experiment with bacteria. Proc Natl Acad Sci U S A 2017; 114:E9026-E9035. [PMID: 29073099 DOI: 10.1073/pnas.1705887114] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Understanding the extreme variation among bacterial genomes remains an unsolved challenge in evolutionary biology, despite long-standing debate about the relative importance of natural selection, mutation, and random drift. A potentially important confounding factor is the variation in mutation rates between lineages and over evolutionary history, which has been documented in several species. Mutation accumulation experiments have shown that hypermutability can erode genomes over short timescales. These results, however, were obtained under conditions of extremely weak selection, casting doubt on their general relevance. Here, we circumvent this limitation by analyzing genomes from mutator populations that arose during a long-term experiment with Escherichia coli, in which populations have been adaptively evolving for >50,000 generations. We develop an analytical framework to quantify the relative contributions of mutation and selection in shaping genomic characteristics, and we validate it using genomes evolved under regimes of high mutation rates with weak selection (mutation accumulation experiments) and low mutation rates with strong selection (natural isolates). Our results show that, despite sustained adaptive evolution in the long-term experiment, the signature of selection is much weaker than that of mutational biases in mutator genomes. This finding suggests that relatively brief periods of hypermutability can play an outsized role in shaping extant bacterial genomes. Overall, these results highlight the importance of genomic draft, in which strong linkage limits the ability of selection to purge deleterious mutations. These insights are also relevant to other biological systems evolving under strong linkage and high mutation rates, including viruses and cancer cells.
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33
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Recombination-Driven Genome Evolution and Stability of Bacterial Species. Genetics 2017; 207:281-295. [PMID: 28751420 DOI: 10.1534/genetics.117.300061] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 07/18/2017] [Indexed: 01/21/2023] Open
Abstract
While bacteria divide clonally, horizontal gene transfer followed by homologous recombination is now recognized as an important contributor to their evolution. However, the details of how the competition between clonality and recombination shapes genome diversity remains poorly understood. Using a computational model, we find two principal regimes in bacterial evolution and identify two composite parameters that dictate the evolutionary fate of bacterial species. In the divergent regime, characterized by either a low recombination frequency or strict barriers to recombination, cohesion due to recombination is not sufficient to overcome the mutational drift. As a consequence, the divergence between pairs of genomes in the population steadily increases in the course of their evolution. The species lacks genetic coherence with sexually isolated clonal subpopulations continuously formed and dissolved. In contrast, in the metastable regime, characterized by a high recombination frequency combined with low barriers to recombination, genomes continuously recombine with the rest of the population. The population remains genetically cohesive and temporally stable. Notably, the transition between these two regimes can be affected by relatively small changes in evolutionary parameters. Using the Multi Locus Sequence Typing (MLST) data, we classify a number of bacterial species to be either the divergent or the metastable type. Generalizations of our framework to include selection, ecologically structured populations, and horizontal gene transfer of nonhomologous regions are discussed as well.
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34
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Fomenkov A, Sun Z, Dila DK, Anton BP, Roberts RJ, Raleigh EA. EcoBLMcrX, a classical modification-dependent restriction enzyme in Escherichia coli B: Characterization in vivo and in vitro with a new approach to cleavage site determination. PLoS One 2017; 12:e0179853. [PMID: 28654677 PMCID: PMC5487053 DOI: 10.1371/journal.pone.0179853] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 06/05/2017] [Indexed: 12/24/2022] Open
Abstract
Here we characterize the modification-dependent restriction enzyme (MDE) EcoBLMcrX in vivo, in vitro and in its genomic environment. MDE cleavage of modified DNAs protects prokaryote populations from lethal infection by bacteriophage with highly modified DNA, and also stabilizes lineages by reducing gene import when sparse modification occurs in the wrong context. The function and distribution of MDE families are thus important. Here we describe the properties of EcoBLMcrX, an enzyme of the E. coli B lineage, in vivo and in vitro. Restriction in vivo and the genome location of its gene, ecoBLmcrX, were determined during construction and sequencing of a B/K-12 hybrid, ER2566. In classical restriction literature, this B system was named r6 or rglAB. Like many genome defense functions, ecoBLmcrX is found within a genomic island, where gene content is variable among natural E. coli isolates. In vitro, EcoBLMcrX was compared with two related enzymes, BceYI and NhoI. All three degrade fully cytosine-modified phage DNA, as expected for EcoBLMcrX from classical T4 genetic data. A new method of characterizing MDE specificity was developed to better understand action on fully-modified targets such as the phage that provide major evolutionary pressure for MDE maintenance. These enzymes also cleave plasmids with m5C in particular motifs, consistent with a role in lineage-stabilization. The recognition sites were characterized using a site-ranking approach that allows visualization of preferred cleavage sites when fully-modified substrates are digested. A technical constraint on the method is that ligation of one-nucleotide 5' extensions favors G:C over A:T approximately five-fold. Taking this bias into account, we conclude that EcoBLMcrX can cleave 3' to the modified base in the motif Rm5C|. This is compatible with, but less specific than, the site reported by others. Highly-modified site contexts, such as those found in base-substituted virulent phages, are strongly preferred.
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Affiliation(s)
- Alexey Fomenkov
- Research Department, New England Biolabs, Ipswich, MA, United States of America
| | - Zhiyi Sun
- Research Department, New England Biolabs, Ipswich, MA, United States of America
| | - Deborah K. Dila
- Research Department, New England Biolabs, Ipswich, MA, United States of America
| | - Brian P. Anton
- Research Department, New England Biolabs, Ipswich, MA, United States of America
| | - Richard J. Roberts
- Research Department, New England Biolabs, Ipswich, MA, United States of America
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Experimental evolution and the dynamics of adaptation and genome evolution in microbial populations. ISME JOURNAL 2017; 11:2181-2194. [PMID: 28509909 DOI: 10.1038/ismej.2017.69] [Citation(s) in RCA: 178] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 03/02/2017] [Accepted: 03/10/2017] [Indexed: 01/01/2023]
Abstract
Evolution is an on-going process, and it can be studied experimentally in organisms with rapid generations. My team has maintained 12 populations of Escherichia coli in a simple laboratory environment for >25 years and 60 000 generations. We have quantified the dynamics of adaptation by natural selection, seen some of the populations diverge into stably coexisting ecotypes, described changes in the bacteria's mutation rate, observed the new ability to exploit a previously untapped carbon source, characterized the dynamics of genome evolution and used parallel evolution to identify the genetic targets of selection. I discuss what the future might hold for this particular experiment, briefly highlight some other microbial evolution experiments and suggest how the fields of experimental evolution and microbial ecology might intersect going forward.
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Sneppen K. Models of life: epigenetics, diversity and cycles. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2017; 80:042601. [PMID: 28106010 DOI: 10.1088/1361-6633/aa5aeb] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
This review emphasizes aspects of biology that can be understood through repeated applications of simple causal rules. The selected topics include perspectives on gene regulation, phage lambda development, epigenetics, microbial ecology, as well as model approaches to diversity and to punctuated equilibrium in evolution. Two outstanding features are repeatedly described. One is the minimal number of rules to sustain specific states of complex systems for a long time. The other is the collapse of such states and the subsequent dynamical cycle of situations that restitute the system to a potentially new metastable state.
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Affiliation(s)
- Kim Sneppen
- Center for Models of Life, Niels Bohr Institute, Blegdamsvej 17, 2100 Copenhagen, Denmark
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Kingston AW, Ponkratz C, Raleigh EA. Rpn (YhgA-Like) Proteins of Escherichia coli K-12 and Their Contribution to RecA-Independent Horizontal Transfer. J Bacteriol 2017; 199:e00787-16. [PMID: 28096446 PMCID: PMC5350276 DOI: 10.1128/jb.00787-16] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 01/09/2017] [Indexed: 01/21/2023] Open
Abstract
Bacteria use a variety of DNA-mobilizing enzymes to facilitate environmental niche adaptation via horizontal gene transfer. This has led to real-world problems, like the spread of antibiotic resistance, yet many mobilization proteins remain undefined. In the study described here, we investigated the uncharacterized family of YhgA-like transposase_31 (Pfam PF04754) proteins. Our primary focus was the genetic and biochemical properties of the five Escherichia coli K-12 members of this family, which we designate RpnA to RpnE, where Rpn represents recombination-promoting nuclease. We employed a conjugal system developed by our lab that demanded RecA-independent recombination following transfer of chromosomal DNA. Overexpression of RpnA (YhgA), RpnB (YfcI), RpnC (YadD), and RpnD (YjiP) increased RecA-independent recombination, reduced cell viability, and induced the expression of reporter of DNA damage. For the exemplar of the family, RpnA, mutational changes in proposed catalytic residues reduced or abolished all three phenotypes in concert. In vitro, RpnA displayed magnesium-dependent, calcium-stimulated DNA endonuclease activity with little, if any, sequence specificity and a preference for double-strand cleavage. We propose that Rpn/YhgA-like family nucleases can participate in gene acquisition processes.IMPORTANCE Bacteria adapt to new environments by obtaining new genes from other bacteria. Here, we characterize a set of genes that can promote the acquisition process by a novel mechanism. Genome comparisons had suggested the horizontal spread of the genes for the YhgA-like family of proteins through bacteria. Although annotated as transposase_31, no member of the family has previously been characterized experimentally. We show that four Escherichia coli K-12 paralogs contribute to a novel RecA-independent recombination mechanism in vivo For RpnA, we demonstrate in vitro action as a magnesium-dependent, calcium-stimulated nonspecific DNA endonuclease. The cleavage products are capable of providing priming sites for DNA polymerase, which can enable DNA joining by primer-template switching.
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Pang TY, Lercher MJ. Supra-operonic clusters of functionally related genes (SOCs) are a source of horizontal gene co-transfers. Sci Rep 2017; 7:40294. [PMID: 28067311 PMCID: PMC5220362 DOI: 10.1038/srep40294] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 12/01/2016] [Indexed: 12/14/2022] Open
Abstract
Adaptation of bacteria occurs predominantly via horizontal gene transfer (HGT). While it is widely recognized that horizontal acquisitions frequently encompass multiple genes, it is unclear what the size distribution of successfully transferred DNA segments looks like and what evolutionary forces shape this distribution. Here, we identified 1790 gene family pairs that were consistently co-gained on the same branches across a phylogeny of 53 E. coli strains. We estimated a lower limit of their genomic distances at the time they were transferred to their host genomes; this distribution shows a sharp upper bound at 30 kb. The same gene-pairs can have larger distances (up to 70 kb) in other genomes. These more distant pairs likely represent recent acquisitions via transduction that involve the co-transfer of excised prophage genes, as they are almost always associated with intervening phage-associated genes. The observed distribution of genomic distances of co-transferred genes is much broader than expected from a model based on the co-transfer of genes within operons; instead, this distribution is highly consistent with the size distribution of supra-operonic clusters (SOCs), groups of co-occurring and co-functioning genes that extend beyond operons. Thus, we propose that SOCs form a basic unit of horizontal gene transfer.
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Affiliation(s)
- Tin Yau Pang
- Institute for Computer Science, Heinrich Heine University, Düsseldorf, 40225, Germany
| | - Martin J Lercher
- Institute for Computer Science, Heinrich Heine University, Düsseldorf, 40225, Germany
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Correlated Mutations and Homologous Recombination Within Bacterial Populations. Genetics 2016; 205:891-917. [PMID: 28007887 DOI: 10.1534/genetics.116.189621] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 12/15/2016] [Indexed: 11/18/2022] Open
Abstract
Inferring the rate of homologous recombination within a bacterial population remains a key challenge in quantifying the basic parameters of bacterial evolution. Due to the high sequence similarity within a clonal population, and unique aspects of bacterial DNA transfer processes, detecting recombination events based on phylogenetic reconstruction is often difficult, and estimating recombination rates using coalescent model-based methods is computationally expensive, and often infeasible for large sequencing data sets. Here, we present an efficient solution by introducing a set of mutational correlation functions computed using pairwise sequence comparison, which characterize various facets of bacterial recombination. We provide analytical expressions for these functions, which precisely recapitulate simulation results of neutral and adapting populations under different coalescent models. We used these to fit correlation functions measured at synonymous substitutions using whole-genome data on Escherichia coli and Streptococcus pneumoniae populations. We calculated and corrected for the effect of sample selection bias, i.e., the uneven sampling of individuals from natural microbial populations that exists in most datasets. Our method is fast and efficient, and does not employ phylogenetic inference or other computationally intensive numerics. By simply fitting analytical forms to measurements from sequence data, we show that recombination rates can be inferred, and the relative ages of different samples can be estimated. Our approach, which is based on population genetic modeling, is broadly applicable to a wide variety of data, and its computational efficiency makes it particularly attractive for use in the analysis of large sequencing datasets.
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40
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He F, Maslov S. Pan- and core- network analysis of co-expression genes in a model plant. Sci Rep 2016; 6:38956. [PMID: 27982071 PMCID: PMC5159811 DOI: 10.1038/srep38956] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 11/14/2016] [Indexed: 01/18/2023] Open
Abstract
Genome-wide gene expression experiments have been performed using the model plant Arabidopsis during the last decade. Some studies involved construction of coexpression networks, a popular technique used to identify groups of co-regulated genes, to infer unknown gene functions. One approach is to construct a single coexpression network by combining multiple expression datasets generated in different labs. We advocate a complementary approach in which we construct a large collection of 134 coexpression networks based on expression datasets reported in individual publications. To this end we reanalyzed public expression data. To describe this collection of networks we introduced concepts of 'pan-network' and 'core-network' representing union and intersection between a sizeable fractions of individual networks, respectively. We showed that these two types of networks are different both in terms of their topology and biological function of interacting genes. For example, the modules of the pan-network are enriched in regulatory and signaling functions, while the modules of the core-network tend to include components of large macromolecular complexes such as ribosomes and photosynthetic machinery. Our analysis is aimed to help the plant research community to better explore the information contained within the existing vast collection of gene expression data in Arabidopsis.
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Affiliation(s)
- Fei He
- Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Sergei Maslov
- Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA
- Department of Bioengineering, Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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41
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Pérez Carrascal OM, VanInsberghe D, Juárez S, Polz MF, Vinuesa P, González V. Population genomics of the symbiotic plasmids of sympatric nitrogen-fixing Rhizobium species associated with Phaseolus vulgaris. Environ Microbiol 2016; 18:2660-76. [PMID: 27312778 DOI: 10.1111/1462-2920.13415] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 06/13/2016] [Indexed: 11/28/2022]
Abstract
Cultivated common beans are the primary protein source for millions of people around the world who subsist on low-input agriculture, enabled by the symbiotic N2 -fixation these legumes perform in association with rhizobia. Within a single agricultural plot, multiple Rhizobium species can nodulate bean roots, but it is unclear how genetically isolated these species remain in sympatry. To better understand this issue, we sequenced and compared the genomes of 33 strains isolated from the rhizosphere and root nodules of a particular bean variety grown in the same agricultural plot. We found that the Rhizobium species we observed coexist with low genetic recombination across their core genomes. Accessory plasmids thought to be necessary for the saprophytic lifestyle in soil show similar levels of genetic isolation, but with higher rates of recombination than the chromosomes. However, the symbiotic plasmids are extremely similar, with high rates of recombination and do not appear to have co-evolved with the chromosome or accessory plasmids. Therefore, while Rhizobium species are genetically isolated units within the microbial community, a common symbiotic plasmid allows all Rhizobium species to engage in symbiosis with the same host in a single agricultural plot.
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Affiliation(s)
- Olga M Pérez Carrascal
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, 62210, México
| | - David VanInsberghe
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Soledad Juárez
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, 62210, México
| | - Martin F Polz
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Pablo Vinuesa
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, 62210, México
| | - Víctor González
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, 62210, México
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42
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Pirogov S, Rybko A, Kalinina A, Gelfand M. Recombination Processes and Nonlinear Markov Chains. J Comput Biol 2016; 23:711-7. [PMID: 27386932 DOI: 10.1089/cmb.2016.0051] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Bacteria are known to exchange genetic information by horizontal gene transfer. Since the frequency of homologous recombination depends on the similarity between the recombining segments, several studies examined whether this could lead to the emergence of subspecies. Most of them simulated fixed-size Wright-Fisher populations, in which the genetic drift should be taken into account. Here, we use nonlinear Markov processes to describe a bacterial population evolving under mutation and recombination. We consider a population structure as a probability measure on the space of genomes. This approach implies the infinite population size limit, and thus, the genetic drift is not assumed. We prove that under these conditions, the emergence of subspecies is impossible.
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Affiliation(s)
- Sergey Pirogov
- 1 A.A. Kharkevich Institute for Information Transmission Problems , RAS, Moscow, Russia
| | - Alexander Rybko
- 1 A.A. Kharkevich Institute for Information Transmission Problems , RAS, Moscow, Russia
| | - Anastasia Kalinina
- 1 A.A. Kharkevich Institute for Information Transmission Problems , RAS, Moscow, Russia
| | - Mikhail Gelfand
- 1 A.A. Kharkevich Institute for Information Transmission Problems , RAS, Moscow, Russia .,2 Department of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State University , Moscow, Russia
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Mitarai N, Brown S, Sneppen K. Population Dynamics of Phage and Bacteria in Spatially Structured Habitats Using Phage λ and Escherichia coli. J Bacteriol 2016; 198:1783-93. [PMID: 27068593 PMCID: PMC4886755 DOI: 10.1128/jb.00965-15] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2015] [Accepted: 04/05/2016] [Indexed: 01/21/2023] Open
Abstract
UNLABELLED Bacteria living in physically structured habitats are exposed heterogeneously to both resources and different types of phages. While there have been numerous experimental approaches to examine spatially distributed bacteria exposed to phages, there is little theory to guide the design of these experiments, interpret their results, or expand the inferences drawn to a broader ecological and evolutionary context. Plaque formation provides a window into understanding phage-bacterium interactions in physically structured populations, including surfaces, semisolids, and biofilms. We develop models to address the plaque dynamics for a temperate phage and its virulent mutants. The models are compared with phage λ-Escherichia coli system to quantify their applicability. We found that temperate phages gave an increasing number of gradually smaller colonies as the distance increased from the plaque center. For low-lysogen frequency this resulted in plaques with most of the visible colonies at an intermediate distance between the center and periphery. Using spot inoculation, where phages in excess of bacteria were inoculated in a circular area, we measured the frequency and spatial distribution of lysogens. The spot morphology of cII-negative (cII(-)) and cIII(-) mutants of phage λ displays concentric rings of high-density lysogenic colonies. The simplest of these ring morphologies was reproduced by including multiplicity of infection (MOI) sensitivity in lysis-lysogeny decisions, but its failure to explain the occasional observation of multiple rings in cIII(-) mutant phages highlights unknown features of this phage. Our findings demonstrated advantages of temperate phages over virulent phages in exploiting limited resources in spatially distributed microbial populations. IMPORTANCE Phages are the most abundant organisms on earth, and yet little is known about how phages and bacterial hosts are influencing each other in density and evolution. Phages can be either virulent or temperate, a difference that is highlighted when a spatially structured bacterial population is infected. Phage λ is a temperate phage, with a capacity for dormancy that can be modified by single gene knockouts. The stochastic bias in the lysis-lysogeny decision's probability is reflected in plaque morphologies on bacterial lawns. We present a model for plaque morphology of both virulent and temperate phages, taking into account the underlying survival of bacterial microcolonies. It reproduces known plaque morphologies and speaks to advantages of temperate phages in a spatially structured environment.
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Affiliation(s)
- Namiko Mitarai
- Center for Models of Life, Niels Bohr Institute, University of Copenhagen, Copenhagen, DenmarkPrinceton University
| | - Stanley Brown
- Center for Models of Life, Niels Bohr Institute, University of Copenhagen, Copenhagen, DenmarkPrinceton University
| | - Kim Sneppen
- Center for Models of Life, Niels Bohr Institute, University of Copenhagen, Copenhagen, DenmarkPrinceton University
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Abstract
We have examined a collection of the free-living marine bacterium Alteromonas genomes with cores diverging in average nucleotide identities ranging from 99.98% to 73.35%, i.e., from microbes that can be considered members of a natural clone (like in a clinical epidemiological outbreak) to borderline genus level. The genomes were largely syntenic allowing a precise delimitation of the core and flexible regions in each. The core was 1.4 Mb (ca. 30% of the typical strain genome size). Recombination rates along the core were high among strains belonging to the same species (37.7-83.7% of all nucleotide polymorphisms) but they decreased sharply between species (18.9-5.1%). Regarding the flexible genome, its main expansion occurred within the boundaries of the species, i.e., strains of the same species already have a large and diverse flexible genome. Flexible regions occupy mostly fixed genomic locations. Four large genomic islands are involved in the synthesis of strain-specific glycosydic receptors that we have called glycotypes. These genomic regions are exchanged by homologous recombination within and between species and there is evidence for their import from distant taxonomic units (other genera within the family). In addition, several hotspots for integration of gene cassettes by illegitimate recombination are distributed throughout the genome. They code for features that give each clone specific properties to interact with their ecological niche and must flow fast throughout the whole genus as they are found, with nearly identical sequences, in different species. Models for the generation of this genomic diversity involving phage predation are discussed.
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Affiliation(s)
- Mario López-Pérez
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, Alicante, Spain
| | - Francisco Rodriguez-Valera
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, Alicante, Spain
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Benefit of transferred mutations is better predicted by the fitness of recipients than by their ecological or genetic relatedness. Proc Natl Acad Sci U S A 2016; 113:5047-52. [PMID: 27091964 DOI: 10.1073/pnas.1524988113] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The effect of a mutation depends on its interaction with the genetic background in which it is assessed. Studies in experimental systems have demonstrated that such interactions are common among beneficial mutations and often follow a pattern consistent with declining evolvability of more fit genotypes. However, these studies generally examine the consequences of interactions between a small number of focal mutations. It is not clear, therefore, that findings can be extrapolated to natural populations, where new mutations may be transferred between genetically divergent backgrounds. We build on work that examined interactions between four beneficial mutations selected in a laboratory-evolved population of Escherichia coli to test how they interact with the genomes of diverse natural isolates of the same species. We find that the fitness effect of transferred mutations depends weakly on the genetic and ecological similarity of recipient strains relative to the donor strain in which the mutations were selected. By contrast, mutation effects were strongly inversely correlated to the initial fitness of the recipient strain. That is, there was a pattern of diminishing returns whereby fit strains benefited proportionally less from an added mutation. Our results strengthen the view that the fitness of a strain can be a major determinant of its ability to adapt. They also support a role for barriers of transmission, rather than differential selection of transferred DNA, as an explanation of observed phylogenetically determined patterns of restricted recombination among E. coli strains.
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Shapiro BJ. How clonal are bacteria over time? Curr Opin Microbiol 2016; 31:116-123. [PMID: 27057964 DOI: 10.1016/j.mib.2016.03.013] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 03/20/2016] [Accepted: 03/22/2016] [Indexed: 11/15/2022]
Abstract
Bacteria and archaea reproduce clonally (vertical descent), but exchange genes by recombination (horizontal transfer). Recombination allows adaptive mutations or genes to spread rapidly within (or even between) species, and reduces the burden of deleterious mutations. Clonality-defined here as the balance between vertical and horizontal inheritance-is therefore a key microbial trait, determining how quickly a population can adapt and the size of its gene pool. Here, I discuss whether clonality varies over time and if it can be considered a stable trait of a given population. I show that, in some cases, clonality is clearly not static. For example, non-clonal (highly recombining) populations can give rise to clonal expansions, often of pathogens. However, an analysis of time-course metagenomic data from a lake suggests that a bacterial population's past clonality (as measured by its genetic diversity) is a good predictor of its future clonality. Clonality therefore appears to be relatively-but not completely-stable over evolutionary time.
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Affiliation(s)
- B Jesse Shapiro
- Département de sciences biologiques, Université de Montréal, Montréal, QC H3C 3J7, Canada.
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47
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Maddamsetti R. Gene flow in microbial communities could explain unexpected patterns of synonymous variation in the Escherichia coli core genome. Mob Genet Elements 2016; 6:e1137380. [PMID: 27066306 PMCID: PMC4802760 DOI: 10.1080/2159256x.2015.1137380] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 12/20/2015] [Accepted: 12/22/2015] [Indexed: 11/27/2022] Open
Abstract
Researchers contest the importance of gene flow in bacterial core genomes, as traditionalists view microbes as predominantly clonal, asexually reproducing organisms. Contrary to the traditional perspective, Escherichia coli core genes vary greatly in their levels of synonymous genetic diversity. This observation indicates that the relative importance of evolutionary forces such as mutation, selection, and recombination varies from gene to gene. In this paper, I highlight why the synonymous diversity observation is broadly relevant to researchers interested in the evolutionary dynamics of microbial populations and communities. I explain how a model of evolution called the coalescent relates neutral diversity (i.e. mutations with negligible fitness effects) to mutation rates, evolutionary time, and a parameter called effective population size. I then describe the possible ways in which mutation, selection, and recombination can explain observed patterns of synonymous diversity in E. coli. Finally, I describe a model for E. coli genome evolution in which different loci are subject to varying levels of gene flow among co-occurring microbes and viruses in the environment. Researchers can falsify the gene flow hypothesis by sequencing genes and strains isolated from stable microbiomes or by carrying out evolution experiments that trace gene genealogies in real-time.
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Affiliation(s)
- Rohan Maddamsetti
- Department of Integrative Biology, Michigan State University, East Lansing, MI, USA; Ecology, Evolutionary Biology, and Behavior Program, Michigan State University, East Lansing, MI, USA; BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI, USA
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Weakly Deleterious Mutations and Low Rates of Recombination Limit the Impact of Natural Selection on Bacterial Genomes. mBio 2015; 6:e01302-15. [PMID: 26670382 PMCID: PMC4701828 DOI: 10.1128/mbio.01302-15] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Free-living bacteria are usually thought to have large effective population sizes, and so tiny selective differences can drive their evolution. However, because recombination is infrequent, “background selection” against slightly deleterious alleles should reduce the effective population size (Ne) by orders of magnitude. For example, for a well-mixed population with 1012 individuals and a typical level of homologous recombination (r/m = 3, i.e., nucleotide changes due to recombination [r] occur at 3 times the mutation rate [m]), we predict that Ne is <107. An argument for high Ne values for bacteria has been the high genetic diversity within many bacterial “species,” but this diversity may be due to population structure: diversity across subpopulations can be far higher than diversity within a subpopulation, which makes it difficult to estimate Ne correctly. Given an estimate of Ne, standard population genetics models imply that selection should be sufficient to drive evolution if Ne × s is >1, where s is the selection coefficient. We found that this remains approximately correct if background selection is occurring or when population structure is present. Overall, we predict that even for free-living bacteria with enormous populations, natural selection is only a significant force if s is above 10−7 or so. Because bacteria form huge populations with trillions of individuals, the simplest theoretical prediction is that the better allele at a site would predominate even if its advantage was just 10−9 per generation. In other words, virtually every nucleotide would be at the local optimum in most individuals. A more sophisticated theory considers that bacterial genomes have millions of sites each and selection events on these many sites could interfere with each other, so that only larger effects would be important. However, bacteria can exchange genetic material, and in principle, this exchange could eliminate the interference between the evolution of the sites. We used simulations to confirm that during multisite evolution with realistic levels of recombination, only larger effects are important. We propose that advantages of less than 10−7 are effectively neutral.
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49
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Maddamsetti R, Hatcher PJ, Cruveiller S, Médigue C, Barrick JE, Lenski RE. Synonymous Genetic Variation in Natural Isolates of Escherichia coli Does Not Predict Where Synonymous Substitutions Occur in a Long-Term Experiment. Mol Biol Evol 2015. [PMID: 26199375 PMCID: PMC4651231 DOI: 10.1093/molbev/msv161] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Synonymous genetic differences vary by more than 20-fold among genes in natural isolates of Escherichia coli. One hypothesis to explain this heterogeneity is that genes with high levels of synonymous variation mutate at higher rates than genes with low synonymous variation. If so, then one would expect to observe similar mutational patterns in evolution experiments. In fact, however, the pattern of synonymous substitutions in a long-term evolution experiment with E. coli does not support this hypothesis. In particular, the extent of synonymous variation across genes in that experiment does not reflect the variation observed in natural isolates of E. coli. Instead, gene length alone predicts with high accuracy the prevalence of synonymous changes in the experimental populations. We hypothesize that patterns of synonymous variation in natural E. coli populations are instead caused by differences across genomic regions in their effective population size that, in turn, reflect different histories of recombination, horizontal gene transfer, selection, and population structure.
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Affiliation(s)
- Rohan Maddamsetti
- Ecology, Evolutionary Biology, and Behavior Program, Michigan State University BEACON Center for the Study of Evolution in Action, Michigan State University
| | | | - Stéphane Cruveiller
- CNRS-UMR 8030 and Commissariat à l'Energie Atomique CEA/DSV/IG/Genoscope LABGeM, Evry, France
| | - Claudine Médigue
- CNRS-UMR 8030 and Commissariat à l'Energie Atomique CEA/DSV/IG/Genoscope LABGeM, Evry, France
| | - Jeffrey E Barrick
- BEACON Center for the Study of Evolution in Action, Michigan State University Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, The University of Texas at Austin
| | - Richard E Lenski
- Ecology, Evolutionary Biology, and Behavior Program, Michigan State University BEACON Center for the Study of Evolution in Action, Michigan State University
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