1
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Mallawaarachchi S, Tonkin-Hill G, Pöntinen A, Calland J, Gladstone R, Arredondo-Alonso S, MacAlasdair N, Thorpe H, Top J, Sheppard S, Balding D, Croucher N, Corander J. Detecting co-selection through excess linkage disequilibrium in bacterial genomes. NAR Genom Bioinform 2024; 6:lqae061. [PMID: 38846349 PMCID: PMC11155488 DOI: 10.1093/nargab/lqae061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Revised: 04/15/2024] [Accepted: 05/14/2024] [Indexed: 06/09/2024] Open
Abstract
Population genomics has revolutionized our ability to study bacterial evolution by enabling data-driven discovery of the genetic architecture of trait variation. Genome-wide association studies (GWAS) have more recently become accompanied by genome-wide epistasis and co-selection (GWES) analysis, which offers a phenotype-free approach to generating hypotheses about selective processes that simultaneously impact multiple loci across the genome. However, existing GWES methods only consider associations between distant pairs of loci within the genome due to the strong impact of linkage-disequilibrium (LD) over short distances. Based on the general functional organisation of genomes it is nevertheless expected that majority of co-selection and epistasis will act within relatively short genomic proximity, on co-variation occurring within genes and their promoter regions, and within operons. Here, we introduce LDWeaver, which enables an exhaustive GWES across both short- and long-range LD, to disentangle likely neutral co-variation from selection. We demonstrate the ability of LDWeaver to efficiently generate hypotheses about co-selection using large genomic surveys of multiple major human bacterial pathogen species and validate several findings using functional annotation and phenotypic measurements. Our approach will facilitate the study of bacterial evolution in the light of rapidly expanding population genomic data.
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Affiliation(s)
| | | | - Anna K Pöntinen
- Department of Biostatistics, University of Oslo, Oslo, Norway
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - Jessica K Calland
- Oslo Centre for Biostatistics and Epidemiology, Oslo University Hospital, Oslo, Norway
| | | | | | | | - Harry A Thorpe
- Department of Biostatistics, University of Oslo, Oslo, Norway
| | - Janetta Top
- Department of Medical Microbiology, UMC Utrecht, Utrecht, The Netherlands
| | - Samuel K Sheppard
- Ineos Oxford Institute of Antimicrobial Research, Department of Biology, University of Oxford, Oxford, United Kingdom
| | - David Balding
- Melbourne Integrative Genomics, School of BioSciences and School of Mathematics & Statistics, University of Melbourne, Parkville, Victoria, Australia
| | - Nicholas J Croucher
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, United Kingdom
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, United Kingdom
| | - Jukka Corander
- Department of Biostatistics, University of Oslo, Oslo, Norway
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK
- Helsinki Institute of Information Technology, Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
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2
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McCutcheon JP, Garber AI, Spencer N, Warren JM. How do bacterial endosymbionts work with so few genes? PLoS Biol 2024; 22:e3002577. [PMID: 38626194 PMCID: PMC11020763 DOI: 10.1371/journal.pbio.3002577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/18/2024] Open
Abstract
The move from a free-living environment to a long-term residence inside a host eukaryotic cell has profound effects on bacterial function. While endosymbioses are found in many eukaryotes, from protists to plants to animals, the bacteria that form these host-beneficial relationships are even more diverse. Endosymbiont genomes can become radically smaller than their free-living relatives, and their few remaining genes show extreme compositional biases. The details of how these reduced and divergent gene sets work, and how they interact with their host cell, remain mysterious. This Unsolved Mystery reviews how genome reduction alters endosymbiont biology and highlights a "tipping point" where the loss of the ability to build a cell envelope coincides with a marked erosion of translation-related genes.
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Affiliation(s)
- John P. McCutcheon
- Biodesign Institute and School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Arkadiy I. Garber
- Biodesign Institute and School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
| | - Noah Spencer
- Biodesign Institute and School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
| | - Jessica M. Warren
- Biodesign Institute and School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
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3
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Wolff R, Garud NR. Pervasive selective sweeps across human gut microbiomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.22.573162. [PMID: 38187688 PMCID: PMC10769429 DOI: 10.1101/2023.12.22.573162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
The human gut microbiome is composed of a highly diverse consortia of species which are continually evolving within and across hosts. The ability to identify adaptations common to many host gut microbiomes would not only reveal shared selection pressures across hosts, but also key drivers of functional differentiation of the microbiome that may affect community structure and host traits. However, to date there has not been a systematic scan for adaptations that have spread across host microbiomes. Here, we develop a novel selection scan statistic, named the integrated linkage disequilibrium score (iLDS), that can detect the spread of adaptive haplotypes across host microbiomes via migration and horizontal gene transfer. Specifically, iLDS leverages signals of hitchhiking of deleterious variants with the beneficial variant, a common feature of adaptive evolution. We find that iLDS is capable of detecting simulated and known cases of selection, and moreover is robust to potential confounders that can also elevate LD. Application of the statistic to ~20 common commensal gut species from a large cohort of healthy, Western adults reveals pervasive spread of selected alleles across human microbiomes mediated by horizontal gene transfer. Among the candidate selective sweeps recovered by iLDS is an enrichment for genes involved in the metabolism of maltodextrin, a synthetic starch that has recently become a widespread component of Western diets. In summary, we demonstrate that selective sweeps across host microbiomes are a common feature of the evolution of the human gut microbiome.
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Affiliation(s)
- Richard Wolff
- Department of Ecology and Evolutionary Biology, UCLA
| | - Nandita R. Garud
- Department of Ecology and Evolutionary Biology, UCLA
- Department of Human Genetics, UCLA
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4
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Mah JC, Lohmueller KE, Garud N. Inference of the demographic histories and selective effects of human gut commensal microbiota over the course of human history. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.09.566454. [PMID: 38014007 PMCID: PMC10680615 DOI: 10.1101/2023.11.09.566454] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Despite the importance of gut commensal microbiota to human health, there is little knowledge about their evolutionary histories, including their population demographic histories and their distributions of fitness effects (DFE) of new mutations. Here, we infer the demographic histories and DFEs of 27 of the most highly prevalent and abundant commensal gut microbial species in North Americans over timescales exceeding human generations using a collection of lineages inferred from a panel of healthy hosts. We find overall reductions in genetic variation among commensal gut microbes sampled from a Western population relative to an African rural population. Additionally, some species in North American microbiomes display contractions in population size and others expansions, potentially occurring at several key historical moments in human history. DFEs across species vary from highly to mildly deleterious, with accessory genes experiencing more drift compared to core genes. Within genera, DFEs tend to be more congruent, reflective of underlying phylogenetic relationships. Taken together, these findings suggest that human commensal gut microbes have distinct evolutionary histories, possibly reflecting the unique roles of individual members of the microbiome.
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5
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Teng W, Liao B, Chen M, Shu W. Genomic Legacies of Ancient Adaptation Illuminate GC-Content Evolution in Bacteria. Microbiol Spectr 2023; 11:e0214522. [PMID: 36511682 PMCID: PMC9927291 DOI: 10.1128/spectrum.02145-22] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Bacterial evolution is characterized by strong purifying selection as well as rapid adaptive evolution in changing environments. In this context, the genomic GC content (genomic GC) varies greatly but presents some level of phylogenetic stability, making it challenging to explain based on current hypotheses. To illuminate the evolutionary mechanisms of the genomic GC, we analyzed the base composition and functional inventory of 11,083 representative genomes. A phylogenetically constrained bimodal distribution of the genomic GC, which mainly originated from parallel divergences in the early evolution, was demonstrated. Such variation of the genomic GC can be well explained by DNA replication and repair (DRR), in which multiple pathways correlate with the genomic GC. Furthermore, the biased conservation of various stress-related genes, especially the DRR-related ones, implies distinct adaptive processes in the ancestral lineages of high- or low-GC clades which are likely induced by major environmental changes. Our findings support that the mutational biases resulting from these legacies of ancient adaptation have changed the course of adaptive evolution and generated great variation in the genomic GC. This highlights the importance of indirect effects of natural selection, which indicates a new model for bacterial evolution. IMPORTANCE GC content has been shown to be an important factor in microbial ecology and evolution, and the genomic GC of bacteria can be characterized by great intergenomic heterogeneity, high intragenomic homogeneity, and strong phylogenetic inertia, as well as being associated with the environment. Current hypotheses concerning direct selection or mutational biases cannot well explain these features simultaneously. Our findings of the genomic GC showing that ancient adaptations have transformed the DRR system and that the resulting mutational biases further contributed to a bimodal distribution of it offer a more reasonable scenario for the mechanism. This would imply that, when thinking about the evolution of life, diverse processes of adaptation exist, and combined effects of natural selection should be considered.
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Affiliation(s)
- Wenkai Teng
- School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Bin Liao
- School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Mengyun Chen
- School of Life Sciences, South China Normal University, Guangzhou, Guangdong, China
| | - Wensheng Shu
- School of Life Sciences, South China Normal University, Guangzhou, Guangdong, China
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6
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Bohlin J. A simple stochastic model describing the evolution of genomic GC content in asexually reproducing organisms. Sci Rep 2022; 12:18569. [PMID: 36329129 PMCID: PMC9631610 DOI: 10.1038/s41598-022-21709-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 09/30/2022] [Indexed: 11/06/2022] Open
Abstract
A genome's nucleotide composition can usually be summarized with (G)uanine + (C)ytosine (GC) or (A)denine + (T)hymine (AT) frequencies as GC% = 100% - AT%. Genomic AT/GC content has been linked to environment and selective processes in asexually reproducing organisms. A model is presented relating the evolution of genomic GC content over time to AT [Formula: see text] GC and GC [Formula: see text] AT mutation rates. By employing Itô calculus it is shown that if mutation rates are subject to random perturbations, that can vary over time, several implications follow. In particular, an extra Brownian motion term appears influencing genomic nucleotide variability; the greater the random perturbations the more genomic nucleotide variability. This can have several interpretations depending on the context. For instance, reducing the influence of the random perturbations on the AT/GC mutation rates and thus genomic nucleotide variability, to limit fitness decreasing and deleterious mutations, will likely suggest channeling of resources. On the other hand, increased genomic nucleotide diversity may be beneficial in variable environments. In asexually reproducing organisms, the Brownian motion term can be considered to be inversely reflective of the selective pressures an organism is subjected to at the molecular level. The presented model is a generalization of a previous model, limited to microbial symbionts, to all asexually reproducing, non-recombining organisms. Last, a connection between the presented model and the classical Luria-Delbrück mutation model is presented in an Itô calculus setting.
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Affiliation(s)
- Jon Bohlin
- grid.418193.60000 0001 1541 4204Division of Infection Control, Department of Methods Development and Analysis, Norwegian Institute of Public Health, Oslo, Norway ,grid.418193.60000 0001 1541 4204Centre for Fertility and Health, Norwegian Institute of Public Health, P.O. Box 4404, Lovisenberggata 8, 0403 Oslo, Norway
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7
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Sen P, Kurmi A, Ray SK, Satapathy SS. Machine learning approach identifies prominent codons from different degenerate groups influencing gene expression in bacteria. Genes Cells 2022; 27:591-601. [DOI: 10.1111/gtc.12977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 07/15/2022] [Accepted: 07/30/2022] [Indexed: 11/29/2022]
Affiliation(s)
- Piyali Sen
- Department of Computer Science and Engineering Tezpur University, Napaam Tezpur Assam India
| | - Annushree Kurmi
- Department of Computer Science and Engineering Tezpur University, Napaam Tezpur Assam India
| | - Suvendra Kumar Ray
- Molecular Biology and Biotechnology Tezpur University, Napaam Tezpur Assam India
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8
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Chen Z, Wang X, Song Y, Zeng Q, Zhang Y, Luo H. Prochlorococcus have low global mutation rate and small effective population size. Nat Ecol Evol 2022; 6:183-194. [PMID: 34949817 DOI: 10.1038/s41559-021-01591-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 10/14/2021] [Indexed: 12/27/2022]
Abstract
Prochlorococcus are the most abundant free-living photosynthetic carbon-fixing organisms in the ocean. Prochlorococcus show small genome sizes, low genomic G+C content, reduced DNA repair gene pool and fast evolutionary rates, which are typical features of endosymbiotic bacteria. Nevertheless, their evolutionary mechanisms are believed to be different. Evolution of endosymbiotic bacteria is dominated by genetic drift owing to repeated population bottlenecks, whereas Prochlorococcus are postulated to have extremely large effective population sizes (Ne) and thus drift has rarely been considered. However, accurately extrapolating Ne requires measuring an unbiased global mutation rate through mutation accumulation, which is challenging for Prochlorococcus. Here, we managed this experiment over 1,065 days using Prochlorococcus marinus AS9601, sequenced genomes of 141 mutant lines and determined its mutation rate to be 3.50 × 10-10 per site per generation. Extrapolating Ne additionally requires identifying population boundaries, which we defined using PopCOGenT and over 400 genomes related to AS9601. Accordingly, we calculated its Ne to be 1.68 × 107, which is only reasonably greater than that of endosymbiotic bacteria but surprisingly smaller than that of many free-living bacteria extrapolated using the same approach. Our results therefore suggest that genetic drift is a key driver of Prochlorococcus evolution.
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Affiliation(s)
- Zhuoyu Chen
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Xiaojun Wang
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR.,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Yu Song
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Qinglu Zeng
- Department of Ocean Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong SAR.,Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Clear Water Bay, Hong Kong SAR
| | - Yao Zhang
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.
| | - Haiwei Luo
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR. .,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China. .,Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Clear Water Bay, Hong Kong SAR.
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9
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Duan B, Ding P, Navarre WW, Liu J, Xia B. Xenogeneic Silencing and Bacterial Genome Evolution: Mechanisms for DNA Recognition Imply Multifaceted Roles of Xenogeneic Silencers. Mol Biol Evol 2021; 38:4135-4148. [PMID: 34003286 PMCID: PMC8476142 DOI: 10.1093/molbev/msab136] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 04/08/2021] [Indexed: 12/14/2022] Open
Abstract
Horizontal gene transfer (HGT) is a major driving force for bacterial evolution. To avoid the deleterious effects due to the unregulated expression of newly acquired foreign genes, bacteria have evolved specific proteins named xenogeneic silencers to recognize foreign DNA sequences and suppress their transcription. As there is considerable diversity in genomic base compositions among bacteria, how xenogeneic silencers distinguish self- from nonself DNA in different bacteria remains poorly understood. This review summarizes the progress in studying the DNA binding preferences and the underlying molecular mechanisms of known xenogeneic silencer families, represented by H-NS of Escherichia coli, Lsr2 of Mycobacterium, MvaT of Pseudomonas, and Rok of Bacillus. Comparative analyses of the published data indicate that the differences in DNA recognition mechanisms enable these xenogeneic silencers to have clear characteristics in DNA sequence preferences, which are further correlated with different host genomic features. These correlations provide insights into the mechanisms of how these xenogeneic silencers selectively target foreign DNA in different genomic backgrounds. Furthermore, it is revealed that the genomic AT contents of bacterial species with the same xenogeneic silencer family proteins are distributed in a limited range and are generally lower than those species without any known xenogeneic silencers in the same phylum/class/genus, indicating that xenogeneic silencers have multifaceted roles on bacterial genome evolution. In addition to regulating horizontal gene transfer, xenogeneic silencers also act as a selective force against the GC to AT mutational bias found in bacterial genomes and help the host genomic AT contents maintained at relatively low levels.
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Affiliation(s)
- Bo Duan
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, and School of Life Sciences, Peking University, Beijing, 100871, China
| | - Pengfei Ding
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, and School of Life Sciences, Peking University, Beijing, 100871, China
| | - William Wiley Navarre
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5G 1M1, Canada
| | - Jun Liu
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5G 1M1, Canada
| | - Bin Xia
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, and School of Life Sciences, Peking University, Beijing, 100871, China
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10
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de Oliveira JL, Morales AC, Hurst LD, Urrutia AO, Thompson CRL, Wolf JB. Inferring Adaptive Codon Preference to Understand Sources of Selection Shaping Codon Usage Bias. Mol Biol Evol 2021; 38:3247-3266. [PMID: 33871580 PMCID: PMC8321536 DOI: 10.1093/molbev/msab099] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Alternative synonymous codons are often used at unequal frequencies. Classically, studies of such codon usage bias (CUB) attempted to separate the impact of neutral from selective forces by assuming that deviations from a predicted neutral equilibrium capture selection. However, GC-biased gene conversion (gBGC) can also cause deviation from a neutral null. Alternatively, selection has been inferred from CUB in highly expressed genes, but the accuracy of this approach has not been extensively tested, and gBGC can interfere with such extrapolations (e.g., if expression and gene conversion rates covary). It is therefore critical to examine deviations from a mutational null in a species with no gBGC. To achieve this goal, we implement such an analysis in the highly AT rich genome of Dictyostelium discoideum, where we find no evidence of gBGC. We infer neutral CUB under mutational equilibrium to quantify "adaptive codon preference," a nontautologous genome wide quantitative measure of the relative selection strength driving CUB. We observe signatures of purifying selection consistent with selection favoring adaptive codon preference. Preferred codons are not GC rich, underscoring the independence from gBGC. Expression-associated "preference" largely matches adaptive codon preference but does not wholly capture the influence of selection shaping patterns across all genes, suggesting selective constraints associated specifically with high expression. We observe patterns consistent with effects on mRNA translation and stability shaping adaptive codon preference. Thus, our approach to quantifying adaptive codon preference provides a framework for inferring the sources of selection that shape CUB across different contexts within the genome.
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Affiliation(s)
- Janaina Lima de Oliveira
- Instituto de Biologia, Universidade Federal da Bahia, Salvador, Bahia, 40170-115, Brazil.,Milner Centre for Evolution and Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Atahualpa Castillo Morales
- Milner Centre for Evolution and Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Laurence D Hurst
- Milner Centre for Evolution and Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Araxi O Urrutia
- Milner Centre for Evolution and Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK.,Instituto de Ecologia, UNAM, Ciudad de Mexico 04510, Mexico
| | - Christopher R L Thompson
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London, WC1E 6BT, UK
| | - Jason B Wolf
- Milner Centre for Evolution and Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK
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11
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Uddin A, Chakraborty S. Analysis of mitochondrial protein-coding genes of Antheraea assamensis: Muga silkworm of Assam. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2021; 106:e21750. [PMID: 33075174 DOI: 10.1002/arch.21750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 09/18/2020] [Accepted: 09/30/2020] [Indexed: 06/11/2023]
Abstract
To understand the synonymous codon usage pattern in mitochondrial genome of Antheraea assamensis, we analyzed the 13 mitochondrial protein-coding genes of this species using a bioinformatic approach as no work was reported yet. The nucleotide composition analysis suggested that the percentages of A, T, G,and C were 33.73, 46.39, 9.7 and 10.17, respectively and the overall GC content was 19.86, that is, lower than 50% and the genes were AT rich. The mean effective number of codons of mitochondrial protein-coding genes was 36.30 and it indicated low codon usage bias (CUB). Relative synonymous codon usage analysis suggested overrepresented and underrepresented codons in each gene and the pattern of codon usage was different among genes. Neutrality plot analysis revealed a narrow range of distribution for GC content at the third codon position and some points were diagonally distributed, suggesting both mutation pressure and natural selection influenced the CUB.
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Affiliation(s)
- Arif Uddin
- Department of Zoology, Moinul Hoque Choudhury Memorial Science College, Algapur, Assam, India
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12
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Abstract
The genomes of bacteria contain fewer genes and substantially less noncoding DNA than those of eukaryotes, and as a result, they have much less raw material to invent new traits. Yet, bacteria are vastly more taxonomically diverse, numerically abundant, and globally successful in colonizing new habitats compared to eukaryotes. Although bacterial genomes are generally considered to be optimized for efficient growth and rapid adaptation, nonadaptive processes have played a major role in shaping the size, contents, and compact organization of bacterial genomes and have allowed the establishment of deleterious traits that serve as the raw materials for genetic innovation.
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Affiliation(s)
- Paul C Kirchberger
- Department of Integrative Biology, University of Texas at Austin, Texas 78712, USA; ; ;
| | - Marian L Schmidt
- Department of Integrative Biology, University of Texas at Austin, Texas 78712, USA; ; ;
| | - Howard Ochman
- Department of Integrative Biology, University of Texas at Austin, Texas 78712, USA; ; ;
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13
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Bohlin J, Rose B, Brynildsrud O, Birgitte Freiesleben De Blasio. A simple stochastic model describing genomic evolution over time of GC content in microbial symbionts. J Theor Biol 2020; 503:110389. [PMID: 32634385 DOI: 10.1016/j.jtbi.2020.110389] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 04/21/2020] [Accepted: 06/24/2020] [Indexed: 11/29/2022]
Abstract
An organism's genomic base composition is usually summarized by its AT or GC content due to Chargaff's parity laws. Variation in prokaryotic GC content can be substantial between taxa but is generally small within microbial genomes. This variation has been found to correlate with both phylogeny and environmental factors. Since novel single-nucleotide polymorphisms (SNPs) within genomes are at least partially linked to the environment through natural selection, SNP GC content can be considered a compound measure of an organism's environmental influences, lifestyle, phylogeny as well as other more or less random processes. While there are several models describing genomic GC content few, if any, consider AT/GC mutation rates subjected to random perturbations. We present a mathematical model that describes how GC content in microbial genomes evolves over time as a function of the AT → GC and GC → AT mutation rates with Gaussian white noise disturbances. The model, which is suited specifically to non-recombining vertically transmitted prokaryotic symbionts, suggests that small differences in the AT/GC mutation rates can lead to profound differences in outcome due to the ensuing stochastic process. In other words, the model indicates that time to extinction could be a consequence of the mutation rate trajectory on which the symbiont embarked early on in its evolutionary history.
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Affiliation(s)
- Jon Bohlin
- Division of Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway; Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway; Department of Production Animals, Faculty of Veterinary Medicine, Norwegian University of Life Science, Oslo, Norway
| | - Brittany Rose
- Division of Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway; Department of Biostatistics, Oslo Centre for Biostatistics and Epidemiology, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Ola Brynildsrud
- Division of Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway; Department of Production Animals, Faculty of Veterinary Medicine, Norwegian University of Life Science, Oslo, Norway
| | - Birgitte Freiesleben De Blasio
- Division of Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway; Department of Biostatistics, Oslo Centre for Biostatistics and Epidemiology, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
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14
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Weissman JL, Fagan WF, Johnson PLF. Linking high GC content to the repair of double strand breaks in prokaryotic genomes. PLoS Genet 2019; 15:e1008493. [PMID: 31703064 PMCID: PMC6867656 DOI: 10.1371/journal.pgen.1008493] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 11/20/2019] [Accepted: 10/25/2019] [Indexed: 01/21/2023] Open
Abstract
Genomic GC content varies widely among microbes for reasons unknown. While mutation bias partially explains this variation, prokaryotes near-universally have a higher GC content than predicted solely by this bias. Debate surrounds the relative importance of the remaining explanations of selection versus biased gene conversion favoring GC alleles. Some environments (e.g. soils) are associated with a high genomic GC content of their inhabitants, which implies that either high GC content is a selective adaptation to particular habitats, or that certain habitats favor increased rates of gene conversion. Here, we report a novel association between the presence of the non-homologous end joining DNA double-strand break repair pathway and GC content; this observation suggests that DNA damage may be a fundamental driver of GC content, leading in part to the many environmental patterns observed to-date. We discuss potential mechanisms accounting for the observed association, and provide preliminary evidence that sites experiencing higher rates of double-strand breaks are under selection for increased GC content relative to the genomic background. The overall nucleotide composition of an organism’s genome varies greatly between species. Previous work has identified certain environmental factors (e.g., oxygen availability) associated with the relative number of GC bases as opposed to AT bases in the genomes of species. Many of these environments that are associated with high GC content are also associated with relatively high rates of DNA damage. We show that organisms possessing the non-homologous end-joining DNA repair pathway, which is one mechanism to repair DNA double-strand breaks, have an elevated GC content relative to expectation. We also show that certain sites on the genome that are particularly susceptible to double strand breaks have an elevated GC content. This leads us to suggest that an important underlying driver of variability in nucleotide composition across environments is the rate of DNA damage (specifically double-strand breaks) to which an organism living in each environment is exposed.
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Affiliation(s)
- JL Weissman
- Department of Biology, University of Maryland - College Park, College Park, Maryland, United States of America
| | - William F. Fagan
- Department of Biology, University of Maryland - College Park, College Park, Maryland, United States of America
| | - Philip L. F. Johnson
- Department of Biology, University of Maryland - College Park, College Park, Maryland, United States of America
- * E-mail:
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15
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Ghalayini M, Magnan M, Dion S, Zatout O, Bourguignon L, Tenaillon O, Lescat M. Long-term evolution of the natural isolate of Escherichia coli 536 in the mouse gut colonized after maternal transmission reveals convergence in the constitutive expression of the lactose operon. Mol Ecol 2019; 28:4470-4485. [PMID: 31482587 DOI: 10.1111/mec.15232] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 07/24/2019] [Indexed: 02/02/2023]
Abstract
In vitro experimental evolution has taught us many lessons on the molecular bases of adaptation. To move towards more natural settings, evolution in the mice gut has been successfully performed. Yet, these experiments suffered from the use of laboratory strains as well as the use of axenic or streptomycin-treated mice to maintain the inoculated strains. To circumvent these limitations, we conducted a one-year experimental evolution in vivo using a natural isolate of E. coli, strain 536, in conditions mimicking as much as possible natural environment with mother-to-offspring microbiota transmission. Mice were then distributed in 24 independent cages and separated into two different diets: a regular one (chow diet, CD) and high-fat and high-sugar one (Western Diet, WD). Genome sequences revealed an early and rapid selection during the breastfeeding period that selected the constitutive expression of the well-characterized lactose operon. E. coli was lost significantly more in CD than WD; however, we could not detect any genomic signature of selection, nor any diet specificities during the later part of the experiments. The apparently neutral evolution presumably due to low population size maintained nevertheless at high frequency the early selected mutations affecting lactose regulation. The rapid loss of lactose operon regulation challenges the idea that plastic gene expression is both optimal and stable in the wild.
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Affiliation(s)
- Mohamed Ghalayini
- IAME, INSERM, Université Paris 13, Bobigny, France.,Service de Réanimation Médico-Chirurgicale, Hôpital Avicenne, AP - HP, Bobigny, France.,IAME, INSERM, Université de Paris, Paris, France
| | - Melanie Magnan
- IAME, INSERM, Université Paris 13, Bobigny, France.,IAME, INSERM, Université de Paris, Paris, France
| | - Sara Dion
- IAME, INSERM, Université Paris 13, Bobigny, France.,IAME, INSERM, Université de Paris, Paris, France
| | | | - Lucie Bourguignon
- IAME, INSERM, Université de Paris, Paris, France.,École de l'Inserm Liliane Bettencourt, Paris, France
| | - Olivier Tenaillon
- IAME, INSERM, Université Paris 13, Bobigny, France.,IAME, INSERM, Université de Paris, Paris, France
| | - Mathilde Lescat
- IAME, INSERM, Université Paris 13, Bobigny, France.,IAME, INSERM, Université de Paris, Paris, France.,Service de Microbiologie, Hôpital Avicenne, AP - HP, Bobigny, France
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16
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Silva JK, Marques LM, Timenetsky J, de Farias ST. Ureaplasma diversum protein interaction networks: evidence of horizontal gene transfer and evolution of reduced genomes among Mollicutes. Can J Microbiol 2019; 65:596-612. [PMID: 31018106 DOI: 10.1139/cjm-2018-0688] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Ureaplasma diversum is a member of the Mollicutes class responsible for urogenital tract infection in cattle and small ruminants. Studies indicate that the process of horizontal gene transfer, the exchange of genetic material among different species, has a crucial role in mollicute evolution, affecting the group's characteristic genomic reduction process and simplification of metabolic pathways. Using bioinformatics tools and the STRING database of known and predicted protein interactions, we constructed the protein-protein interaction network of U. diversum and compared it with the networks of other members of the Mollicutes class. We also investigated horizontal gene transfer events in subnetworks of interest involved in purine and pyrimidine metabolism and urease function, chosen because of their intrinsic importance for host colonization and virulence. We identified horizontal gene transfer events among Mollicutes and from Ureaplasma to Staphylococcus aureus and Corynebacterium, bacterial groups that colonize the urogenital niche. The overall tendency of genome reduction and simplification in the Mollicutes is echoed in their protein interaction networks, which tend to be more generalized and less selective. Our data suggest that the process was permitted (or enabled) by an increase in host dependence and the available gene repertoire in the urogenital tract shared via horizontal gene transfer.
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Affiliation(s)
- Joana Kästle Silva
- a Department of Molecular Biology, Federal University of Paraíba, João Pessoa, Brazil
| | - Lucas Miranda Marques
- b Multidisciplinary Institute of Health, Universidade Federal da Bahia, Vitória da Conquista, Brazil.,c Department of Microbiology, Institute of Biomedical Science, University of São Paulo, São Paulo, Brazil
| | - Jorge Timenetsky
- c Department of Microbiology, Institute of Biomedical Science, University of São Paulo, São Paulo, Brazil
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17
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Venev SV, Zeldovich KB. Thermophilic Adaptation in Prokaryotes Is Constrained by Metabolic Costs of Proteostasis. Mol Biol Evol 2019; 35:211-224. [PMID: 29106597 PMCID: PMC5850847 DOI: 10.1093/molbev/msx282] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Prokaryotes evolved to thrive in an extremely diverse set of habitats, and their proteomes bear signatures of environmental conditions. Although correlations between amino acid usage and environmental temperature are well-documented, understanding of the mechanisms of thermal adaptation remains incomplete. Here, we couple the energetic costs of protein folding and protein homeostasis to build a microscopic model explaining both the overall amino acid composition and its temperature trends. Low biosynthesis costs lead to low diversity of physical interactions between amino acid residues, which in turn makes proteins less stable and drives up chaperone activity to maintain appropriate levels of folded, functional proteins. Assuming that the cost of chaperone activity is proportional to the fraction of unfolded client proteins, we simulated thermal adaptation of model proteins subject to minimization of the total cost of amino acid synthesis and chaperone activity. For the first time, we predicted both the proteome-average amino acid abundances and their temperature trends simultaneously, and found strong correlations between model predictions and 402 genomes of bacteria and archaea. The energetic constraint on protein evolution is more apparent in highly expressed proteins, selected by codon adaptation index. We found that in bacteria, highly expressed proteins are similar in composition to thermophilic ones, whereas in archaea no correlation between predicted expression level and thermostability was observed. At the same time, thermal adaptations of highly expressed proteins in bacteria and archaea are nearly identical, suggesting that universal energetic constraints prevail over the phylogenetic differences between these domains of life.
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Affiliation(s)
- Sergey V Venev
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, 368 Plantation St, Worcester, MA
| | - Konstantin B Zeldovich
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, 368 Plantation St, Worcester, MA
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18
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Aslam S, Lan XR, Zhang BW, Chen ZL, Wang L, Niu DK. Aerobic prokaryotes do not have higher GC contents than anaerobic prokaryotes, but obligate aerobic prokaryotes have. BMC Evol Biol 2019; 19:35. [PMID: 30691392 PMCID: PMC6350292 DOI: 10.1186/s12862-019-1365-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 01/17/2019] [Indexed: 12/17/2022] Open
Abstract
Background Among the four bases, guanine is the most susceptible to damage from oxidative stress. Replication of DNA containing damaged guanines results in G to T mutations. Therefore, the mutations resulting from oxidative DNA damage are generally expected to predominantly consist of G to T (and C to A when the damaged guanine is not in the reference strand) and result in decreased GC content. However, the opposite pattern was reported 16 years ago in a study of prokaryotic genomes. Although that result has been widely cited and confirmed by nine later studies with similar methods, the omission of the effect of shared ancestry requires a re-examination of the reliability of the results. Results When aerobic and obligate aerobic prokaryotes were mixed together and anaerobic and obligate anaerobic prokaryotes were mixed together, phylogenetic controlled analyses did not detect significant difference in GC content between aerobic and anaerobic prokaryotes. This result is consistent with two generally neglected studied that had accounted for the phylogenetic relationship. However, when obligate aerobic prokaryotes were compared with aerobic prokaryotes, anaerobic prokaryotes, and obligate anaerobic prokaryotes separately using phylogenetic regression analysis, a significant positive association was observed between aerobiosis and GC content, no matter it was calculated from whole genome sequences or the 4-fold degenerate sites of protein-coding genes. Obligate aerobes have significantly higher GC content than aerobes, anaerobes, and obligate anaerobes. Conclusions The positive association between aerobiosis and GC content could be attributed to a mutational force resulting from incorporation of damaged deoxyguanosine during DNA replication rather than oxidation of the guanine nucleotides within DNA sequences. Our results indicate a grade in the aerobiosis-associated mutational force, strong in obligate aerobes, moderate in aerobes, weak in anaerobes and obligate anaerobes. Electronic supplementary material The online version of this article (10.1186/s12862-019-1365-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sidra Aslam
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Xin-Ran Lan
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Bo-Wen Zhang
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Zheng-Lin Chen
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Li Wang
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Deng-Ke Niu
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, 100875, China.
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19
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Sinha I, Woodrow CJ. Forces acting on codon bias in malaria parasites. Sci Rep 2018; 8:15984. [PMID: 30374097 PMCID: PMC6206010 DOI: 10.1038/s41598-018-34404-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 10/16/2018] [Indexed: 11/09/2022] Open
Abstract
Malaria parasite genomes have a range of codon biases, with Plasmodium falciparum one of the most AT-biased genomes known. We examined the make up of synonymous coding sites and stop codons in the core genomes of representative malaria parasites, showing first that local DNA context influences codon bias similarly across P. falciparum, P. vivax and P. berghei, with suppression of CpG dinucleotides and enhancement of CpC dinucleotides, both within and aross codons. Intense asexual phase gene expression in P. falciparum and P. berghei is associated with increased A3:G3 bias but reduced T3:C3 bias at 2-fold sites, consistent with adaptation of codons to tRNA pools and avoidance of wobble tRNA interactions that potentially slow down translation. In highly expressed genes, the A3:G3 ratio can exceed 30-fold while the T3:C3 ratio can be less than 1, according to the encoded amino acid and subsequent base. Lysine codons (AAA/G) show distinctive behaviour with substantially reduced A3:G3 bias in highly expressed genes, perhaps because of selection against frameshifting when the AAA codon is followed by another adenine. Intense expression is also associated with a strong bias towards TAA stop codons (found in 94% and 89% of highly expressed P. falciparum and P. berghei genes respectively) and a proportional rise in the TAAA stop ‘tetranucleotide’. The presence of these expression-linked effects in the relatively AT-rich malaria parasite species adds weight to the suggestion that AT-richness in the Plasmodium genus might be a fitness adaptation. Potential explanations for the relative lack of codon bias in P. vivax include the distinct features of its lifecycle and its effective population size over evolutionary time.
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Affiliation(s)
- I Sinha
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Mahidol University, Bangkok, Thailand.,Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | - C J Woodrow
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Mahidol University, Bangkok, Thailand. .,Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK.
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20
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Bobay LM, Ochman H. Factors driving effective population size and pan-genome evolution in bacteria. BMC Evol Biol 2018; 18:153. [PMID: 30314447 PMCID: PMC6186134 DOI: 10.1186/s12862-018-1272-4] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 10/04/2018] [Indexed: 02/07/2023] Open
Abstract
Background Knowledge of population-level processes is essential to understanding the efficacy of selection operating within a species. However, attempts at estimating effective population sizes (Ne) are particularly challenging in bacteria due to their extremely large census populations sizes, varying rates of recombination and arbitrary species boundaries. Results In this study, we estimated Ne for 153 species (152 bacteria and one archaeon) defined under a common framework and found that ecological lifestyle and growth rate were major predictors of Ne; and that contrary to theoretical expectations, Ne was unaffected by recombination rate. Additionally, we found that Ne shapes the evolution and diversity of total gene repertoires of prokaryotic species. Conclusion Together, these results point to a new model of genome architecture evolution in prokaryotes, in which pan-genome sizes, not individual genome sizes, are governed by drift-barrier evolution. Electronic supplementary material The online version of this article (10.1186/s12862-018-1272-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Louis-Marie Bobay
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78712, USA. .,Department of Biology, University of North Carolina at Greensboro, 321 McIver Street, PO Box 26170, Greensboro, NC, 27402, USA.
| | - Howard Ochman
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78712, USA
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21
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Bohlin J, Eldholm V, Brynildsrud O, Petterson JHO, Alfsnes K. Modeling of the GC content of the substituted bases in bacterial core genomes. BMC Genomics 2018; 19:589. [PMID: 30081825 PMCID: PMC6080486 DOI: 10.1186/s12864-018-4984-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 07/31/2018] [Indexed: 12/13/2022] Open
Abstract
Background The purpose of the present study was to examine the GC content of substituted bases (sbGC) in the core genomes of 35 bacterial species. Each species, or core genome, constituted genomes from at least 10 strains. We also wanted to explore whether sbGC for each strain was associated with the corresponding species’ core genome GC content (cgGC). We present a simple mathematical model that estimates sbGC from cgGC. The model assumes only that the estimated sbGC is a function of cgGC proportional to fixed AT→GC (α) and GC → AT (β) mutation rates. Non-linear regression was used to estimate parameters α and β from the empirical data described above. Results We found that sbGC for each strain showed a non-linear association with the corresponding cgGC with a bias towards higher GC content for most core genomes (66.3% of the strains), assuming as a null-hypothesis that sbGC should be approximately equal to cgGC. The most GC rich core genomes (i.e. approximately %GC > 60), on the other hand, exhibited slightly less GC-biased sbGC than expected. The best fitted regression model indicates that GC → AT mutation rates β = (1.91 ± 0.13) p < 0.001 are approximately (1.91/0.79) = 2.42 times as high, on average, as AT→GC α = (− 0.79 ± 0.25) p < 0.001 mutation rates. Whether the observed sbGC GC-bias for all but the most GC-rich prokaryotic species is due to selection, compensating for the GC → AT mutation bias, and/or selective neutral processes is currently debated. Residual standard error was found to be σ = 0.076 indicating estimated errors of sbGC to be approximately within ±15.2% GC (95% confidence interval) for the strains of all species in the study. Conclusion Not only did our mathematical model give reasonable estimates of sbGC it also provides further support to previous observations that mutation rates in prokaryotes exhibit a universal GC → AT bias that appears to be remarkably consistent between taxa. Electronic supplementary material The online version of this article (10.1186/s12864-018-4984-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jon Bohlin
- Norwegian Institute of Public Health, Lovisenberggata 8, P.O. Box 4404, 0403, Oslo, Norway.
| | - Vegard Eldholm
- Norwegian Institute of Public Health, Lovisenberggata 8, P.O. Box 4404, 0403, Oslo, Norway
| | - Ola Brynildsrud
- Norwegian Institute of Public Health, Lovisenberggata 8, P.O. Box 4404, 0403, Oslo, Norway
| | - John H-O Petterson
- Norwegian Institute of Public Health, Lovisenberggata 8, P.O. Box 4404, 0403, Oslo, Norway
| | - Kristian Alfsnes
- Norwegian Institute of Public Health, Lovisenberggata 8, P.O. Box 4404, 0403, Oslo, Norway
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22
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Dasgupta D, Jasmine J, Mukherji S. Characterization, phylogenetic distribution and evolutionary trajectories of diverse hydrocarbon degrading microorganisms isolated from refinery sludge. 3 Biotech 2018; 8:273. [PMID: 29868311 DOI: 10.1007/s13205-018-1297-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 05/20/2018] [Indexed: 12/01/2022] Open
Abstract
Phylogenic association between bacteria living under harsh conditions can provide important information on adaptive mechanism, survival strategy and their potential application. Indigenous microorganisms isolated from toxic refinery oily sludge with ability to degrade a diverse range of hydrocarbons were identified and characterized. The strains including Pseudomonas aeruginosa RS1, Microbacterium sp. RS2, Bacillus sp. RS3, Acinetobacter baumannii RS4 and Stenotrophomonas sp. RS5 could utilize n-alkanes, cycloalkanes, polynuclear aromatic hydrocarbons (PAHs) with 2-4 rings and also substituted PAHs as sole substrate. The phylogenetic position of Bacillus sp. RS3 and Pseudomonas sp. RS1 was tested by applying the maximum likelihood (ML) method to the aligned 16S rRNA nucleotide sequences of PAH and aliphatic hydrocarbon degrading strains belonging to the corresponding genus. The base substitution matrix created with each set of organisms capable of degrading aromatic and aliphatic hydrocarbons showed significant transitional event with high values of transition: transversion ratio (R) under all conditions. The guanine-cytosine (GC) content of the hydrocarbon degrading test strains was also found to be highest for the clade which harbored them. The test strains consistently occupied a distinct terminal end within the phylogenetic tree constructed by ML analysis. This study reveals that the refinery sludge imposed environmental stress on the bacterial strains which possibly caused significant genetic alteration and phenotypic adaptation. Due to the divergent evolution of the Pseudomonas and Bacillus strains in the sludge, they appeared distinctly different from other hydrocarbon degrading strains of the same genus.
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Affiliation(s)
- Debdeep Dasgupta
- 1Centre for Environmental Science and Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, Maharashtra 400076 India
- 2Present Address: Amity Institute of Biotechnology, Amity University Mumbai, Bhatan, Post-Somathne, Panvel, Mumbai, Maharashtra 410206 India
| | - Jublee Jasmine
- 1Centre for Environmental Science and Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, Maharashtra 400076 India
| | - Suparna Mukherji
- 1Centre for Environmental Science and Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, Maharashtra 400076 India
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23
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Rocha EPC. Neutral Theory, Microbial Practice: Challenges in Bacterial Population Genetics. Mol Biol Evol 2018; 35:1338-1347. [DOI: 10.1093/molbev/msy078] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Eduardo P C Rocha
- Microbial Evolutionary Genomics, Institut Pasteur, Paris, France
- CNRS, UMR3525, Paris, France
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24
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Long H, Sung W, Kucukyildirim S, Williams E, Miller SF, Guo W, Patterson C, Gregory C, Strauss C, Stone C, Berne C, Kysela D, Shoemaker WR, Muscarella ME, Luo H, Lennon JT, Brun YV, Lynch M. Evolutionary determinants of genome-wide nucleotide composition. Nat Ecol Evol 2018; 2:237-240. [PMID: 29292397 PMCID: PMC6855595 DOI: 10.1038/s41559-017-0425-y] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Accepted: 11/21/2017] [Indexed: 12/30/2022]
Abstract
One of the long-standing mysteries of evolutionary genomics is the source of the wide phylogenetic diversity in genome nucleotide composition (G + C versus A + T), which must be a consequence of interspecific differences in mutation bias, the efficiency of selection for different nucleotides or a combination of the two. We demonstrate that although genomic G + C composition is strongly driven by mutation bias, it is also substantially modified by direct selection and/or as a by-product of biased gene conversion. Moreover, G + C composition at fourfold redundant sites is consistently elevated above the neutral expectation-more so than for any other class of sites.
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Affiliation(s)
- Hongan Long
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, China
| | - Way Sung
- Department of Bioinformatics and Genomics, University of North Carolina, Charlotte, NC, USA
| | | | - Emily Williams
- Center for Mechanisms of Evolution, Arizona State University, PO Box 877701, Tempe, AZ, USA
| | - Samuel F Miller
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - Wanfeng Guo
- Center for Mechanisms of Evolution, Arizona State University, PO Box 877701, Tempe, AZ, USA
| | | | - Colin Gregory
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - Chloe Strauss
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - Casey Stone
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - Cécile Berne
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - David Kysela
- Department of Biology, Indiana University, Bloomington, IN, USA
| | | | - Mario E Muscarella
- Department of Plant Biology, University of Illinois, Urbana-Champaign, Champaign, IL, USA
| | - Haiwei Luo
- School of Life Sciences and Partner State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Jay T Lennon
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - Yves V Brun
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - Michael Lynch
- Center for Mechanisms of Evolution, Arizona State University, PO Box 877701, Tempe, AZ, USA.
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25
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Quandt EM, Traverse CC, Ochman H. Local genic base composition impacts protein production and cellular fitness. PeerJ 2018; 6:e4286. [PMID: 29362699 PMCID: PMC5774297 DOI: 10.7717/peerj.4286] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 01/01/2018] [Indexed: 01/25/2023] Open
Abstract
The maintenance of a G + C content that is higher than the mutational input to a genome provides support for the view that selection serves to increase G + C contents in bacteria. Recent experimental evidence from Escherichia coli demonstrated that selection for increasing G + C content operates at the level of translation, but the precise mechanism by which this occurs is unknown. To determine the substrate of selection, we asked whether selection on G + C content acts across all sites within a gene or is confined to particular genic regions or nucleotide positions. We systematically altered the G + C contents of the GFP gene and assayed its effects on the fitness of strains harboring each variant. Fitness differences were attributable to the base compositional variation in the terminal portion of the gene, suggesting a connection to the folding of a specific protein feature. Variants containing sequence features that are thought to result in rapid translation, such as low G + C content and high levels of codon adaptation, displayed highly reduced growth rates. Taken together, our results show that purifying selection acting against A and T mutations most likely results from their tendency to increase the rate of translation, which can perturb the dynamics of protein folding.
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Affiliation(s)
- Erik M Quandt
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, United States of America
| | - Charles C Traverse
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, United States of America
| | - Howard Ochman
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, United States of America
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26
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Shakya M, Soucy SM, Zhaxybayeva O. Insights into origin and evolution of α-proteobacterial gene transfer agents. Virus Evol 2017; 3:vex036. [PMID: 29250433 PMCID: PMC5721377 DOI: 10.1093/ve/vex036] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Several bacterial and archaeal lineages produce nanostructures that morphologically resemble small tailed viruses, but, unlike most viruses, contain apparently random pieces of the host genome. Since these elements can deliver the packaged DNA to other cells, they were dubbed gene transfer agents (GTAs). Because many genes involved in GTA production have viral homologs, it has been hypothesized that the GTA ancestor was a virus. Whether GTAs represent an atypical virus, a defective virus, or a virus co-opted by the prokaryotes for some function, remains to be elucidated. To evaluate these possibilities, we examined the distribution and evolutionary histories of genes that encode a GTA in the α-proteobacterium Rhodobacter capsulatus (RcGTA). We report that although homologs of many individual RcGTA genes are abundant across bacteria and their viruses, RcGTA-like genomes are mainly found in one subclade of α-proteobacteria. When compared with the viral homologs, genes of the RcGTA-like genomes evolve significantly slower, and do not have higher %A+T nucleotides than their host chromosomes. Moreover, they appear to reside in stable regions of the bacterial chromosomes that are generally conserved across taxonomic orders. These findings argue against RcGTA being an atypical or a defective virus. Our phylogenetic analyses suggest that RcGTA ancestor likely originated in the lineage that gave rise to contemporary α-proteobacterial orders Rhizobiales, Rhodobacterales, Caulobacterales, Parvularculales, and Sphingomonadales, and since that time the RcGTA-like element has co-evolved with its host chromosomes. Such evolutionary history is compatible with maintenance of these elements by bacteria due to some selective advantage. As for many other prokaryotic traits, horizontal gene transfer played a substantial role in the evolution of RcGTA-like elements, not only in shaping its genome components within the orders, but also in occasional dissemination of RcGTA-like regions across the orders and even to different bacterial phyla.
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Affiliation(s)
- Migun Shakya
- Department of Biological Sciences, Dartmouth College, 78 College Street, Hanover, NH 03755, USA
| | - Shannon M Soucy
- Department of Biological Sciences, Dartmouth College, 78 College Street, Hanover, NH 03755, USA
| | - Olga Zhaxybayeva
- Department of Biological Sciences, Dartmouth College, 78 College Street, Hanover, NH 03755, USA.,Department of Computer Science, Dartmouth College, 6211 Sudikoff Lab, Hanover, NH 03755, USA
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27
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Abstract
The mutational process in bacteria is biased toward A and T, and most species are GC-rich relative to the mutational input to their genome. It has been proposed that the shift in base composition is an adaptive process-that natural selection operates to increase GC-contents-and there is experimental evidence that bacterial strains with GC-rich versions of genes have higher growth rates than those strains with AT-rich versions expressing identical proteins. Alternatively, a nonadaptive process, GC-biased gene conversion (gBGC), could also increase the GC-content of DNA due to the mechanistic bias of gene conversion events during recombination. To determine what role recombination plays in the base composition of bacterial genomes, we compared the spectrum of nucleotide polymorphisms introduced by recombination in all microbial species represented by large numbers of sequenced strains. We found that recombinant alleles are consistently biased toward A and T, and that the magnitude of AT-bias introduced by recombination is similar to that of mutations. These results indicate that recombination alone, without the intervention of selection, is unlikely to counteract the AT-enrichment of bacterial genomes.
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Affiliation(s)
- Louis-Marie Bobay
- Department of Integrative Biology, University of Texas at Austin, Austin, TX
| | - Howard Ochman
- Department of Integrative Biology, University of Texas at Austin, Austin, TX
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Weinert LA, Welch JJ. Why Might Bacterial Pathogens Have Small Genomes? Trends Ecol Evol 2017; 32:936-947. [PMID: 29054300 DOI: 10.1016/j.tree.2017.09.006] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 09/19/2017] [Accepted: 09/20/2017] [Indexed: 12/31/2022]
Abstract
Bacteria that cause serious disease often have smaller genomes, and fewer genes, than their nonpathogenic, or less pathogenic relatives. Here, we review evidence for the generality of this association, and summarise the various reasons why the association might hold. We focus on the population genetic processes that might lead to reductive genome evolution, and show how several of these could be connected to pathogenicity. We find some evidence for most of the processes having acted in bacterial pathogens, including several different modes of genome reduction acting in the same lineage. We argue that predictable processes of genome evolution might not reflect any common underlying process.
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Affiliation(s)
- Lucy A Weinert
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK.
| | - John J Welch
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
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29
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Abstract
Organisms often encounter stressful conditions, some of which damage their DNA. In response, some organisms show a high expression of error-prone DNA repair machinery, causing a temporary increase in the genome-wide mutation rate. Although we now have a detailed map of the molecular mechanisms underlying such stress-induced mutagenesis (SIM), it has been hotly debated whether SIM alters evolutionary dynamics. Key to this controversy is our poor understanding about which stresses increase mutagenesis and their long-term consequences for adaptation. In a new study with Escherichia coli, Maharjan and Ferenci show that while only some nutritional stresses (phosphorous and carbon limitation) increase total mutation rates, each stress generates a unique spectrum of mutations. Their results suggest the potential for specific stresses to shape evolutionary dynamics and highlight the necessity for explicit tests of the long-term evolutionary impacts of SIM.
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30
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Bobay LM, Ochman H. The Evolution of Bacterial Genome Architecture. Front Genet 2017; 8:72. [PMID: 28611826 PMCID: PMC5447742 DOI: 10.3389/fgene.2017.00072] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 05/12/2017] [Indexed: 11/15/2022] Open
Abstract
The genome architecture of bacteria and eukaryotes evolves in opposite directions when subject to genetic drift, a difference that can be ascribed to the fact that bacteria exhibit a mutational bias that deletes superfluous sequences, whereas eukaryotes are biased toward large insertions. Expansion of eukaryotic genomes occurs through the addition of non-functional sequences, such as repetitive sequences and transposable elements, whereas variation in bacterial genome size is largely due to the acquisition and loss of functional accessory genes. These properties create the situation in which eukaryotes with very similar numbers of genes can have vastly different genome sizes, while in bacteria, gene number scales linearly with genome size. Some bacterial genomes, however, particularly those of species that undergo bottlenecks due to recent association with hosts, accumulate pseudogenes and mobile elements, conferring them a low gene content relative to their genome size. These non-functional sequences are gradually eroded and eliminated after long-term association with hosts, with the result that obligate symbionts have the smallest genomes of any cellular organism. The architecture of bacterial genomes is shaped by complex and diverse processes, but for most bacterial species, genome size is governed by a non-adaptive process, i.e., genetic drift coupled with a mutational bias toward deletions. Thus, bacteria with small effective population sizes typically have the smallest genomes. Some marine bacteria counter this near-universal trend: despite having immense population sizes, selection, not drift, acts to reduce genome size in response to metabolic constraints in their nutrient-limited environment.
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Affiliation(s)
- Louis-Marie Bobay
- Department of Integrative Biology, University of Texas, AustinTX, United States
| | - Howard Ochman
- Department of Integrative Biology, University of Texas, AustinTX, United States
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31
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Comparative Analyses of Selection Operating on Nontranslated Intergenic Regions of Diverse Bacterial Species. Genetics 2017; 206:363-376. [PMID: 28280056 DOI: 10.1534/genetics.116.195784] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 02/26/2017] [Indexed: 12/31/2022] Open
Abstract
Nontranslated intergenic regions (IGRs) compose 10-15% of bacterial genomes, and contain many regulatory elements with key functions. Despite this, there are few systematic studies on the strength and direction of selection operating on IGRs in bacteria using whole-genome sequence data sets. Here we exploit representative whole-genome data sets from six diverse bacterial species: Staphylococcus aureus, Streptococcus pneumoniae, Mycobacterium tuberculosis, Salmonella enterica, Klebsiella pneumoniae, and Escherichia coli We compare patterns of selection operating on IGRs using two independent methods: the proportion of singleton mutations and the dI/dS ratio, where dI is the number of intergenic SNPs per intergenic site. We find that the strength of purifying selection operating over all intergenic sites is consistently intermediate between that operating on synonymous and nonsynonymous sites. Ribosome binding sites and noncoding RNAs tend to be under stronger selective constraint than promoters and Rho-independent terminators. Strikingly, a clear signal of purifying selection remains even when all these major categories of regulatory elements are excluded, and this constraint is highest immediately upstream of genes. While a paucity of variation means that the data for M. tuberculosis are more equivocal than for the other species, we find strong evidence for positive selection within promoters of this species. This points to a key adaptive role for regulatory changes in this important pathogen. Our study underlines the feasibility and utility of gauging the selective forces operating on bacterial IGRs from whole-genome sequence data, and suggests that our current understanding of the functionality of these sequences is far from complete.
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Bohlin J, Eldholm V, Pettersson JHO, Brynildsrud O, Snipen L. The nucleotide composition of microbial genomes indicates differential patterns of selection on core and accessory genomes. BMC Genomics 2017; 18:151. [PMID: 28187704 PMCID: PMC5303225 DOI: 10.1186/s12864-017-3543-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 02/02/2017] [Indexed: 12/02/2022] Open
Abstract
Background The core genome consists of genes shared by the vast majority of a species and is therefore assumed to have been subjected to substantially stronger purifying selection than the more mobile elements of the genome, also known as the accessory genome. Here we examine intragenic base composition differences in core genomes and corresponding accessory genomes in 36 species, represented by the genomes of 731 bacterial strains, to assess the impact of selective forces on base composition in microbes. We also explore, in turn, how these results compare with findings for whole genome intragenic regions. Results We found that GC content in coding regions is significantly higher in core genomes than accessory genomes and whole genomes. Likewise, GC content variation within coding regions was significantly lower in core genomes than in accessory genomes and whole genomes. Relative entropy in coding regions, measured as the difference between observed and expected trinucleotide frequencies estimated from mononucleotide frequencies, was significantly higher in the core genomes than in accessory and whole genomes. Relative entropy was positively associated with coding region GC content within the accessory genomes, but not within the corresponding coding regions of core or whole genomes. Conclusion The higher intragenic GC content and relative entropy, as well as the lower GC content variation, observed in the core genomes is most likely associated with selective constraints. It is unclear whether the positive association between GC content and relative entropy in the more mobile accessory genomes constitutes signatures of selection or selective neutral processes. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3543-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jon Bohlin
- Infectious Disease Control and Environmental Health, Norwegian Institute of Public Health, Lovisenberggata 8, P.O. Box 4404, 0403, Oslo, Norway.
| | - Vegard Eldholm
- Infectious Disease Control and Environmental Health, Norwegian Institute of Public Health, Lovisenberggata 8, P.O. Box 4404, 0403, Oslo, Norway
| | - John H O Pettersson
- Infectious Disease Control and Environmental Health, Norwegian Institute of Public Health, Lovisenberggata 8, P.O. Box 4404, 0403, Oslo, Norway
| | - Ola Brynildsrud
- Infectious Disease Control and Environmental Health, Norwegian Institute of Public Health, Lovisenberggata 8, P.O. Box 4404, 0403, Oslo, Norway
| | - Lars Snipen
- Department of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, 1430, Ås, Norway
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Satapathy SS, Sahoo AK, Ray SK, Ghosh TC. Codon degeneracy and amino acid abundance influence the measures of codon usage bias: improved Nc (N̂c) and ENCprime (N̂′c) measures. Genes Cells 2017; 22:277-283. [DOI: 10.1111/gtc.12474] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 01/02/2017] [Indexed: 01/22/2023]
Affiliation(s)
| | - Ajit Kumar Sahoo
- Department of Molecular Biology and Biotechnology; Tezpur University; Napaam Tezpur 784028 Assam India
| | - Suvendra Kumar Ray
- Department of Molecular Biology and Biotechnology; Tezpur University; Napaam Tezpur 784028 Assam India
| | - Tapash Chandra Ghosh
- Bioinformatics Centre; Bose Institute; P-1/12, C.I.T. Scheme VII M Kolkata 700054 India
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Seward EA, Kelly S. Dietary nitrogen alters codon bias and genome composition in parasitic microorganisms. Genome Biol 2016; 17:226. [PMID: 27842572 PMCID: PMC5109750 DOI: 10.1186/s13059-016-1087-9] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 10/12/2016] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Genomes are composed of long strings of nucleotide monomers (A, C, G and T) that are either scavenged from the organism's environment or built from metabolic precursors. The biosynthesis of each nucleotide differs in atomic requirements with different nucleotides requiring different quantities of nitrogen atoms. However, the impact of the relative availability of dietary nitrogen on genome composition and codon bias is poorly understood. RESULTS Here we show that differential nitrogen availability, due to differences in environment and dietary inputs, is a major determinant of genome nucleotide composition and synonymous codon use in both bacterial and eukaryotic microorganisms. Specifically, low nitrogen availability species use nucleotides that require fewer nitrogen atoms to encode the same genes compared to high nitrogen availability species. Furthermore, we provide a novel selection-mutation framework for the evaluation of the impact of metabolism on gene sequence evolution and show that it is possible to predict the metabolic inputs of related organisms from an analysis of the raw nucleotide sequence of their genes. CONCLUSIONS Taken together, these results reveal a previously hidden relationship between cellular metabolism and genome evolution and provide new insight into how genome sequence evolution can be influenced by adaptation to different diets and environments.
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Affiliation(s)
- Emily A Seward
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Steven Kelly
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK.
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35
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Pouyet F, Bailly-Bechet M, Mouchiroud D, Guéguen L. SENCA: A Multilayered Codon Model to Study the Origins and Dynamics of Codon Usage. Genome Biol Evol 2016; 8:2427-41. [PMID: 27401173 PMCID: PMC5010899 DOI: 10.1093/gbe/evw165] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Gene sequences are the target of evolution operating at different levels, including the nucleotide, codon, and amino acid levels. Disentangling the impact of those different levels on gene sequences requires developing a probabilistic model with three layers. Here we present SENCA (site evolution of nucleotides, codons, and amino acids), a codon substitution model that separately describes 1) nucleotide processes which apply on all sites of a sequence such as the mutational bias, 2) preferences between synonymous codons, and 3) preferences among amino acids. We argue that most synonymous substitutions are not neutral and that SENCA provides more accurate estimates of selection compared with more classical codon sequence models. We study the forces that drive the genomic content evolution, intraspecifically in the core genome of 21 prokaryotes and interspecifically for five Enterobacteria. We retrieve the existence of a universal mutational bias toward AT, and that taking into account selection on synonymous codon usage has consequences on the measurement of selection on nonsynonymous substitutions. We also confirm that codon usage bias is mostly driven by selection on preferred codons. We propose new summary statistics to measure the relative importance of the different evolutionary processes acting on sequences.
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Affiliation(s)
- Fanny Pouyet
- Laboratoire de Biologie et Biométrie Evolutive, University Claude Bernard Lyon 1-University of Lyon, Villeurbanne, France
| | - Marc Bailly-Bechet
- Laboratoire de Biologie et Biométrie Evolutive, University Claude Bernard Lyon 1-University of Lyon, Villeurbanne, France
| | - Dominique Mouchiroud
- Laboratoire de Biologie et Biométrie Evolutive, University Claude Bernard Lyon 1-University of Lyon, Villeurbanne, France
| | - Laurent Guéguen
- Laboratoire de Biologie et Biométrie Evolutive, University Claude Bernard Lyon 1-University of Lyon, Villeurbanne, France
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36
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Lapierre M, Blin C, Lambert A, Achaz G, Rocha EPC. The Impact of Selection, Gene Conversion, and Biased Sampling on the Assessment of Microbial Demography. Mol Biol Evol 2016; 33:1711-25. [PMID: 26931140 PMCID: PMC4915353 DOI: 10.1093/molbev/msw048] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Recent studies have linked demographic changes and epidemiological patterns in bacterial populations using coalescent-based approaches. We identified 26 studies using skyline plots and found that 21 inferred overall population expansion. This surprising result led us to analyze the impact of natural selection, recombination (gene conversion), and sampling biases on demographic inference using skyline plots and site frequency spectra (SFS). Forward simulations based on biologically relevant parameters from Escherichia coli populations showed that theoretical arguments on the detrimental impact of recombination and especially natural selection on the reconstructed genealogies cannot be ignored in practice. In fact, both processes systematically lead to spurious interpretations of population expansion in skyline plots (and in SFS for selection). Weak purifying selection, and especially positive selection, had important effects on skyline plots, showing patterns akin to those of population expansions. State-of-the-art techniques to remove recombination further amplified these biases. We simulated three common sampling biases in microbiological research: uniform, clustered, and mixed sampling. Alone, or together with recombination and selection, they further mislead demographic inferences producing almost any possible skyline shape or SFS. Interestingly, sampling sub-populations also affected skyline plots and SFS, because the coalescent rates of populations and their sub-populations had different distributions. This study suggests that extreme caution is needed to infer demographic changes solely based on reconstructed genealogies. We suggest that the development of novel sampling strategies and the joint analyzes of diverse population genetic methods are strictly necessary to estimate demographic changes in populations where selection, recombination, and biased sampling are present.
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Affiliation(s)
- Marguerite Lapierre
- Atelier de Bioinformatique, UMR7205 ISYEB, MNHN-UPMC-CNRS-EPHE, Muséum National d'Histoire Naturelle, Paris, France Collège de France, Center for Interdisciplinary Research in Biology (CIRB), CNRS UMR 7241, Paris, France
| | - Camille Blin
- Sorbonne Universités, UPMC Univ Paris06, IFD, 4 Place Jussieu, Paris Cedex05, France Institut Pasteur, Microbial Evolutionary Genomics, Paris, France CNRS, UMR3525, Paris, France
| | - Amaury Lambert
- Collège de France, Center for Interdisciplinary Research in Biology (CIRB), CNRS UMR 7241, Paris, France UPMC Univ Paris 06, Laboratoire de Probabilités et Modèles Aléatoires (LPMA), CNRS UMR 7599, Paris, France
| | - Guillaume Achaz
- Atelier de Bioinformatique, UMR7205 ISYEB, MNHN-UPMC-CNRS-EPHE, Muséum National d'Histoire Naturelle, Paris, France Collège de France, Center for Interdisciplinary Research in Biology (CIRB), CNRS UMR 7241, Paris, France
| | - Eduardo P C Rocha
- Institut Pasteur, Microbial Evolutionary Genomics, Paris, France CNRS, UMR3525, Paris, France
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37
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Dettman JR, Sztepanacz JL, Kassen R. The properties of spontaneous mutations in the opportunistic pathogen Pseudomonas aeruginosa. BMC Genomics 2016; 17:27. [PMID: 26732503 PMCID: PMC4702332 DOI: 10.1186/s12864-015-2244-3] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 11/25/2015] [Indexed: 12/23/2022] Open
Abstract
Background Natural genetic variation ultimately arises from the process of mutation. Knowledge of how the raw material for evolution is produced is necessary for a full understanding of several fundamental evolutionary concepts. We performed a mutation accumulation experiment with wild-type and mismatch-repair deficient, mutator lines of the pathogenic bacterium Pseudomonas aeruginosa, and used whole-genome sequencing to reveal the genome-wide rate, spectrum, distribution, leading/lagging bias, and context-dependency of spontaneous mutations. Results Wild-type base-pair mutation and indel rates were ~10−10 and ~10−11 per nucleotide per generation, respectively, and deficiencies in the mismatch-repair system caused rates to increase by over two orders of magnitude. A universal bias towards AT was observed in wild-type lines, but was reversed in mutator lines to a bias towards GC. Biases for which types of mutations occurred during replication of the leading versus lagging strand were detected reciprocally in both replichores. The distribution of mutations along the chromosome was non-random, with peaks near the terminus of replication and at positions intermediate to the replication origin and terminus. A similar distribution bias was observed along the chromosome in natural populations of P. aeruginosa. Site-specific mutation rates were higher when the focal nucleotide was immediately flanked by C:G pairings. Conclusions Whole-genome sequencing of mutation accumulation lines allowed the comprehensive identification of mutations and revealed what factors of molecular and genomic architecture affect the mutational process. Our study provides a more complete view of how several mechanisms of mutation, mutation repair, and bias act simultaneously to produce the raw material for evolution. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2244-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jeremy R Dettman
- Department of Biology and Centre for Advanced Research in Environmental Genomics, University of Ottawa, Ottawa, ON, K1N 6N5, Canada.
| | | | - Rees Kassen
- Department of Biology and Centre for Advanced Research in Environmental Genomics, University of Ottawa, Ottawa, ON, K1N 6N5, Canada.
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38
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Supek F. The Code of Silence: Widespread Associations Between Synonymous Codon Biases and Gene Function. J Mol Evol 2015; 82:65-73. [PMID: 26538122 DOI: 10.1007/s00239-015-9714-8] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2015] [Accepted: 10/30/2015] [Indexed: 02/07/2023]
Abstract
Some mutations in gene coding regions exchange one synonymous codon for another, and thus do not alter the amino acid sequence of the encoded protein. Even though they are often called 'silent,' these mutations may exhibit a plethora of effects on the living cell. Therefore, they are often selected during evolution, causing synonymous codon usage biases in genomes. Comparative analyses of bacterial, archaeal, fungal, and human cancer genomes have found many links between a gene's biological role and the accrual of synonymous mutations during evolution. In particular, highly expressed genes in certain functional categories are enriched with optimal codons, which are decoded by the abundant tRNAs, thus enhancing the speed and accuracy of the translating ribosome. The set of genes exhibiting codon adaptation differs between genomes, and these differences show robust associations to organismal phenotypes. In addition to selection for translation efficiency, other distinct codon bias patterns have been found in: amino acid starvation genes, cyclically expressed genes, tissue-specific genes in animals and plants, oxidative stress response genes, cellular differentiation genes, and oncogenes. In addition, genomes of organisms harboring tRNA modifications exhibit particular codon preferences. The evolutionary trace of codon bias patterns across orthologous genes may be examined to learn about a gene's relevance to various phenotypes, or, more generally, its function in the cell.
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Affiliation(s)
- Fran Supek
- Division of electronics, Rudjer Boskovic Institute, 10000, Zagreb, Croatia.
- EMBL-CRG Systems Biology Unit, Centre for Genomic Regulation (CRG), 08003, Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain.
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39
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Bohlin J. Genome expansion in bacteria: the curios case of Chlamydia trachomatis. BMC Res Notes 2015; 8:512. [PMID: 26423146 PMCID: PMC4589037 DOI: 10.1186/s13104-015-1464-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 09/21/2015] [Indexed: 11/23/2022] Open
Abstract
Background Recent findings indicated that a correlation between genomic % AT and genome size within strains of microbial species was predominantly associated with the uptake of foreign DNA. One species however, Chlamydia trachomatis, defied any explanation. In the present study 79 fully sequenced C. trachomatis genomes, representing ocular- (nine strains), urogenital- (36 strains) and lymphogranuloma venereum strains (LGV, 22 strains), in three pathogroups, in addition to 12 laboratory isolates, were scrutinized with the intent of elucidating the positive correlation between genomic AT content and genome size. Results The average size difference between the strains of each pathogroup was largely explained by the incorporation of genetic fragments. These fragments were slightly more AT rich than their corresponding host genomes, but not enough to justify the difference in AT content between the strains of the smaller genomes lacking the fragments. In addition, a genetic region predominantly found in the ocular strains, which had the largest genomes, was on average more GC rich than the host genomes of the urogenital strains (58.64 % AT vs. 58.69 % AT), which had the second largest genomes, implying that the foreign genetic regions cannot alone explain the association between genome size and AT content in C. trachomatis. 23,492 SNPs were identified for all 79 genomes, and although the SNPs were on average slightly GC rich (~47 % AT), a significant association was found between genome-wide SNP AT content, for each pathogroup, and genome size (p < 0.001, R2 = 0.86) in the C. trachomatis strains. Conclusions The correlation between genome size and AT content, with respect to the C. trachomatis pathogroups, was explained by the incorporation of genetic fragments unique to the ocular and/or urogenital strains into the LGV- and urogential strains in addition to the genome-wide SNP AT content differences between the three pathogroups. Electronic supplementary material The online version of this article (doi:10.1186/s13104-015-1464-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jon Bohlin
- Department of Bacteriology and Immunology, Norwegian Institute of Public Health, Lovisenberggata 6, P.O. Box 4404, 0403, Oslo, Norway.
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40
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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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41
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Luo H, Thompson LR, Stingl U, Hughes AL. Selection Maintains Low Genomic GC Content in Marine SAR11 Lineages. Mol Biol Evol 2015; 32:2738-48. [DOI: 10.1093/molbev/msv149] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
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42
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Brbić M, Warnecke T, Kriško A, Supek F. Global Shifts in Genome and Proteome Composition Are Very Tightly Coupled. Genome Biol Evol 2015; 7:1519-32. [PMID: 25971281 PMCID: PMC4494046 DOI: 10.1093/gbe/evv088] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/09/2015] [Indexed: 02/05/2023] Open
Abstract
The amino acid composition (AAC) of proteomes differs greatly between microorganisms and is associated with the environmental niche they inhabit, suggesting that these changes may be adaptive. Similarly, the oligonucleotide composition of genomes varies and may confer advantages at the DNA/RNA level. These influences overlap in protein-coding sequences, making it difficult to gauge their relative contributions. We disentangle these effects by systematically evaluating the correspondence between intergenic nucleotide composition, where protein-level selection is absent, the AAC, and ecological parameters of 909 prokaryotes. We find that G + C content, the most frequently used measure of genomic composition, cannot capture diversity in AAC and across ecological contexts. However, di-/trinucleotide composition in intergenic DNA predicts amino acid frequencies of proteomes to the point where very little cross-species variability remains unexplained (91% of variance accounted for). Qualitatively similar results were obtained for 49 fungal genomes, where 80% of the variability in AAC could be explained by the composition of introns and intergenic regions. Upon factoring out oligonucleotide composition and phylogenetic inertia, the residual AAC is poorly predictive of the microbes' ecological preferences, in stark contrast with the original AAC. Moreover, highly expressed genes do not exhibit more prominent environment-related AAC signatures than lowly expressed genes, despite contributing more to the effective proteome. Thus, evolutionary shifts in overall AAC appear to occur almost exclusively through factors shaping the global oligonucleotide content of the genome. We discuss these results in light of contravening evidence from biophysical data and further reading frame-specific analyses that suggest that adaptation takes place at the protein level.
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Affiliation(s)
- Maria Brbić
- Division of Electronics, Rudjer Boskovic Institute, Zagreb, Croatia Molecular Basis of Ageing, Mediterranean Institute for Life Sciences (MedILS), Split, Croatia
| | - Tobias Warnecke
- MRC Clinical Sciences Centre, Imperial College, Hammersmith Campus, London, United Kingdom
| | - Anita Kriško
- Molecular Basis of Ageing, Mediterranean Institute for Life Sciences (MedILS), Split, Croatia
| | - Fran Supek
- Division of Electronics, Rudjer Boskovic Institute, Zagreb, Croatia EMBL/CRG Systems Biology Unit, Centre for Genomic Regulation, Barcelona, Spain
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Abstract
The source and significance of the wide variation in the genomic base composition of bacteria have been a matter of continued debate. Although the variation was originally attributed to a strictly neutral process, i.e., species-specific differences in mutational patterns, recent genomic comparisons have shown that bacteria with G+C-rich genomes experience a mutational bias toward A+T. This difference between the mutational input to a genome and its overall base composition suggests the action of natural selection. Here, we examine if selection acts on G+C contents in Caulobacter crescentus and Pseudomonas aeruginosa, which both have very G+C-rich genomes, by testing whether the expression of gene variants that differ only in their base compositions at synonymous sites affects cellular growth rates. In C. crescentus, expression of the more A+T-rich gene variants decelerated growth, indicating that selection on genic base composition is, in part, responsible for the high G+C content of this genome. In contrast, no comparable effect was observed in P. aeruginosa, which has similarly high genome G+C contents. Selection for increased genic G+C-contents in C. crescentus acts independently of the species-specific codon usage pattern and represents an additional selective force operating in bacterial genomes.
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Wernegreen JJ. Endosymbiont evolution: predictions from theory and surprises from genomes. Ann N Y Acad Sci 2015; 1360:16-35. [PMID: 25866055 DOI: 10.1111/nyas.12740] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Revised: 01/27/2015] [Accepted: 02/11/2015] [Indexed: 10/23/2022]
Abstract
Genome data have created new opportunities to untangle evolutionary processes shaping microbial variation. Among bacteria, long-term mutualists of insects represent the smallest and (typically) most AT-rich genomes. Evolutionary theory provides a context to predict how an endosymbiotic lifestyle may alter fundamental evolutionary processes--mutation, selection, genetic drift, and recombination--and thus contribute to extreme genomic outcomes. These predictions can then be explored by comparing evolutionary rates, genome size and stability, and base compositional biases across endosymbiotic and free-living bacteria. Recent surprises from such comparisons include genome reduction among uncultured, free-living species. Some studies suggest that selection generally drives this streamlining, while drift drives genome reduction in endosymbionts; however, this remains an hypothesis requiring additional data. Unexpected evidence of selection acting on endosymbiont GC content hints that even weak selection may be effective in some long-term mutualists. Moving forward, intraspecific analysis offers a promising approach to distinguish underlying mechanisms, by testing the null hypothesis of neutrality and by quantifying mutational spectra. Such analyses may clarify whether endosymbionts and free-living bacteria occupy distinct evolutionary trajectories or, alternatively, represent varied outcomes of similar underlying forces.
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Affiliation(s)
- Jennifer J Wernegreen
- Nicholas School of the Environment and Center for Genomic and Computational Biology, Duke University, Durham, North Carolina
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Lassalle F, Périan S, Bataillon T, Nesme X, Duret L, Daubin V. GC-Content evolution in bacterial genomes: the biased gene conversion hypothesis expands. PLoS Genet 2015; 11:e1004941. [PMID: 25659072 PMCID: PMC4450053 DOI: 10.1371/journal.pgen.1004941] [Citation(s) in RCA: 135] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Accepted: 12/08/2014] [Indexed: 11/29/2022] Open
Abstract
The characterization of functional elements in genomes relies on the identification of the footprints of natural selection. In this quest, taking into account neutral evolutionary processes such as mutation and genetic drift is crucial because these forces can generate patterns that may obscure or mimic signatures of selection. In mammals, and probably in many eukaryotes, another such confounding factor called GC-Biased Gene Conversion (gBGC) has been documented. This mechanism generates patterns identical to what is expected under selection for higher GC-content, specifically in highly recombining genomic regions. Recent results have suggested that a mysterious selective force favouring higher GC-content exists in Bacteria but the possibility that it could be gBGC has been excluded. Here, we show that gBGC is probably at work in most if not all bacterial species. First we find a consistent positive relationship between the GC-content of a gene and evidence of intra-genic recombination throughout a broad spectrum of bacterial clades. Second, we show that the evolutionary force responsible for this pattern is acting independently from selection on codon usage, and could potentially interfere with selection in favor of optimal AU-ending codons. A comparison with data from human populations shows that the intensity of gBGC in Bacteria is comparable to what has been reported in mammals. We propose that gBGC is not restricted to sexual Eukaryotes but also widespread among Bacteria and could therefore be an ancestral feature of cellular organisms. We argue that if gBGC occurs in bacteria, it can account for previously unexplained observations, such as the apparent non-equilibrium of base substitution patterns and the heterogeneity of gene composition within bacterial genomes. Because gBGC produces patterns similar to positive selection, it is essential to take this process into account when studying the evolutionary forces at work in bacterial genomes. Classical population genetics models indicate that the efficiency of selection, and hence adaptation, depends on a number of non-selective factors, such as the size of a population or the intensity of recombination. In the last 10 years, evidence has accumulated that another mechanism called GC-Biased Gene Conversion (gBGC) can interfere with selection and even mimic its effects. This phenomenon, which arises from a particularity of the recombination machinery, was first thought to be restricted to sexual eukaryotic organisms. Here, we show that this mechanism probably exists in Bacteria and has a strong impact on their genome evolution. This discovery not only explains many previously unconnected features of bacterial genome evolution, but also highlights the importance of non-adaptive evolutionary processes in Bacteria.
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Affiliation(s)
- Florent Lassalle
- Université de Lyon, Lyon, France
- Université Lyon 1, Villeurbanne, France
- CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, Villeurbanne, France
- CNRS, UMR 5557, Ecologie Microbienne, Villeurbanne, France
- INRA, USC 1364, Ecologie Microbienne, Villeurbanne, France
- Ecole Normale Supérieure de Lyon, Lyon, France
| | - Séverine Périan
- Université de Lyon, Lyon, France
- Université Lyon 1, Villeurbanne, France
- CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, Villeurbanne, France
| | - Thomas Bataillon
- Aarhus University, Bioinformatics Research Center, Århus Denmark1 Université de Lyon, Lyon, France
| | - Xavier Nesme
- Université de Lyon, Lyon, France
- Université Lyon 1, Villeurbanne, France
- CNRS, UMR 5557, Ecologie Microbienne, Villeurbanne, France
- INRA, USC 1364, Ecologie Microbienne, Villeurbanne, France
| | - Laurent Duret
- Université de Lyon, Lyon, France
- Université Lyon 1, Villeurbanne, France
- CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, Villeurbanne, France
| | - Vincent Daubin
- Université de Lyon, Lyon, France
- Université Lyon 1, Villeurbanne, France
- CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, Villeurbanne, France
- * E-mail:
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46
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Goncearenco A, Berezovsky IN. The fundamental tradeoff in genomes and proteomes of prokaryotes established by the genetic code, codon entropy, and physics of nucleic acids and proteins. Biol Direct 2014; 9:29. [PMID: 25496919 PMCID: PMC4273451 DOI: 10.1186/s13062-014-0029-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 12/01/2014] [Indexed: 11/26/2022] Open
Abstract
Background Mutations in nucleotide sequences provide a foundation for genetic variability, and selection is the driving force of the evolution and molecular adaptation. Despite considerable progress in the understanding of selective forces and their compositional determinants, the very nature of underlying mutational biases remains unclear. Results We explore here a fundamental tradeoff, which analytically describes mutual adjustment of the nucleotide and amino acid compositions and its possible effect on the mutational biases. The tradeoff is determined by the interplay between the genetic code, optimization of the codon entropy, and demands on the structure and stability of nucleic acids and proteins. Conclusion The tradeoff is the unifying property of all prokaryotes regardless of the differences in their phylogenies, life styles, and extreme environments. It underlies mutational biases characteristic for genomes with different nucleotide and amino acid compositions, providing foundation for evolution and adaptation. Reviewers This article was reviewed by Eugene Koonin, Michael Gromiha, and Alexander Schleiffer. Electronic supplementary material The online version of this article (doi:10.1186/s13062-014-0029-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alexander Goncearenco
- Computational Biology Unit and Department of Informatics, University of Bergen, N-5008, Bergen, Norway. .,Current address: Computational Biology Branch of the National Center for Biotechnology Information in Bethesda, Maryland, USA.
| | - Igor N Berezovsky
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, Singapore, 138671, Singapore. .,Department of Biological Sciences (DBS), National University of Singapore (NUS), 8 Medical Drive, 117597, Singapore, Singapore.
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Bohlin J, Brynildsrud OB, Sekse C, Snipen L. An evolutionary analysis of genome expansion and pathogenicity in Escherichia coli. BMC Genomics 2014; 15:882. [PMID: 25297974 PMCID: PMC4200225 DOI: 10.1186/1471-2164-15-882] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 09/29/2014] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND There are several studies describing loss of genes through reductive evolution in microbes, but how selective forces are associated with genome expansion due to horizontal gene transfer (HGT) has not received similar attention. The aim of this study was therefore to examine how selective pressures influence genome expansion in 53 fully sequenced and assembled Escherichia coli strains. We also explored potential connections between genome expansion and the attainment of virulence factors. This was performed using estimations of several genomic parameters such as AT content, genomic drift (measured using relative entropy), genome size and estimated HGT size, which were subsequently compared to analogous parameters computed from the core genome consisting of 1729 genes common to the 53 E. coli strains. Moreover, we analyzed how selective pressures (quantified using relative entropy and dN/dS), acting on the E. coli core genome, influenced lineage and phylogroup formation. RESULTS Hierarchical clustering of dS and dN estimations from the E. coli core genome resulted in phylogenetic trees with topologies in agreement with known E. coli taxonomy and phylogroups. High values of dS, compared to dN, indicate that the E. coli core genome has been subjected to substantial purifying selection over time; significantly more than the non-core part of the genome (p<0.001). This is further supported by a linear association between strain-wise dS and dN values (β = 26.94 ± 0.44, R2~0.98, p<0.001). The non-core part of the genome was also significantly more AT-rich (p<0.001) than the core genome and E. coli genome size correlated with estimated HGT size (p<0.001). In addition, genome size (p<0.001), AT content (p<0.001) as well as estimated HGT size (p<0.005) were all associated with the presence of virulence factors, suggesting that pathogenicity traits in E. coli are largely attained through HGT. No associations were found between selective pressures operating on the E. coli core genome, as estimated using relative entropy, and genome size (p~0.98). CONCLUSIONS On a larger time frame, genome expansion in E. coli, which is significantly associated with the acquisition of virulence factors, appears to be independent of selective forces operating on the core genome.
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Affiliation(s)
- Jon Bohlin
- Division of Epidemiology, Norwegian Institute of Public Health, Marcus Thranes gate 6, P,O, Box 4404, Oslo 0403, Norway.
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Merhej V, Angelakis E, Socolovschi C, Raoult D. Genotyping, evolution and epidemiological findings of Rickettsia species. INFECTION GENETICS AND EVOLUTION 2014; 25:122-37. [DOI: 10.1016/j.meegid.2014.03.014] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Revised: 03/10/2014] [Accepted: 03/12/2014] [Indexed: 01/12/2023]
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Botha AM, Burger NFV, Van Eck L. Hypervirulent Diuraphis noxia (Hemiptera: Aphididae) biotype SAM avoids triggering defenses in its host (Triticum aestivum) (Poales: Poaceae) during feeding. ENVIRONMENTAL ENTOMOLOGY 2014; 43:672-81. [PMID: 24874154 DOI: 10.1603/en13331] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
In the molecular arms race between aphids and plants, both organisms rely on adaptive strategies to outcompete their evolutionary rival. In the current study, we investigated the difference in elicited defense responses of wheat (Triticum aestivum L.) near-isogenic lines with different Dn resistance genes, upon feeding by an avirulent and hypervirulent Diuraphis noxia Kurdjumov biotype. After measuring the activity of a suite of enzymes associated with plant defense, it became apparent that the host does not recognize the invasion by the hypervirulent aphid because none of these were induced, while feeding by the avirulent biotype did result in induction of enzyme activity. Genomic plasticity in D. noxia may be a likely explanation for the observed differences in virulence between D. noxia biotype SA1 and SAM, as demonstrated in the current study.
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Affiliation(s)
- Anna-Maria Botha
- Genetics Department, Stellenbosch University, Private Bag X1, Matieland, 7601, South Africa
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50
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Bohlin J, Sekse C, Skjerve E, Brynildsrud O. Positive correlations between genomic %AT and genome size within strains of bacterial species. ENVIRONMENTAL MICROBIOLOGY REPORTS 2014; 6:278-286. [PMID: 24983532 DOI: 10.1111/1758-2229.12145] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Accepted: 12/23/2013] [Indexed: 06/03/2023]
Abstract
Genomic %AT has been found to correlate negatively with genome size in microbes. While microbes with large genomes are often GC rich and free living, AT-rich bacteria tend to be host associated with smaller genomes. With over 2000 fully sequenced and assembled microbial genomes available, we explored the relationship among genomic %AT, genome size, relative entropy (a measure associated with genetic drift) and fraction of genome islands (GIs) in microbial species with the genomes of more than 10 strains available. A negative correlation with genome size was found in six out of 12 phylogenetic groups and subphyla and a positive correlation in only two. At the species level, we found a trend of positive correlations between genomic %AT and genome size in eight out of 20 species, while only four showed a negative correlation. Estimated chromosomal fractions of GIs were found to correlate positively with genome size in the strains of 14 out of 18 species and genomic %AT in the strains of seven species (two correlated negatively). Although GIs explain most of the observed positive correlations between genomic %AT and size, Chlamydia trachomatis seem to be an exception; therefore, these findings needs to be further explored.
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Affiliation(s)
- Jon Bohlin
- Division of Epidemiology, Norwegian Institute of Public Health, Marcus Thranes Gate 6, P.O. Box 4404, 0403, Oslo, Norway; Epi-Centre, Department of Food-Safety and Infection Biology, Norwegian School of Veterinary Science, Ullevålsveien 72, P.O. Box 8146 Dep, NO-0033, Oslo, Norway
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