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Radical genome remodelling accompanied the emergence of a novel host-restricted bacterial pathogen. PLoS Pathog 2021; 17:e1009606. [PMID: 34015034 PMCID: PMC8171923 DOI: 10.1371/journal.ppat.1009606] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 06/02/2021] [Accepted: 05/03/2021] [Indexed: 11/19/2022] Open
Abstract
The emergence of new pathogens is a major threat to public and veterinary health. Changes in bacterial habitat such as a switch in host or disease tropism are typically accompanied by genetic diversification. Staphylococcus aureus is a multi-host bacterial species associated with human and livestock infections. A microaerophilic subspecies, Staphylococcus aureus subsp. anaerobius, is responsible for Morel’s disease, a lymphadenitis restricted to sheep and goats. However, the evolutionary history of S. aureus subsp. anaerobius and its relatedness to S. aureus are unknown. Population genomic analyses of clinical S. aureus subsp. anaerobius isolates revealed a highly conserved clone that descended from a S. aureus progenitor about 1000 years ago before differentiating into distinct lineages that contain African and European isolates. S. aureus subsp. anaerobius has undergone limited clonal expansion, with a restricted population size, and an evolutionary rate 10-fold slower than S. aureus. The transition to its current restricted ecological niche involved acquisition of a pathogenicity island encoding a ruminant host-specific effector of abscess formation, large chromosomal re-arrangements, and the accumulation of at least 205 pseudogenes, resulting in a highly fastidious metabolism. Importantly, expansion of ~87 insertion sequences (IS) located largely in intergenic regions provided distinct mechanisms for the control of expression of flanking genes, including a novel mechanism associated with IS-mediated anti-anti-sense decoupling of ancestral gene repression. Our findings reveal the remarkable evolutionary trajectory of a host-restricted bacterial pathogen that resulted from extensive remodelling of the S. aureus genome through an array of diverse mechanisms in parallel. The emergence of new pathogens is a major threat to public and veterinary health. Some bacteria such as Staphylococcus aureus, have the capacity to infect many different host species including humans and livestock while others such as the closely-related S. aureus subsp. anaerobius, associated with a single type of pathology called Morel’s disease in small ruminants, are highly niche-restricted. However, our understanding of the genetic basis for such differences in bacterial host-tropism is very limited. Here, we discovered that S. aureus subsp. anaerobius evolved from an S. aureus ancestor and underwent an array of extensive changes to its genome that accompanied the transition to its current restricted lifestyle. We observed genome decay involving loss of function of hundreds of genes, large intra-chromosomal rearrangements affecting most of the genome, acquisition of a pathogenicity island, and expansion of large numbers of insertion sequences that are inserted at intergenic sites around the genome. Importantly, we found that IS elements affect the expression of neighbouring genes in different ways including a novel mechanism of IS-enabled disruption of ancestral gene repression. Taken together, we provide a remarkable example of radical genomic changes associated with evolutionary transition from a multi-host to highly restricted host ecology.
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Michel CJ. Genes on the circular code alphabet. Biosystems 2021; 206:104431. [PMID: 33894288 DOI: 10.1016/j.biosystems.2021.104431] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 04/15/2021] [Accepted: 04/15/2021] [Indexed: 02/07/2023]
Abstract
The X motifs, motifs from the circular code X, are enriched in the (protein coding) genes of bacteria, archaea, eukaryotes, plasmids and viruses, moreover, in the minimal gene set belonging to the three domains of life, as well as in tRNA and rRNA sequences. They allow to retrieve, maintain and synchronize the reading frame in genes, and contribute to the regulation of gene expression. These results lead here to a theoretical study of genes based on the circular code alphabet. A new occurrence relation of the circular code X under the hypothesis of an equiprobable (balanced) strand pairing is given. Surprisingly, a statistical analysis of a large set of bacterial genes retrieves this relation on the circular code alphabet, but not on the DNA alphabet. Furthermore, the circular code X has the strongest balanced circular code pairing among 216 maximal C3 self-complementary trinucleotide circular codes, a new property of this circular code X. As an application of this theory, different tRNAs studied on the circular code alphabet reveal an unexpected stem structure. Thus, the circular code X would have constructed a coding stem in tRNAs as an outline of the future gene structure and the future DNA double helix.
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Affiliation(s)
- Christian J Michel
- Theoretical Bioinformatics, ICube, CNRS, University of Strasbourg, 300 Boulevard Sébastien Brant, 67400 Illkirch, France.
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Abstract
Host-adapted microorganisms are generally assumed to have evolved from free-living, environmental microorganisms, as examples of the reverse process are rare. In the phylum Gammaproteobacteria, family Moraxellaceae, the genus Psychrobacter includes strains from a broad ecological distribution including animal bodies as well as sea ice and other nonhost environments. To elucidate the relationship between these ecological niches and Psychrobacter's evolutionary history, we performed tandem genomic analyses with phenotyping of 85 Psychrobacter accessions. Phylogenomic analysis of the family Moraxellaceae reveals that basal members of the Psychrobacter clade are Moraxella spp., a group of often-pathogenic organisms. Psychrobacter exhibited two broad growth patterns in our phenotypic screen: one group that we called the "flexible ecotype" (FE) had the ability to grow between 4 and 37°C, and the other, which we called the "restricted ecotype" (RE), could grow between 4 and 25°C. The FE group includes phylogenetically basal strains, and FE strains exhibit increased transposon copy numbers, smaller genomes, and a higher likelihood to be bile salt resistant. The RE group contains only phylogenetically derived strains and has increased proportions of lipid metabolism and biofilm formation genes, functions that are adaptive to cold stress. In a 16S rRNA gene survey of polar bear fecal samples, we detect both FE and RE strains, but in in vivo colonizations of gnotobiotic mice, only FE strains persist. Our results indicate the ability to grow at 37°C, seemingly necessary for mammalian gut colonization, is an ancestral trait for Psychrobacter, which likely evolved from a pathobiont.IMPORTANCE Host-associated microbes are generally assumed to have evolved from free-living ones. The evolutionary transition of microbes in the opposite direction, from host associated toward free living, has been predicted based on phylogenetic data but not studied in depth. Here, we provide evidence that the genus Psychrobacter, particularly well known for inhabiting low-temperature, high-salt environments such as sea ice, permafrost soils, and frozen foodstuffs, has evolved from a mammalian-associated ancestor. We show that some Psychrobacter strains retain seemingly ancestral genomic and phenotypic traits that correspond with host association while others have diverged to psychrotrophic or psychrophilic lifestyles.
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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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Contribution of horizontal gene transfer to the functionality of microbial biofilm on a macroalgae. THE ISME JOURNAL 2021; 15:807-817. [PMID: 33558686 PMCID: PMC8027169 DOI: 10.1038/s41396-020-00815-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 10/12/2020] [Accepted: 10/15/2020] [Indexed: 01/30/2023]
Abstract
Horizontal gene transfer (HGT) is thought to be an important driving force for microbial evolution and niche adaptation and has been show in vitro to occur frequently in biofilm communities. However, the extent to which HGT takes place and what functions are being transferred in more complex and natural biofilm systems remains largely unknown. To address this issue, we investigated here HGT and enrichment of gene functions in the biofilm community of the common kelp (macroalgae) Ecklonia radiata in comparison to microbial communities in the surrounding seawater. We found that HGTs in the macroalgal biofilms were dominated by transfers between bacterial members of the same class or order and frequently involved genes for nutrient transport, sugar and phlorotannin degradation as well as stress responses, all functions that would be considered beneficial for bacteria living in this particular niche. HGT did not appear to be driven by mobile gene elements, indicating rather an involvement of unspecific DNA uptake (e.g. natural transformation). There was also a low overlap between the gene functions subject to HGT and those enriched in the biofilm community in comparison to planktonic community members. This indicates that much of the functionality required for bacteria to live in an E. radiata biofilm might be derived from vertical or environmental transmissions of symbionts. This study enhances our understanding of the relative role of evolutionary and ecological processes in driving community assembly and genomic diversity of biofilm communities.
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Lobb B, Tremblay BJM, Moreno-Hagelsieb G, Doxey AC. An assessment of genome annotation coverage across the bacterial tree of life. Microb Genom 2020; 6. [PMID: 32124724 PMCID: PMC7200070 DOI: 10.1099/mgen.0.000341] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Although gene-finding in bacterial genomes is relatively straightforward, the automated assignment of gene function is still challenging, resulting in a vast quantity of hypothetical sequences of unknown function. But how prevalent are hypothetical sequences across bacteria, what proportion of genes in different bacterial genomes remain unannotated, and what factors affect annotation completeness? To address these questions, we surveyed over 27 000 bacterial genomes from the Genome Taxonomy Database, and measured genome annotation completeness as a function of annotation method, taxonomy, genome size, 'research bias' and publication date. Our analysis revealed that 52 and 79 % of the average bacterial proteome could be functionally annotated based on protein and domain-based homology searches, respectively. Annotation coverage using protein homology search varied significantly from as low as 14 % in some species to as high as 98 % in others. We found that taxonomy is a major factor influencing annotation completeness, with distinct trends observed across the microbial tree (e.g. the lowest level of completeness was found in the Patescibacteria lineage). Most lineages showed a significant association between genome size and annotation incompleteness, likely reflecting a greater degree of uncharacterized sequences in 'accessory' proteomes than in 'core' proteomes. Finally, research bias, as measured by publication volume, was also an important factor influencing genome annotation completeness, with early model organisms showing high completeness levels relative to other genomes in their own taxonomic lineages. Our work highlights the disparity in annotation coverage across the bacterial tree of life and emphasizes a need for more experimental characterization of accessory proteomes as well as understudied lineages.
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Affiliation(s)
- Briallen Lobb
- Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1, Canada
| | | | - Gabriel Moreno-Hagelsieb
- Department of Biology, Wilfrid Laurier University, 75 University Avenue West, Waterloo, ON, Canada
| | - Andrew C Doxey
- Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1, Canada
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Liu Z, Feng J, Yu B, Ma Q, Liu B. The functional determinants in the organization of bacterial genomes. Brief Bioinform 2020; 22:5892344. [PMID: 32793986 DOI: 10.1093/bib/bbaa172] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 06/30/2020] [Accepted: 07/07/2020] [Indexed: 12/13/2022] Open
Abstract
Bacterial genomes are now recognized as interacting intimately with cellular processes. Uncovering organizational mechanisms of bacterial genomes has been a primary focus of researchers to reveal the potential cellular activities. The advances in both experimental techniques and computational models provide a tremendous opportunity for understanding these mechanisms, and various studies have been proposed to explore the organization rules of bacterial genomes associated with functions recently. This review focuses mainly on the principles that shape the organization of bacterial genomes, both locally and globally. We first illustrate local structures as operons/transcription units for facilitating co-transcription and horizontal transfer of genes. We then clarify the constraints that globally shape bacterial genomes, such as metabolism, transcription and replication. Finally, we highlight challenges and opportunities to advance bacterial genomic studies and provide application perspectives of genome organization, including pathway hole assignment and genome assembly and understanding disease mechanisms.
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Affiliation(s)
| | | | - Bin Yu
- College of Mathematics and Physics, Qingdao University of Science and Technology
| | - Qin Ma
- Department of Biomedical Informatics, the Ohio State University
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58
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Owusu-Darko R, Allam M, Ismail A, Ferreira CAS, de Oliveira SD, Buys EM. Comparative Genome Analysis of Bacillus sporothermodurans with Its Closest Phylogenetic Neighbor, Bacillus oleronius, and Bacillus cereus and Bacillus subtilis Groups. Microorganisms 2020; 8:microorganisms8081185. [PMID: 32759699 PMCID: PMC7464528 DOI: 10.3390/microorganisms8081185] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 07/22/2020] [Accepted: 07/23/2020] [Indexed: 12/26/2022] Open
Abstract
Bacillus sporothermodurans currently possesses one of the most highly heat-resistant spores (HRS), which can withstand ultra-high temperature (UHT) processing. Determination of multiple whole genome sequences of B. sporothermodurans provided an opportunity to perform the first comparative genome analysis between strains and with B. oleronius, B. cereus, and B. subtilis groups. In this study, five whole genome sequences of B. sporothermodurans strains, including those belonging to the HRS clone (SAD and BR12) normally isolated from UHT milk, were compared with the aforementioned Bacillus species for gene clusters responsible for heat resistance. In the phylogenomic analysis, B. sporothermodurans, with its closest phylogenetic neighbor, B. oleronius, clustered with B. thermoamylovorans and B. thermotolerans. Heat shock proteins GrpE, GroES, GroEL, and DnaK presented identical sequences for all B. sporothermodurans strains, indicating that differences in functional efficiency are not involved in the thermal resistance variations. However, comparing all species evaluated, B. sporothermodurans exhibited a different gene configuration in the chromosomal region of the heat shock protein GrpE. Furthermore, only B. sporothermodurans strains presented the stage II sporulation protein P gene located in this region. Multisequence alignment and phylogenetic analysis of the ClpB protein showed differences for HRS and non-HRS strains. The study identified ClpC, ClpE, and ClpX as the three ATPases putatively involved in protein disaggregation in B. sporothermodurans. Bacillussporothermodurans exhibits high homology with other Bacillus species in the DnaK, DnaJ, GroEL, and GroES cluster of genes involved in heat resistance. The data presented here pave the way to select and evaluate the phenotypic effects of genes putatively involved in heat resistance.
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Affiliation(s)
- Rodney Owusu-Darko
- Department of Consumer and Food Sciences, University of Pretoria, Private Bag X20, Hatfield, Pretoria 0028, South Africa;
| | - Mushal Allam
- National Institute for Communicable Diseases, Private Bag X4, Sandringham, Johannesburg 2131, South Africa; (M.A.); (A.I.)
| | - Arshad Ismail
- National Institute for Communicable Diseases, Private Bag X4, Sandringham, Johannesburg 2131, South Africa; (M.A.); (A.I.)
| | - Carlos A. S. Ferreira
- Laboratory of Immunology and Microbiology, School of Health and Life Sciences, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre 90619-900, Brazil;
| | - Sílvia D. de Oliveira
- Laboratory of Immunology and Microbiology, School of Health and Life Sciences, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre 90619-900, Brazil;
- Correspondence: (S.D.d.O.); (E.M.B.)
| | - Elna M. Buys
- Department of Consumer and Food Sciences, University of Pretoria, Private Bag X20, Hatfield, Pretoria 0028, South Africa;
- Correspondence: (S.D.d.O.); (E.M.B.)
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59
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Boguszewska K, Szewczuk M, Kaźmierczak-Barańska J, Karwowski BT. The Similarities between Human Mitochondria and Bacteria in the Context of Structure, Genome, and Base Excision Repair System. Molecules 2020; 25:E2857. [PMID: 32575813 PMCID: PMC7356350 DOI: 10.3390/molecules25122857] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 06/17/2020] [Accepted: 06/19/2020] [Indexed: 02/06/2023] Open
Abstract
Mitochondria emerged from bacterial ancestors during endosymbiosis and are crucial for cellular processes such as energy production and homeostasis, stress responses, cell survival, and more. They are the site of aerobic respiration and adenosine triphosphate (ATP) production in eukaryotes. However, oxidative phosphorylation (OXPHOS) is also the source of reactive oxygen species (ROS), which are both important and dangerous for the cell. Human mitochondria contain mitochondrial DNA (mtDNA), and its integrity may be endangered by the action of ROS. Fortunately, human mitochondria have repair mechanisms that allow protecting mtDNA and repairing lesions that may contribute to the occurrence of mutations. Mutagenesis of the mitochondrial genome may manifest in the form of pathological states such as mitochondrial, neurodegenerative, and/or cardiovascular diseases, premature aging, and cancer. The review describes the mitochondrial structure, genome, and the main mitochondrial repair mechanism (base excision repair (BER)) of oxidative lesions in the context of common features between human mitochondria and bacteria. The authors present a holistic view of the similarities of mitochondria and bacteria to show that bacteria may be an interesting experimental model for studying mitochondrial diseases, especially those where the mechanism of DNA repair is impaired.
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Affiliation(s)
| | | | | | - Bolesław T. Karwowski
- DNA Damage Laboratory of Food Science Department, Faculty of Pharmacy, Medical University of Lodz, ul. Muszynskiego 1, 90-151 Lodz, Poland; (K.B.); (M.S.); (J.K.-B.)
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Gonçalves OS, Campos KF, de Assis JCS, Fernandes AS, Souza TS, do Carmo Rodrigues LG, Queiroz MVD, Santana MF. Transposable elements contribute to the genome plasticity of Ralstonia solanacearum species complex. Microb Genom 2020; 6. [PMID: 32379020 PMCID: PMC7371123 DOI: 10.1099/mgen.0.000374] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The extensive genetic diversity of Ralstonia solanacearum, a serious soil-borne phytopathogen, has led to the concept that R. solanacearum encompasses a species complex [R. solanacearum species complex (RSSC)]. Insertion sequences (ISs) are suggested to play an important role in the genome evolution of this pathogen. Here, we identified and analysed transposable elements (TEs), ISs and transposons, in 106 RSSC genomes and 15 Ralstonia spp. We mapped 10 259 IS elements in the complete genome of 62 representative RSSC strains and closely related Ralstonia spp. A unique set of 20 IS families was widespread across the strains, IS5 and IS3 being the most abundant. Our results showed six novel transposon sequences belonging to the Tn3 family carrying passenger genes encoding antibiotic resistance and avirulence proteins. In addition, internal rearrangement events associated with ISs were demonstrated in Ralstonia pseudosolanacearum strains. We also mapped IS elements interrupting avirulence genes, which provided evidence that ISs plays an important role in virulence evolution of RSSC. Additionally, the activity of ISs was demonstrated by transcriptome analysis and DNA hybridization in R. solanacearum isolates. Altogether, we have provided collective data of TEs in RSSC genomes, opening a new path for understanding their evolutionary impact on the genome evolution and diversity of this important plant pathogen.
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Affiliation(s)
- Osiel Silva Gonçalves
- Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO), Universidade Federal de Viçosa, Viçosa, MG 36570-000, Brazil
| | - Kiara França Campos
- Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO), Universidade Federal de Viçosa, Viçosa, MG 36570-000, Brazil
| | - Jéssica Catarine Silva de Assis
- Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO), Universidade Federal de Viçosa, Viçosa, MG 36570-000, Brazil
| | - Alexia Suellen Fernandes
- Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO), Universidade Federal de Viçosa, Viçosa, MG 36570-000, Brazil
| | - Thamires Santos Souza
- Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO), Universidade Federal de Viçosa, Viçosa, MG 36570-000, Brazil
| | - Luiz Guilherme do Carmo Rodrigues
- Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO), Universidade Federal de Viçosa, Viçosa, MG 36570-000, Brazil
| | - Marisa Vieira de Queiroz
- Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO), Universidade Federal de Viçosa, Viçosa, MG 36570-000, Brazil
| | - Mateus Ferreira Santana
- Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO), Universidade Federal de Viçosa, Viçosa, MG 36570-000, Brazil
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Bandoy DJDR, Weimer BC. Biological Machine Learning Combined with Campylobacter Population Genomics Reveals Virulence Gene Allelic Variants Cause Disease. Microorganisms 2020; 8:E549. [PMID: 32290186 PMCID: PMC7232492 DOI: 10.3390/microorganisms8040549] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 04/07/2020] [Accepted: 04/08/2020] [Indexed: 01/17/2023] Open
Abstract
Highly dimensional data generated from bacterial whole-genome sequencing is providing an unprecedented scale of information that requires an appropriate statistical analysis framework to infer biological function from populations of genomes. The application of genome-wide association study (GWAS) methods is an appropriate framework for bacterial population genome analysis that yields a list of candidate genes associated with a phenotype, but it provides an unranked measure of importance. Here, we validated a novel framework to define infection mechanism using the combination of GWAS, machine learning, and bacterial population genomics that ranked allelic variants that accurately identified disease. This approach parsed a dataset of 1.2 million single nucleotide polymorphisms (SNPs) and indels that resulted in an importance ranked list of associated alleles of porA in Campylobacter jejuni using spatiotemporal analysis over 30 years. We validated this approach using previously proven laboratory experimental alleles from an in vivo guinea pig abortion model. This framework, termed µPathML, defined intestinal and extraintestinal groups that have differential allelic porA variants that cause abortion. Divergent variants containing indels that defeated automated annotation were rescued using biological context and knowledge that resulted in defining rare, divergent variants that were maintained in the population over two continents and 30 years. This study defines the capability of machine learning coupled with GWAS and population genomics to simultaneously identify and rank alleles to define their role in infectious disease mechanisms.
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Affiliation(s)
- DJ Darwin R. Bandoy
- 100 K Pathogen Genome Project, Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, USA
- Department of Veterinary, Paraclinical Sciences, College of Veterinary Medicine, University of the Philippines Los Baños, Los Baños 4031, Philippines;
| | - Bart C. Weimer
- 100 K Pathogen Genome Project, Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, USA
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Yousuf M, Iuliani I, Veetil RT, Seshasayee A, Sclavi B, Cosentino Lagomarsino M. Early fate of exogenous promoters in E. coli. Nucleic Acids Res 2020; 48:2348-2356. [PMID: 31960057 PMCID: PMC7049719 DOI: 10.1093/nar/gkz1196] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 12/05/2019] [Accepted: 12/20/2019] [Indexed: 01/12/2023] Open
Abstract
Gene gain by horizontal gene transfer is a major pathway of genome innovation in bacteria. The current view posits that acquired genes initially need to be silenced and that a bacterial chromatin protein, H-NS, plays a role in this silencing. However, we lack direct observation of the early fate of a horizontally transferred gene to prove this theory. We combine sequencing, flow cytometry and sorting, followed by microscopy to monitor gene expression and its variability after large-scale random insertions of a reporter gene in a population of Escherichia coli bacteria. We find that inserted promoters have a wide range of gene-expression variability related to their location. We find that high-expression clones carry insertions that are not correlated with H-NS binding. Conversely, binding of H-NS correlates with silencing. Finally, while most promoters show a common level of extrinsic noise, some insertions show higher noise levels. Analysis of these high-noise clones supports a scenario of switching due to transcriptional interference from divergent ribosomal promoters. Altogether, our findings point to evolutionary pathways where newly-acquired genes are not necessarily silenced, but may immediately explore a wide range of expression levels to probe the optimal ones.
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Affiliation(s)
- Malikmohamed Yousuf
- LBPA, UMR 8113, CNRS, ENS Paris-Saclay, 61 Avenue du President Wilson, 94235 Cachan, France
- Current Affiliation: Centre for Clinical Brain Sciences, The University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Ilaria Iuliani
- LBPA, UMR 8113, CNRS, ENS Paris-Saclay, 61 Avenue du President Wilson, 94235 Cachan, France
- Current Affiliation: LCQB, UMR 7238, Sorbonne Université, 4 Place Jussieu, 75005 Paris, France
| | - Reshma T Veetil
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, Karnataka, India
- School of Life science, The University of Trans-Disciplinary Health Sciences and Technology (TDU), Bengaluru 560064, Karnataka, India
| | - Aswin Sai Narain Seshasayee
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, Karnataka, India
| | - Bianca Sclavi
- LBPA, UMR 8113, CNRS, ENS Paris-Saclay, 61 Avenue du President Wilson, 94235 Cachan, France
- Current Affiliation: LCQB, UMR 7238, Sorbonne Université, 4 Place Jussieu, 75005 Paris, France
| | - Marco Cosentino Lagomarsino
- Sorbonne Université, Campus Pierre and Marie Curie, 4 Place Jussieu, 75005 Paris, France
- CNRS, UMR7238, 4 Place Jussieu, 75005 Paris, France
- Current Affiliation: IFOM, FIRC Institute of Molecular Oncology, Via Adamello 16, 20143 Milan, Italy
- Current Affiliation: Physics Department, University of Milan, and I.N.F.N., Via Celoria 16, 20133 Milan, Italy
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Complete Genome Sequence Reveals Evolutionary and Comparative Genomic Features of Xanthomonas albilineans Causing Sugarcane Leaf Scald. Microorganisms 2020; 8:microorganisms8020182. [PMID: 32012870 PMCID: PMC7074728 DOI: 10.3390/microorganisms8020182] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Revised: 01/22/2020] [Accepted: 01/24/2020] [Indexed: 12/02/2022] Open
Abstract
Leaf scald (caused by Xanthomonas albilineans) is an important bacterial disease affecting sugarcane in most sugarcane growing countries, including China. High genetic diversity exists among strains of X. albilineans from diverse geographic regions. To highlight the genomic features associated with X. albilineans from China, we sequenced the complete genome of a representative strain (Xa-FJ1) of this pathogen using the PacBio and Illumina platforms. The complete genome of strain Xa-FJ1 consists of a circular chromosome of 3,724,581 bp and a plasmid of 31,536 bp. Average nucleotide identity analysis revealed that Xa-FJ1 was closest to five strains from the French West Indies and the USA, particularly to the strain GPE PC73 from Guadeloupe. Comparative genomic analysis between Xa-FJ1 and GPE PC73 revealed prophage integration, homologous recombination, transposable elements, and a clustered regulatory interspaced short palindromic repeats (CRISPR) system that were linked with 16 insertions/deletions (InDels). Ten and 82 specific genes were found in Xa-FJ1 and GPE PC73, respectively, and some of these genes were subjected to phage-related proteins, zona occludens toxin, and DNA methyltransferases. Our findings highlight intra-species genetic variability of the leaf scald pathogen and provide additional genomic resources to investigate its fitness and virulence.
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64
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Isolation and Identification of Microvirga thermotolerans HR1, a Novel Thermo-Tolerant Bacterium, and Comparative Genomics among Microvirga Species. Microorganisms 2020; 8:microorganisms8010101. [PMID: 31936875 PMCID: PMC7022394 DOI: 10.3390/microorganisms8010101] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 12/30/2019] [Accepted: 01/09/2020] [Indexed: 12/12/2022] Open
Abstract
Members of the Microvirga genus are metabolically versatile and widely distributed in Nature. However, knowledge of the bacteria that belong to this genus is currently limited to biochemical characteristics. Herein, a novel thermo-tolerant bacterium named Microvirga thermotolerans HR1 was isolated and identified. Based on the 16S rRNA gene sequence analysis, the strain HR1 belonged to the genus Microvirga and was highly similar to Microvirga sp. 17 mud 1-3. The strain could grow at temperatures ranging from 15 to 50 °C with a growth optimum at 40 °C. It exhibited tolerance to pH range of 6.0–8.0 and salt concentrations up to 0.5% (w/v). It contained ubiquinone 10 as the predominant quinone and added group 8 as the main fatty acids. Analysis of 11 whole genomes of Microvirga species revealed that Microvirga segregated into two main distinct clades (soil and root nodule) as affected by the isolation source. Members of the soil clade had a high ratio of heat- or radiation-resistant genes, whereas members of the root nodule clade were characterized by a significantly higher abundance of genes involved in symbiotic nitrogen fixation or nodule formation. The taxonomic clustering of Microvirga strains indicated strong functional differentiation and niche-specific adaption.
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65
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Haag KL, Pombert JF, Sun Y, de Albuquerque NRM, Batliner B, Fields P, Lopes TF, Ebert D. Microsporidia with Vertical Transmission Were Likely Shaped by Nonadaptive Processes. Genome Biol Evol 2020; 12:3599-3614. [PMID: 31825473 PMCID: PMC6944219 DOI: 10.1093/gbe/evz270] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/05/2019] [Indexed: 12/14/2022] Open
Abstract
Microsporidia have the leanest genomes among eukaryotes, and their physiological and genomic simplicity has been attributed to their intracellular, obligate parasitic life-style. However, not all microsporidia genomes are small or lean, with the largest dwarfing the smallest ones by at least an order of magnitude. To better understand the evolutionary mechanisms behind this genomic diversification, we explore here two clades of microsporidia with distinct life histories, Ordospora and Hamiltosporidium, parasitizing the same host species, Daphnia magna. Based on seven newly assembled genomes, we show that mixed-mode transmission (the combination of horizontal and vertical transmission), which occurs in Hamiltosporidium, is found to be associated with larger and AT-biased genomes, more genes, and longer intergenic regions, as compared with the exclusively horizontally transmitted Ordospora. Furthermore, the Hamiltosporidium genome assemblies contain a variety of repetitive elements and long segmental duplications. We show that there is an excess of nonsynonymous substitutions in the microsporidia with mixed-mode transmission, which cannot be solely attributed to the lack of recombination, suggesting that bursts of genome size in these microsporidia result primarily from genetic drift. Overall, these findings suggest that the switch from a horizontal-only to a mixed mode of transmission likely produces population bottlenecks in Hamiltosporidium species, therefore reducing the effectiveness of natural selection, and allowing their genomic features to be largely shaped by nonadaptive processes.
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Affiliation(s)
- Karen L Haag
- Department of Genetics and Post-Graduation Program of Genetics and Molecular Biology, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | | | - Yukun Sun
- Department of Biology, Illinois Institute of Technology
| | - Nathalia Rammé M de Albuquerque
- Department of Genetics and Post-Graduation Program of Genetics and Molecular Biology, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | | | - Peter Fields
- Department of Environmental Sciences, Zoology, Basel University, Switzerland
| | - Tiago Falcon Lopes
- Department of Genetics and Post-Graduation Program of Genetics and Molecular Biology, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Dieter Ebert
- Department of Environmental Sciences, Zoology, Basel University, Switzerland
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66
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Hernandez-Guerrero R, Galán-Vásquez E, Pérez-Rueda E. The protein architecture in Bacteria and Archaea identifies a set of promiscuous and ancient domains. PLoS One 2019; 14:e0226604. [PMID: 31856202 PMCID: PMC6922389 DOI: 10.1371/journal.pone.0226604] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 11/29/2019] [Indexed: 11/19/2022] Open
Abstract
In this work, we describe a systematic comparative genomic analysis of promiscuous domains in genomes of Bacteria and Archaea. A quantitative measure of domain promiscuity, the weighted domain architecture score (WDAS), was used and applied to 1317 domains in 1320 genomes of Bacteria and Archaea. A functional analysis associated with the WDAS per genome showed that 18 of 50 functional categories were identified as significantly enriched in the promiscuous domains; in particular, small-molecule binding domains, transferases domains, DNA binding domains (transcription factors), and signal transduction domains were identified as promiscuous. In contrast, non-promiscuous domains were identified as associated with 6 of 50 functional categories, and the category Function unknown was enriched. In addition, the WDASs of 52 domains correlated with genome size, i.e., WDAS values decreased as the genome size increased, suggesting that the number of combinations at larger domains increases, including domains in the superfamilies Winged helix-turn-helix and P-loop-containing nucleoside triphosphate hydrolases. Finally, based on classification of the domains according to their ancestry, we determined that the set of 52 promiscuous domains are also ancient and abundant among all the genomes, in contrast to the non-promiscuous domains. In summary, we consider that the association between these two classes of protein domains (promiscuous and non-promiscuous) provides bacterial and archaeal cells with the ability to respond to diverse environmental challenges.
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Affiliation(s)
- Rafael Hernandez-Guerrero
- Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Unidad Académica Yucatán, Mérida, Yucatán, México
| | - Edgardo Galán-Vásquez
- Departamento de Ingeniería de Sistemas Computacionales y Automatización, Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Ciudad Universitaria, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Ernesto Pérez-Rueda
- Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Unidad Académica Yucatán, Mérida, Yucatán, México
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
- * E-mail:
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67
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Iranzo J, Wolf YI, Koonin EV, Sela I. Gene gain and loss push prokaryotes beyond the homologous recombination barrier and accelerate genome sequence divergence. Nat Commun 2019; 10:5376. [PMID: 31772262 PMCID: PMC6879757 DOI: 10.1038/s41467-019-13429-2] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 11/07/2019] [Indexed: 02/05/2023] Open
Abstract
Bacterial and archaeal evolution involve extensive gene gain and loss. Thus, phylogenetic trees of prokaryotes can be constructed both by traditional sequence-based methods (gene trees) and by comparison of gene compositions (genome trees). Comparing the branch lengths in gene and genome trees with identical topologies for 34 clusters of closely related bacterial and archaeal genomes, we show here that terminal branches of gene trees are systematically compressed compared to those of genome trees. Thus, sequence evolution is delayed compared to genome evolution by gene gain and loss. The extent of this delay differs widely among bacteria and archaea. Mathematical modeling shows that the divergence delay can result from sequence homogenization by homologous recombination. The model explains how homologous recombination maintains the cohesiveness of the core genome of a species while allowing extensive gene gain and loss within the accessory genome. Once evolving genomes become isolated by barriers impeding homologous recombination, gene and genome evolution processes settle into parallel trajectories, and genomes diverge, resulting in speciation. A significant proportion of the molecular evolution of bacteria and archaea occurs through gene gain and loss. Here Iranzo et al. develop a mathematical model that explains observed differential patterns of sequence evolution vs. gene content evolution as a consequence of homologous recombination.
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Affiliation(s)
- Jaime Iranzo
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA.,Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo-UPM, Pozuelo de Alarcón, 28223, Madrid, Spain
| | - 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.
| | - Itamar Sela
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA.
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68
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Dokland T. Molecular Piracy: Redirection of Bacteriophage Capsid Assembly by Mobile Genetic Elements. Viruses 2019; 11:v11111003. [PMID: 31683607 PMCID: PMC6893505 DOI: 10.3390/v11111003] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 10/29/2019] [Accepted: 10/30/2019] [Indexed: 01/21/2023] Open
Abstract
Horizontal transfer of mobile genetic elements (MGEs) is a key aspect of the evolution of bacterial pathogens. Transduction by bacteriophages is especially important in this process. Bacteriophages—which assemble a machinery for efficient encapsidation and transfer of genetic material—often transfer MGEs and other chromosomal DNA in a more-or-less nonspecific low-frequency process known as generalized transduction. However, some MGEs have evolved highly specific mechanisms to take advantage of bacteriophages for their own propagation and high-frequency transfer while strongly interfering with phage production—“molecular piracy”. These mechanisms include the ability to sense the presence of a phage entering lytic growth, specific recognition and packaging of MGE genomes into phage capsids, and the redirection of the phage assembly pathway to form capsids with a size more appropriate for the size of the MGE. This review focuses on the process of assembly redirection, which has evolved convergently in many different MGEs from across the bacterial universe. The diverse mechanisms that exist suggest that size redirection is an evolutionarily advantageous strategy for many MGEs.
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Affiliation(s)
- Terje Dokland
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35242, USA.
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69
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Passarelli-Araujo H, Palmeiro JK, Moharana KC, Pedrosa-Silva F, Dalla-Costa LM, Venancio TM. Genomic analysis unveils important aspects of population structure, virulence, and antimicrobial resistance in Klebsiella aerogenes. FEBS J 2019; 286:3797-3810. [PMID: 31319017 DOI: 10.1111/febs.15005] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 06/03/2019] [Accepted: 07/16/2019] [Indexed: 12/22/2022]
Abstract
Klebsiella aerogenes is an important pathogen in healthcare-associated infections. Nevertheless, in comparison to other clinically important pathogens, K. aerogenes population structure, genetic diversity, and pathogenicity remain poorly understood. Here, we elucidate K. aerogenes clonal complexes (CCs) and genomic features associated with resistance and virulence. We present a detailed description of the population structure of K. aerogenes based on 97 publicly available genomes by using both multilocus sequence typing and single-nucleotide polymorphisms extracted from the core genome. We also assessed virulence and resistance profiles using Virulence Finder Database and Comprehensive Antibiotic Resistance Database, respectively. We show that K. aerogenes has an open pangenome and a large effective population size, which account for its high genomic diversity and support that negative selection prevents fixation of most deleterious alleles. The population is structured in at least 10 CCs, including two novel ones identified here, CC9 and CC10. The repertoires of resistance genes comprise a high number of antibiotic efflux proteins as well as narrow- and extended-spectrum β-lactamases. Regarding the population structure, we identified two clusters based on virulence profiles because of the presence of the toxin-encoding clb operon and the siderophore production genes, irp and ybt. Notably, CC3 comprises the majority of K. aerogenes isolates associated with hospital outbreaks, emphasizing the importance of constant monitoring of this pathogen. Collectively, our results may provide a foundation for the development of new therapeutic and surveillance strategies worldwide.
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Affiliation(s)
- Hemanoel Passarelli-Araujo
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil.,Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Jussara K Palmeiro
- Laboratório de Microbiologia Clínica, Departamento de Análises Clínicas, Centro de Ciências da Saúde, Universidade Federal de Santa Catarina, Florianópolis, Brazil.,Faculdade Pequeno Príncipe, Instituto de Pesquisa Pelé Pequeno Príncipe, Curitiba, Brazil
| | - Kanhu C Moharana
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
| | - Francisnei Pedrosa-Silva
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
| | - Libera M Dalla-Costa
- Faculdade Pequeno Príncipe, Instituto de Pesquisa Pelé Pequeno Príncipe, Curitiba, Brazil
| | - Thiago M Venancio
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
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70
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Fimmel E, Michel CJ, Pirot F, Sereni JS, Strüngmann L. Mixed circular codes. Math Biosci 2019; 317:108231. [PMID: 31325443 DOI: 10.1016/j.mbs.2019.108231] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 07/16/2019] [Accepted: 07/17/2019] [Indexed: 12/11/2022]
Abstract
By an extensive statistical analysis in genes of bacteria, archaea, eukaryotes, plasmids and viruses, a maximal C3-self-complementary trinucleotide circular code has been found to have the highest average occurrence in the reading frame of the ribosome during translation. Circular codes may play an important role in maintaining the correct reading frame. On the other hand, as several evolutionary theories propose primeval codes based on dinucleotides, trinucleotides and tetranucleotides, mixed circular codes were investigated. By using a graph-theoretical approach of circular codes recently developed, we study mixed circular codes, which are the union of a dinucleotide circular code, a trinucleotide circular code and a tetranucleotide circular code. Maximal mixed circular codes of (di,tri)-nucleotides, (tri,tetra)-nucleotides and (di,tri,tetra)-nucleotides are constructed, respectively. In particular, we show that any maximal dinucleotide circular code of size 6 can be embedded into a maximal mixed (di,tri)-nucleotide circular code such that its trinucleotide component is a maximal C3-comma-free code. The growth function of self-complementary mixed circular codes of dinucleotides and trinucleotides is given. Self-complementary mixed circular codes could have been involved in primitive genetic processes.
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Affiliation(s)
- Elena Fimmel
- Institute of Mathematical Biology, Faculty for Computer Sciences, Mannheim University of Applied Sciences, Mannheim 68163, Germany.
| | - Christian J Michel
- Theoretical Bioinformatics, ICube, C.N.R.S., University of Strasbourg, 300 Boulevard Sébastien Brant, Illkirch 67400, France.
| | - François Pirot
- Theoretical Bioinformatics, ICube, C.N.R.S., University of Strasbourg, 300 Boulevard Sébastien Brant, Illkirch 67400, France; LORIA (Orpailleur) and Dept. of Mathematics, University of Lorraine and Radboud University, Vandœuvre-lès-Nancy, France and Nijmegen, Netherlands.
| | - Jean-Sébastien Sereni
- Theoretical Bioinformatics, ICube, C.N.R.S., University of Strasbourg, 300 Boulevard Sébastien Brant, Illkirch 67400, France.
| | - Lutz Strüngmann
- Institute of Mathematical Biology, Faculty for Computer Sciences, Mannheim University of Applied Sciences, Mannheim 68163, Germany.
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71
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Liao J, Orsi RH, Carroll LM, Kovac J, Ou H, Zhang H, Wiedmann M. Serotype-specific evolutionary patterns of antimicrobial-resistant Salmonella enterica. BMC Evol Biol 2019; 19:132. [PMID: 31226931 PMCID: PMC6588947 DOI: 10.1186/s12862-019-1457-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 06/11/2019] [Indexed: 12/28/2022] Open
Abstract
Background The emergence of antimicrobial-resistant (AMR) strains of the important human and animal pathogen Salmonella enterica poses a growing threat to public health. Here, we studied the genome-wide evolution of 90 S. enterica AMR isolates, representing one host adapted serotype (S. Dublin) and two broad host range serotypes (S. Newport and S. Typhimurium). Results AMR S. Typhimurium had a large effective population size, a large and diverse genome, AMR profiles with high diversity, and frequent positive selection and homologous recombination. AMR S. Newport showed a relatively low level of diversity and a relatively clonal population structure. AMR S. Dublin showed evidence for a recent population bottleneck, and the genomes were characterized by a larger number of genes and gene ontology terms specifically absent from this serotype and a significantly higher number of pseudogenes as compared to other two serotypes. Approximately 50% of accessory genes, including specific AMR and putative prophage genes, were significantly over- or under-represented in a given serotype. Approximately 65% of the core genes showed phylogenetic clustering by serotype, including the AMR gene aac (6′)-Iaa. While cell surface proteins were shown to be the main target of positive selection, some proteins with possible functions in AMR and virulence also showed evidence for positive selection. Homologous recombination mainly acted on prophage-associated proteins. Conclusions Our data indicates a strong association between genome content of S. enterica and serotype. Evolutionary patterns observed in S. Typhimurium are consistent with multiple emergence events of AMR strains and/or ecological success of this serotype in different hosts or habitats. Evolutionary patterns of S. Newport suggested that antimicrobial resistance emerged in one single lineage, Lineage IIC. A recent population bottleneck and genome decay observed in AMR S. Dublin are congruent with its narrow host range. Finally, our results suggest the potentially important role of positive selection in the evolution of antimicrobial resistance, host adaptation and serotype diversification in S. enterica. Electronic supplementary material The online version of this article (10.1186/s12862-019-1457-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jingqiu Liao
- Department of Food Science, 341 Stocking Hall, Cornell University, Ithaca, NY, 14853, USA.,Graduate Field of Microbiology, Cornell University, Ithaca, NY, 14853, USA
| | - Renato Hohl Orsi
- Department of Food Science, 341 Stocking Hall, Cornell University, Ithaca, NY, 14853, USA
| | - Laura M Carroll
- Department of Food Science, 341 Stocking Hall, Cornell University, Ithaca, NY, 14853, USA
| | - Jasna Kovac
- Department of Food Science, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Hongyu Ou
- School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hailong Zhang
- Department of Computer Science & Engineering, Ohio State University, Columbus, OH, 43210, USA
| | - Martin Wiedmann
- Department of Food Science, 341 Stocking Hall, Cornell University, Ithaca, NY, 14853, USA.
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72
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Fillinger RJ, Anderson MZ. Seasons of change: Mechanisms of genome evolution in human fungal pathogens. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2019; 70:165-174. [PMID: 30826447 DOI: 10.1016/j.meegid.2019.02.031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 02/23/2019] [Accepted: 02/26/2019] [Indexed: 06/09/2023]
Abstract
Fungi are a diverse kingdom of organisms capable of thriving in various niches across the world including those in close association with multicellular eukaryotes. Fungal pathogens that contribute to human disease reside both within the host as commensal organisms of the microbiota and the environment. Their niche of origin dictates how infection initiates but also places specific selective pressures on the fungal pathogen that contributes to its genome organization and genetic repertoire. Recent efforts to catalogue genomic variation among major human fungal pathogens have unveiled evolutionary themes that shape the fungal genome. Mechanisms ranging from large scale changes such as aneuploidy and ploidy cycling as well as more targeted mutations like base substitutions and gene copy number variations contribute to the evolution of these species, which are often under multiple competing selective pressures with their host, environment, and other microbes. Here, we provide an overview of the major selective pressures and mechanisms acting to evolve the genome of clinically important fungal pathogens of humans.
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Affiliation(s)
- Robert J Fillinger
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH 43210, USA
| | - Matthew Z Anderson
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH 43210, USA; Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA.
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73
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Ellegaard KM, Brochet S, Bonilla‐Rosso G, Emery O, Glover N, Hadadi N, Jaron KS, Meer JR, Robinson‐Rechavi M, Sentchilo V, Tagini F, Engel P. Genomic changes underlying host specialization in the bee gut symbiont
Lactobacillus
Firm5. Mol Ecol 2019; 28:2224-2237. [DOI: 10.1111/mec.15075] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 02/21/2019] [Accepted: 03/04/2019] [Indexed: 01/08/2023]
Affiliation(s)
- Kirsten M. Ellegaard
- Department of Fundamental Microbiology University of Lausanne Lausanne Switzerland
| | - Silvia Brochet
- Department of Fundamental Microbiology University of Lausanne Lausanne Switzerland
| | - German Bonilla‐Rosso
- Department of Fundamental Microbiology University of Lausanne Lausanne Switzerland
| | - Olivier Emery
- Department of Fundamental Microbiology University of Lausanne Lausanne Switzerland
| | - Natasha Glover
- Department of Ecology and Evolution University of Lausanne Lausanne Switzerland
| | - Noushin Hadadi
- Department of Fundamental Microbiology University of Lausanne Lausanne Switzerland
| | - Kamil S. Jaron
- Department of Ecology and Evolution University of Lausanne Lausanne Switzerland
- Swiss Institute of Bioinformatics Lausanne Switzerland
| | - Jan R. Meer
- Department of Fundamental Microbiology University of Lausanne Lausanne Switzerland
| | - Marc Robinson‐Rechavi
- Department of Ecology and Evolution University of Lausanne Lausanne Switzerland
- Swiss Institute of Bioinformatics Lausanne Switzerland
| | - Vladimir Sentchilo
- Department of Fundamental Microbiology University of Lausanne Lausanne Switzerland
| | - Florian Tagini
- Institute of Microbiology, Department of Laboratory Medicine University of Lausanne & Lausanne University Hospital Lausanne Switzerland
| | - Philipp Engel
- Department of Fundamental Microbiology University of Lausanne Lausanne Switzerland
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74
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Nepal S, Bonn F, Grasso S, Stobernack T, de Jong A, Zhou K, Wedema R, Rosema S, Becher D, Otto A, Rossen JW, van Dijl JM, Bathoorn E. An ancient family of mobile genomic islands introducing cephalosporinase and carbapenemase genes in Enterobacteriaceae. Virulence 2019; 9:1377-1389. [PMID: 30101693 PMCID: PMC6177240 DOI: 10.1080/21505594.2018.1509666] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The exchange of mobile genomic islands (MGIs) between microorganisms is often mediated by phages, which may provide benefits to the phage’s host. The present study started with the identification of Enterobacter cloacae, Klebsiella pneumoniae and Escherichia coli isolates with exceptional cephalosporin and carbapenem resistance phenotypes from patients in a neonatal ward. To identify possible molecular connections between these isolates and their β-lactam resistance phenotypes, the respective bacterial genome sequences were compared. This unveiled the existence of a family of ancient MGIs that were probably exchanged before the species E. cloacae, K. pneumoniae and E. coli emerged from their common ancestry. A representative MGI from E. cloacae was named MIR17-GI, because it harbors the novel β-lactamase gene variant blaMIR17. Importantly, our observations show that the MIR17-GI-like MGIs harbor genes associated with high-level resistance to cephalosporins. Among them, MIR17-GI stands out because MIR17 also displays carbapenemase activity. As shown by mass spectrometry, the MIR17 carbapenemase is among the most abundantly expressed proteins of the respective E. cloacae isolate. Further, we show that MIR17-GI-like islands are associated with integrated P4-like prophages. This implicates phages in the spread of cephalosporin and carbapenem resistance amongst Enterobacteriaceae. The discovery of an ancient family of MGIs, mediating the spread of cephalosporinase and carbapenemase genes, is of high clinical relevance, because high-level cephalosporin and carbapenem resistance have serious implications for the treatment of patients with enterobacteriaceal infections.
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Affiliation(s)
- Suruchi Nepal
- a Department of Medical Microbiology , University of Groningen, University Medical Center Groningen , Groningen , the Netherlands
| | - Florian Bonn
- b Institute for Microbiology , Ernst-Moritz-Arndt-University Greifswald , Greifswald , Germany
| | - Stefano Grasso
- a Department of Medical Microbiology , University of Groningen, University Medical Center Groningen , Groningen , the Netherlands
| | - Tim Stobernack
- a Department of Medical Microbiology , University of Groningen, University Medical Center Groningen , Groningen , the Netherlands
| | - Anne de Jong
- c Department of Molecular Genetics , University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute , Groningen , The Netherlands
| | - Kai Zhou
- a Department of Medical Microbiology , University of Groningen, University Medical Center Groningen , Groningen , the Netherlands.,d State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital , Zhejiang University , Hangzhou , China
| | - Ronald Wedema
- a Department of Medical Microbiology , University of Groningen, University Medical Center Groningen , Groningen , the Netherlands
| | - Sigrid Rosema
- a Department of Medical Microbiology , University of Groningen, University Medical Center Groningen , Groningen , the Netherlands
| | - Dörte Becher
- b Institute for Microbiology , Ernst-Moritz-Arndt-University Greifswald , Greifswald , Germany
| | - Andreas Otto
- b Institute for Microbiology , Ernst-Moritz-Arndt-University Greifswald , Greifswald , Germany
| | - John W Rossen
- a Department of Medical Microbiology , University of Groningen, University Medical Center Groningen , Groningen , the Netherlands
| | - Jan Maarten van Dijl
- a Department of Medical Microbiology , University of Groningen, University Medical Center Groningen , Groningen , the Netherlands
| | - Erik Bathoorn
- a Department of Medical Microbiology , University of Groningen, University Medical Center Groningen , Groningen , the Netherlands
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75
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Elhenawy W, Tsai CN, Coombes BK. Host-Specific Adaptive Diversification of Crohn's Disease-Associated Adherent-Invasive Escherichia coli. Cell Host Microbe 2019; 25:301-312.e5. [PMID: 30683582 DOI: 10.1016/j.chom.2018.12.010] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 10/05/2018] [Accepted: 12/13/2018] [Indexed: 12/12/2022]
Abstract
Crohn's disease (CD) is an inflammatory bowel disease influenced by bacteria. Adherent-invasive E. coli (AIEC) is associated with CD, yet the adaptations facilitating AIEC gut colonization are unknown. AIEC isolates exhibit high genetic diversity, suggesting strains evolve independently across different gut environments. We tracked the adaptive evolution of AIEC in a murine model of chronic colonization across multiple hosts and transmission events. We detected evolved lineages that outcompeted the ancestral strain in the host through independent mechanisms. One lineage was hypermotile because of a mobile insertion sequence upstream of the master flagellar regulator, flhDC, which enhanced AIEC invasion and establishment of a mucosal niche. Another lineage outcompeted the ancestral strain through improved use of acetate, a short-chain fatty acid in the gut. The presence of hypermotile and acetate-consuming lineages discriminated E. coli isolated from CD patients from healthy controls, suggesting an evolutionary trajectory that distinguishes AIEC from commensal E. coli.
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Affiliation(s)
- Wael Elhenawy
- Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, ON, Canada
| | - Caressa N Tsai
- Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, ON, Canada
| | - Brian K Coombes
- Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, ON, Canada; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Hamilton, ON, Canada.
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76
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Viana MVC, Sahm A, Góes Neto A, Figueiredo HCP, Wattam AR, Azevedo V. Rapidly evolving changes and gene loss associated with host switching in Corynebacterium pseudotuberculosis. PLoS One 2018; 13:e0207304. [PMID: 30419061 PMCID: PMC6231662 DOI: 10.1371/journal.pone.0207304] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 10/28/2018] [Indexed: 02/01/2023] Open
Abstract
Phylogenomics and genome scale positive selection analyses were performed on 29 Corynebacterium pseudotuberculosis genomes that were isolated from different hosts, including representatives of the Ovis and Equi biovars. A total of 27 genes were identified as undergoing adaptive changes. An analysis of the clades within this species and these biovars, the genes specific to each branch, and the genes responding to selective pressure show clear differences, indicating that adaptation and specialization is occurring in different clades. These changes are often correlated with the isolation host but could indicate responses to some undetermined factor in the respective niches. The fact that some of these more-rapidly evolving genes have homology to known virulence factors, antimicrobial resistance genes and drug targets shows that this type of analysis could be used to identify novel targets, and that these could be used as a way to control this pathogen.
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Affiliation(s)
| | - Arne Sahm
- Leibniz Institute on Aging, Fritz Lipmann Institute, Jena, Germany
| | - Aristóteles Góes Neto
- Department of Microbiology, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Henrique Cesar Pereira Figueiredo
- AQUACEN, National Reference Laboratory for Aquatic Animal Diseases, Ministry of Fisheries and Aquaculture, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Alice Rebecca Wattam
- Biocomplexity Institute of Virginia Tech, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Vasco Azevedo
- Department of General Biology, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
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77
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Bobay LM, Ochman H. Factors driving effective population size and pan-genome evolution in bacteria. BMC Evol Biol 2018; 18:153. [PMID: 30314447 PMCID: PMC6186134 DOI: 10.1186/s12862-018-1272-4] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 10/04/2018] [Indexed: 02/07/2023] Open
Abstract
Background Knowledge of population-level processes is essential to understanding the efficacy of selection operating within a species. However, attempts at estimating effective population sizes (Ne) are particularly challenging in bacteria due to their extremely large census populations sizes, varying rates of recombination and arbitrary species boundaries. Results In this study, we estimated Ne for 153 species (152 bacteria and one archaeon) defined under a common framework and found that ecological lifestyle and growth rate were major predictors of Ne; and that contrary to theoretical expectations, Ne was unaffected by recombination rate. Additionally, we found that Ne shapes the evolution and diversity of total gene repertoires of prokaryotic species. Conclusion Together, these results point to a new model of genome architecture evolution in prokaryotes, in which pan-genome sizes, not individual genome sizes, are governed by drift-barrier evolution. Electronic supplementary material The online version of this article (10.1186/s12862-018-1272-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Louis-Marie Bobay
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78712, USA. .,Department of Biology, University of North Carolina at Greensboro, 321 McIver Street, PO Box 26170, Greensboro, NC, 27402, USA.
| | - Howard Ochman
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78712, USA
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Abstract
Current understanding of many animal-microbial symbioses involving unculturable bacterial symbionts with much-reduced genomes derives almost entirely from nonquantitative inferences from genome data. To overcome this limitation, we reconstructed multipartner metabolic models that quantify both the metabolic fluxes within and between three xylem-feeding insects and their bacterial symbionts. This revealed near-complete metabolic segregation between cooccurring bacterial symbionts, despite extensive metabolite exchange between each symbiont and the host, suggestive of strict host controls over the metabolism of its symbionts. We extended the model analysis to investigate metabolic costs. The positive relationship between symbiont genome size and the metabolic cost incurred by the host points to fitness benefits to the host of bearing symbionts with small genomes. The multicompartment metabolic models developed here can be applied to other symbioses that are not readily tractable to experimental approaches. Various intracellular bacterial symbionts that provide their host with essential nutrients have much-reduced genomes, attributed largely to genomic decay and relaxed selection. To obtain quantitative estimates of the metabolic function of these bacteria, we reconstructed genome- and transcriptome-informed metabolic models of three xylem-feeding insects that bear two bacterial symbionts with complementary metabolic functions: a primary symbiont, Sulcia, that has codiversified with the insects, and a coprimary symbiont of distinct taxonomic origin and with different degrees of genome reduction in each insect species (Hodgkinia in a cicada, Baumannia in a sharpshooter, and Sodalis in a spittlebug). Our simulations reveal extensive bidirectional flux of multiple metabolites between each symbiont and the host, but near-complete metabolic segregation (i.e., near absence of metabolic cross-feeding) between the two symbionts, a likely mode of host control over symbiont metabolism. Genome reduction of the symbionts is associated with an increased number of host metabolic inputs to the symbiont and also reduced metabolic cost to the host. In particular, Sulcia and Hodgkinia with genomes of ≤0.3 Mb are calculated to recycle ∼30 to 80% of host-derived nitrogen to essential amino acids returned to the host, while Baumannia and Sodalis with genomes of ≥0.6 Mb recycle 10 to 15% of host nitrogen. We hypothesize that genome reduction of symbionts may be driven by selection for increased host control and reduced host costs, as well as by the stochastic process of genomic decay and relaxed selection.
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Abstract
Some bacteria can transfer to new host species, and this poses a risk to human health. Indeed, an estimated 60% of all human pathogens have originated from other animal species. Similarly, human-to-animal transitions are recognized as a major threat to sustainable livestock production, and emerging pathogens impose an increasing burden on crop yield and global food security. Recent advances in high-throughput sequencing technologies have enabled comparative genomic analyses of bacterial populations from multiple hosts. Such studies are providing new insights into the evolutionary processes that underpin the establishment of bacteria in new host niches. A better understanding of the genetic and mechanistic basis for bacterial host adaptation may reveal novel targets for controlling infection or inform the design of approaches to limit the emergence of new pathogens.
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Affiliation(s)
- Samuel K Sheppard
- Milner Centre for Evolution, Department of Biology & Biotechnology, University of Bath, Claverton Down, Bath, UK
| | - David S Guttman
- Department of Cell & Systems Biology, University of Toronto, Toronto, Ontario, Canada
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, Ontario, Canada
| | - J Ross Fitzgerald
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Edinburgh, UK.
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80
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Aguilar A, Mora Y, Dávalos A, Girard L, Mora J, Peralta H. Analysis of genome sequence and symbiotic ability of rhizobial strains isolated from seeds of common bean (Phaseolus vulgaris). BMC Genomics 2018; 19:645. [PMID: 30165827 PMCID: PMC6117902 DOI: 10.1186/s12864-018-5023-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 08/21/2018] [Indexed: 12/14/2022] Open
Abstract
Background Rhizobia are alpha-proteobacteria commonly found in soil and root nodules of legumes. It was recently reported that nitrogen-fixing rhizobia also inhabit legume seeds. In this study, we examined whole-genome sequences of seven strains of rhizobia isolated from seeds of common bean (Phaseolus vulgaris). Results Rhizobial strains included in this study belonged to three different species, including Rhizobium phaseoli, R. leguminosarum, and R. grahamii. Genome sequence analyses revealed that six of the strains formed three pairs of highly related strains. Both strains comprising a pair shared all but one plasmid. In two out of three pairs, one of the member strains was effective in nodulation and nitrogen fixation, whereas the other was ineffective. The genome of the ineffective strain in each pair lacked several genes responsible for symbiosis, including nod, nif, and fix genes, whereas that of the effective strain harbored the corresponding genes in clusters, suggesting that recombination events provoked gene loss in ineffective strains. Comparisons of genomic sequences between seed strains and nodule strains of the same species showed high conservation of chromosomal sequences and lower conservation of plasmid sequences. Approximately 70% of all genes were shared among the strains of each species. However, paralogs were more abundant in seed strains than in nodule strains. Functional analysis showed that seed strains were particularly enriched in genes involved in the transport and metabolism of amino acids and carbohydrates, biosynthesis of cofactors and in transposons and prophages. Genomes of seed strains harbored several intact prophages, one of which was inserted at exactly the same genomic position in three strains of R. phaseoli and R. leguminosarum. The R. grahamii strain carried a prophage similar to a gene transfer agent (GTA); this represents the first GTA reported for this genus. Conclusions Seeds represent a niche for bacteria; their access by rhizobia possibly triggered the infection of phages, recombination, loss or gain of plasmids, and loss of symbiosis genes. This process probably represents ongoing evolution that will eventually convert these strains into obligate endophytes. Electronic supplementary material The online version of this article (10.1186/s12864-018-5023-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alejandro Aguilar
- Functional Genomics of Prokaryotes, Center for Genomic Sciences, National University of Mexico, Av. Universidad, CP 62210, Cuernavaca, Morelos, Mexico
| | - Yolanda Mora
- Functional Genomics of Prokaryotes, Center for Genomic Sciences, National University of Mexico, Av. Universidad, CP 62210, Cuernavaca, Morelos, Mexico
| | - Araceli Dávalos
- Genome Dynamics, Center for Genomic Sciences, National University of Mexico, Av. Universidad, CP 62210, Cuernavaca, Morelos, Mexico
| | - Lourdes Girard
- Systems Biology and Synthetic Biology, Center for Genomic Sciences, National University of Mexico, Av. Universidad, CP 62210, Cuernavaca, Morelos, Mexico
| | - Jaime Mora
- Functional Genomics of Prokaryotes, Center for Genomic Sciences, National University of Mexico, Av. Universidad, CP 62210, Cuernavaca, Morelos, Mexico
| | - Humberto Peralta
- Functional Genomics of Prokaryotes, Center for Genomic Sciences, National University of Mexico, Av. Universidad, CP 62210, Cuernavaca, Morelos, Mexico.
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Quentin Y, Siguier P, Chandler M, Fichant G. Single-strand DNA processing: phylogenomics and sequence diversity of a superfamily of potential prokaryotic HuH endonucleases. BMC Genomics 2018; 19:475. [PMID: 29914351 PMCID: PMC6006769 DOI: 10.1186/s12864-018-4836-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 05/29/2018] [Indexed: 12/11/2022] Open
Abstract
Background Some mobile genetic elements target the lagging strand template during DNA replication. Bacterial examples are insertion sequences IS608 and ISDra2 (IS200/IS605 family members). They use obligatory single-stranded circular DNA intermediates for excision and insertion and encode a transposase, TnpAIS200, which recognizes subterminal secondary structures at the insertion sequence ends. Similar secondary structures, Repeated Extragenic Palindromes (REP), are present in many bacterial genomes. TnpAIS200-related proteins, TnpAREP, have been identified and could be responsible for REP sequence proliferation. These proteins share a conserved HuH/Tyrosine core domain responsible for catalysis and are involved in processes of ssDNA cleavage and ligation. Our goal is to characterize the diversity of these proteins collectively referred as the TnpAY1 family. Results A genome-wide analysis of sequences similar to TnpAIS200 and TnpAREP in prokaryotes revealed a large number of family members with a wide taxonomic distribution. These can be arranged into three distinct classes and 12 subclasses based on sequence similarity. One subclass includes sequences similar to TnpAIS200. Proteins from other subclasses are not associated with typical insertion sequence features. These are characterized by specific additional domains possibly involved in protein/DNA or protein/protein interactions. Their genes are found in more than 25% of species analyzed. They exhibit a patchy taxonomic distribution consistent with dissemination by horizontal gene transfers followed by loss. The tnpAREP genes of five subclasses are flanked by typical REP sequences in a REPtron-like arrangement. Four distinct REP types were characterized with a subclass specific distribution. Other subclasses are not associated with REP sequences but have a large conserved domain located in C-terminal end of their sequence. This unexpected diversity suggests that, while most likely involved in processing single-strand DNA, proteins from different subfamilies may play a number of different roles. Conclusions We established a detailed classification of TnpAY1 proteins, consolidated by the analysis of the conserved core domains and the characterization of additional domains. The data obtained illustrate the unexpected diversity of the TnpAY1 family and provide a strong framework for future evolutionary and functional studies. By their potential function in ssDNA editing, they may confer adaptive responses to host cell physiology and metabolism. Electronic supplementary material The online version of this article (10.1186/s12864-018-4836-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yves Quentin
- Laboratoire de Microbiologie et Génétique Moléculaires, UMR5100, Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique (CNRS), Université de Toulouse, UPS, F-31062, Toulouse, France.
| | - Patricia Siguier
- Laboratoire de Microbiologie et Génétique Moléculaires, UMR5100, Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique (CNRS), Université de Toulouse, UPS, F-31062, Toulouse, France
| | - Mick Chandler
- Laboratoire de Microbiologie et Génétique Moléculaires, UMR5100, Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique (CNRS), Université de Toulouse, UPS, F-31062, Toulouse, France.
| | - Gwennaele Fichant
- Laboratoire de Microbiologie et Génétique Moléculaires, UMR5100, Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique (CNRS), Université de Toulouse, UPS, F-31062, Toulouse, France
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82
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Willemsen A, Carrasco JL, Elena SF, Zwart MP. Going, going, gone: predicting the fate of genomic insertions in plant RNA viruses. Heredity (Edinb) 2018; 121:499-509. [PMID: 29743566 DOI: 10.1038/s41437-018-0086-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 03/28/2018] [Accepted: 03/29/2018] [Indexed: 11/09/2022] Open
Abstract
Horizontal gene transfer is common among viruses, while they also have highly compact genomes and tend to lose artificial genomic insertions rapidly. Understanding the stability of genomic insertions in viral genomes is therefore relevant for explaining and predicting their evolutionary patterns. Here, we revisit a large body of experimental research on a plant RNA virus, tobacco etch potyvirus (TEV), to identify the patterns underlying the stability of a range of homologous and heterologous insertions in the viral genome. We obtained a wide range of estimates for the recombination rate-the rate at which deletions removing the insertion occur-and these appeared to be independent of the type of insertion and its location. Of the factors we considered, recombination rate was the best predictor of insertion stability, although we could not identify the specific sequence characteristics that would help predict insertion instability. We also considered experimentally the possibility that functional insertions lead to higher mutational robustness through increased redundancy. However, our observations suggest that both functional and non-functional increases in genome size decreased the mutational robustness. Our results therefore demonstrate the importance of recombination rates for predicting the long-term stability and evolution of viral RNA genomes and suggest that there are unexpected drawbacks to increases in genome size for mutational robustness.
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Affiliation(s)
- Anouk Willemsen
- Laboratory MIVEGEC (UMR CNRS 5290, IRD 224, UM), National Center for Scientific Research (CNRS), Montpellier, France
| | - José L Carrasco
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València, València, Spain
| | - Santiago F Elena
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València, València, Spain.,Instituto de Biología Integrativa de Sistemas (I2SysBio), Consejo Superior de Investigaciones Científicas-Universitat de València, Paterna, Spain.,The Santa Fe Institute, Santa Fe, NM, 87501, USA
| | - Mark P Zwart
- Microbial Ecology Department, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands. .,Laboratory of Genetics, Wageningen University, Wageningen, The Netherlands.
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83
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Scherlach K, Hertweck C. Mediators of mutualistic microbe–microbe interactions. Nat Prod Rep 2018; 35:303-308. [DOI: 10.1039/c7np00035a] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
This viewpoint summarizes recent advances in understanding the role of natural products as regulators of mutualistic microbial interactions.
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Affiliation(s)
- Kirstin Scherlach
- Department of Biomolecular Chemistry
- Leibniz Institute for Natural Product Chemistry
- Infection Biology (HKI)
- 07745 Jena
- Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry
- Leibniz Institute for Natural Product Chemistry
- Infection Biology (HKI)
- 07745 Jena
- Germany
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