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Lund D, Coertze RD, Parras-Moltó M, Berglund F, Flach CF, Johnning A, Larsson DGJ, Kristiansson E. Extensive screening reveals previously undiscovered aminoglycoside resistance genes in human pathogens. Commun Biol 2023; 6:812. [PMID: 37537271 PMCID: PMC10400643 DOI: 10.1038/s42003-023-05174-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 07/24/2023] [Indexed: 08/05/2023] Open
Abstract
Antibiotic resistance is a growing threat to human health, caused in part by pathogens accumulating antibiotic resistance genes (ARGs) through horizontal gene transfer. New ARGs are typically not recognized until they have become widely disseminated, which limits our ability to reduce their spread. In this study, we use large-scale computational screening of bacterial genomes to identify previously undiscovered mobile ARGs in pathogens. From ~1 million genomes, we predict 1,071,815 genes encoding 34,053 unique aminoglycoside-modifying enzymes (AMEs). These cluster into 7,612 families (<70% amino acid identity) of which 88 are previously described. Fifty new AME families are associated with mobile genetic elements and pathogenic hosts. From these, 24 of 28 experimentally tested AMEs confer resistance to aminoglycoside(s) in Escherichia coli, with 17 providing resistance above clinical breakpoints. This study greatly expands the range of clinically relevant aminoglycoside resistance determinants and demonstrates that computational methods enable early discovery of potentially emerging ARGs.
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Affiliation(s)
- David Lund
- Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Roelof Dirk Coertze
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Marcos Parras-Moltó
- Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Fanny Berglund
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Carl-Fredrik Flach
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Anna Johnning
- Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
- Department of Systems and Data Analysis, Fraunhofer-Chalmers Centre, Gothenburg, Sweden
| | - D G Joakim Larsson
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Erik Kristiansson
- Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, Gothenburg, Sweden.
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden.
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2
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Picard MAL, Leblay F, Cassan C, Willemsen A, Daron J, Bauffe F, Decourcelle M, Demange A, Bravo IG. Transcriptomic, proteomic, and functional consequences of codon usage bias in human cells during heterologous gene expression. Protein Sci 2023; 32:e4576. [PMID: 36692287 PMCID: PMC9926478 DOI: 10.1002/pro.4576] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 01/12/2023] [Accepted: 01/14/2023] [Indexed: 01/25/2023]
Abstract
Differences in codon frequency between genomes, genes, or positions along a gene, modulate transcription and translation efficiency, leading to phenotypic and functional differences. Here, we present a multiscale analysis of the effects of synonymous codon recoding during heterologous gene expression in human cells, quantifying the phenotypic consequences of codon usage bias at different molecular and cellular levels, with an emphasis on translation elongation. Six synonymous versions of an antibiotic resistance gene were generated, fused to a fluorescent reporter, and independently expressed in HEK293 cells. Multiscale phenotype was analyzed by means of quantitative transcriptome and proteome assessment, as proxies for gene expression; cellular fluorescence, as a proxy for single-cell level expression; and real-time cell proliferation in absence or presence of antibiotic, as a proxy for the cell fitness. We show that differences in codon usage bias strongly impact the molecular and cellular phenotype: (i) they result in large differences in mRNA levels and protein levels, leading to differences of over 15 times in translation efficiency; (ii) they introduce unpredicted splicing events; (iii) they lead to reproducible phenotypic heterogeneity; and (iv) they lead to a trade-off between the benefit of antibiotic resistance and the burden of heterologous expression. In human cells in culture, codon usage bias modulates gene expression by modifying mRNA availability and suitability for translation, leading to differences in protein levels and eventually eliciting functional phenotypic changes.
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Affiliation(s)
- Marion A. L. Picard
- French National Center for Scientific ResearchLaboratory MIVEGEC (CNRS, IRD, University of Montpellier)MontpellierFrance
| | - Fiona Leblay
- French National Center for Scientific ResearchLaboratory MIVEGEC (CNRS, IRD, University of Montpellier)MontpellierFrance
| | - Cécile Cassan
- French National Center for Scientific ResearchLaboratory MIVEGEC (CNRS, IRD, University of Montpellier)MontpellierFrance
| | - Anouk Willemsen
- French National Center for Scientific ResearchLaboratory MIVEGEC (CNRS, IRD, University of Montpellier)MontpellierFrance
| | - Josquin Daron
- French National Center for Scientific ResearchLaboratory MIVEGEC (CNRS, IRD, University of Montpellier)MontpellierFrance
| | - Frédérique Bauffe
- French National Center for Scientific ResearchLaboratory MIVEGEC (CNRS, IRD, University of Montpellier)MontpellierFrance
| | - Mathilde Decourcelle
- BioCampus Montpellier (University of Montpellier, CNRS, INSERM)MontpellierFrance
| | - Antonin Demange
- French National Center for Scientific ResearchLaboratory MIVEGEC (CNRS, IRD, University of Montpellier)MontpellierFrance
| | - Ignacio G. Bravo
- French National Center for Scientific ResearchLaboratory MIVEGEC (CNRS, IRD, University of Montpellier)MontpellierFrance
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Chandra S, Gupta K, Khare S, Kohli P, Asok A, Mohan SV, Gowda H, Varadarajan R. The High Mutational Sensitivity of ccdA Antitoxin Is Linked to Codon Optimality. Mol Biol Evol 2022; 39:6693774. [PMID: 36069948 PMCID: PMC9555053 DOI: 10.1093/molbev/msac187] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Deep mutational scanning studies suggest that synonymous mutations are typically silent and that most exposed, nonactive-site residues are tolerant to mutations. Here, we show that the ccdA antitoxin component of the Escherichia coli ccdAB toxin-antitoxin system is unusually sensitive to mutations when studied in the operonic context. A large fraction (∼80%) of single-codon mutations, including many synonymous mutations in the ccdA gene shows inactive phenotype, but they retain native-like binding affinity towards cognate toxin, CcdB. Therefore, the observed phenotypic effects are largely not due to alterations in protein structure/stability, consistent with a large region of CcdA being intrinsically disordered. E. coli codon preference and strength of ribosome-binding associated with translation of downstream ccdB gene are found to be major contributors of the observed ccdA mutant phenotypes. In select cases, proteomics studies reveal altered ratios of CcdA:CcdB protein levels in vivo, suggesting that the ccdA mutations likely alter relative translation efficiencies of the two genes in the operon. We extend these results by studying single-site synonymous mutations that lead to loss of function phenotypes in the relBE operon upon introduction of rarer codons. Thus, in their operonic context, genes are likely to be more sensitive to both synonymous and nonsynonymous point mutations than inferred previously.
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Affiliation(s)
| | | | - Shruti Khare
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Pehu Kohli
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Aparna Asok
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | | | - Harsha Gowda
- Institute of Bioinformatics, Bangalore 560100, India
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4
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Sarkar I, Dey P, Rathore SS, Singh GD, Singh RP. Global genomic and proteomic analysis indicates co-evolution of Neisseria species and with their human host. World J Microbiol Biotechnol 2022; 38:149. [PMID: 35773545 DOI: 10.1007/s11274-022-03338-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 06/11/2022] [Indexed: 11/30/2022]
Abstract
Neisseria, a genus from the beta-proteobacteria class, is of potential clinical importance. This genus contains both pathogenic and commensal strains. Gonorrhea and meningitis are two major diseases caused by pathogens belonging to this genus. With the increased use of antimicrobial agents against these pathogens they have evolved the antimicrobial resistance capacity making these diseases nearly untreatable. The set of anti-bacterial resistance genes (resistome) and genes associated with signal processing (secretomes) are crucial for the host-microbial interaction. With the virtue of whole-genome sequences and computational biology, it is now possible to study the genomic and proteomic riddles of Neisseria along with their comprehensive evolutionary and metabolic profiling. We have studied relative synonymous codon usage, amino acid usage, reverse ecology, comparative genomics, evolutionary analysis and pathogen-host (Neisseria-human) interaction through bioinformatics analysis. Our analysis revealed the co-evolution of Neisseria genomes with the human host. Moreover, the co-occurrence of Neisseria and humans has been supported through reverse ecology analysis. A differential pattern of the evolutionary rate of resistomes and secretomes was evident among the pathogenic and commensal strains. Comparative genomics supported the presence of virulent genes in both pathogenic and commensal strains of the select genus. Our analysis also indicated a transition from commensal to pathogenic Neisseria strains through the long run of evolution.
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Affiliation(s)
- Indrani Sarkar
- Salim Ali Centre for Ornithology and Natural History, Anaikatty, Coimbatore, Tamil Nadu, 641 108, India
| | - Prateek Dey
- Salim Ali Centre for Ornithology and Natural History, Anaikatty, Coimbatore, Tamil Nadu, 641 108, India
| | | | | | - Ram Pratap Singh
- Department of Life Science, Central University of South Bihar, Gaya, Bihar, 824236, India.
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5
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Baquero F, Martínez JL, F. Lanza V, Rodríguez-Beltrán J, Galán JC, San Millán A, Cantón R, Coque TM. Evolutionary Pathways and Trajectories in Antibiotic Resistance. Clin Microbiol Rev 2021; 34:e0005019. [PMID: 34190572 PMCID: PMC8404696 DOI: 10.1128/cmr.00050-19] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Evolution is the hallmark of life. Descriptions of the evolution of microorganisms have provided a wealth of information, but knowledge regarding "what happened" has precluded a deeper understanding of "how" evolution has proceeded, as in the case of antimicrobial resistance. The difficulty in answering the "how" question lies in the multihierarchical dimensions of evolutionary processes, nested in complex networks, encompassing all units of selection, from genes to communities and ecosystems. At the simplest ontological level (as resistance genes), evolution proceeds by random (mutation and drift) and directional (natural selection) processes; however, sequential pathways of adaptive variation can occasionally be observed, and under fixed circumstances (particular fitness landscapes), evolution is predictable. At the highest level (such as that of plasmids, clones, species, microbiotas), the systems' degrees of freedom increase dramatically, related to the variable dispersal, fragmentation, relatedness, or coalescence of bacterial populations, depending on heterogeneous and changing niches and selective gradients in complex environments. Evolutionary trajectories of antibiotic resistance find their way in these changing landscapes subjected to random variations, becoming highly entropic and therefore unpredictable. However, experimental, phylogenetic, and ecogenetic analyses reveal preferential frequented paths (highways) where antibiotic resistance flows and propagates, allowing some understanding of evolutionary dynamics, modeling and designing interventions. Studies on antibiotic resistance have an applied aspect in improving individual health, One Health, and Global Health, as well as an academic value for understanding evolution. Most importantly, they have a heuristic significance as a model to reduce the negative influence of anthropogenic effects on the environment.
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Affiliation(s)
- F. Baquero
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Network Center for Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - J. L. Martínez
- National Center for Biotechnology (CNB-CSIC), Madrid, Spain
| | - V. F. Lanza
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Network Center for Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
- Central Bioinformatics Unit, Ramón y Cajal Institute for Health Research (IRYCIS), Madrid, Spain
| | - J. Rodríguez-Beltrán
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Network Center for Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - J. C. Galán
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Network Center for Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - A. San Millán
- National Center for Biotechnology (CNB-CSIC), Madrid, Spain
| | - R. Cantón
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Network Center for Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - T. M. Coque
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Network Center for Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
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6
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Chevin LM, Leung C, Le Rouzic A, Uller T. Using phenotypic plasticity to understand the structure and evolution of the genotype-phenotype map. Genetica 2021; 150:209-221. [PMID: 34617196 DOI: 10.1007/s10709-021-00135-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 09/22/2021] [Indexed: 10/20/2022]
Abstract
Deciphering the genotype-phenotype map necessitates relating variation at the genetic level to variation at the phenotypic level. This endeavour is inherently limited by the availability of standing genetic variation, the rate of spontaneous mutation to novo genetic variants, and possible biases associated with induced mutagenesis. An interesting alternative is to instead rely on the environment as a source of variation. Many phenotypic traits change plastically in response to the environment, and these changes are generally underlain by changes in gene expression. Relating gene expression plasticity to the phenotypic plasticity of more integrated organismal traits thus provides useful information about which genes influence the development and expression of which traits, even in the absence of genetic variation. We here appraise the prospects and limits of such an environment-for-gene substitution for investigating the genotype-phenotype map. We review models of gene regulatory networks, and discuss the different ways in which they can incorporate the environment to mechanistically model phenotypic plasticity and its evolution. We suggest that substantial progress can be made in deciphering this genotype-environment-phenotype map, by connecting theory on gene regulatory network to empirical patterns of gene co-expression, and by more explicitly relating gene expression to the expression and development of phenotypes, both theoretically and empirically.
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Affiliation(s)
- Luis-Miguel Chevin
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier 3, Montpellier, France.
| | - Christelle Leung
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier 3, Montpellier, France
| | - Arnaud Le Rouzic
- Laboratoire Évolution, Génomes, Comportement, Écologie, CNRS, IRD, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Tobias Uller
- Department of Biology, Lund University, Lund, Sweden
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7
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Bailey SF, Alonso Morales LA, Kassen R. Effects of synonymous mutations beyond codon bias: The evidence for adaptive synonymous substitutions from microbial evolution experiments. Genome Biol Evol 2021; 13:6300525. [PMID: 34132772 PMCID: PMC8410137 DOI: 10.1093/gbe/evab141] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/10/2021] [Indexed: 12/22/2022] Open
Abstract
Synonymous mutations are often assumed to be neutral with respect to fitness because they do not alter the encoded amino acid and so cannot be 'seen' by natural selection. Yet a growing body of evidence suggests that synonymous mutations can have fitness effects that drive adaptive evolution through their impacts on gene expression and protein folding. Here, we review what microbial experiments have taught us about the contribution of synonymous mutations to adaptation. A survey of site-directed mutagenesis experiments reveals the distributions of fitness effects for nonsynonymous and synonymous mutations are more similar, especially for beneficial mutations, than expected if all synonymous mutations were neutral, suggesting they should drive adaptive evolution more often than is typically observed. A review of experimental evolution studies where synonymous mutations have contributed to adaptation shows they can impact fitness through a range of mechanisms including the creation of illicit RNA polymerase binding sites impacting transcription and changes to mRNA folding stability that modulate translation. We suggest that clonal interference in evolving microbial populations may be the reason synonymous mutations play a smaller role in adaptive evolution than expected based on their observed fitness effects. We finish by discussing the impacts of falsely assuming synonymous mutations are neutral and discuss directions for future work exploring the role of synonymous mutations in adaptive evolution.
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Affiliation(s)
- Susan F Bailey
- Department of Biology, Clarkson University, Potsdam, NY 13699, USA
| | | | - Rees Kassen
- Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
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8
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Callens M, Scornavacca C, Bedhomme S. Evolutionary responses to codon usage of horizontally transferred genes in Pseudomonas aeruginosa: gene retention, amelioration and compensatory evolution. Microb Genom 2021; 7:000587. [PMID: 34165421 PMCID: PMC8461475 DOI: 10.1099/mgen.0.000587] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 04/19/2021] [Indexed: 12/18/2022] Open
Abstract
Prokaryote genome evolution is characterized by the frequent gain of genes through horizontal gene transfer (HGT). For a gene, being horizontally transferred can represent a strong change in its genomic and physiological context. If the codon usage of a transferred gene deviates from that of the receiving organism, the fitness benefits it provides can be reduced due to a mismatch with the expression machinery. Consequently, transferred genes with a deviating codon usage can be selected against or elicit evolutionary responses that enhance their integration, such as gene amelioration and compensatory evolution. Within bacterial species, the extent and relative importance of these different mechanisms has never been considered altogether. In this study, a phylogeny-based method was used to investigate the occurrence of these different evolutionary responses in Pseudomonas aeruginosa. Selection on codon usage of genes acquired through HGT was observed over evolutionary time, with the overall codon usage converging towards that of the core genome. Gene amelioration, through the accumulation of synonymous mutations after HGT, did not seem to systematically affect transferred genes. This pattern therefore seemed to be mainly driven by selective retention of transferred genes with an initial codon usage similar to that of the core genes. Additionally, variation in the copy number of tRNA genes was often associated with the acquisition of genes for which the observed variation could enhance their expression. This provides evidence that compensatory evolution might be an important mechanism for the integration of horizontally transferred genes.
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Affiliation(s)
- Martijn Callens
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier 3, Montpellier, France
| | - Celine Scornavacca
- Institut des Sciences de l’Evolution, Université Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Stéphanie Bedhomme
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier 3, Montpellier, France
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9
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Tabima JF, Trautman IA, Chang Y, Wang Y, Mondo S, Kuo A, Salamov A, Grigoriev IV, Stajich JE, Spatafora JW. Phylogenomic Analyses of Non-Dikarya Fungi Supports Horizontal Gene Transfer Driving Diversification of Secondary Metabolism in the Amphibian Gastrointestinal Symbiont, Basidiobolus. G3 (Bethesda) 2020; 10:3417-33. [PMID: 32727924 DOI: 10.1534/g3.120.401516] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Research into secondary metabolism (SM) production by fungi has resulted in the discovery of diverse, biologically active compounds with significant medicinal applications. The fungi rich in SM production are taxonomically concentrated in the subkingdom Dikarya, which comprises the phyla Ascomycota and Basidiomycota. Here, we explore the potential for SM production in Mucoromycota and Zoopagomycota, two phyla of nonflagellated fungi that are not members of Dikarya, by predicting and identifying core genes and gene clusters involved in SM. The majority of non-Dikarya have few genes and gene clusters involved in SM production except for the amphibian gut symbionts in the genus Basidiobolus. Basidiobolus genomes exhibit an enrichment of SM genes involved in siderophore, surfactin-like, and terpene cyclase production, all these with evidence of constitutive gene expression. Gene expression and chemical assays also confirm that Basidiobolus has significant siderophore activity. The expansion of SMs in Basidiobolus are partially due to horizontal gene transfer from bacteria, likely as a consequence of its ecology as an amphibian gut endosymbiont.
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10
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Gophna U. The unbearable ease of expression-how avoidance of spurious transcription can shape G+C content in bacterial genomes. FEMS Microbiol Lett 2019; 365:5181332. [PMID: 30423131 DOI: 10.1093/femsle/fny267] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 11/11/2018] [Indexed: 12/28/2022] Open
Affiliation(s)
- Uri Gophna
- Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Levanon Street, Tel Aviv 69000, Israel
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11
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Frumkin I, Yofe I, Bar-Ziv R, Gurvich Y, Lu YY, Voichek Y, Towers R, Schirman D, Krebber H, Pilpel Y. Evolution of intron splicing towards optimized gene expression is based on various Cis- and Trans-molecular mechanisms. PLoS Biol 2019; 17:e3000423. [PMID: 31442222 PMCID: PMC6728054 DOI: 10.1371/journal.pbio.3000423] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 09/05/2019] [Accepted: 08/08/2019] [Indexed: 01/09/2023] Open
Abstract
Splicing expands, reshapes, and regulates the transcriptome of eukaryotic organisms. Despite its importance, key questions remain unanswered, including the following: Can splicing evolve when organisms adapt to new challenges? How does evolution optimize inefficiency of introns’ splicing and of the splicing machinery? To explore these questions, we evolved yeast cells that were engineered to contain an inefficiently spliced intron inside a gene whose protein product was under selection for an increased expression level. We identified a combination of mutations in Cis (within the gene of interest) and in Trans (in mRNA-maturation machinery). Surprisingly, the mutations in Cis resided outside of known intronic functional sites and improved the intron’s splicing efficiency potentially by easing tight mRNA structures. One of these mutations hampered a protein’s domain that was not under selection, demonstrating the evolutionary flexibility of multi-domain proteins as one domain functionality was improved at the expense of the other domain. The Trans adaptations resided in two proteins, Npl3 and Gbp2, that bind pre-mRNAs and are central to their maturation. Interestingly, these mutations either increased or decreased the affinity of these proteins to mRNA, presumably allowing faster spliceosome recruitment or increased time before degradation of the pre-mRNAs, respectively. Altogether, our work reveals various mechanistic pathways toward optimizations of intron splicing to ultimately adapt gene expression patterns to novel demands. An experimental evolution study involving an inefficiently spliced intron reveals that the splicing machinery, introns, and RNA quality control factors evolve in Cis and in Trans when cells optimize their transcriptome to new challenges.
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Affiliation(s)
- Idan Frumkin
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
- * E-mail: (IF); (YP)
| | - Ido Yofe
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Raz Bar-Ziv
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Yonat Gurvich
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Yen-Yun Lu
- Abteilung für Molekulare Genetik, Institut für Mikrobiologie und Genetik, Göttinger Zentrum für Molekulare Biowissenschaften (GZMB), Georg-August Universität Göttingen, Göttingen, Germany
| | - Yoav Voichek
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Ruth Towers
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Dvir Schirman
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Heike Krebber
- Abteilung für Molekulare Genetik, Institut für Mikrobiologie und Genetik, Göttinger Zentrum für Molekulare Biowissenschaften (GZMB), Georg-August Universität Göttingen, Göttingen, Germany
| | - Yitzhak Pilpel
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
- * E-mail: (IF); (YP)
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12
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Bedhomme S, Amorós-Moya D, Valero LM, Bonifaci N, Pujana MÀ, Bravo IG. Evolutionary Changes after Translational Challenges Imposed by Horizontal Gene Transfer. Genome Biol Evol 2019; 11:814-831. [PMID: 30753446 PMCID: PMC6427688 DOI: 10.1093/gbe/evz031] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/07/2019] [Indexed: 01/24/2023] Open
Abstract
Genes acquired by horizontal gene transfer (HGT) may provide the recipient organism with potentially new functions, but proper expression level and integration of the transferred genes in the novel environment are not granted. Notably, transferred genes can differ from the receiving genome in codon usage preferences, leading to impaired translation and reduced functionality. Here, we characterize the genomic and proteomic changes undergone during experimental evolution of Escherichia coli after HGT of three synonymous versions, presenting very different codon usage preference, of an antibiotic resistance gene. The experimental evolution was conducted with and without the corresponding antibiotic and the mutational patterns and proteomic profiles after 1,000 generations largely depend on the experimental growth conditions (e.g., mutations in antibiotic off-target genes), and on the synonymous gene version transferred (e.g., mutations in genes responsive to translational stress). The transfer of an exogenous gene extensively modifies the whole proteome, and these proteomic changes are different for the different version of the transferred gene. Additionally, we identified conspicuous changes in global regulators and in intermediate metabolism, confirmed the evolutionary ratchet generated by mutations in DNA repair genes and highlighted the plasticity of bacterial genomes accumulating large and occasionally transient duplications. Our results support a central role of HGT in fuelling evolution as a powerful mechanism promoting rapid, often dramatic genotypic and phenotypic changes. The profound reshaping of the pre-existing geno/phenotype allows the recipient bacteria to explore new ways of functioning, far beyond the mere acquisition of a novel function.
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Affiliation(s)
- Stéphanie Bedhomme
- CEFE, CNRS, Univ Montpellier, Univ Paul Valéry Montpellier 3, EPHE, IRD, France
| | - Dolors Amorós-Moya
- Experimental Molecular Evolution, Institute for Evolution and Biodiversity, Westfälische-Wilhelms Universität Münster, Germany
| | - Luz M Valero
- Secció de Proteomica, SCSIE Universitat de Valencia, Spain
| | - Nùria Bonifaci
- ProCURE, Catalan Institute of Oncology (ICO), Bellvitge Institute of Biomedical Research (IDIBELL), Barcelona, Spain
| | - Miquel-Àngel Pujana
- ProCURE, Catalan Institute of Oncology (ICO), Bellvitge Institute of Biomedical Research (IDIBELL), Barcelona, Spain
| | - Ignacio G Bravo
- Centre National de la Recherche Scientifique (CNRS), Laboratory MIVEGEC (UMR CNRS, IRD, UM), Montpellier, France
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diCenzo GC, Wellappili D, Golding GB, Finan TM. Inter-replicon Gene Flow Contributes to Transcriptional Integration in the Sinorhizobium meliloti Multipartite Genome. G3 (Bethesda) 2018; 8:1711-20. [PMID: 29563186 DOI: 10.1534/g3.117.300405] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Integration of newly acquired genes into existing regulatory networks is necessary for successful horizontal gene transfer (HGT). Ten percent of bacterial species contain at least two DNA replicons over 300 kilobases in size, with the secondary replicons derived predominately through HGT. The Sinorhizobium meliloti genome is split between a 3.7 Mb chromosome, a 1.7 Mb chromid consisting largely of genes acquired through ancient HGT, and a 1.4 Mb megaplasmid consisting primarily of recently acquired genes. Here, RNA-sequencing is used to examine the transcriptional consequences of massive, synthetic genome reduction produced through the removal of the megaplasmid and/or the chromid. Removal of the pSymA megaplasmid influenced the transcription of only six genes. In contrast, removal of the chromid influenced expression of ∼8% of chromosomal genes and ∼4% of megaplasmid genes. This was mediated in part by the loss of the ETR DNA region whose presence on pSymB is due to a translocation from the chromosome. No obvious functional bias among the up-regulated genes was detected, although genes with putative homologs on the chromid were enriched. Down-regulated genes were enriched in motility and sensory transduction pathways. Four transcripts were examined further, and in each case the transcriptional change could be traced to loss of specific pSymB regions. In particularly, a chromosomal transporter was induced due to deletion of bdhA likely mediated through 3-hydroxybutyrate accumulation. These data provide new insights into the evolution of the multipartite bacterial genome, and more generally into the integration of horizontally acquired genes into the transcriptome.
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Alonso‐Gutierrez J, Koma D, Hu Q, Yang Y, Chan LJG, Petzold CJ, Adams PD, Vickers CE, Nielsen LK, Keasling JD, Lee TS. Toward industrial production of isoprenoids in
Escherichia coli
: Lessons learned from CRISPR‐Cas9 based optimization of a chromosomally integrated mevalonate pathway. Biotechnol Bioeng 2018; 115:1000-1013. [DOI: 10.1002/bit.26530] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 12/18/2017] [Accepted: 12/22/2017] [Indexed: 01/13/2023]
Affiliation(s)
- Jorge Alonso‐Gutierrez
- Joint BioEnergy Institute (JBEI)EmeryvilleCalifornia
- Biological Systems and Engineering DivisionLawrence Berkeley National LaboratoryBerkeleyCalifornia
| | - Daisuke Koma
- Joint BioEnergy Institute (JBEI)EmeryvilleCalifornia
- Biological Systems and Engineering DivisionLawrence Berkeley National LaboratoryBerkeleyCalifornia
- Osaka Municipal Technical Research InstituteOsakaJapan
| | - Qijun Hu
- Joint BioEnergy Institute (JBEI)EmeryvilleCalifornia
- Biological Systems and Engineering DivisionLawrence Berkeley National LaboratoryBerkeleyCalifornia
| | - Yuchen Yang
- Joint BioEnergy Institute (JBEI)EmeryvilleCalifornia
- Biological Systems and Engineering DivisionLawrence Berkeley National LaboratoryBerkeleyCalifornia
| | - Leanne J. G. Chan
- Joint BioEnergy Institute (JBEI)EmeryvilleCalifornia
- Biological Systems and Engineering DivisionLawrence Berkeley National LaboratoryBerkeleyCalifornia
| | - Christopher J. Petzold
- Joint BioEnergy Institute (JBEI)EmeryvilleCalifornia
- Biological Systems and Engineering DivisionLawrence Berkeley National LaboratoryBerkeleyCalifornia
| | - Paul D. Adams
- Joint BioEnergy Institute (JBEI)EmeryvilleCalifornia
- Molecular Biophysics and Integrated Bioimaging DivisionLawrence Berkeley National LaboratoryBerkeleyCalifornia
| | - Claudia E. Vickers
- Australian Institute for Bioengineering and NanotechnologyThe University of QueenslandSt. LuciaQueenslandAustralia
| | - Lars K. Nielsen
- Australian Institute for Bioengineering and NanotechnologyThe University of QueenslandSt. LuciaQueenslandAustralia
| | - Jay D. Keasling
- Joint BioEnergy Institute (JBEI)EmeryvilleCalifornia
- Biological Systems and Engineering DivisionLawrence Berkeley National LaboratoryBerkeleyCalifornia
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of DenmarkHorsholmDenmark
- Department of Chemical and Biomolecular EngineeringUniversity of CaliforniaBerkeleyCalifornia
- Department of BioengineeringUniversity of CaliforniaBerkeleyCalifornia
| | - Taek S. Lee
- Joint BioEnergy Institute (JBEI)EmeryvilleCalifornia
- Biological Systems and Engineering DivisionLawrence Berkeley National LaboratoryBerkeleyCalifornia
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15
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Porse A, Schou TS, Munck C, Ellabaan MMH, Sommer MOA. Biochemical mechanisms determine the functional compatibility of heterologous genes. Nat Commun 2018; 9:522. [PMID: 29410400 PMCID: PMC5802803 DOI: 10.1038/s41467-018-02944-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 01/09/2018] [Indexed: 11/28/2022] Open
Abstract
Elucidating the factors governing the functional compatibility of horizontally transferred genes is important to understand bacterial evolution, including the emergence and spread of antibiotic resistance, and to successfully engineer biological systems. In silico efforts and work using single-gene libraries have suggested that sequence composition is a strong barrier for the successful integration of heterologous genes. Here we sample 200 diverse genes, representing >80% of sequenced antibiotic resistance genes, to interrogate the factors governing genetic compatibility in new hosts. In contrast to previous work, we find that GC content, codon usage, and mRNA-folding energy are of minor importance for the compatibility of mechanistically diverse gene products at moderate expression. Instead, we identify the phylogenetic origin, and the dependence of a resistance mechanism on host physiology, as major factors governing the functionality and fitness of antibiotic resistance genes. These findings emphasize the importance of biochemical mechanism for heterologous gene compatibility, and suggest physiological constraints as a pivotal feature orienting the evolution of antibiotic resistance. Sequence composition is thought to be a major factor governing the functionality of horizontally transferred genes. In contrast, Porse et al. show that phylogenetic origin, and the type of resistance mechanism, are major factors affecting the functionality of horizontally transferred antibiotic resistance genes.
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Affiliation(s)
- Andreas Porse
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, DK-2800, Denmark
| | - Thea S Schou
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, DK-2800, Denmark
| | - Christian Munck
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, DK-2800, Denmark
| | - Mostafa M H Ellabaan
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, DK-2800, Denmark
| | - Morten O A Sommer
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, DK-2800, Denmark.
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Weissenbach J, Ilhan J, Bogumil D, Hülter N, Stucken K, Dagan T. Evolution of Chaperonin Gene Duplication in Stigonematalean Cyanobacteria (Subsection V). Genome Biol Evol 2017; 9:241-252. [PMID: 28082600 PMCID: PMC5381637 DOI: 10.1093/gbe/evw287] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/23/2016] [Indexed: 12/15/2022] Open
Abstract
Chaperonins promote protein folding and are known to play a role in the maintenance of cellular stability under stress conditions. The group I bacterial chaperonin complex comprises GroEL, that forms a barrel-like oligomer, and GroES that forms the lid. In most eubacteria the GroES/GroEL chaperonin is encoded by a single-copy bicistronic operon, whereas in cyanobacteria up to three groES/groEL paralogs have been documented. Here we study the evolution and functional diversification of chaperonin paralogs in the heterocystous, multi-seriate filament forming cyanobacterium Chlorogloeopsis fritschii PCC 6912. The genome of C. fritschii encodes two groES/groEL operons (groESL1, groESL1.2) and a monocistronic groEL gene (groEL2). A phylogenetic reconstruction reveals that the groEL2 duplication is as ancient as cyanobacteria, whereas the groESL1.2 duplication occurred at the ancestor of heterocystous cyanobacteria. A comparison of the groEL paralogs transcription levels under different growth conditions shows that they have adapted distinct transcriptional regulation. Our results reveal that groEL1 and groEL1.2 are upregulated during diazotrophic conditions and the localization of their promoter activity points towards a role in heterocyst differentiation. Furthermore, protein–protein interaction assays suggest that paralogs encoded in the two operons assemble into hybrid complexes. The monocistronic encoded GroEL2 is not forming oligomers nor does it interact with the co-chaperonins. Interaction between GroES1.2 and GroEL1.2 could not be documented, suggesting that the groESL1.2 operon does not encode a functional chaperonin complex. Functional complementation experiments in Escherichia coli show that only GroES1/GroEL1 and GroES1/GroEL1.2 can substitute the native operon. In summary, the evolutionary consequences of chaperonin duplication in cyanobacteria include the retention of groESL1 as a housekeeping gene, subfunctionalization of groESL1.2 and neofunctionalization of the monocistronic groEL2 paralog.
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Affiliation(s)
- Julia Weissenbach
- Institute of General Microbiology, Christian-Albrechts University of Kiel, Am Botanischen Garten 11, Kiel, Germany
| | - Judith Ilhan
- Institute of General Microbiology, Christian-Albrechts University of Kiel, Am Botanischen Garten 11, Kiel, Germany
| | - David Bogumil
- Institute of General Microbiology, Christian-Albrechts University of Kiel, Am Botanischen Garten 11, Kiel, Germany
| | - Nils Hülter
- Institute of General Microbiology, Christian-Albrechts University of Kiel, Am Botanischen Garten 11, Kiel, Germany
| | - Karina Stucken
- Institute of General Microbiology, Christian-Albrechts University of Kiel, Am Botanischen Garten 11, Kiel, Germany
| | - Tal Dagan
- Institute of General Microbiology, Christian-Albrechts University of Kiel, Am Botanischen Garten 11, Kiel, Germany
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17
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Bedhomme S, Perez Pantoja D, Bravo IG. Plasmid and clonal interference during post horizontal gene transfer evolution. Mol Ecol 2017; 26:1832-1847. [PMID: 28206693 DOI: 10.1111/mec.14056] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 01/31/2017] [Accepted: 02/08/2017] [Indexed: 01/12/2023]
Abstract
Plasmids are nucleic acid molecules that can drive their own replication in a living cell. They can be transmitted horizontally and can thrive in the host cell to high-copy numbers. Plasmid replication and gene expression consume cellular resources and cells carrying plasmids incur fitness costs. But many plasmids carry genes that can be beneficial under certain conditions, allowing the cell to endure in the presence of antibiotics, toxins, competitors or parasites. Horizontal transfer of plasmid-encoded genes can thus instantaneously confer differential adaptation to local or transient selection conditions. This conflict between cellular fitness and plasmid spread sets the scene for multilevel selection processes. We have engineered a system to study the short-term evolutionary impact of different synonymous versions of a plasmid-encoded antibiotic resistance gene. Applying experimental evolution under different selection conditions and deep sequencing allowed us to show rapid local adaptation to the presence of antibiotic and to the specific version of the resistance gene transferred. We describe the presence of clonal interference at two different levels: at the within-cell level, because a single cell can carry several plasmids, and at the between-cell level, because a bacterial population may contain several clones carrying different plasmids and displaying different fitness in the presence/absence of antibiotic. Understanding the within-cell and between-cell dynamics of plasmids after horizontal gene transfer is essential to unravel the dense network of mobile elements underlying the worldwide threat to public health of antibiotic resistance.
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Affiliation(s)
- S Bedhomme
- Centre d'Ecologie Fonctionnelle et Evolutive, UMR CNRS 5175, 34293, Montpellier, France.,Laboratory MIVEGEC, UMR CNRS 5290, IRD 224, UM, Centre National de la Recherche Scientifique, 911 avenue Agropolis, BP64501, 34394, Montpellier Cedex 05, France
| | - D Perez Pantoja
- Programa Institucional de Fomento a la Investigación, Desarrollo e Innovación, Universidad Tecnológica Metropolitana, Ignacio Valdivieso 2409, P.O. Box 8940577, San Joaquín, Santiago, Chile
| | - I G Bravo
- Laboratory MIVEGEC, UMR CNRS 5290, IRD 224, UM, Centre National de la Recherche Scientifique, 911 avenue Agropolis, BP64501, 34394, Montpellier Cedex 05, France
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18
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Choudoir MJ, Panke-Buisse K, Andam CP, Buckley DH. Genome Surfing As Driver of Microbial Genomic Diversity. Trends Microbiol 2017; 25:624-636. [PMID: 28283403 DOI: 10.1016/j.tim.2017.02.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 02/03/2017] [Accepted: 02/10/2017] [Indexed: 01/20/2023]
Abstract
Historical changes in population size, such as those caused by demographic range expansions, can produce nonadaptive changes in genomic diversity through mechanisms such as gene surfing. We propose that demographic range expansion of a microbial population capable of horizontal gene exchange can result in genome surfing, a mechanism that can cause widespread increase in the pan-genome frequency of genes acquired by horizontal gene exchange. We explain that patterns of genetic diversity within Streptomyces are consistent with genome surfing, and we describe several predictions for testing this hypothesis both in Streptomyces and in other microorganisms.
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Affiliation(s)
- Mallory J Choudoir
- School of Integrative Plant Science, Cornell University, Ithaca, NY 14850 USA
| | - Kevin Panke-Buisse
- School of Integrative Plant Science, Cornell University, Ithaca, NY 14850 USA
| | - Cheryl P Andam
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham NH 03824, USA
| | - Daniel H Buckley
- School of Integrative Plant Science, Cornell University, Ithaca, NY 14850 USA.
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19
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Agashe D, Sane M, Phalnikar K, Diwan GD, Habibullah A, Martinez-Gomez NC, Sahasrabuddhe V, Polachek W, Wang J, Chubiz LM, Marx CJ. Large-Effect Beneficial Synonymous Mutations Mediate Rapid and Parallel Adaptation in a Bacterium. Mol Biol Evol 2016; 33:1542-53. [PMID: 26908584 PMCID: PMC4868122 DOI: 10.1093/molbev/msw035] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Contrary to previous understanding, recent evidence indicates that synonymous codon changes may sometimes face strong selection. However, it remains difficult to generalize the nature, strength, and mechanism(s) of such selection. Previously, we showed that synonymous variants of a key enzyme-coding gene (fae) of Methylobacterium extorquens AM1 decreased enzyme production and reduced fitness dramatically. We now show that during laboratory evolution, these variants rapidly regained fitness via parallel yet variant-specific, highly beneficial point mutations in the N-terminal region of fae. These mutations (including four synonymous mutations) had weak but consistently positive impacts on transcript levels, enzyme production, or enzyme activity. However, none of the proposed mechanisms (including internal ribosome pause sites or mRNA structure) predicted the fitness impact of evolved or additional, engineered point mutations. This study shows that synonymous mutations can be fixed through strong positive selection, but the mechanism for their benefit varies depending on the local sequence context.
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Affiliation(s)
- Deepa Agashe
- National Center for Biological Sciences, Tata Institute of Fundamental Research, GKVK, Bangalore, India Department of Organismic and Evolutionary Biology, Harvard University
| | - Mrudula Sane
- National Center for Biological Sciences, Tata Institute of Fundamental Research, GKVK, Bangalore, India
| | - Kruttika Phalnikar
- National Center for Biological Sciences, Tata Institute of Fundamental Research, GKVK, Bangalore, India
| | - Gaurav D Diwan
- National Center for Biological Sciences, Tata Institute of Fundamental Research, GKVK, Bangalore, India SASTRA University, Thanjavur, India
| | - Alefiyah Habibullah
- National Center for Biological Sciences, Tata Institute of Fundamental Research, GKVK, Bangalore, India
| | | | - Vinaya Sahasrabuddhe
- National Center for Biological Sciences, Tata Institute of Fundamental Research, GKVK, Bangalore, India
| | - William Polachek
- Department of Organismic and Evolutionary Biology, Harvard University
| | - Jue Wang
- Department of Organismic and Evolutionary Biology, Harvard University Systems Biology Graduate Program, Harvard University
| | - Lon M Chubiz
- Department of Organismic and Evolutionary Biology, Harvard University
| | - Christopher J Marx
- Department of Organismic and Evolutionary Biology, Harvard University Faculty of Arts and Sciences Center for Systems Biology, Harvard University Department of Biological Sciences, University of Idaho Institute for Bioinformatics and Evolutionary Studies, University of Idaho
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20
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Higashi K, Tobe T, Kanai A, Uyar E, Ishikawa S, Suzuki Y, Ogasawara N, Kurokawa K, Oshima T. H-NS Facilitates Sequence Diversification of Horizontally Transferred DNAs during Their Integration in Host Chromosomes. PLoS Genet 2016; 12:e1005796. [PMID: 26789284 PMCID: PMC4720273 DOI: 10.1371/journal.pgen.1005796] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Accepted: 12/20/2015] [Indexed: 01/06/2023] Open
Abstract
Bacteria can acquire new traits through horizontal gene transfer. Inappropriate expression of transferred genes, however, can disrupt the physiology of the host bacteria. To reduce this risk, Escherichia coli expresses the nucleoid-associated protein, H-NS, which preferentially binds to horizontally transferred genes to control their expression. Once expression is optimized, the horizontally transferred genes may actually contribute to E. coli survival in new habitats. Therefore, we investigated whether and how H-NS contributes to this optimization process. A comparison of H-NS binding profiles on common chromosomal segments of three E. coli strains belonging to different phylogenetic groups indicated that the positions of H-NS-bound regions have been conserved in E. coli strains. The sequences of the H-NS-bound regions appear to have diverged more so than H-NS-unbound regions only when H-NS-bound regions are located upstream or in coding regions of genes. Because these regions generally contain regulatory elements for gene expression, sequence divergence in these regions may be associated with alteration of gene expression. Indeed, nucleotide substitutions in H-NS-bound regions of the ybdO promoter and coding regions have diversified the potential for H-NS-independent negative regulation among E. coli strains. The ybdO expression in these strains was still negatively regulated by H-NS, which reduced the effect of H-NS-independent regulation under normal growth conditions. Hence, we propose that, during E. coli evolution, the conservation of H-NS binding sites resulted in the diversification of the regulation of horizontally transferred genes, which may have facilitated E. coli adaptation to new ecological niches. Horizontal gene transfer among bacteria is the major means of acquiring genetic diversity and has been a central factor in bacterial evolution. The expression of horizontally transferred genes could potentially be optimized to permit the host bacteria to expand their habitat. The results of our study suggest that DNA regions bound by the nucleoid-associated protein, H-NS, which preferentially binds to horizontally transferred genes, have been conserved during Escherichia coli evolution. Interestingly, H-NS-bound regions have evolved faster than H-NS-unbound regions, but only in gene regulatory and coding regions. We show that DNA sequence substitutions in H-NS-bound regions actually alter the regulation of gene expression in different E. coli strains. Thus, our results support the hypothesis that H-NS accelerates the diversification of the regulation of horizontally transferred genes such that their selective expression could potentially allow E. coli strains to adapt to new habitats.
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Affiliation(s)
- Koichi Higashi
- Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Meguro-ku, Tokyo, Japan
| | - Toru Tobe
- Department of Biomedical Informatics, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
- * E-mail: (TT); (KK); (TO)
| | - Akinori Kanai
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa-shi, Chiba, Japan
| | - Ebru Uyar
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Nara, Japan
| | - Shu Ishikawa
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Nara, Japan
| | - Yutaka Suzuki
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa-shi, Chiba, Japan
| | - Naotake Ogasawara
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Nara, Japan
| | - Ken Kurokawa
- Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Meguro-ku, Tokyo, Japan
- Earth-Life Science Institute, Tokyo Institute of Technology, Meguro-ku, Tokyo, Japan
- * E-mail: (TT); (KK); (TO)
| | - Taku Oshima
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Nara, Japan
- * E-mail: (TT); (KK); (TO)
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21
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Pelchovich G, Nadejda S, Dana A, Tuller T, Bravo IG, Gophna U. Ribosomal mutations affecting the translation of genes that use non-optimal codons. FEBS J 2014; 281:3701-18. [PMID: 24966114 DOI: 10.1111/febs.12892] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Revised: 06/10/2014] [Accepted: 06/23/2014] [Indexed: 01/26/2023]
Abstract
Genes that are laterally acquired by a new host species often contain codons that are non-optimal to the tRNA repertoire of the new host, which may lead to insufficient translational levels. Inefficient translation can be overcome by different mechanisms, such as incremental amelioration of the coding sequence, compensatory mutations in the regulatory sequences leading to increased transcription or increase in gene copy number. However, there is also a possibility that ribosomal mutations can improve the expression of such genes. To test this hypothesis, we examined the effects of point mutations in the endogenous ribosomal proteins S12 and S5 in Escherichia coli, which are known to be involved in the decoding of the mRNA, on the efficiency of translation of exogenous genes that use non-optimal codons, in vivo. We show that an S12 mutant in E. coli is able to express exogenous genes, with non-optimal codons, to higher levels than the wild-type, and explore the mechanisms underlying this phenomenon in this mutant. Our results suggest that the transient emergence of mutants that allow efficient expression of exogenous genes with non-optimal codons could also increase the chances of fixation of laterally transferred genes.
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Affiliation(s)
- Gidi Pelchovich
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Israel
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22
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Baltrus DA. Exploring the costs of horizontal gene transfer. Trends Ecol Evol 2013; 28:489-95. [DOI: 10.1016/j.tree.2013.04.002] [Citation(s) in RCA: 261] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Revised: 04/15/2013] [Accepted: 04/25/2013] [Indexed: 11/20/2022]
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23
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Abstract
In vitro studies of the haloarchaeal genus Haloferax have demonstrated
their ability to frequently exchange DNA between species, whereas rates of homologous
recombination estimated from natural populations in the genus Halorubrum
are high enough to maintain random association of alleles between five loci. To quantify
the effects of gene transfer and recombination of commonly held (relaxed core) genes
during the evolution of the class Halobacteria (haloarchaea), we reconstructed the history
of 21 genomes representing all major groups. Using a novel algorithm and a concatenated
ribosomal protein phylogeny as a reference, we created a directed horizontal genetic
transfer (HGT) network of contemporary and ancestral genomes. Gene order analysis revealed
that 90% of testable HGTs were by direct homologous replacement, rather than
nonhomologous integration followed by a loss. Network analysis revealed an inverse
log-linear relationship between HGT frequency and ribosomal protein evolutionary distance
that is maintained across the deepest divergences in Halobacteria. We use this
mathematical relationship to estimate the total transfers and amino acid substitutions
delivered by HGTs in each genome, providing a measure of chimerism. For the relaxed core
genes of each genome, we conservatively estimate that 11–20% of their
evolution occurred in other haloarchaea. Our findings are unexpected, because the transfer
and homologous recombination of relaxed core genes between members of the class
Halobacteria disrupts the coevolution of genes; however, the generation of new
combinations of divergent but functionally related genes may lead to adaptive phenotypes
not available through cumulative mutations and recombination within a single
population.
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Affiliation(s)
- David Williams
- Department of Molecular and Cell Biology, University of Connecticut, CT, USA
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24
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Bedhomme S, Lafforgue G, Elena SF. Genotypic but not phenotypic historical contingency revealed by viral experimental evolution. BMC Evol Biol 2013; 13:46. [PMID: 23421472 PMCID: PMC3598485 DOI: 10.1186/1471-2148-13-46] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2012] [Accepted: 02/15/2013] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND The importance of historical contingency in determining the potential of viral populations to evolve has been largely unappreciated. Identifying the constraints imposed by past adaptations is, however, of importance for understanding many questions in evolutionary biology, such as the evolution of host usage dynamics by multi-host viruses or the emergence of escape mutants that persist in the absence of antiviral treatments. To address this issue, we undertook an experimental approach in which sixty lineages of Tobacco etch potyvirus that differ in their past evolutionary history and degree of adaptation to Nicotiana tabacum were allowed to adapt to this host for 15 rounds of within host multiplication and transfer. We thereafter evaluated the degree of adaptation to the new host as well as to the original ones and characterized the consensus sequence of each lineage. RESULTS We found that past evolutionary history did not determine the phenotypic outcome of this common host evolution phase, and that the signal of local adaptation to past hosts had largely disappeared. By contrast, evolutionary history left footprints at the genotypic level, since the majority of host-specific mutations present at the beginning of this experiment were retained in the end-point populations and may have affected which new mutations were consequently fixed. This resulted in further divergence between the sequences despite a shared selective environment. CONCLUSIONS The present experiment reinforces the idea that the answer to the question "How important is historical contingency in evolution?" strongly depends on the level of integration of the traits studied. A strong historical contingency was found for TEV genotype, whereas a weak effect of on phenotypic evolution was revealed. In an applied context, our results imply that viruses are not easily trapped into suboptimal phenotypes and that (re)emergence is not evolutionarily constrained.
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Affiliation(s)
- Stéphanie Bedhomme
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-UPV, 46022, València, Spain
- Present address: Infections and Cancer, Catalan Institute of Oncology (ICO), Barcelona, Spain
| | - Guillaume Lafforgue
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-UPV, 46022, València, Spain
| | - Santiago F Elena
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-UPV, 46022, València, Spain
- The Santa Fe Institute, Santa Fe, 87501, New Mexico
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Agashe D, Martinez-Gomez NC, Drummond DA, Marx CJ. Good codons, bad transcript: large reductions in gene expression and fitness arising from synonymous mutations in a key enzyme. Mol Biol Evol 2012; 30:549-60. [PMID: 23223712 PMCID: PMC3563975 DOI: 10.1093/molbev/mss273] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Biased codon usage in protein-coding genes is pervasive, whereby amino acids are largely encoded by a specific subset of possible codons. Within individual genes, codon bias is stronger at evolutionarily conserved residues, favoring codons recognized by abundant tRNAs. Although this observation suggests an overall pattern of selection for translation speed and/or accuracy, other work indicates that transcript structure or binding motifs drive codon usage. However, our understanding of codon bias evolution is constrained by limited experimental data on the fitness effects of altering codons in functional genes. To bridge this gap, we generated synonymous variants of a key enzyme-coding gene in Methylobacterium extorquens. We found that mutant gene expression, enzyme production, enzyme activity, and fitness were all significantly lower than wild-type. Surprisingly, encoding the gene using only rare codons decreased fitness by 40%, whereas an allele coded entirely by frequent codons decreased fitness by more than 90%. Increasing gene expression restored mutant fitness to varying degrees, demonstrating that the fitness disadvantage of synonymous mutants arose from a lack of beneficial protein rather than costs of protein production. Protein production was negatively correlated with the frequency of motifs with high affinity for the anti-Shine-Dalgarno sequence, suggesting ribosome pausing as the dominant cause of low mutant fitness. Together, our data support the idea that, although a particular set of codons are favored on average across a genome, in an individual gene selection can either act for or against codons depending on their local context.
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Affiliation(s)
- Deepa Agashe
- Department of Organismic and Evolutionary Biology, Biological Laboratories, Harvard University, MA, USA.
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Francino MP. The ecology of bacterial genes and the survival of the new. Int J Evol Biol 2012; 2012:394026. [PMID: 22900231 DOI: 10.1155/2012/394026] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/21/2012] [Accepted: 06/26/2012] [Indexed: 11/18/2022]
Abstract
Much of the observed variation among closely related bacterial genomes is attributable to gains and losses of genes that are acquired horizontally as well as to gene duplications and larger amplifications. The genomic flexibility that results from these mechanisms certainly contributes to the ability of bacteria to survive and adapt in varying environmental challenges. However, the duplicability and transferability of individual genes imply that natural selection should operate, not only at the organismal level, but also at the level of the gene. Genes can be considered semiautonomous entities that possess specific functional niches and evolutionary dynamics. The evolution of bacterial genes should respond both to selective pressures that favor competition, mostly among orthologs or paralogs that may occupy the same functional niches, and cooperation, with the majority of other genes coexisting in a given genome. The relative importance of either type of selection is likely to vary among different types of genes, based on the functional niches they cover and on the tightness of their association with specific organismal lineages. The frequent availability of new functional niches caused by environmental changes and biotic evolution should enable the constant diversification of gene families and the survival of new lineages of genes.
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Huang Q, Cheng X, Cheung MK, Kiselev SS, Ozoline ON, Kwan HS. High-density transcriptional initiation signals underline genomic islands in bacteria. PLoS One 2012; 7:e33759. [PMID: 22448273 PMCID: PMC3309015 DOI: 10.1371/journal.pone.0033759] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Accepted: 02/21/2012] [Indexed: 02/07/2023] Open
Abstract
Genomic islands (GIs), frequently associated with the pathogenicity of bacteria and having a substantial influence on bacterial evolution, are groups of "alien" elements which probably undergo special temporal-spatial regulation in the host genome. Are there particular hallmark transcriptional signals for these "exotic" regions? We here explore the potential transcriptional signals that underline the GIs beyond the conventional views on basic sequence composition, such as codon usage and GC property bias. It showed that there is a significant enrichment of the transcription start positions (TSPs) in the GI regions compared to the whole genome of Salmonella enterica and Escherichia coli. There was up to a four-fold increase for the 70% GIs, implying high-density TSPs profile can potentially differentiate the GI regions. Based on this feature, we developed a new sliding window method GIST, Genomic-island Identification by Signals of Transcription, to identify these regions. Subsequently, we compared the known GI-associated features of the GIs detected by GIST and by the existing method Islandviewer to those of the whole genome. Our method demonstrates high sensitivity in detecting GIs harboring genes with biased GI-like function, preferred subcellular localization, skewed GC property, shorter gene length and biased "non-optimal" codon usage. The special transcriptional signals discovered here may contribute to the coordinate expression regulation of foreign genes. Finally, by using GIST, we detected many interesting GIs in the 2011 German E. coli O104:H4 outbreak strain TY-2482, including the microcin H47 system and gene cluster ycgXEFZ-ymgABC that activates the production of biofilm matrix. The aforesaid findings highlight the power of GIST to predict GIs with distinct intrinsic features to the genome. The heterogeneity of cumulative TSPs profiles may not only be a better identity for "alien" regions, but also provide hints to the special evolutionary course and transcriptional regulation of GI regions.
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Affiliation(s)
- Qianli Huang
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Xuanjin Cheng
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Man Kit Cheung
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Sergey S. Kiselev
- Institute of Cell Biophysics, Russian Academy of Sciences, Moscow, Russia
| | - Olga N. Ozoline
- Institute of Cell Biophysics, Russian Academy of Sciences, Moscow, Russia
| | - Hoi Shan Kwan
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
- * E-mail:
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Bedhomme S, Lafforgue G, Elena SF. Multihost Experimental Evolution of a Plant RNA Virus Reveals Local Adaptation and Host-Specific Mutations. Mol Biol Evol 2011; 29:1481-92. [DOI: 10.1093/molbev/msr314] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
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29
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Popa O, Dagan T. Trends and barriers to lateral gene transfer in prokaryotes. Curr Opin Microbiol 2011; 14:615-23. [PMID: 21856213 DOI: 10.1016/j.mib.2011.07.027] [Citation(s) in RCA: 185] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2011] [Revised: 07/19/2011] [Accepted: 07/25/2011] [Indexed: 11/19/2022]
Abstract
Gene acquisition by lateral gene transfer (LGT) is an important mechanism for natural variation among prokaryotes. Laboratory experiments show that protein-coding genes can be laterally transferred extremely fast among microbial cells, inherited to most of their descendants, and adapt to a new regulatory regime within a short time. Recent advance in the phylogenetic analysis of microbial genomes using networks approach reveals a substantial impact of LGT during microbial genome evolution. Phylogenomic networks of LGT among prokaryotes reconstructed from completely sequenced genomes uncover barriers to LGT in multiple levels. Here we discuss the kinds of barriers to gene acquisition in nature including physical barriers for gene transfer between cells, genomic barriers for the integration of acquired DNA, and functional barriers for the acquisition of new genes.
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Affiliation(s)
- Ovidiu Popa
- Institute of Molecular Evolution, Heinrich-Heine University of Düsseldorf, Universitätstr. 1 40225, Düsseldorf, Germany
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