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Peng K, Liu YX, Sun X, Wang Q, Song L, Wang Z, Li R. Large-scale bacterial genomic and metagenomic analysis reveals Pseudomonas aeruginosa as potential ancestral source of tigecycline resistance gene cluster tmexCD-toprJ. Microbiol Res 2024; 285:127747. [PMID: 38739956 DOI: 10.1016/j.micres.2024.127747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 04/04/2024] [Accepted: 05/02/2024] [Indexed: 05/16/2024]
Abstract
BACKGROUND The global dissemination of the multidrug resistance efflux pump gene cluster tmexCD-toprJ has greatly weakened the effects of multiple antibiotics, including tigecycline. However, the potential origin and transmission mechanisms of the gene cluster remain unclear. METHODS Here, we concluded a comprehensive bioinformatics analysis on integrated 73,498 bacterial genomes, including Pseudomonas spp., Klebsiella spp., Aeromonas spp., Proteus spp., and Citrobacter spp., along with 1,152 long-read metagenomic datasets to trace the origin and propagation of tmexCD-toprJ. RESULTS Our results demonstrated that tmexCD-toprJ was predominantly found in Pseudomonas aeruginosa sourced from human hosts in Asian countries and North American countries. Phylogenetic and genomic feature analyses showed that tmexCD-toprJ was likely evolved from mexCD-oprJ of some special clones of P. aeruginosa. Furthermore, metagenomic analysis confirmed that P. aeruginosa is the only potential ancestral bacterium for tmexCD-toprJ. A putative mobile genetic structure harboring tmexCD-toprJ, int-int-hp-hp-tnfxB-tmexCD-toprJ, was the predominant genetic context of tmexCD-toprJ across various bacterial genera, suggesting that the two integrase genes play a pivotal role in the horizontal transmission of tmexCD-toprJ. CONCLUSIONS Based on these findings, it is almost certain that the tmexCD-toprJ gene cluster was derived from P. aeruginosa and further spread to other bacteria.
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Affiliation(s)
- Kai Peng
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
| | - Yong-Xin Liu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Xinran Sun
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
| | - Qiaojun Wang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
| | - Luyang Song
- College of Plant Protection, Henan Agricultural University, Zhengzhou, Henan, China
| | - Zhiqiang Wang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu, China.
| | - Ruichao Li
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China; Institute of Comparative Medicine, Yangzhou University, Yangzhou, Jiangsu, China.
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2
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Dmitrijeva M, Tackmann J, Matias Rodrigues JF, Huerta-Cepas J, Coelho LP, von Mering C. A global survey of prokaryotic genomes reveals the eco-evolutionary pressures driving horizontal gene transfer. Nat Ecol Evol 2024; 8:986-998. [PMID: 38443606 DOI: 10.1038/s41559-024-02357-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 02/05/2024] [Indexed: 03/07/2024]
Abstract
Horizontal gene transfer, the exchange of genetic material through means other than reproduction, is a fundamental force in prokaryotic genome evolution. Genomic persistence of horizontally transferred genes has been shown to be influenced by both ecological and evolutionary factors. However, there is limited availability of ecological information about species other than the habitats from which they were isolated, which has prevented a deeper exploration of ecological contributions to horizontal gene transfer. Here we focus on transfers detected through comparison of individual gene trees to the species tree, assessing the distribution of gene-exchanging prokaryotes across over a million environmental sequencing samples. By analysing detected horizontal gene transfer events, we show distinct functional profiles for recent versus old events. Although most genes transferred are part of the accessory genome, genes transferred earlier in evolution tend to be more ubiquitous within present-day species. We find that co-occurring, interacting and high-abundance species tend to exchange more genes. Finally, we show that host-associated specialist species are most likely to exchange genes with other host-associated specialist species, whereas species found across different habitats have similar gene exchange rates irrespective of their preferred habitat. Our study covers an unprecedented scale of integrated horizontal gene transfer and environmental information, highlighting broad eco-evolutionary trends.
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Affiliation(s)
- Marija Dmitrijeva
- Department of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zürich, Zurich, Switzerland
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zurich, Switzerland
| | - Janko Tackmann
- Department of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zürich, Zurich, Switzerland
| | | | - Jaime Huerta-Cepas
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Campus de Montegancedo-UPM, Madrid, Spain
| | - Luis Pedro Coelho
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China.
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology, Translational Research Institute, Woolloongabba, Queensland, Australia.
| | - Christian von Mering
- Department of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zürich, Zurich, Switzerland.
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3
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Sengupta A, Bandyopadhyay A, Sarkar D, Hendry JI, Schubert MG, Liu D, Church GM, Maranas CD, Pakrasi HB. Genome streamlining to improve performance of a fast-growing cyanobacterium Synechococcus elongatus UTEX 2973. mBio 2024; 15:e0353023. [PMID: 38358263 PMCID: PMC10936165 DOI: 10.1128/mbio.03530-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 01/22/2024] [Indexed: 02/16/2024] Open
Abstract
Cyanobacteria are photosynthetic organisms that have garnered significant recognition as potential hosts for sustainable bioproduction. However, their complex regulatory networks pose significant challenges to major metabolic engineering efforts, thereby limiting their feasibility as production hosts. Genome streamlining has been demonstrated to be a successful approach for improving productivity and fitness in heterotrophs but is yet to be explored to its full potential in phototrophs. Here, we present the systematic reduction of the genome of the cyanobacterium exhibiting the fastest exponential growth, Synechococcus elongatus UTEX 2973. This work, the first of its kind in a photoautotroph, involved an iterative process using state-of-the-art genome-editing technology guided by experimental analysis and computational tools. CRISPR-Cas3 enabled large, progressive deletions of predicted dispensable regions and aided in the identification of essential genes. The large deletions were combined to obtain a strain with 55-kb genome reduction. The strains with streamlined genome showed improvement in growth (up to 23%) and productivity (by 22.7%) as compared to the wild type (WT). This streamlining strategy not only has the potential to develop cyanobacterial strains with improved growth and productivity traits but can also facilitate a better understanding of their genome-to-phenome relationships.IMPORTANCEGenome streamlining is an evolutionary strategy used by natural living systems to dispense unnecessary genes from their genome as a mechanism to adapt and evolve. While this strategy has been successfully borrowed to develop synthetic heterotrophic microbial systems with desired phenotype, it has not been extensively explored in photoautotrophs. Genome streamlining strategy incorporates both computational predictions to identify the dispensable regions and experimental validation using genome-editing tool, and in this study, we have employed a modified strategy with the goal to minimize the genome size to an extent that allows optimal cellular fitness under specified conditions. Our strategy has explored a novel genome-editing tool in photoautotrophs, which, unlike other existing tools, enables large, spontaneous optimal deletions from the genome. Our findings demonstrate the effectiveness of this modified strategy in obtaining strains with streamlined genome, exhibiting improved fitness and productivity.
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Affiliation(s)
- Annesha Sengupta
- Department of Biology, Washington University, St. Louis, Missouri, USA
| | | | - Debolina Sarkar
- Department of Chemical Engineering, Pennsylvania State University, State College, Pennsylvania, USA
| | - John I. Hendry
- Department of Chemical Engineering, Pennsylvania State University, State College, Pennsylvania, USA
| | - Max G. Schubert
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, Massachusetts, USA
| | - Deng Liu
- Department of Biology, Washington University, St. Louis, Missouri, USA
| | - George M. Church
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, Massachusetts, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Costas D. Maranas
- Department of Chemical Engineering, Pennsylvania State University, State College, Pennsylvania, USA
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4
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Douglas GM, Shapiro BJ. Pseudogenes act as a neutral reference for detecting selection in prokaryotic pangenomes. Nat Ecol Evol 2024; 8:304-314. [PMID: 38177690 DOI: 10.1038/s41559-023-02268-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 11/10/2023] [Indexed: 01/06/2024]
Abstract
A long-standing question is to what degree genetic drift and selection drive the divergence in rare accessory gene content between closely related bacteria. Rare genes, including singletons, make up a large proportion of pangenomes (all genes in a set of genomes), but it remains unclear how many such genes are adaptive, deleterious or neutral to their host genome. Estimates of species' effective population sizes (Ne) are positively associated with pangenome size and fluidity, which has independently been interpreted as evidence for both neutral and adaptive pangenome models. We hypothesized that pseudogenes, used as a neutral reference, could be used to distinguish these models. We find that most functional categories are depleted for rare pseudogenes when a genome encodes only a single intact copy of a gene family. In contrast, transposons are enriched in pseudogenes, suggesting they are mostly neutral or deleterious to the host genome. Thus, even if individual rare accessory genes vary in their effects on host fitness, we can confidently reject a model of entirely neutral or deleterious rare genes. We also define the ratio of singleton intact genes to singleton pseudogenes (si/sp) within a pangenome, compare this measure across 668 prokaryotic species and detect a signal consistent with the adaptive value of many rare accessory genes. Taken together, our work demonstrates that comparing with pseudogenes can improve inferences of the evolutionary forces driving pangenome variation.
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Affiliation(s)
- Gavin M Douglas
- Department of Microbiology and Immunology, McGill University, Montréal, Québec, Canada.
- McGill Genome Centre, McGill University, Montréal, Québec, Canada.
| | - B Jesse Shapiro
- Department of Microbiology and Immunology, McGill University, Montréal, Québec, Canada.
- McGill Genome Centre, McGill University, Montréal, Québec, Canada.
- McGill Centre for Microbiome Research, McGill University, Montréal, Québec, Canada.
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5
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Zhang H, Hellweger FL, Luo H. Genome reduction occurred in early Prochlorococcus with an unusually low effective population size. THE ISME JOURNAL 2024; 18:wrad035. [PMID: 38365237 PMCID: PMC10837832 DOI: 10.1093/ismejo/wrad035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 12/14/2023] [Accepted: 12/20/2023] [Indexed: 02/18/2024]
Abstract
In the oligotrophic sunlit ocean, the most abundant free-living planktonic bacterial lineages evolve convergently through genome reduction. The cyanobacterium Prochlorococcus responsible for 10% global oxygen production is a prominent example. The dominant theory known as "genome streamlining" posits that they have extremely large effective population sizes (Ne) such that selection for metabolic efficiency acts to drive genome reduction. Because genome reduction largely took place anciently, this theory builds on the assumption that their ancestors' Ne was similarly large. Constraining Ne for ancient ancestors is challenging because experimental measurements of extinct organisms are impossible and alternatively reconstructing ancestral Ne with phylogenetic models gives large uncertainties. Here, we develop a new strategy that leverages agent-based modeling to simulate the changes in the genome-wide ratio of radical to conservative nonsynonymous nucleotide substitution rate (dR/dC) in a possible range of Ne in ancestral populations. This proxy shows expected increases with decreases of Ne only when Ne falls to about 10 k - 100 k or lower, magnitudes characteristic of Ne of obligate endosymbiont species where drift drives genome reduction. Our simulations therefore strongly support a scenario where the primary force of Prochlorococcus genome reduction is drift rather than selection.
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Affiliation(s)
- Hao Zhang
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, 999077, Hong Kong SAR
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, 518000, China
| | - Ferdi L Hellweger
- Water Quality Engineering, Technical University of Berlin, Berlin, 10623, Germany
| | - 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, 999077, Hong Kong SAR
- Institute of Environment, Energy and Sustainability, The Chinese University of Hong Kong, Shatin, 999077, Hong Kong SAR
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6
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Dimonaco NJ, Clare A, Kenobi K, Aubrey W, Creevey CJ. StORF-Reporter: finding genes between genes. Nucleic Acids Res 2023; 51:11504-11517. [PMID: 37897345 PMCID: PMC10682499 DOI: 10.1093/nar/gkad814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 09/04/2023] [Accepted: 09/27/2023] [Indexed: 10/30/2023] Open
Abstract
Large regions of prokaryotic genomes are currently without any annotation, in part due to well-established limitations of annotation tools. For example, it is routine for genes using alternative start codons to be misreported or completely omitted. Therefore, we present StORF-Reporter, a tool that takes an annotated genome and returns regions that may contain missing CDS genes from unannotated regions. StORF-Reporter consists of two parts. The first begins with the extraction of unannotated regions from an annotated genome. Next, Stop-ORFs (StORFs) are identified in these unannotated regions. StORFs are open reading frames that are delimited by stop codons and thus can capture those genes most often missing in genome annotations. We show this methodology recovers genes missing from canonical genome annotations. We inspect the results of the genomes of model organisms, the pangenome of Escherichia coli, and a set of 5109 prokaryotic genomes of 247 genera from the Ensembl Bacteria database. StORF-Reporter extended the core, soft-core and accessory gene collections, identified novel gene families and extended families into additional genera. The high levels of sequence conservation observed between genera suggest that many of these StORFs are likely to be functional genes that should now be considered for inclusion in canonical annotations.
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Affiliation(s)
- Nicholas J Dimonaco
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth SY23 3PD, Wales, UK
- Department of Computer Science, Aberystwyth University, Aberystwyth SY23 3DB, Wales, UK
- Department of Medicine, McMaster University, Hamilton, ON, Canada
- Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, ON, Canada
- School of Biological Sciences, Queen’s University Belfast, Belfast BT7 1NN, Northern Ireland, UK
| | - Amanda Clare
- Department of Computer Science, Aberystwyth University, Aberystwyth SY23 3DB, Wales, UK
| | - Kim Kenobi
- Department of Mathematics, Aberystwyth University, Aberystwyth SY23 3BZ, Wales, UK
| | - Wayne Aubrey
- Department of Computer Science, Aberystwyth University, Aberystwyth SY23 3DB, Wales, UK
| | - Christopher J Creevey
- School of Biological Sciences, Queen’s University Belfast, Belfast BT7 1NN, Northern Ireland, UK
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7
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Manzano-Morales S, Liu Y, González-Bodí S, Huerta-Cepas J, Iranzo J. Comparison of gene clustering criteria reveals intrinsic uncertainty in pangenome analyses. Genome Biol 2023; 24:250. [PMID: 37904249 PMCID: PMC10614367 DOI: 10.1186/s13059-023-03089-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 10/16/2023] [Indexed: 11/01/2023] Open
Abstract
BACKGROUND A key step for comparative genomics is to group open reading frames into functionally and evolutionarily meaningful gene clusters. Gene clustering is complicated by intraspecific duplications and horizontal gene transfers that are frequent in prokaryotes. In consequence, gene clustering methods must deal with a trade-off between identifying vertically transmitted representatives of multicopy gene families, which are recognizable by synteny conservation, and retrieving complete sets of species-level orthologs. We studied the implications of adopting homology, orthology, or synteny conservation as formal criteria for gene clustering by performing comparative analyses of 125 prokaryotic pangenomes. RESULTS Clustering criteria affect pangenome functional characterization, core genome inference, and reconstruction of ancestral gene content to different extents. Species-wise estimates of pangenome and core genome sizes change by the same factor when using different clustering criteria, allowing robust cross-species comparisons regardless of the clustering criterion. However, cross-species comparisons of genome plasticity and functional profiles are substantially affected by inconsistencies among clustering criteria. Such inconsistencies are driven not only by mobile genetic elements, but also by genes involved in defense, secondary metabolism, and other accessory functions. In some pangenome features, the variability attributed to methodological inconsistencies can even exceed the effect sizes of ecological and phylogenetic variables. CONCLUSIONS Choosing an appropriate criterion for gene clustering is critical to conduct unbiased pangenome analyses. We provide practical guidelines to choose the right method depending on the research goals and the quality of genome assemblies, and a benchmarking dataset to assess the robustness and reproducibility of future comparative studies.
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Affiliation(s)
- Saioa Manzano-Morales
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain
- Barcelona Supercomputing Centre (BSC-CNS) - Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Yang Liu
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Sara González-Bodí
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain
| | - Jaime Huerta-Cepas
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain.
| | - Jaime Iranzo
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain.
- Institute for Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, Zaragoza, Spain.
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8
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Page CA, Pérez-Díaz IM, Pan M, Barrangou R. Genome-Wide Comparative Analysis of Lactiplantibacillus pentosus Isolates Autochthonous to Cucumber Fermentation Reveals Subclades of Divergent Ancestry. Foods 2023; 12:2455. [PMID: 37444193 DOI: 10.3390/foods12132455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/07/2023] [Accepted: 06/13/2023] [Indexed: 07/15/2023] Open
Abstract
Lactiplantibacillus pentosus, commonly isolated from commercial cucumber fermentation, is a promising candidate for starter culture formulation due to its ability to achieve complete sugar utilization to an end pH of 3.3. In this study, we conducted a comparative genomic analysis encompassing 24 L. pentosus and 3 Lactiplantibacillus plantarum isolates autochthonous to commercial cucumber fermentation and 47 lactobacillales reference genomes to determine species specificity and provide insights into niche adaptation. Results showed that metrics such as average nucleotide identity score, emulated Rep-PCR-(GTG)5, computed multi-locus sequence typing (MLST), and multiple open reading frame (ORF)-based phylogenetic trees can robustly and consistently distinguish the two closely related species. Phylogenetic trees based on the alignment of 587 common ORFs separated the L. pentosus autochthonous cucumber isolates from olive fermentation isolates into clade A and B, respectively. The L. pentosus autochthonous clade partitions into subclades A.I, A.II, and A.III, suggesting substantial intraspecies diversity in the cucumber fermentation habitat. The hypervariable sequences within CRISPR arrays revealed recent evolutionary history, which aligns with the L. pentosus subclades identified in the phylogenetic trees constructed. While L. plantarum autochthonous to cucumber fermentation only encode for Type II-A CRISPR arrays, autochthonous L. pentosus clade B codes for Type I-E and L. pentosus clade A hosts both types of arrays. L. pentosus 7.8.2, for which phylogeny could not be defined using the varied methods employed, was found to uniquely encode for four distinct Type I-E CRISPR arrays and a Type II-A array. Prophage sequences in varied isolates evidence the presence of adaptive immunity in the candidate starter cultures isolated from vegetable fermentation as observed in dairy counterparts. This study provides insight into the genomic features of industrial Lactiplantibacillus species, the level of species differentiation in a vegetable fermentation habitat, and diversity profile of relevance in the selection of functional starter cultures.
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Affiliation(s)
- Clinton A Page
- United States Department of Agriculture, Agricultural Research Service, SEA Food Science and Market Quality and Handling Research Unit, 322 Schaub Hall, Box 7624, Raleigh, NC 27695-7624, USA
| | - Ilenys M Pérez-Díaz
- United States Department of Agriculture, Agricultural Research Service, SEA Food Science and Market Quality and Handling Research Unit, 322 Schaub Hall, Box 7624, Raleigh, NC 27695-7624, USA
| | - Meichen Pan
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, 322 Schaub Hall, Box 7624, Raleigh, NC 27695-7624, USA
| | - Rodolphe Barrangou
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, 322 Schaub Hall, Box 7624, Raleigh, NC 27695-7624, USA
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9
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Madhu S, Sengupta A, Sarnaik AP, Sahasrabuddhe D, Wangikar PP. Global Transcriptome-Guided Identification of Neutral Sites for Engineering Synechococcus elongatus PCC 11801. ACS Synth Biol 2023; 12:1677-1685. [PMID: 37252895 DOI: 10.1021/acssynbio.3c00019] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Engineered cyanobacteria are attractive hosts for the phototrophic conversion of CO2 to chemicals. Synechococcus elongatus PCC11801, a novel, fast-growing, and stress-tolerant cyanobacterium, has the potential to be a platform cell factory, and hence, it necessitates the development of a synthetic biology toolbox. Considering the widely followed cyanobacterial engineering strategy of chromosomal integration of heterologous DNA, it is of interest to discover and validate new chromosomal neutral sites (NSs) in this strain. To that end, global transcriptome analysis was performed using RNA Seq under the conditions of high temperature (HT), carbon (HC), and salt (HS) and ambient growth conditions. We found upregulation of 445, 138, and 87 genes and downregulation of 333, 125, and 132 genes, under HC, HT, and HS, respectively. Following nonhierarchical clustering, gene enrichment, and bioinformatics analysis, 27 putative NSs were predicted. Six of them were experimentally tested, and five showed confirmed neutrality, based on unaltered cell growth. Thus, global transcriptomic analysis was effectively exploited for NS annotation and would be advantageous for multiplexed genome editing.
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Affiliation(s)
- Swati Madhu
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076 India
| | - Annesha Sengupta
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076 India
| | - Aditya P Sarnaik
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076 India
| | - Deepti Sahasrabuddhe
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076 India
| | - Pramod P Wangikar
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076 India
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10
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Abondio P, Cilli E, Luiselli D. Human Pangenomics: Promises and Challenges of a Distributed Genomic Reference. Life (Basel) 2023; 13:1360. [PMID: 37374141 DOI: 10.3390/life13061360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/02/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
A pangenome is a collection of the common and unique genomes that are present in a given species. It combines the genetic information of all the genomes sampled, resulting in a large and diverse range of genetic material. Pangenomic analysis offers several advantages compared to traditional genomic research. For example, a pangenome is not bound by the physical constraints of a single genome, so it can capture more genetic variability. Thanks to the introduction of the concept of pangenome, it is possible to use exceedingly detailed sequence data to study the evolutionary history of two different species, or how populations within a species differ genetically. In the wake of the Human Pangenome Project, this review aims at discussing the advantages of the pangenome around human genetic variation, which are then framed around how pangenomic data can inform population genetics, phylogenetics, and public health policy by providing insights into the genetic basis of diseases or determining personalized treatments, targeting the specific genetic profile of an individual. Moreover, technical limitations, ethical concerns, and legal considerations are discussed.
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Affiliation(s)
- Paolo Abondio
- Laboratory of Ancient DNA, Department of Cultural Heritage, University of Bologna, Via degli Ariani 1, 48121 Ravenna, Italy
| | - Elisabetta Cilli
- Laboratory of Ancient DNA, Department of Cultural Heritage, University of Bologna, Via degli Ariani 1, 48121 Ravenna, Italy
| | - Donata Luiselli
- Laboratory of Ancient DNA, Department of Cultural Heritage, University of Bologna, Via degli Ariani 1, 48121 Ravenna, Italy
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11
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Ngugi DK, Acinas SG, Sánchez P, Gasol JM, Agusti S, Karl DM, Duarte CM. Abiotic selection of microbial genome size in the global ocean. Nat Commun 2023; 14:1384. [PMID: 36914646 PMCID: PMC10011403 DOI: 10.1038/s41467-023-36988-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 02/27/2023] [Indexed: 03/14/2023] Open
Abstract
Strong purifying selection is considered a major evolutionary force behind small microbial genomes in the resource-poor photic ocean. However, very little is currently known about how the size of prokaryotic genomes evolves in the global ocean and whether patterns reflect shifts in resource availability in the epipelagic and relatively stable deep-sea environmental conditions. Using 364 marine microbial metagenomes, we investigate how the average genome size of uncultured planktonic prokaryotes varies across the tropical and polar oceans to the hadal realm. We find that genome size is highest in the perennially cold polar ocean, reflecting elongation of coding genes and gene dosage effects due to duplications in the interior ocean microbiome. Moreover, the rate of change in genome size due to temperature is 16-fold higher than with depth up to 200 m. Our results demonstrate how environmental factors can influence marine microbial genome size selection and ecological strategies of the microbiome.
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Affiliation(s)
- David K Ngugi
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.
| | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, CSIC, Barcelona, Spain
| | - Pablo Sánchez
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, CSIC, Barcelona, Spain
| | - Josep M Gasol
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, CSIC, Barcelona, Spain
| | - Susana Agusti
- King Abdullah University of Science and Technology, Red Sea Research Center, Thuwal, Saudi Arabia
| | - David M Karl
- Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawaií at Mãnoa, Honolulu, USA
| | - Carlos M Duarte
- King Abdullah University of Science and Technology, Red Sea Research Center, Thuwal, Saudi Arabia
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12
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Kugarajah V, Nisha KN, Jayakumar R, Sahabudeen S, Ramakrishnan P, Mohamed SB. Significance of microbial genome in environmental remediation. Microbiol Res 2023; 271:127360. [PMID: 36931127 DOI: 10.1016/j.micres.2023.127360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 02/27/2023] [Accepted: 03/08/2023] [Indexed: 03/11/2023]
Abstract
Environmental pollutants seriously threaten the ecosystem and health of various life forms, particularly with the rapid industrialization and emerging population. Conventionally physical and chemical strategies are being opted for the removal of these pollutants. Bioremediation, through several advancements, has been a boon to combat the existing threat faced today. Microbes with enzymes degrade various pollutants and utilize them as a carbon and energy source. With the existing demand and through several research explorations, Genetically Engineered Microorganisms (GEMs) have paved to be a successful approach to abate pollution through bioremediation. The genome of the microbe determines its biodegradative nature. Thus, methods including pure culture techniques and metagenomics are used for analyzing the genome of microbes, which provides information about catabolic genes. The information obtained along with the aid of biotechnology helps to construct GEMs that are cost-effective and safer thereby exhibiting higher degradation of pollutants. The present review focuses on the role of microbes in the degradation of environmental pollutants, role of evolution in habitat and adaptation of microbes, microbial degenerative genes, their pathways, and the efficacy of recombinant DNA (rDNA) technology for creating GEMs for bioremediation. The present review also provides a gist of existing GEMs for bioremediation and their limitations, thereby providing a future scope of implementation of these GEMs for a sustainable environment.
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Affiliation(s)
- Vaidhegi Kugarajah
- Department of Nanobiomaterials, Institute for Biomedical Engineering, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Chennai 602015, India
| | | | - R Jayakumar
- Department of Nanobiomaterials, Institute for Biomedical Engineering, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Chennai 602015, India
| | - S Sahabudeen
- Department of Biotechnology, SRM Institute of Science and Technology, Kanchipuram Dist, Kattankulathur, Tamil Nadu, India; Medical Team, Doctoral Institute for Evidence Based Policy, Tokyo, Japan
| | - P Ramakrishnan
- Department of Nanobiomaterials, Institute for Biomedical Engineering, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Chennai 602015, India.
| | - S B Mohamed
- Department of Materials Science, School of Technology, Central University of Tamil Nadu, Thiruvarur 610005, Tamil Nadu, India.
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13
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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: 0] [Impact Index Per Article: 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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14
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McInerney JO. Prokaryotic Pangenomes Act as Evolving Ecosystems. Mol Biol Evol 2022; 40:6775222. [PMID: 36288801 PMCID: PMC9851318 DOI: 10.1093/molbev/msac232] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/11/2022] [Accepted: 10/20/2022] [Indexed: 01/24/2023] Open
Abstract
Understanding adaptation to the local environment is a central tenet and a major focus of evolutionary biology. But this is only part of the adaptionist story. In addition to the external environment, one of the main drivers of genome composition is genetic background. In this perspective, I argue that there is a growing body of evidence that intra-genomic selective pressures play a significant part in the composition of prokaryotic genomes and play a significant role in the origin, maintenance and structuring of prokaryotic pangenomes.
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15
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Grouzdev D, Gaisin V, Lunina O, Krutkina M, Krasnova E, Voronov D, Baslerov R, Sigalevich P, Savvichev A, Gorlenko V. Microbial communities of stratified aquatic ecosystems of Kandalaksha Bay (White Sea) shed light on the evolutionary history of green and brown morphotypes of Chlorobiota. FEMS Microbiol Ecol 2022; 98:6693937. [PMID: 36073352 DOI: 10.1093/femsec/fiac103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 08/30/2022] [Accepted: 09/01/2022] [Indexed: 12/14/2022] Open
Abstract
Anoxygenic photoautotrophic metabolism of green sulfur bacteria of the family Chlorobiaceae played a significant role in establishing the Earth's biosphere. Two known major ecological forms of these phototrophs differ in their pigment composition and, therefore, in color: the green and brown forms. The latter form often occurs in low-light environments and is specialized to harvest blue light, which can penetrate to the greatest depth in the water column. In the present work, metagenomic sequencing was used to investigate the natural population of brown Chl. phaeovibrioides ZM in a marine stratified Zeleny Mys lagoon in the Kandalaksha Bay (the White Sea) to supplement the previously obtained genomes of brown Chlorobiaceae. The genomes of brown and green Chlorobiaceae were investigated using comparative genome analysis and phylogenetic and reconciliation analysis to reconstruct the evolution of these ecological forms. Our results support the suggestion that the last common ancestor of Chlorobiaceae belonged to the brown form, i.e. it was adapted to the conditions of low illumination. However, despite the vertical inheritance of these characteristics, among modern Chlorobiaceae populations, the genes responsible for synthesizing the pigments of the brown form are subject to active horizontal transfer.
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Affiliation(s)
- Denis Grouzdev
- SciBear OU, 10115 Tallinn, Estonia.,School of Marine and Atmospheric Sciences, Stony Brook University, 11794, Stony Brook, USA
| | - Vasil Gaisin
- Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russia.,Current affiliation: Institute of Molecular Biology & Biophysics, Eidgenössische Technische Hochschule Zürich, Zurich, Switzerland
| | - Olga Lunina
- Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russia
| | | | - Elena Krasnova
- Pertsov White Sea Biological Station, 184042, Republic Karelia, Russia
| | - Dmitry Voronov
- Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, 127051, Moscow, Russia
| | - Roman Baslerov
- Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russia
| | - Pavel Sigalevich
- Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russia
| | - Alexander Savvichev
- Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russia
| | - Vladimir Gorlenko
- Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russia
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16
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Wackett LP. Strategies for the Biodegradation of Polyfluorinated Compounds. Microorganisms 2022; 10:microorganisms10081664. [PMID: 36014082 PMCID: PMC9415301 DOI: 10.3390/microorganisms10081664] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/14/2022] [Accepted: 08/16/2022] [Indexed: 01/01/2023] Open
Abstract
Many cite the strength of C–F bonds for the poor microbial biodegradability of polyfluorinated organic compounds (PFCs). However, commercial PFCs almost invariably contain more functionality than fluorine. The additional functionality provides a weak entry point for reactions that activate C–F bonds and lead to their eventual cleavage. This metabolic activation strategy is common in microbial biodegradation pathways and is observed with aromatic hydrocarbons, chlorinated compounds, phosphonates and many other compounds. Initial metabolic activation precedes critical bond breakage and assimilation of nutrients. A similar strategy with commercial PFCs proceeds via initial attack at the non-fluorinated functionalities: sulfonates, carboxylates, chlorines, phenyl rings, or phosphonates. Metabolic transformation of these non-fluorinated groups can activate the C–F bonds, allowing more facile cleavage than a direct attack on the C–F bonds. Given that virtually all compounds denoted as “PFAS” are not perfluorinated and are not alkanes, it is posited here that considering their individual chemical classes is more useful for both chemical and microbiological considerations of their fate.
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Affiliation(s)
- Lawrence P Wackett
- Department of Biochemistry, Molecular Biology and Biophysics and BioTechnology Institute, University of Minnesota, Minneapolis, MN 55455, USA
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17
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Garza DR, von Meijenfeldt FAB, van Dijk B, Boleij A, Huynen MA, Dutilh BE. Nutrition or nature: using elementary flux modes to disentangle the complex forces shaping prokaryote pan-genomes. BMC Ecol Evol 2022; 22:101. [PMID: 35974327 PMCID: PMC9382767 DOI: 10.1186/s12862-022-02052-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 07/22/2022] [Indexed: 11/15/2022] Open
Abstract
Background Microbial pan-genomes are shaped by a complex combination of stochastic and deterministic forces. Even closely related genomes exhibit extensive variation in their gene content. Understanding what drives this variation requires exploring the interactions of gene products with each other and with the organism’s external environment. However, to date, conceptual models of pan-genome dynamics often represent genes as independent units and provide limited information about their mechanistic interactions. Results We simulated the stochastic process of gene-loss using the pooled genome-scale metabolic reaction networks of 46 taxonomically diverse bacterial and archaeal families as proxies for their pan-genomes. The frequency by which reactions are retained in functional networks when stochastic gene loss is simulated in diverse environments allowed us to disentangle the metabolic reactions whose presence depends on the metabolite composition of the external environment (constrained by “nutrition”) from those that are independent of the environment (constrained by “nature”). By comparing the frequency of reactions from the first group with their observed frequencies in bacterial and archaeal families, we predicted the metabolic niches that shaped the genomic composition of these lineages. Moreover, we found that the lineages that were shaped by a more diverse metabolic niche also occur in more diverse biomes as assessed by global environmental sequencing datasets. Conclusion We introduce a computational framework for analyzing and interpreting pan-reactomes that provides novel insights into the ecological and evolutionary drivers of pan-genome dynamics. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-022-02052-3.
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18
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Bremer N, Knopp M, Martin WF, Tria FDK. Realistic Gene Transfer to Gene Duplication Ratios Identify Different Roots in the Bacterial Phylogeny Using a Tree Reconciliation Method. LIFE (BASEL, SWITZERLAND) 2022; 12:life12070995. [PMID: 35888084 PMCID: PMC9322720 DOI: 10.3390/life12070995] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 06/29/2022] [Accepted: 07/01/2022] [Indexed: 11/29/2022]
Abstract
The rooting of phylogenetic trees permits important inferences about ancestral states and the polarity of evolutionary events. Recently, methods that reconcile discordance between gene-trees and species-trees—tree reconciliation methods—are becoming increasingly popular for rooting species trees. Rooting via reconciliation requires values for a particular parameter, the gene transfer to gene duplication ratio (T:D), which in current practice is estimated on the fly from discordances observed in the trees. To date, the accuracy of T:D estimates obtained by reconciliation analyses has not been compared to T:D estimates obtained by independent means, hence the effect of T:D upon inferences of species tree roots is altogether unexplored. Here we investigated the issue in detail by performing tree reconciliations of more than 10,000 gene trees under a variety of T:D ratios for two phylogenetic cases: a bacterial (prokaryotic) tree with 265 species and a fungal-metazoan (eukaryotic) tree with 31 species. We show that the T:D ratios automatically estimated by a current tree reconciliation method, ALE, generate virtually identical T:D ratios across bacterial genes and fungal-metazoan genes. The T:D ratios estimated by ALE differ 10- to 100-fold from robust, ALE-independent estimates from real data. More important is our finding that the root inferences using ALE in both datasets are strongly dependent upon T:D. Using more realistic T:D ratios, the number of roots inferred by ALE consistently increases and, in some cases, clearly incorrect roots are inferred. Furthermore, our analyses reveal that gene duplications have a far greater impact on ALE’s preferences for phylogenetic root placement than gene transfers or gene losses do. Overall, we show that obtaining reliable species tree roots with ALE is only possible when gene duplications are abundant in the data and the number of falsely inferred gene duplications is low. Finding a sufficient sample of true gene duplications for rooting species trees critically depends on the T:D ratios used in the analyses. T:D ratios, while being important parameters of genome evolution in their own right, affect the root inferences with tree reconciliations to an unanticipated degree.
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19
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Hogle SL, Hackl T, Bundy RM, Park J, Satinsky B, Hiltunen T, Biller S, Berube PM, Chisholm SW. Siderophores as an iron source for picocyanobacteria in deep chlorophyll maximum layers of the oligotrophic ocean. THE ISME JOURNAL 2022; 16:1636-1646. [PMID: 35241788 PMCID: PMC9122953 DOI: 10.1038/s41396-022-01215-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 02/08/2022] [Accepted: 02/14/2022] [Indexed: 11/09/2022]
Abstract
Prochlorococcus and Synechococcus are the most abundant photosynthesizing organisms in the oceans. Gene content variation among picocyanobacterial populations in separate ocean basins often mirrors the selective pressures imposed by the region's distinct biogeochemistry. By pairing genomic datasets with trace metal concentrations from across the global ocean, we show that the genomic capacity for siderophore-mediated iron uptake is widespread in Synechococcus and low-light adapted Prochlorococcus populations from deep chlorophyll maximum layers of iron-depleted regions of the oligotrophic Pacific and S. Atlantic oceans: Prochlorococcus siderophore consumers were absent in the N. Atlantic ocean (higher new iron flux) but constituted up to half of all Prochlorococcus genomes from metagenomes in the N. Pacific (lower new iron flux). Picocyanobacterial siderophore consumers, like many other bacteria with this trait, also lack siderophore biosynthesis genes indicating that they scavenge exogenous siderophores from seawater. Statistical modeling suggests that the capacity for siderophore uptake is endemic to remote ocean regions where atmospheric iron fluxes are the smallest, especially at deep chlorophyll maximum and primary nitrite maximum layers. We argue that abundant siderophore consumers at these two common oceanographic features could be a symptom of wider community iron stress, consistent with prior hypotheses. Our results provide a clear example of iron as a selective force driving the evolution of marine picocyanobacteria.
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Affiliation(s)
- Shane L Hogle
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA. .,Department of Biology, University of Turku, Turku, Finland.
| | - Thomas Hackl
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Randelle M Bundy
- School of Oceanography, University of Washington, Seattle, WA, USA
| | - Jiwoon Park
- School of Oceanography, University of Washington, Seattle, WA, USA
| | - Brandon Satinsky
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Teppo Hiltunen
- Department of Biology, University of Turku, Turku, Finland
| | - Steven Biller
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Biological Sciences, Wellesley College, Wellesley, MA, USA
| | - Paul M Berube
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sallie W Chisholm
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA. .,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
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20
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Botas J, Rodríguez Del Río Á, Giner-Lamia J, Huerta-Cepas J. GeCoViz: genomic context visualisation of prokaryotic genes from a functional and evolutionary perspective. Nucleic Acids Res 2022; 50:W352-W357. [PMID: 35639770 PMCID: PMC9252766 DOI: 10.1093/nar/gkac367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 04/14/2022] [Accepted: 05/05/2022] [Indexed: 11/14/2022] Open
Abstract
Synteny conservation analysis is a well-established methodology to investigate the potential functional role of unknown prokaryotic genes. However, bioinformatic tools to reconstruct and visualise genomic contexts usually depend on slow computations, are restricted to narrow taxonomic ranges, and/or do not allow for the functional and interactive exploration of neighbouring genes across different species. Here, we present GeCoViz, an online resource built upon 12 221 reference prokaryotic genomes that provides fast and interactive visualisation of custom genomic regions anchored by any target gene, which can be sought by either name, orthologous group (KEGGs, eggNOGs), protein domain (PFAM) or sequence. To facilitate functional and evolutionary interpretation, GeCoViz allows to customise the taxonomic scope of each analysis and provides comprehensive annotations of the neighbouring genes. Interactive visualisation options include, among others, the scaled representations of gene lengths and genomic distances, and on the fly calculation of synteny conservation of neighbouring genes, which can be highlighted based on custom thresholds. The resulting plots can be downloaded as high-quality images for publishing purposes. Overall, GeCoViz offers an easy-to-use, comprehensive, fast and interactive web-based tool for investigating the genomic context of prokaryotic genes, and is freely available at https://gecoviz.cgmlab.org.
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Affiliation(s)
- Jorge Botas
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Campus de Montegancedo-UPM, Madrid, 28223, Spain
| | - Álvaro Rodríguez Del Río
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Campus de Montegancedo-UPM, Madrid, 28223, Spain
| | - Joaquín Giner-Lamia
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Campus de Montegancedo-UPM, Madrid, 28223, Spain.,Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), Madrid, 28040, Spain
| | - Jaime Huerta-Cepas
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Campus de Montegancedo-UPM, Madrid, 28223, Spain
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21
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Martinez-Gutierrez CA, Aylward FO. Genome size distributions in bacteria and archaea are strongly linked to evolutionary history at broad phylogenetic scales. PLoS Genet 2022; 18:e1010220. [PMID: 35605022 PMCID: PMC9166353 DOI: 10.1371/journal.pgen.1010220] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 06/03/2022] [Accepted: 04/26/2022] [Indexed: 12/30/2022] Open
Abstract
The evolutionary forces that determine genome size in bacteria and archaea have been the subject of intense debate over the last few decades. Although the preferential loss of genes observed in prokaryotes is explained through the deletional bias, factors promoting and preventing the fixation of such gene losses often remain unclear. Importantly, statistical analyses on this topic typically do not consider the potential bias introduced by the shared ancestry of many lineages, which is critical when using species as data points because of the potential dependence on residuals. In this study, we investigated the genome size distributions across a broad diversity of bacteria and archaea to evaluate if this trait is phylogenetically conserved at broad phylogenetic scales. After model fit, Pagel’s lambda indicated a strong phylogenetic signal in genome size data, suggesting that the diversification of this trait is influenced by shared evolutionary histories. We used a phylogenetic generalized least-squares analysis (PGLS) to test whether phylogeny influences the predictability of genome size from dN/dS ratios and 16S copy number, two variables that have been previously linked to genome size. These results confirm that failure to account for evolutionary history can lead to biased interpretations of genome size predictors. Overall, our results indicate that although bacteria and archaea can rapidly gain and lose genetic material through gene transfers and deletions, respectively, phylogenetic signal for genome size distributions can still be recovered at broad phylogenetic scales that should be taken into account when inferring the drivers of genome size evolution. The evolutionary forces driving genome size in bacteria and archaea have been subject to debate during the last decades. Typically, independent comparative analyses have suggested that unique variables, such as the strength of selection, environmental complexity, and mutation rate, are the main drivers of this trait, without considering for potential biases derived from shared ancestry. Here, we applied a phylogeny-based statistical approach to assess how tightly genome size in bacteria and archaea is linked to evolutionary history. Moreover, we also evaluated the predictability of genome size from the strength of purifying selection and ecological strategy on a broad diversity of bacteria and archaea genomes under a phylogenetic comparative framework. Our approach indicates that despite the ability of bacteria and archaea to rapidly exchange genes, a strong phylogenetic signal to genome size distributions can be recovered at broad phylogenetic scales.
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Affiliation(s)
| | - Frank O. Aylward
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, United States of America
- Center for Emerging, Zoonotic, and Arthropod-borne Pathogens, Virginia Tech, Blacksburg, Virginia, United States of America
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22
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Importance of RpoD- and Non-RpoD-Dependent Expression of Horizontally Acquired Genes in Cupriavidus metallidurans. Microbiol Spectr 2022; 10:e0012122. [PMID: 35311568 PMCID: PMC9045368 DOI: 10.1128/spectrum.00121-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The genome of the metal-resistant, hydrogen-oxidizing bacterium Cupriavidus metallidurans contains a large number of horizontally acquired plasmids and genomic islands that were integrated into its chromosome or chromid. For the C. metallidurans CH34 wild-type strain growing under nonchallenging conditions, 5,763 transcriptional starting sequences (TSSs) were determined. Using a custom-built motif discovery software based on hidden Markov models, patterns upstream of the TSSs were identified. The pattern TTGACA, −35.6 ± 1.6 bp upstream of the TSSs, in combination with a TATAAT sequence 15.8 ± 1.4 bp upstream occurred frequently, especially upstream of the TSSs for 48 housekeeping genes, and these were assigned to promoters used by RNA polymerase containing the main housekeeping sigma factor RpoD. From patterns upstream of the housekeeping genes, a score for RpoD-dependent promoters in C. metallidurans was derived and applied to all 5,763 TSSs. Among these, 2,572 TSSs could be associated with RpoD with high probability, 373 with low probability, and 2,818 with no probability. In a detailed analysis of horizontally acquired genes involved in metal resistance and not involved in this process, the TSSs responsible for the expression of these genes under nonchallenging conditions were assigned to RpoD- or non-RpoD-dependent promoters. RpoD-dependent promoters occurred frequently in horizontally acquired metal resistance and other determinants, which should allow their initial expression in a new host. However, other sigma factors and sense/antisense effects also contribute—maybe to mold in subsequent adaptation steps the assimilated gene into the regulatory network of the cell. IMPORTANCE In their natural environment, bacteria are constantly acquiring genes by horizontal gene transfer. To be of any benefit, these genes should be expressed. We show here that the main housekeeping sigma factor RpoD plays an important role in the expression of horizontally acquired genes in the metal-resistant hydrogen-oxidizing bacterium C. metallidurans. By conservation of the RpoD recognition consensus sequence, a newly arriving gene has a high probability to be expressed in the new host cell. In addition to integrons and genes travelling together with that for their sigma factor, conservation of the RpoD consensus sequence may be an important contributor to the overall evolutionary success of horizontal gene transfer in bacteria. Using C. metallidurans as an example, this publication sheds some light on the fate and function of horizontally acquired genes in bacteria.
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23
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Abstract
Horizontal gene transfer (HGT) is arguably the most conspicuous feature of bacterial evolution. Evidence for HGT is found in most bacterial genomes. Although HGT can considerably alter bacterial genomes, not all transfer events may be biologically significant and may instead represent the outcome of an incessant evolutionary process that only occasionally has a beneficial purpose. When adaptive transfers occur, HGT and positive selection may result in specific, detectable signatures in genomes, such as gene-specific sweeps or increased transfer rates for genes that are ecologically relevant. In this Review, we first discuss the various mechanisms whereby HGT occurs, how the genetic signatures shape patterns of genomic variation and the distinct bioinformatic algorithms developed to detect these patterns. We then discuss the evolutionary theory behind HGT and positive selection in bacteria, and discuss the approaches developed over the past decade to detect transferred DNA that may be involved in adaptation to new environments.
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24
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Csűrös M. Gain-loss-duplication models for copy number evolution on a phylogeny: Exact algorithms for computing the likelihood and its gradient. Theor Popul Biol 2022; 145:80-94. [DOI: 10.1016/j.tpb.2022.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 03/07/2022] [Accepted: 03/10/2022] [Indexed: 10/18/2022]
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25
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Abstract
We apply the theory of learning to physically renormalizable systems in an attempt to outline a theory of biological evolution, including the origin of life, as multilevel learning. We formulate seven fundamental principles of evolution that appear to be necessary and sufficient to render a universe observable and show that they entail the major features of biological evolution, including replication and natural selection. It is shown that these cornerstone phenomena of biology emerge from the fundamental features of learning dynamics such as the existence of a loss function, which is minimized during learning. We then sketch the theory of evolution using the mathematical framework of neural networks, which provides for detailed analysis of evolutionary phenomena. To demonstrate the potential of the proposed theoretical framework, we derive a generalized version of the Central Dogma of molecular biology by analyzing the flow of information during learning (back propagation) and predicting (forward propagation) the environment by evolving organisms. The more complex evolutionary phenomena, such as major transitions in evolution (in particular, the origin of life), have to be analyzed in the thermodynamic limit, which is described in detail in the paper by Vanchurin et al. [V. Vanchurin, Y. I. Wolf, E. V. Koonin, M. I. Katsnelson, Proc. Natl. Acad. Sci. U.S.A. 119, 10.1073/pnas.2120042119 (2022)].
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Dong Y, Wu S, Fan H, Li X, Li Y, Xu S, Bai Z, Zhuang X. Ecological selection of bacterial taxa with larger genome sizes in response to polycyclic aromatic hydrocarbons stress. J Environ Sci (China) 2022; 112:82-93. [PMID: 34955225 DOI: 10.1016/j.jes.2021.04.027] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 04/24/2021] [Accepted: 04/25/2021] [Indexed: 05/15/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous priority pollutants that cause great damage to the natural environment and health. Average genome size in a community is critical for shedding light on microbiome's functional response to pollution stress within an environment. Here, microcosms under different concentrations were performed to evaluate the selection of PAHs stress on the average genome size in a community. We found the distinct communities of significantly larger genome size with the increase of PAHs concentration gradients in soils, and consistent trends were discovered in soils at different latitudes. The abundance of Proteobacteria and Deinococcus-Thermus with relatively larger genomes increased along with PAHs stress and well adapted to polluted environments. In contrast, the abundance of Patescibacteria with a highly streamlined and smaller genome decreased, implying complex interactions between environmental selection and functional fitness resulted in bacteria with larger genomes becoming more abundant. Moreover, we confirmed the increased capacity for horizontal transfer of degrading genes between communities by showing an increased connection number per node positively related to the nidA gene along the concentration gradients in the co-occurrence network. Our findings suggest PAHs tend to select bacterial taxa with larger genome sizes, with significant consequences for community stability and potential biodegradation strategies.
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Affiliation(s)
- Yuzhu Dong
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shanghua Wu
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haonan Fan
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xianglong Li
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yijing Li
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Sino-Danish Center, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shengjun Xu
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhihui Bai
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xuliang Zhuang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China.
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27
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Environmental stress leads to genome streamlining in a widely distributed species of soil bacteria. THE ISME JOURNAL 2022; 16:423-434. [PMID: 34408268 PMCID: PMC8776746 DOI: 10.1038/s41396-021-01082-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 07/14/2021] [Accepted: 07/28/2021] [Indexed: 02/07/2023]
Abstract
Bacteria have highly flexible pangenomes, which are thought to facilitate evolutionary responses to environmental change, but the impacts of environmental stress on pangenome evolution remain unclear. Using a landscape pangenomics approach, I demonstrate that environmental stress leads to consistent, continuous reduction in genome content along four environmental stress gradients (acidity, aridity, heat, salinity) in naturally occurring populations of Bradyrhizobium diazoefficiens (widespread soil-dwelling plant mutualists). Using gene-level network and duplication functional traits to predict accessory gene distributions across environments, genes predicted to be superfluous are more likely lost in high stress, while genes with multi-functional roles are more likely retained. Genes with higher probabilities of being lost with stress contain significantly higher proportions of codons under strong purifying and positive selection. Gene loss is widespread across the entire genome, with high gene-retention hotspots in close spatial proximity to core genes, suggesting Bradyrhizobium has evolved to cluster essential-function genes (accessory genes with multifunctional roles and core genes) in discrete genomic regions, which may stabilise viability during genomic decay. In conclusion, pangenome evolution through genome streamlining are important evolutionary responses to environmental change. This raises questions about impacts of genome streamlining on the adaptive capacity of bacterial populations facing rapid environmental change.
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28
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Cummins EA, Hall RJ, McInerney JO, McNally A. Prokaryote pangenomes are dynamic entities. Curr Opin Microbiol 2022; 66:73-78. [PMID: 35104691 DOI: 10.1016/j.mib.2022.01.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 01/07/2022] [Accepted: 01/11/2022] [Indexed: 11/24/2022]
Abstract
Prokaryote pangenomes are influenced heavily by environmental factors and the opportunity for gene gain and loss events. As the field of pangenome analysis has expanded, so has the need to fully understand the complexity of how eco-evolutionary dynamics shape pangenomes. Here, we describe current models of pangenome evolution and discuss their suitability and accuracy. We suggest that pangenomes are dynamic entities under constant flux, highlighting the influence of two-way interactions between pangenome and environment. New classifications of core and accessory genes are also considered, underscoring the need for continuous evaluation of nomenclature in a fast-moving field. We conclude that future models of pangenome evolution should incorporate eco-evolutionary dynamics to fully encompass their dynamic, changeable nature.
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Affiliation(s)
- Elizabeth A Cummins
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Rebecca J Hall
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK.
| | - James O McInerney
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Alan McNally
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK.
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29
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van Dijk B, Bertels F, Stolk L, Takeuchi N, Rainey PB. Transposable elements promote the evolution of genome streamlining. Philos Trans R Soc Lond B Biol Sci 2022; 377:20200477. [PMID: 34839699 PMCID: PMC8628081 DOI: 10.1098/rstb.2020.0477] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Accepted: 08/30/2021] [Indexed: 12/25/2022] Open
Abstract
Eukaryotes and prokaryotes have distinct genome architectures, with marked differences in genome size, the ratio of coding/non-coding DNA, and the abundance of transposable elements (TEs). As TEs replicate independently of their hosts, the proliferation of TEs is thought to have driven genome expansion in eukaryotes. However, prokaryotes also have TEs in intergenic spaces, so why do prokaryotes have small, streamlined genomes? Using an in silico model describing the genomes of single-celled asexual organisms that coevolve with TEs, we show that TEs acquired from the environment by horizontal gene transfer can promote the evolution of genome streamlining. The process depends on local interactions and is underpinned by rock-paper-scissors dynamics in which populations of cells with streamlined genomes beat TEs, which beat non-streamlined genomes, which beat streamlined genomes, in continuous and repeating cycles. Streamlining is maladaptive to individual cells, but improves lineage viability by hindering the proliferation of TEs. Streamlining does not evolve in sexually reproducing populations because recombination partially frees TEs from the deleterious effects they cause. This article is part of the theme issue 'The secret lives of microbial mobile genetic elements'.
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Affiliation(s)
- Bram van Dijk
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Frederic Bertels
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Lianne Stolk
- Theoretical Biology, Department of Biology, Utrecht University, The Netherlands
| | - Nobuto Takeuchi
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Paul B. Rainey
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany
- Laboratory of Biophysics and Evolution, CBI, ESPCI Paris, Université PSL, CNRS, Paris, France
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30
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Coelho LP, Alves R, del Río ÁR, Myers PN, Cantalapiedra CP, Giner-Lamia J, Schmidt TS, Mende DR, Orakov A, Letunic I, Hildebrand F, Van Rossum T, Forslund SK, Khedkar S, Maistrenko OM, Pan S, Jia L, Ferretti P, Sunagawa S, Zhao XM, Nielsen HB, Huerta-Cepas J, Bork P. Towards the biogeography of prokaryotic genes. Nature 2022; 601:252-256. [PMID: 34912116 PMCID: PMC7613196 DOI: 10.1038/s41586-021-04233-4] [Citation(s) in RCA: 61] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Accepted: 11/12/2021] [Indexed: 12/19/2022]
Abstract
Microbial genes encode the majority of the functional repertoire of life on earth. However, despite increasing efforts in metagenomic sequencing of various habitats1-3, little is known about the distribution of genes across the global biosphere, with implications for human and planetary health. Here we constructed a non-redundant gene catalogue of 303 million species-level genes (clustered at 95% nucleotide identity) from 13,174 publicly available metagenomes across 14 major habitats and use it to show that most genes are specific to a single habitat. The small fraction of genes found in multiple habitats is enriched in antibiotic-resistance genes and markers for mobile genetic elements. By further clustering these species-level genes into 32 million protein families, we observed that a small fraction of these families contain the majority of the genes (0.6% of families account for 50% of the genes). The majority of species-level genes and protein families are rare. Furthermore, species-level genes, and in particular the rare ones, show low rates of positive (adaptive) selection, supporting a model in which most genetic variability observed within each protein family is neutral or nearly neutral.
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Affiliation(s)
- Luis Pedro Coelho
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China. .,MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, and MOE Frontiers Center for Brain Science, Shanghai, China. .,Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
| | - Renato Alves
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Álvaro Rodríguez del Río
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain
| | - Pernille Neve Myers
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Carlos P. Cantalapiedra
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain
| | - Joaquín Giner-Lamia
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain,Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), Madrid, Spain
| | - Thomas Sebastian Schmidt
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Daniel R. Mende
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany,Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawai’i at Mānoa, Honolulu, HI, USA
| | - Askarbek Orakov
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | | | - Falk Hildebrand
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany,Earlham Institute, Norwich Research Park, Norwich, UK,Gut Health and Microbes Programme, Quadram Institute, Norwich Research Park, Norwich, UK
| | - Thea Van Rossum
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Sofia K. Forslund
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany,Experimental and Clinical Research Center (ECRC), a joint venture of the Max Delbrück Centre (MDC) and Charité University Hospital, Berlin, Germany,Berlin Initiative of Health, Berlin, Germany
| | - Supriya Khedkar
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Oleksandr M. Maistrenko
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Shaojun Pan
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China,MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, and MOE Frontiers Center for Brain Science, Shanghai, China
| | - Longhao Jia
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China,MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, and MOE Frontiers Center for Brain Science, Shanghai, China
| | - Pamela Ferretti
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Shinichi Sunagawa
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany,Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich, Switzerland
| | - Xing-Ming Zhao
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China,MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, and MOE Frontiers Center for Brain Science, Shanghai, China
| | | | - Jaime Huerta-Cepas
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany. .,Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain.
| | - Peer Bork
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany. .,Max Delbrück Centre for Molecular Medicine, Berlin, Germany. .,Yonsei Frontier Lab (YFL), Yonsei University, Seoul, South Korea. .,Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany.
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31
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Li Y, Jiang B, Dai W. A large-scale whole-genome sequencing analysis reveals false positives of bacterial essential genes. Appl Microbiol Biotechnol 2021; 106:341-347. [PMID: 34889987 DOI: 10.1007/s00253-021-11702-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 11/05/2021] [Accepted: 11/15/2021] [Indexed: 11/26/2022]
Abstract
Essential genes are crucial for bacterial viability and represent attractive targets for novel anti-pathogen drug discovery. However, essential genes determined by the transposon insertion sequencing (Tn-seq) approach often contain many false positives. We hypothesized that some of those false positives are genes that are actually deleted from the genome, so they do not present any transposon insertion in the course of Tn-seq analysis. Based on this assumption, we performed a large-scale whole-genome sequencing analysis for the bacterium of interest. Our analysis revealed that some "essential genes" are indeed removed from the analyzed bacterial genomes. Since these genes were kicked out by bacteria, they should not be defined as essential. Our work showed that gene deletion is one of the false positive sources of essentiality determination, which is apparently underestimated in previous studies. We suggest subtracting the genome backgrounds before the evaluation of Tn-seq, and created a list of false positive gene essentiality as a reference for the downstream application. KEY POINTS: • Discovery of false positives of essential genes defined previously through the analyses of a large scale of whole-genome sequencing data • These false positives are the results of gene deletions in the studied genomes • Sequencing the target genome before Tn-seq analysis is of importance while some studies neglected it.
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Affiliation(s)
- Yuanhao Li
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510006, China
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou, 510642, China
| | - Bo Jiang
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510006, China
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou, 510642, China
| | - Weijun Dai
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510006, China.
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou, 510642, China.
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32
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Dimonaco NJ, Aubrey W, Kenobi K, Clare A, Creevey CJ. No one tool to rule them all: prokaryotic gene prediction tool annotations are highly dependent on the organism of study. Bioinformatics 2021; 38:1198-1207. [PMID: 34875010 PMCID: PMC8825762 DOI: 10.1093/bioinformatics/btab827] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 11/13/2021] [Accepted: 12/02/2021] [Indexed: 01/06/2023] Open
Abstract
MOTIVATION The biases in CoDing Sequence (CDS) prediction tools, which have been based on historic genomic annotations from model organisms, impact our understanding of novel genomes and metagenomes. This hinders the discovery of new genomic information as it results in predictions being biased towards existing knowledge. To date, users have lacked a systematic and replicable approach to identify the strengths and weaknesses of any CDS prediction tool and allow them to choose the right tool for their analysis. RESULTS We present an evaluation framework (ORForise) based on a comprehensive set of 12 primary and 60 secondary metrics that facilitate the assessment of the performance of CDS prediction tools. This makes it possible to identify which performs better for specific use-cases. We use this to assess 15 ab initio- and model-based tools representing those most widely used (historically and currently) to generate the knowledge in genomic databases. We find that the performance of any tool is dependent on the genome being analysed, and no individual tool ranked as the most accurate across all genomes or metrics analysed. Even the top-ranked tools produced conflicting gene collections, which could not be resolved by aggregation. The ORForise evaluation framework provides users with a replicable, data-led approach to make informed tool choices for novel genome annotations and for refining historical annotations. AVAILABILITY AND IMPLEMENTATION Code and datasets for reproduction and customisation are available at https://github.com/NickJD/ORForise. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Nicholas J Dimonaco
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth SY23 3PD, UK,To whom correspondence should be addressed.
| | - Wayne Aubrey
- Department of Computer Science, Aberystwyth University, Aberystwyth SY23 3DB, UK
| | - Kim Kenobi
- Department of Mathematics, Aberystwyth University, Aberystwyth SY23 3BZ, UK
| | - Amanda Clare
- Department of Computer Science, Aberystwyth University, Aberystwyth SY23 3DB, UK
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33
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Heringer P, Kuhn GCS. Pif1 helicases and the evidence for a prokaryotic origin of Helitrons. Mol Biol Evol 2021; 39:6440065. [PMID: 34850089 PMCID: PMC8788227 DOI: 10.1093/molbev/msab334] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Helitrons are the only group of rolling-circle transposons that encode a transposase with a helicase domain (Hel), which belongs to the Pif1 family. Because Pif1 helicases are important components of eukaryotic genomes, it has been suggested that Hel domains probably originated after a host eukaryotic Pif1 gene was captured by a Helitron ancestor. However, the few analyses exploring the evolution of Helitron transposases (RepHel) have focused on its Rep domain, which is also present in other mobile genetic elements. Here, we used phylogenetic and nonmetric multidimensional scaling analyses to investigate the relationship between Hel domains and Pif1-like helicases from a variety of organisms. Our results reveal that Hel domains are only distantly related to genomic helicases from eukaryotes and prokaryotes, and thus are unlikely to have originated from a captured Pif1 gene. Based on this evidence, and on recent studies indicating that Rep domains are more closely related to rolling-circle plasmids and phages, we suggest that Helitrons are descendants of a RepHel-encoding prokaryotic plasmid element that invaded eukaryotic genomes before the radiation of its major groups. We discuss how a Pif1-like helicase domain might have favored the transposition of Helitrons in eukaryotes beyond simply unwinding DNA intermediates. Finally, we demonstrate that some examples in the literature describing genomic helicases from eukaryotes actually consist of Hel domains from Helitrons, a finding that underscores how transposons can hamper the analysis of eukaryotic genes. This investigation also revealed that two groups of land plants appear to have lost genomic Pif1 helicases independently.
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Affiliation(s)
- Pedro Heringer
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, CEP, 31270-901, Brazil
| | - Gustavo C S Kuhn
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, CEP, 31270-901, Brazil
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34
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Lee IPA, Eldakar OT, Gogarten JP, Andam CP. Bacterial cooperation through horizontal gene transfer. Trends Ecol Evol 2021; 37:223-232. [PMID: 34815098 DOI: 10.1016/j.tree.2021.11.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/27/2021] [Accepted: 11/01/2021] [Indexed: 11/16/2022]
Abstract
Cooperation exists across all scales of biological organization, from genetic elements to complex human societies. Bacteria cooperate by secreting molecules that benefit all individuals in the population (i.e., public goods). Genes associated with cooperation can spread among strains through horizontal gene transfer (HGT). We discuss recent findings on how HGT mediated by mobile genetic elements promotes bacterial cooperation, how cooperation in turn can facilitate more frequent HGT, and how the act of HGT itself may be considered as a form of cooperation. We propose that HGT is an important enforcement mechanism in bacterial populations, thus creating a positive feedback loop that further maintains cooperation. To enforce cooperation, HGT serves as a homogenizing force by transferring the cooperative trait, effectively eliminating cheaters.
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Affiliation(s)
- Isaiah Paolo A Lee
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA
| | - Omar Tonsi Eldakar
- Department of Biological Sciences, Nova Southeastern University, Fort Lauderdale, FL 33314, USA
| | - J Peter Gogarten
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA.
| | - Cheryl P Andam
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY 12222, USA.
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35
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Douglas GM, Shapiro BJ. Genic Selection Within Prokaryotic Pangenomes. Genome Biol Evol 2021; 13:6402011. [PMID: 34665261 PMCID: PMC8598171 DOI: 10.1093/gbe/evab234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/14/2021] [Indexed: 11/13/2022] Open
Abstract
Understanding the evolutionary forces shaping prokaryotic pangenome structure is a major goal of microbial evolution research. Recent work has highlighted that a substantial proportion of accessory genes appear to confer niche-specific adaptations. This work has primarily focused on selection acting at the level of individual cells. Herein, we discuss a lower level of selection that also contributes to pangenome variation: genic selection. This refers to cases where genetic elements, rather than individual cells, are the entities under selection. The clearest examples of this form of selection are selfish mobile genetic elements, which are those that have either a neutral or a deleterious effect on host fitness. We review the major classes of these and other mobile elements and discuss the characteristic features of such elements that could be under genic selection. We also discuss how genetic elements that are beneficial to hosts can also be under genic selection, a scenario that may be more prevalent but not widely appreciated, because disentangling the effects of selection at different levels (i.e., organisms vs. genes) is challenging. Nonetheless, an appreciation for the potential action and implications of genic selection is important to better understand the evolution of prokaryotic pangenomes.
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Affiliation(s)
- Gavin M Douglas
- Department of Microbiology and Immunology, McGill University, Montréal, Québec, Canada
| | - B Jesse Shapiro
- Department of Microbiology and Immunology, McGill University, Montréal, Québec, Canada
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36
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Shukla N, Prasad A, Kanga U, Suravajhala R, Nigam VK, Kishor PBK, Polavarapu R, Chaubey G, Singh KK, Suravajhala P. SARS-CoV-2 transgressing LncRNAs uncovers the known unknowns. Physiol Genomics 2021; 53:433-440. [PMID: 34492207 PMCID: PMC8562947 DOI: 10.1152/physiolgenomics.00075.2021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/27/2021] [Accepted: 08/31/2021] [Indexed: 12/21/2022] Open
Abstract
SARS-CoV-2 harbors many known unknown regions in the form of hypothetical open reading frames (ORFs). Although the mechanisms underlying the disease pathogenesis are not clearly understood, molecules such as long noncoding RNAs (lncRNAs) play a key regulatory role in the viral pathogenesis from endocytosis. We asked whether or not the lncRNAs in the host are associated with the viral proteins and argue that lncRNA-mRNAs molecules related to viral infection may regulate SARS-CoV-2 pathogenesis. Toward the end of the perspective, we provide challenges and insights into investigating these transgression pathways.
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Affiliation(s)
- Nidhi Shukla
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Jaipur, India
- Department of Chemistry, Manipal University Jaipur, Jaipur, India
| | - Anchita Prasad
- Department of Bioengineering, Birla Institute of Technology Mesra, Ranchi, India
| | - Uma Kanga
- Department of Transplant Immunology and Immunogenetics, AIIMS, New Delhi, India
| | | | - Vinod Kumar Nigam
- Department of Bioengineering, Birla Institute of Technology Mesra, Ranchi, India
| | - P B Kavi Kishor
- Department of Biotechnology, Vignan's Foundation for Science, Technology & Research (VFSTR), Guntur, India
| | | | - Gyaneshwer Chaubey
- Cytogenetics Lab, Department of Zoology, Banaras Hindu University, Varanasi, India
| | - Keshav K Singh
- Department of Genetics, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Prashanth Suravajhala
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Jaipur, India
- Bioclues Organization, Hyderabad, India
- Amrita School of Biotechnology, Amrita University, Amritapuri, Kerala, India
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37
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Tria FDK, Martin WF. Gene Duplications Are At Least 50 Times Less Frequent than Gene Transfers in Prokaryotic Genomes. Genome Biol Evol 2021; 13:6380140. [PMID: 34599337 PMCID: PMC8536544 DOI: 10.1093/gbe/evab224] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/22/2021] [Indexed: 12/20/2022] Open
Abstract
The contribution of gene duplications to the evolution of eukaryotic genomes is well studied. By contrast, studies of gene duplications in prokaryotes are scarce and generally limited to a handful of genes or careful analysis of a few prokaryotic lineages. Systematic broad-scale studies of prokaryotic genomes that sample available data are lacking, leaving gaps in our understanding of the contribution of gene duplications as a source of genetic novelty in the prokaryotic world. Here, we report conservative and robust estimates for the frequency of recent gene duplications within prokaryotic genomes relative to recent lateral gene transfer (LGT), as mechanisms to generate multiple copies of related sequences in the same genome. We obtain our estimates by focusing on evolutionarily recent events among 5,655 prokaryotic genomes, thereby avoiding vagaries of deep phylogenetic inference and confounding effects of ancient events and differential loss. We find that recent, genome-specific gene duplications are at least 50 times less frequent and probably 100 times less frequent than recent, genome-specific, gene acquisitions via LGT. The frequency of gene duplications varies across lineages and functional categories. The findings improve our understanding of genome evolution in prokaryotes and have far-reaching implications for evolutionary models that entail LGT to gene duplications ratio as a parameter.
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Affiliation(s)
- Fernando D K Tria
- Department of Biology, Institute for Molecular Evolution, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - William F Martin
- Department of Biology, Institute for Molecular Evolution, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
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38
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Banerjee R, Chaudhari NM, Lahiri A, Gautam A, Bhowmik D, Dutta C, Chattopadhyay S, Huson DH, Paul S. Interplay of Various Evolutionary Modes in Genome Diversification and Adaptive Evolution of the Family Sulfolobaceae. Front Microbiol 2021; 12:639995. [PMID: 34248865 PMCID: PMC8267890 DOI: 10.3389/fmicb.2021.639995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 05/06/2021] [Indexed: 11/21/2022] Open
Abstract
Sulfolobaceae family, comprising diverse thermoacidophilic and aerobic sulfur-metabolizing Archaea from various geographical locations, offers an ideal opportunity to infer the evolutionary dynamics across the members of this family. Comparative pan-genomics coupled with evolutionary analyses has revealed asymmetric genome evolution within the Sulfolobaceae family. The trend of genome streamlining followed by periods of differential gene gains resulted in an overall genome expansion in some species of this family, whereas there was reduction in others. Among the core genes, both Sulfolobus islandicus and Saccharolobus solfataricus showed a considerable fraction of positively selected genes and also higher frequencies of gene acquisition. In contrast, Sulfolobus acidocaldarius genomes experienced substantial amount of gene loss and strong purifying selection as manifested by relatively lower genome size and higher genome conservation. Central carbohydrate metabolism and sulfur metabolism coevolved with the genome diversification pattern of this archaeal family. The autotrophic CO2 fixation with three significant positively selected enzymes from S. islandicus and S. solfataricus was found to be more imperative than heterotrophic CO2 fixation for Sulfolobaceae. Overall, our analysis provides an insight into the interplay of various genomic adaptation strategies including gene gain-loss, mutation, and selection influencing genome diversification of Sulfolobaceae at various taxonomic levels and geographical locations.
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Affiliation(s)
- Rachana Banerjee
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Narendrakumar M. Chaudhari
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Abhishake Lahiri
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Anupam Gautam
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, Kolkata, India
| | - Debaleena Bhowmik
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Chitra Dutta
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Sujay Chattopadhyay
- JIS Institute of Advanced Studies and Research, JIS University, Kolkata, India
| | - Daniel H. Huson
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, Germany
- Cluster of Excellence: Controlling Microbes to Fight Infection, Tübingen, Germany
| | - Sandip Paul
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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39
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N'Guessan A, Brito IL, Serohijos AWR, Shapiro BJ. Mobile Gene Sequence Evolution within Individual Human Gut Microbiomes Is Better Explained by Gene-Specific Than Host-Specific Selective Pressures. Genome Biol Evol 2021; 13:6300526. [PMID: 34132784 PMCID: PMC8358218 DOI: 10.1093/gbe/evab142] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/10/2021] [Indexed: 01/03/2023] Open
Abstract
Pangenomes—the cumulative set of genes encoded by a population or species—arise from the interplay of horizontal gene transfer, drift, and selection. The balance of these forces in shaping pangenomes has been debated, and studies to date focused on ancient evolutionary time scales have suggested that pangenomes generally confer niche adaptation to their bacterial hosts. To shed light on pangenome evolution on shorter evolutionary time scales, we inferred the selective pressures acting on mobile genes within individual human microbiomes from 176 Fiji islanders. We mapped metagenomic sequence reads to a set of known mobile genes to identify single nucleotide variants (SNVs) and calculated population genetic metrics to infer deviations from a neutral evolutionary model. We found that mobile gene sequence evolution varied more by gene family than by human social attributes, such as household or village. Patterns of mobile gene sequence evolution could be qualitatively recapitulated with a simple evolutionary simulation without the need to invoke the adaptive value of mobile genes to either bacterial or human hosts. These results stand in contrast with the apparent adaptive value of pangenomes over longer evolutionary time scales. In general, the most highly mobile genes (i.e., those present in more distinct bacterial host genomes) tend to have higher metagenomic read coverage and an excess of low-frequency SNVs, consistent with their rapid spread across multiple bacterial species in the gut. However, a subset of mobile genes—including those involved in defense mechanisms and secondary metabolism—showed a contrasting signature of intermediate-frequency SNVs, indicating species-specific selective pressures or negative frequency-dependent selection on these genes. Together, our evolutionary models and population genetic data show that gene-specific selective pressures predominate over human or bacterial host-specific pressures during the relatively short time scales of a human lifetime.
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Affiliation(s)
- Arnaud N'Guessan
- Departement de Biochimie, Université de Montréal, Québec, Canada.,Centre Robert-Cedergren en Bio-informatique et Génomique, Université de Montréal, Québec, Canada
| | - Ilana Lauren Brito
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York, USA
| | - Adrian W R Serohijos
- Departement de Biochimie, Université de Montréal, Québec, Canada.,Centre Robert-Cedergren en Bio-informatique et Génomique, Université de Montréal, Québec, Canada
| | - B Jesse Shapiro
- Département de Sciences Biologiques, Complexe des Sciences, Université de Montréal, Québec, Canada.,Department of Microbiology and Immunology, McGill University, Montreal, Québec, Canada.,McGill Genome Centre, Montreal, Québec, Canada
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40
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Unexpectedly high mutation rate of a deep-sea hyperthermophilic anaerobic archaeon. THE ISME JOURNAL 2021; 15:1862-1869. [PMID: 33452477 PMCID: PMC8163891 DOI: 10.1038/s41396-020-00888-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 12/14/2020] [Accepted: 12/16/2020] [Indexed: 01/29/2023]
Abstract
Deep-sea hydrothermal vents resemble the early Earth, and thus the dominant Thermococcaceae inhabitants, which occupy an evolutionarily basal position of the archaeal tree and take an obligate anaerobic hyperthermophilic free-living lifestyle, are likely excellent models to study the evolution of early life. Here, we determined that unbiased mutation rate of a representative species, Thermococcus eurythermalis, exceeded that of all known free-living prokaryotes by 1-2 orders of magnitude, and thus rejected the long-standing hypothesis that low mutation rates were selectively favored in hyperthermophiles. We further sequenced multiple and diverse isolates of this species and calculated that T. eurythermalis has a lower effective population size than other free-living prokaryotes by 1-2 orders of magnitude. These data collectively indicate that the high mutation rate of this species is not selectively favored but instead driven by random genetic drift. The availability of these unusual data also helps explore mechanisms underlying microbial genome size evolution. We showed that genome size is negatively correlated with mutation rate and positively correlated with effective population size across 30 bacterial and archaeal lineages, suggesting that increased mutation rate and random genetic drift are likely two important mechanisms driving microbial genome reduction. Future determinations of the unbiased mutation rate of more representative lineages with highly reduced genomes such as Prochlorococcus and Pelagibacterales that dominate marine microbial communities are essential to test these hypotheses.
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Coleman GA, Davín AA, Mahendrarajah TA, Szánthó LL, Spang A, Hugenholtz P, Szöllősi GJ, Williams TA. A rooted phylogeny resolves early bacterial evolution. Science 2021; 372:372/6542/eabe0511. [PMID: 33958449 DOI: 10.1126/science.abe0511] [Citation(s) in RCA: 89] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 11/05/2020] [Accepted: 04/01/2021] [Indexed: 12/17/2022]
Abstract
A rooted bacterial tree is necessary to understand early evolution, but the position of the root is contested. Here, we model the evolution of 11,272 gene families to identify the root, extent of horizontal gene transfer (HGT), and the nature of the last bacterial common ancestor (LBCA). Our analyses root the tree between the major clades Terrabacteria and Gracilicutes and suggest that LBCA was a free-living flagellated, rod-shaped double-membraned organism. Contrary to recent proposals, our analyses reject a basal placement of the Candidate Phyla Radiation, which instead branches sister to Chloroflexota within Terrabacteria. While most gene families (92%) have evidence of HGT, overall, two-thirds of gene transmissions have been vertical, suggesting that a rooted tree provides a meaningful frame of reference for interpreting bacterial evolution.
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Affiliation(s)
- Gareth A Coleman
- School of Biological Sciences, University of Bristol, Bristol BS8 1TQ, UK
| | - Adrián A Davín
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Tara A Mahendrarajah
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, 1790 AB Den Burg, Netherlands
| | - Lénárd L Szánthó
- Department of Biological Physics, Eötvös Loránd University, 1117 Budapest, Hungary.,MTA-ELTE "Lendület" Evolutionary Genomics Research Group, 1117 Budapest, Hungary
| | - Anja Spang
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, 1790 AB Den Burg, Netherlands.,Department of Cell- and Molecular Biology, Uppsala University, SE-75123 Uppsala, Sweden
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia.
| | - Gergely J Szöllősi
- Department of Biological Physics, Eötvös Loránd University, 1117 Budapest, Hungary. .,MTA-ELTE "Lendület" Evolutionary Genomics Research Group, 1117 Budapest, Hungary.,Institute of Evolution, Centre for Ecological Research, 1121 Budapest, Hungary
| | - Tom A Williams
- School of Biological Sciences, University of Bristol, Bristol BS8 1TQ, UK.
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42
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Abstract
Plasmids play an important role in bacterial evolution by transferring niche-adaptive functional genes between lineages, thus driving genomic diversification. Bacterial genomes commonly contain multiple, coexisting plasmid replicons, which could fuel adaptation by increasing the range of gene functions available to selection and allowing their recombination. However, plasmid coexistence is difficult to explain because the acquisition of plasmids typically incurs high fitness costs for the host cell. Here, we show that plasmid coexistence was stably maintained without positive selection for plasmid-borne gene functions and was associated with compensatory evolution to reduce fitness costs. In contrast, with positive selection, plasmid coexistence was unstable despite compensatory evolution. Positive selection discriminated between differential fitness benefits of functionally redundant plasmid replicons, retaining only the more beneficial plasmid. These data suggest that while the efficiency of negative selection against plasmid fitness costs declines over time due to compensatory evolution, positive selection to maximize plasmid-derived fitness benefits remains efficient. Our findings help to explain the forces structuring bacterial genomes: coexistence of multiple plasmids in a genome is likely to require either rare positive selection in nature or nonredundancy of accessory gene functions among the coexisting plasmids.
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43
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Thompson CL, Alberti M, Barve S, Battistuzzi FU, Drake JL, Goncalves GC, Govaert L, Partridge C, Yang Y. Back to the future: Reintegrating biology to understand how past eco-evolutionary change can predict future outcomes. Integr Comp Biol 2021; 61:2218-2232. [PMID: 33964141 DOI: 10.1093/icb/icab068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
During the last few decades, biologists have made remarkable progress in understanding the fundamental processes that shape life. But despite the unprecedented level of knowledge now available, large gaps still remain in our understanding of the complex interplay of eco-evolutionary mechanisms across scales of life. Rapidly changing environments on Earth provide a pressing need to understand the potential implications of eco-evolutionary dynamics, which can be achieved by improving existing eco-evolutionary models and fostering convergence among the sub-fields of biology. We propose a new, data-driven approach that harnesses our knowledge of the functioning of biological systems to expand current conceptual frameworks and develop corresponding models that can more accurately represent and predict future eco-evolutionary outcomes. We suggest a roadmap toward achieving this goal. This long-term vision will move biology in a direction that can wield these predictive models for scientific applications that benefit humanity and increase the resilience of natural biological systems. We identify short, medium, and long-term key objectives to connect our current state of knowledge to this long-term vision, iteratively progressing across three stages: 1) utilizing knowledge of biological systems to better inform eco-evolutionary models, 2) generating models with more accurate predictions, and 3) applying predictive models to benefit the biosphere. Within each stage, we outline avenues of investigation and scientific applications related to the timescales over which evolution occurs, the parameter space of eco-evolutionary processes, and the dynamic interactions between these mechanisms. The ability to accurately model, monitor, and anticipate eco-evolutionary changes would be transformational to humanity's interaction with the global environment, providing novel tools to benefit human health, protect the natural world, and manage our planet's biosphere.
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Affiliation(s)
| | - Marina Alberti
- Department of Urban Design and Planning, University of Washington,
| | - Sahas Barve
- Smithsonian National Museum of Natural History,
| | | | - Jeana L Drake
- Department of Earth, Planetary, and Space Sciences, University of California Los Angeles,
| | | | - Lynn Govaert
- Department of Evolutionary Biology and Environmental Studies, University of Zurich; Department of Aquatic Ecology, Swiss Federal Institute of Aquatic Science and Technology, URPP Global Change and Biodiversity, University of Zurich,
| | | | - Ya Yang
- Department of Plant and Microbial Biology, University of Minnesota,
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44
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Shaw LP, Chau KK, Kavanagh J, AbuOun M, Stubberfield E, Gweon HS, Barker L, Rodger G, Bowes MJ, Hubbard ATM, Pickford H, Swann J, Gilson D, Smith RP, Hoosdally SJ, Sebra R, Brett H, Peto TEA, Bailey MJ, Crook DW, Read DS, Anjum MF, Walker AS, Stoesser N. Niche and local geography shape the pangenome of wastewater- and livestock-associated Enterobacteriaceae. SCIENCE ADVANCES 2021; 7:eabe3868. [PMID: 33837077 PMCID: PMC8034854 DOI: 10.1126/sciadv.abe3868] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 02/22/2021] [Indexed: 05/07/2023]
Abstract
Escherichia coli and other Enterobacteriaceae are diverse species with "open" pangenomes, where genes move intra- and interspecies via horizontal gene transfer. However, most analyses focus on clinical isolates. The pangenome dynamics of natural populations remain understudied, despite their suggested role as reservoirs for antimicrobial resistance (AMR) genes. Here, we analyze near-complete genomes for 827 Enterobacteriaceae (553 Escherichia and 274 non-Escherichia spp.) with 2292 circularized plasmids in total, collected from 19 locations (livestock farms and wastewater treatment works in the United Kingdom) within a 30-km radius at three time points over a year. We find different dynamics for chromosomal and plasmid-borne genes. Plasmids have a higher burden of AMR genes and insertion sequences, and AMR-gene-carrying plasmids show evidence of being under stronger selective pressure. Environmental niche and local geography both play a role in shaping plasmid dynamics. Our results highlight the importance of local strategies for controlling the spread of AMR.
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Affiliation(s)
- Liam P Shaw
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK.
| | - Kevin K Chau
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
| | - James Kavanagh
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
| | - Manal AbuOun
- Department of Bacteriology, Animal and Plant Health Agency (APHA), Woodham Lane, Addlestone, Surrey KT15 3NB, UK
| | - Emma Stubberfield
- Department of Bacteriology, Animal and Plant Health Agency (APHA), Woodham Lane, Addlestone, Surrey KT15 3NB, UK
| | - H Soon Gweon
- UK Centre for Ecology & Hydrology (UKCEH), Benson Lane, Crowmarsh Gifford, Wallingford OX10 8BB, UK
- School of Biological Sciences, University of Reading, Reading RG6 6AS, UK
| | - Leanne Barker
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Gillian Rodger
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Mike J Bowes
- UK Centre for Ecology & Hydrology (UKCEH), Benson Lane, Crowmarsh Gifford, Wallingford OX10 8BB, UK
| | - Alasdair T M Hubbard
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
| | - Hayleah Pickford
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Jeremy Swann
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford OX4 9DU, UK
| | - Daniel Gilson
- Department of Epidemiological Sciences, The Animal and Plant Health Agency (APHA), Woodham Lane, Addlestone, Surrey KT15 3NB, UK
| | - Richard P Smith
- Department of Epidemiological Sciences, The Animal and Plant Health Agency (APHA), Woodham Lane, Addlestone, Surrey KT15 3NB, UK
| | - Sarah J Hoosdally
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Sema4, a Mount Sinai venture, 333 Ludlow Street, North Tower, 8th floor, Stamford, CT 06902, USA
| | - Howard Brett
- Thames Water Utilities, Clearwater Court, Vastern Road, Reading RG1 8DB, UK
| | - Tim E A Peto
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford OX3 9DU, UK
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford OX4 9DU, UK
| | - Mark J Bailey
- UK Centre for Ecology & Hydrology (UKCEH), Benson Lane, Crowmarsh Gifford, Wallingford OX10 8BB, UK
| | - Derrick W Crook
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford OX3 9DU, UK
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford OX4 9DU, UK
| | - Daniel S Read
- UK Centre for Ecology & Hydrology (UKCEH), Benson Lane, Crowmarsh Gifford, Wallingford OX10 8BB, UK
| | - Muna F Anjum
- Department of Bacteriology, Animal and Plant Health Agency (APHA), Woodham Lane, Addlestone, Surrey KT15 3NB, UK
| | - A Sarah Walker
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford OX3 9DU, UK
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford OX4 9DU, UK
| | - Nicole Stoesser
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK.
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford OX3 9DU, UK
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Ionescu D, Zoccarato L, Zaduryan A, Schorn S, Bizic M, Pinnow S, Cypionka H, Grossart HP. Heterozygous, Polyploid, Giant Bacterium, Achromatium, Possesses an Identical Functional Inventory Worldwide across Drastically Different Ecosystems. Mol Biol Evol 2021; 38:1040-1059. [PMID: 33169788 PMCID: PMC7947748 DOI: 10.1093/molbev/msaa273] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Achromatium is large, hyperpolyploid and the only known heterozygous bacterium. Single cells contain approximately 300 different chromosomes with allelic diversity far exceeding that typically harbored by single bacteria genera. Surveying all publicly available sediment sequence archives, we show that Achromatium is common worldwide, spanning temperature, salinity, pH, and depth ranges normally resulting in bacterial speciation. Although saline and freshwater Achromatium spp. appear phylogenetically separated, the genus Achromatium contains a globally identical, complete functional inventory regardless of habitat. Achromatium spp. cells from differing ecosystems (e.g., from freshwater to saline) are, unexpectedly, equally functionally equipped but differ in gene expression patterns by transcribing only relevant genes. We suggest that environmental adaptation occurs by increasing the copy number of relevant genes across the cell's hundreds of chromosomes, without losing irrelevant ones, thus maintaining the ability to survive in any ecosystem type. The functional versatility of Achromatium and its genomic features reveal alternative genetic and evolutionary mechanisms, expanding our understanding of the role and evolution of polyploidy in bacteria while challenging the bacterial species concept and drivers of bacterial speciation.
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Affiliation(s)
- Danny Ionescu
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Neuglobsow, Germany
- Berlin Brandenburg Institute of Biodiversity, Berlin, Germany
| | - Luca Zoccarato
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Neuglobsow, Germany
| | - Artur Zaduryan
- Department of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Sina Schorn
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Mina Bizic
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Neuglobsow, Germany
- Berlin Brandenburg Institute of Biodiversity, Berlin, Germany
| | - Solvig Pinnow
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Neuglobsow, Germany
| | - Heribert Cypionka
- Institute for Chemistry and Biology of the Marine Environment, Oldenburg, Germany
| | - Hans-Peter Grossart
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Neuglobsow, Germany
- Berlin Brandenburg Institute of Biodiversity, Berlin, Germany
- Institute of Biochemistry and Biology, Potsdam University, Potsdam, Germany
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46
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Sela I, Wolf YI, Koonin EV. Assessment of assumptions underlying models of prokaryotic pangenome evolution. BMC Biol 2021; 19:27. [PMID: 33563283 PMCID: PMC7874442 DOI: 10.1186/s12915-021-00960-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 01/15/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The genomes of bacteria and archaea evolve by extensive loss and gain of genes which, for any group of related prokaryotic genomes, result in the formation of a pangenome with the universal, asymmetrical U-shaped distribution of gene commonality. However, the evolutionary factors that define the specific shape of this distribution are not thoroughly understood. RESULTS We investigate the fit of simple models of genome evolution to the empirically observed gene commonality distributions and genome intersections for 33 groups of closely related bacterial genomes. A model with an infinite external gene pool available for gene acquisition and constant genome size (IGP-CGS model), and two gene turnover rates, one for slow- and the other one for fast-evolving genes, allows two approaches to estimate the parameters for gene content dynamics. One is by fitting the model prediction to the distribution of the number of genes shared by precisely k genomes (gene commonality distribution) and another by analyzing the distribution of the number of genes common for k genome sets (k-cores). Both approaches produce a comparable overall quality of fit, although the former significantly overestimates the number of the universally conserved genes, while the latter overestimates the number of singletons. We further explore the effect of dropping each of the assumptions of the IGP-CGS model on the fit to the gene commonality distributions and show that models with either a finite gene pool or unequal rates of gene loss and gain (greater gene loss rate) eliminate the overestimate of the number of singletons or the core genome size. CONCLUSIONS We examine the assumptions that are usually adopted for modeling the evolution of the U-shaped gene commonality distributions in prokaryote genomes, namely, those of infinitely many genes and constant genome size. The combined analysis of genome intersections and gene commonality suggests that at least one of these assumptions is invalid. The violation of both these assumptions reflects the limited ability of prokaryotes to gain new genes. This limitation seems to stem, at least partly, from the horizontal gene transfer barrier, i.e., the cost of accommodation of foreign genes by prokaryotes. Further development of models taking into account the complexity of microbial evolution is necessary for an improved understanding of the evolution of prokaryotes.
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Affiliation(s)
- Itamar Sela
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA.
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA.
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47
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Nielsen DA, Fierer N, Geoghegan JL, Gillings MR, Gumerov V, Madin JS, Moore L, Paulsen IT, Reddy TBK, Tetu SG, Westoby M. Aerobic bacteria and archaea tend to have larger and more versatile genomes. OIKOS 2021. [DOI: 10.1111/oik.07912] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
| | - Noah Fierer
- Dept of Ecology and Evolutionary Biology, Cooperative Inst. for Research in Environmental Sciences, Univ. of Colorado Boulder CO USA
| | - Jemma L. Geoghegan
- Dept of Biological Sciences, Macquarie Univ. Sydney NSW Australia
- Dept of Microbiology and Immunology, Univ. of Otago New Zealand
| | | | - Vadim Gumerov
- Dept of Microbiology, Ohio State Univ. Columbus Ohio USA
| | - Joshua S. Madin
- Hawaii Inst. of Marine Biology, Univ. of Hawaii Kaneohe HI USA
| | - Lisa Moore
- Dept of Molecular Sciences, Macquarie Univ. Sydney NSW Australia
| | | | - T. B. K. Reddy
- Dept of Molecular Sciences, Macquarie Univ. Sydney NSW Australia
| | - Sasha G. Tetu
- Dept of Molecular Sciences, Macquarie Univ. Sydney NSW Australia
| | - Mark Westoby
- Dept of Biological Sciences, Macquarie Univ. Sydney NSW Australia
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48
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Koonin EV, Makarova KS, Wolf YI. Evolution of Microbial Genomics: Conceptual Shifts over a Quarter Century. Trends Microbiol 2021; 29:582-592. [PMID: 33541841 DOI: 10.1016/j.tim.2021.01.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 01/07/2021] [Accepted: 01/08/2021] [Indexed: 12/20/2022]
Abstract
Prokaryote genomics started in earnest in 1995, with the complete sequences of two small bacterial genomes, those of Haemophilus influenzae and Mycoplasma genitalium. During the next quarter century, the prokaryote genome database has been growing exponentially, with no saturation in sight. For most of these 25 years, genome sequencing remained limited to cultivable microbes. Together with next-generation sequencing methods, advances in metagenomics and single-cell genomics have lifted this limitation, providing for an increasingly unbiased characterization of the global prokaryote diversity. Advances in computational genomics followed the progress of genome sequencing, even if occasionally lagging behind. Several major new branches of bacteria and archaea were discovered, including Asgard archaea, the apparent closest relatives of eukaryotes and expansive groups of bacteria and archaea with small genomes thought to be symbionts of other prokaryotes. Comparative analysis of numerous prokaryote genomes spanning a wide range of evolutionary distances changed the conceptual foundations of microbiology, supplanting the notion of species genomes with fixed gene sets with that of dynamic pangenomes and the notion of a single Tree of Life (ToL) with a statistical tree-like trend among individual gene trees. Strides were also made towards a theory and quantitative laws of prokaryote genome evolution.
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Affiliation(s)
- Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA.
| | - Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
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49
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Domingo-Sananes MR, McInerney JO. Mechanisms That Shape Microbial Pangenomes. Trends Microbiol 2021; 29:493-503. [PMID: 33423895 DOI: 10.1016/j.tim.2020.12.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 12/09/2020] [Accepted: 12/10/2020] [Indexed: 01/02/2023]
Abstract
Analyses of multiple whole-genome sequences from the same species have revealed that differences in gene content can be substantial, particularly in prokaryotes. Such variation has led to the recognition of pangenomes, the complete set of genes present in a species - consisting of core genes, present in all individuals, and accessory genes whose presence is variable. Questions now arise about how pangenomes originate and evolve. We describe how gene content variation can arise as a result of the combination of several processes, including random drift, selection, gain/loss balance, and the influence of ecological and epistatic interactions. We believe that identifying the contributions of these processes to pangenomes will need novel theoretical approaches and empirical data.
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Affiliation(s)
- Maria Rosa Domingo-Sananes
- School of Life Sciences, University of Nottingham, Nottingham, UK; School of Science and Technology, Nottingham Trent University, Nottingham, UK.
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50
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Benler S, Koonin EV. Phage lysis‐lysogeny switches and programmed cell death: Danse macabre. Bioessays 2020; 42:e2000114. [DOI: 10.1002/bies.202000114] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 08/25/2020] [Indexed: 01/04/2023]
Affiliation(s)
- Sean Benler
- National Center for Biotechnology Information National Library of Medicine National Institutes of Health Bethesda Maryland USA
| | - Eugene V. Koonin
- National Center for Biotechnology Information National Library of Medicine National Institutes of Health Bethesda Maryland USA
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