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Kirsch JM, Hryckowian AJ, Duerkop BA. A metagenomics pipeline reveals insertion sequence-driven evolution of the microbiota. Cell Host Microbe 2024; 32:739-754.e4. [PMID: 38565143 PMCID: PMC11081829 DOI: 10.1016/j.chom.2024.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 02/06/2024] [Accepted: 03/08/2024] [Indexed: 04/04/2024]
Abstract
Insertion sequence (IS) elements are mobile genetic elements in bacterial genomes that support adaptation. We developed a database of IS elements coupled to a computational pipeline that identifies IS element insertions in the microbiota. We discovered that diverse IS elements insert into the genomes of intestinal bacteria regardless of human host lifestyle. These insertions target bacterial accessory genes that aid in their adaptation to unique environmental conditions. Using IS expansion in Bacteroides, we show that IS activity leads to the insertion of "hot spots" in accessory genes. We show that IS insertions are stable and can be transferred between humans. Extreme environmental perturbations force IS elements to fall out of the microbiota, and many fail to rebound following homeostasis. Our work shows that IS elements drive bacterial genome diversification within the microbiota and establishes a framework for understanding how strain-level variation within the microbiota impacts human health.
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Affiliation(s)
- Joshua M Kirsch
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, School of Medicine, Aurora, CO 80045, USA
| | - Andrew J Hryckowian
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA; Department of Medical Microbiology & Immunology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA
| | - Breck A Duerkop
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, School of Medicine, Aurora, CO 80045, USA.
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2
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Fernandes AS, Campos KF, de Assis JCS, Gonçalves OS, Queiroz MVD, Bazzolli DMS, Santana MF. Investigating the impact of insertion sequences and transposons in the genomes of the most significant phytopathogenic bacteria. Microb Genom 2024; 10. [PMID: 38568199 DOI: 10.1099/mgen.0.001219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024] Open
Abstract
Genetic variability in phytopathogens is one of the main problems encountered for effective plant disease control. This fact may be related to the presence of transposable elements (TEs), but little is known about their role in host genomes. Here, we performed the most comprehensive analysis of insertion sequences (ISs) and transposons (Tns) in the genomes of the most important bacterial plant pathogens. A total of 35 692 ISs and 71 transposons were identified in 270 complete genomes. The level of pathogen-host specialization was found to be a significant determinant of the element distribution among the species. Some Tns were identified as carrying virulence factors, such as genes encoding effector proteins of the type III secretion system and resistance genes for the antimicrobial streptomycin. Evidence for IS-mediated ectopic recombination was identified in Xanthomonas genomes. Moreover, we found that IS elements tend to be inserted in regions near virulence and fitness genes, such ISs disrupting avirulence genes in X. oryzae genomes. In addition, transcriptome analysis under different stress conditions revealed differences in the expression of genes encoding transposases in the Ralstonia solanacearum, X. oryzae, and P. syringae species. Lastly, we also investigated the role of Tns in regulation via small noncoding regulatory RNAs and found these elements may target plant-cell transcriptional activators. Taken together, the results indicate that TEs may have a fundamental role in variability and virulence in plant pathogenic bacteria.
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3
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Zhong J, Osborn T, Del Rosario Hernández T, Kyrysyuk O, Tully BJ, Anderson RE. Increasing transposase abundance with ocean depth correlates with a particle-associated lifestyle. mSystems 2024; 9:e0006724. [PMID: 38380923 PMCID: PMC10949469 DOI: 10.1128/msystems.00067-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 01/25/2024] [Indexed: 02/22/2024] Open
Abstract
Transposases are mobile genetic elements that move within and between genomes, promoting genomic plasticity in microorganisms. In marine microbial communities, the abundance of transposases increases with depth, but the reasons behind this trend remain unclear. Our analysis of metagenomes from the Tara Oceans and Malaspina Expeditions suggests that a particle-associated lifestyle is the main covariate for the high occurrence of transposases in the deep ocean, and this trend holds true for individual genomes as well as in a community-wide sense. We observed a strong and depth-independent correlation between transposase abundance and the presence of biofilm-associated genes, as well as the prevalence of secretory enzymes. This suggests that mobile genetic elements readily propagate among microbial communities within crowded biofilms. Furthermore, we show that particle association positively correlates with larger genome size, which is in turn associated with higher transposase abundance. Cassette sequences associated with transposons are enriched with genes related to defense mechanisms, which are more highly expressed in the deep sea. Thus, while transposons spread at the expense of their microbial hosts, they also introduce novel genes and potentially benefit the hosts in helping to compete for limited resources. Overall, our results suggest a new understanding of deep ocean particles as highways for gene sharing among defensively oriented microbial genomes.IMPORTANCEGenes can move within and between microbial genomes via mobile genetic elements, which include transposases and transposons. In the oceans, there is a puzzling increase in transposase abundance in microbial genomes as depth increases. To gain insight into this trend, we conducted an extensive analysis of marine microbial metagenomes and metatranscriptomes. We found a significant correlation between transposase abundance and a particle-associated lifestyle among marine microbes at both the metagenome and genome-resolved levels. We also observed a link between transposase abundance and genes related to defense mechanisms. These results suggest that as microbes become densely packed into crowded particles, mobile genes are more likely to spread and carry genetic material that provides a competitive advantage in crowded habitats. This may enable deep sea microbes to effectively compete in such environments.
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Affiliation(s)
- Juntao Zhong
- Carleton College, Northfield, Minnesota, USA
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Troy Osborn
- Carleton College, Northfield, Minnesota, USA
| | - Thais Del Rosario Hernández
- Carleton College, Northfield, Minnesota, USA
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island, USA
| | - Oleksandr Kyrysyuk
- Carleton College, Northfield, Minnesota, USA
- Yale School of Medicine, Yale University, New Haven, Connecticut, USA
| | - Benjamin J. Tully
- Marine & Environmental Biology, Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
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4
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Saini P, Bandsode V, Singh A, Mendem SK, Semmler T, Alam M, Ahmed N. Genomic insights into virulence, antimicrobial resistance, and adaptation acumen of Escherichia coli isolated from an urban environment. mBio 2024; 15:e0354523. [PMID: 38376265 PMCID: PMC10936179 DOI: 10.1128/mbio.03545-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 01/23/2024] [Indexed: 02/21/2024] Open
Abstract
Populations of common commensal bacteria such as Escherichia coli undergo genetic changes by the acquisition of certain virulence and antimicrobial resistance (AMR) encoding genetic elements leading to the emergence of pathogenic strains capable of surviving in the previously uninhabited or protected niches. These bacteria are also reported to be prevalent in the environment where they survive by adopting various recombination strategies to counter microflora of the soil and water, under constant selection pressure(s). In this study, we performed molecular characterization, phenotypic AMR analysis, and whole genome sequencing (WGS) of E. coli (n = 37) isolated from soil and surface water representing the urban and peri-urban areas. The primary aim of this study was to understand the genetic architecture and pathogenic acumen exhibited by environmental E. coli. WGS-based analysis entailing resistome and virulome profiling indicated the presence of various virulence (adherence, iron uptake, and toxins) and AMR encoding genes, including blaNDM-5 in the environmental isolates. A majority of our isolates belonged to phylogroup B1 (73%). A few isolates in our collection were of sequence type(s) (ST) 58 and 224 that could have emerged recently as clonal lineages and might pose risk of infection/transmission. Mobile genetic elements (MGEs) such as plasmids (predominantly) of the IncF family, prophages, pipolins, and insertion elements such as IS1 and IS5 were also observed to exist, which may presumably aid in the propagation of genes encoding resistance against antimicrobial drugs. The observed high prevalence of MGEs associated with multidrug resistance in pathogenic E. coli isolates belonging to the phylogroup B1 underscores the need for extended surveillance to keep track of and prevent the transmission of the bacterium to certain vulnerable human and animal populations. IMPORTANCE Evolutionary patterns of E. coli bacteria convey that they evolve into highly pathogenic forms by acquiring fitness advantages, such as AMR, and various virulence factors through the horizontal gene transfer (HGT)-mediated acquisition of MGEs. However, limited research on the genetic profiles of environmental E. coli, particularly from India, hinders our understanding of their transition to pathogenic forms and impedes the adoption of a comprehensive approach to address the connection between environmentally dwelling E. coli populations and human and veterinary public health. This study focuses on high-resolution genomic analysis of the environmental E. coli isolates aiming to understand the genetic similarities and differences among isolates from different environmental niches and uncover the survival strategies employed by these bacteria to thrive in their surroundings. Our approach involved molecular characterization of environmental samples using PCR-based DNA fingerprinting and subsequent WGS analysis. This multidisciplinary approach is likely to provide valuable insights into the understanding of any potential spill-over to human and animal populations and locales. Investigating these environmental isolates has significant potential for developing epidemiological strategies against transmission and understanding niche-specific evolutionary patterns.
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Affiliation(s)
- Poorvi Saini
- Department of Biotechnology and Bioinformatics, Pathogen Biology Laboratory, University of Hyderabad, Hyderabad, Telangana State, India
| | - Viraj Bandsode
- Department of Biotechnology and Bioinformatics, Pathogen Biology Laboratory, University of Hyderabad, Hyderabad, Telangana State, India
| | - Anuradha Singh
- Department of Biotechnology and Bioinformatics, Pathogen Biology Laboratory, University of Hyderabad, Hyderabad, Telangana State, India
| | - Suresh Kumar Mendem
- Department of Biotechnology and Bioinformatics, Pathogen Biology Laboratory, University of Hyderabad, Hyderabad, Telangana State, India
| | | | - Munirul Alam
- International Centre for Diarrheal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Niyaz Ahmed
- Department of Biotechnology and Bioinformatics, Pathogen Biology Laboratory, University of Hyderabad, Hyderabad, Telangana State, India
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5
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Pfeifer E, Rocha EPC. Phage-plasmids promote recombination and emergence of phages and plasmids. Nat Commun 2024; 15:1545. [PMID: 38378896 PMCID: PMC10879196 DOI: 10.1038/s41467-024-45757-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 02/01/2024] [Indexed: 02/22/2024] Open
Abstract
Phages and plasmids are regarded as distinct types of mobile genetic elements that drive bacterial evolution by horizontal gene transfer. However, the distinction between both types is blurred by the existence of elements known as prophage-plasmids or phage-plasmids, which transfer horizontally between cells as viruses and vertically within cellular lineages as plasmids. Here, we study gene flow between the three types of elements. We show that the gene repertoire of phage-plasmids overlaps with those of phages and plasmids. By tracking recent recombination events, we find that phage-plasmids exchange genes more frequently with plasmids than with phages, and that direct gene exchange between plasmids and phages is less frequent in comparison. The results suggest that phage-plasmids can mediate gene flow between plasmids and phages, including exchange of mobile element core functions, defense systems, and antibiotic resistance. Moreover, a combination of gene transfer and gene inactivation may result in the conversion of elements. For example, gene loss turns P1-like phage-plasmids into integrative prophages or into plasmids (that are no longer phages). Remarkably, some of the latter have acquired conjugation-related functions to became mobilisable by conjugation. Thus, our work indicates that phage-plasmids can play a key role in the transfer of genes across mobile elements within their hosts, and can act as intermediates in the conversion of one type of element into another.
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Affiliation(s)
- Eugen Pfeifer
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, 75015, Paris, France.
| | - Eduardo P C Rocha
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, 75015, Paris, France.
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Sánchez‐Costa M, Gola S, Rodríguez‐Sáiz M, Barredo J, Hidalgo A, Berenguer J. From accurate genome sequence to biotechnological application: The thermophile Mycolicibacterium hassiacum as experimental model. Microb Biotechnol 2024; 17:e14290. [PMID: 37498289 PMCID: PMC10832570 DOI: 10.1111/1751-7915.14290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 05/18/2023] [Accepted: 05/19/2023] [Indexed: 07/28/2023] Open
Abstract
Mycobacteria constitute a large group of microorganisms belonging to the phylum Actinobacteria encompassing some of the most relevant pathogenic bacteria and many saprophytic isolates that share a unique and complex cell envelope. Also unique to this group is the extensive capability to use and synthesize sterols, a class of molecules that include active signalling compounds of pharmaceutical use. However, few mycobacterial species and strains have been established as laboratory models to date, Mycolicibacterium smegmatis mc2 155 being the most common one. In this work, we focus on the use of a thermophilic mycobacterium, Mycolicibacterium hassiacum, which grows optimally above 50°C, as an emerging experimental model valid to extend our general knowledge of mycobacterial biology as well as for application purposes. To that end, accurate genomic sequences are key for gene mining, the study of pathogenicity or lack thereof and the potential for gene transfer. The combination of long- and short-massive sequencing technologies is strictly necessary to remove biases caused by errors specific to long-reads technology. By doing so in M. hassiacum, we obtained from the curated genome clues regarding the genetic manipulation potential of this microorganism from the presence of insertion sequences, CRISPR-Cas, type VII ESX secretion systems, as well as lack of plasmids. Finally, as a proof of concept of the applicability of M. hassiacum as a laboratory and industrial model, we used this high-quality genome of M. hassiacum to successfully knockout a gene involved in the use of phytosterols as source of carbon and energy, using an improved gene cassette for thermostable selection and a transformation protocol at high temperature.
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Affiliation(s)
- Mercedes Sánchez‐Costa
- Department of Molecular Biology, Faculty of SciencesCentre for Molecular Biology (UAM‐CSIC)University Institute for Molecular BiologyMadridSpain
| | - Susanne Gola
- Department of Medical Technology and BiotechnologyErnst‐Abbe‐Hochschule Jena, University of Applied SciencesJenaGermany
| | | | - José‐Luis Barredo
- Department of BiotechnologyCuria, Parque Tecnológico de LeónLeónSpain
| | - Aurelio Hidalgo
- Department of Molecular Biology, Faculty of SciencesCentre for Molecular Biology (UAM‐CSIC)University Institute for Molecular BiologyMadridSpain
| | - José Berenguer
- Department of Molecular Biology, Faculty of SciencesCentre for Molecular Biology (UAM‐CSIC)University Institute for Molecular BiologyMadridSpain
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van Dijk B, Buffard P, Farr AD, Giersdorf F, Meijer J, Dutilh BE, Rainey PB. Identifying and tracking mobile elements in evolving compost communities yields insights into the nanobiome. ISME COMMUNICATIONS 2023; 3:90. [PMID: 37640834 PMCID: PMC10462680 DOI: 10.1038/s43705-023-00294-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 08/02/2023] [Accepted: 08/08/2023] [Indexed: 08/31/2023]
Abstract
Microbial evolution is driven by rapid changes in gene content mediated by horizontal gene transfer (HGT). While mobile genetic elements (MGEs) are important drivers of gene flux, the nanobiome-the zoo of Darwinian replicators that depend on microbial hosts-remains poorly characterised. New approaches are necessary to increase our understanding beyond MGEs shaping individual populations, towards their impacts on complex microbial communities. A bioinformatic pipeline (xenoseq) was developed to cross-compare metagenomic samples from microbial consortia evolving in parallel, aimed at identifying MGE dissemination, which was applied to compost communities which underwent periodic mixing of MGEs. We show that xenoseq can distinguish movement of MGEs from demographic changes in community composition that otherwise confounds identification, and furthermore demonstrate the discovery of various unexpected entities. Of particular interest was a nanobacterium of the candidate phylum radiation (CPR) which is closely related to a species identified in groundwater ecosystems (Candidatus Saccharibacterium), and appears to have a parasitic lifestyle. We also highlight another prolific mobile element, a 313 kb plasmid hosted by a Cellvibrio lineage. The host was predicted to be capable of nitrogen fixation, and acquisition of the plasmid coincides with increased ammonia production. Taken together, our data show that new experimental strategies combined with bioinformatic analyses of metagenomic data stand to provide insight into the nanobiome as a driver of microbial community evolution.
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Affiliation(s)
- Bram van Dijk
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany.
- Theoretical Biology and Bioinformatics, Department of Biology, Science for Life, Utrecht University, Utrecht, the Netherlands.
| | - Pauline Buffard
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Andrew D Farr
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Franz Giersdorf
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Jeroen Meijer
- Theoretical Biology and Bioinformatics, Department of Biology, Science for Life, Utrecht University, Utrecht, the Netherlands
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Department of Biology, Science for Life, Utrecht University, Utrecht, the Netherlands
- Institute of Biodiversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich Schiller University, Jena, Germany
| | - Paul B Rainey
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany.
- Laboratory of Biophysics and Evolution, CBI, ESPCI Paris, Université PSL CNRS, Paris, France.
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8
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Fusi M, Ngugi DK, Marasco R, Booth JM, Cardinale M, Sacchi L, Clementi E, Yang X, Garuglieri E, Fodelianakis S, Michoud G, Daffonchio D. Gill-associated bacteria are homogeneously selected in amphibious mangrove crabs to sustain host intertidal adaptation. MICROBIOME 2023; 11:189. [PMID: 37612775 PMCID: PMC10463870 DOI: 10.1186/s40168-023-01629-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 07/20/2023] [Indexed: 08/25/2023]
Abstract
BACKGROUND The transition from water to air is a key event in the evolution of many marine organisms to access new food sources, escape water hypoxia, and exploit the higher and temperature-independent oxygen concentration of air. Despite the importance of microorganisms in host adaptation, their contribution to overcoming the challenges posed by the lifestyle changes from water to land is not well understood. To address this, we examined how microbial association with a key multifunctional organ, the gill, is involved in the intertidal adaptation of fiddler crabs, a dual-breathing organism. RESULTS Electron microscopy revealed a rod-shaped bacterial layer tightly connected to the gill lamellae of the five crab species sampled across a latitudinal gradient from the central Red Sea to the southern Indian Ocean. The gill bacterial community diversity assessed with 16S rRNA gene amplicon sequencing was consistently low across crab species, and the same actinobacterial group, namely Ilumatobacter, was dominant regardless of the geographic location of the host. Using metagenomics and metatranscriptomics, we detected that these members of actinobacteria are potentially able to convert ammonia to amino acids and may help eliminate toxic sulphur compounds and carbon monoxide to which crabs are constantly exposed. CONCLUSIONS These results indicate that bacteria selected on gills can play a role in the adaptation of animals in dynamic intertidal ecosystems. Hence, this relationship is likely to be important in the ecological and evolutionary processes of the transition from water to air and deserves further attention, including the ontogenetic onset of this association. Video Abstract.
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Affiliation(s)
- Marco Fusi
- Red Sea Research Center, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia.
- Centre for Conservation and Restoration Science, Edinburgh Napier University, Edinburgh, UK.
| | - David K Ngugi
- Red Sea Research Center, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, D-38124, Braunschweig, Germany
| | - Ramona Marasco
- Red Sea Research Center, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Jenny Marie Booth
- Red Sea Research Center, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Massimiliano Cardinale
- Institute of Applied Microbiology Research Center for BioSystems, Land Use, and Nutrition (IFZ) Justus-Liebig-University Giessen, D-35392, Giessen, Germany
- Department of Biological and Environmental Sciences and Technologies, University of Salento, via Prov.le Lecce-Monteroni, I-73100, Lecce, Italy
| | - Luciano Sacchi
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, I-27100, Pavia, Italy
| | - Emanuela Clementi
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, I-27100, Pavia, Italy
| | - Xinyuan Yang
- Red Sea Research Center, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Elisa Garuglieri
- Red Sea Research Center, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Stilianos Fodelianakis
- Red Sea Research Center, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Grégoire Michoud
- Red Sea Research Center, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Daniele Daffonchio
- Red Sea Research Center, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia.
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9
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Kim JJ, Seong HJ, Johnson TA, Cha CJ, Sul WJ, Chae JC. Persistence of antibiotic resistance from animal agricultural effluents to surface water revealed by genome-centric metagenomics. JOURNAL OF HAZARDOUS MATERIALS 2023; 457:131761. [PMID: 37290355 DOI: 10.1016/j.jhazmat.2023.131761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 05/25/2023] [Accepted: 06/01/2023] [Indexed: 06/10/2023]
Abstract
Concerns about antibiotic resistance genes (ARGs) released from wastewaters of livestock or fish farming into the natural environment are increasing, but studies on unculturable bacteria related to the dissemination of antibiotic resistance are limited. Here, we reconstructed 1100 metagenome-assembled genomes (MAGs) to assess the impact of microbial antibiotic resistome and mobilome in wastewaters discharged to Korean rivers. Our results indicate that ARGs harbored in the MAGs were disseminated from wastewater effluents into downstream rivers. Moreover, it was found that ARGs are more commonly co-localized with mobile genetic elements (MGEs) in agricultural wastewater than in river water. Among the effluent-derived phyla, uncultured members of the superphylum Patescibacteria possessed a high number of MGEs, along with co-localized ARGs. Our findings suggest that members of the Patesibacteria are a potential vector for propagating ARGs into the environmental community. Therefore, we propose that the dissemination of ARGs by uncultured bacteria should be further investigated in multiple environments.
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Affiliation(s)
- Jin Ju Kim
- Department of Systems Biotechnology, Chung-Ang University, Anseong 17546, Republic of Korea
| | - Hoon Je Seong
- Department of Systems Biotechnology, Chung-Ang University, Anseong 17546, Republic of Korea; Korean Medicine Data Division, Korea Institute of Oriental Medicine, Daejeon 34054, Republic of Korea
| | - Timothy A Johnson
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, United States
| | - Chang-Jun Cha
- Department of Systems Biotechnology, Chung-Ang University, Anseong 17546, Republic of Korea
| | - Woo Jun Sul
- Department of Systems Biotechnology, Chung-Ang University, Anseong 17546, Republic of Korea.
| | - Jong-Chan Chae
- Division of Biotechnology, Jeonbuk National University, Iksan 54596, Republic of Korea.
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10
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Kirsch JM, Ely S, Stellfox ME, Hullahalli K, Luong P, Palmer KL, Van Tyne D, Duerkop BA. Targeted IS-element sequencing uncovers transposition dynamics during selective pressure in enterococci. PLoS Pathog 2023; 19:e1011424. [PMID: 37267422 PMCID: PMC10266640 DOI: 10.1371/journal.ppat.1011424] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 06/14/2023] [Accepted: 05/15/2023] [Indexed: 06/04/2023] Open
Abstract
Insertion sequences (IS) are simple transposons implicated in the genome evolution of diverse pathogenic bacterial species. Enterococci have emerged as important human intestinal pathogens with newly adapted virulence potential and antibiotic resistance. These genetic features arose in tandem with large-scale genome evolution mediated by mobile elements. Pathoadaptation in enterococci is thought to be mediated in part by the IS element IS256 through gene inactivation and recombination events. However, the regulation of IS256 and the mechanisms controlling its activation are not well understood. Here, we adapt an IS256-specfic deep sequencing method to describe how chronic lytic phage infection drives widespread diversification of IS256 in E. faecalis and how antibiotic exposure is associated with IS256 diversification in E. faecium during a clinical human infection. We show through comparative genomics that IS256 is primarily found in hospital-adapted enterococcal isolates. Analyses of IS256 transposase gene levels reveal that IS256 mobility is regulated at the transcriptional level by multiple mechanisms in E. faecalis, indicating tight control of IS256 activation in the absence of selective pressure. Our findings reveal that stressors such as phages and antibiotic exposure drives rapid genome-scale transposition in the enterococci. IS256 diversification can therefore explain how selective pressures mediate evolution of the enterococcal genome, ultimately leading to the emergence of dominant nosocomial lineages that threaten human health.
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Affiliation(s)
- Joshua M. Kirsch
- Department of Immunology and Microbiology, University of Colorado–Anschutz Medical Campus, School of Medicine, Aurora, Colorado, United States of America
| | - Shannon Ely
- Department of Immunology and Microbiology, University of Colorado–Anschutz Medical Campus, School of Medicine, Aurora, Colorado, United States of America
| | - Madison E. Stellfox
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Karthik Hullahalli
- Department of Biological Sciences, University of Texas at Dallas, Richardson, Texas, United States of America
| | - Phat Luong
- Department of Immunology and Microbiology, University of Colorado–Anschutz Medical Campus, School of Medicine, Aurora, Colorado, United States of America
| | - Kelli L. Palmer
- Department of Biological Sciences, University of Texas at Dallas, Richardson, Texas, United States of America
| | - Daria Van Tyne
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Breck A. Duerkop
- Department of Immunology and Microbiology, University of Colorado–Anschutz Medical Campus, School of Medicine, Aurora, Colorado, United States of America
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11
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Huang S, Li H, Ma L, Liu R, Li Y, Wang H, Lu X, Huang X, Wu X, Liu X. Insertion sequence contributes to the evolution and environmental adaptation of Acidithiobacillus. BMC Genomics 2023; 24:282. [PMID: 37231368 DOI: 10.1186/s12864-023-09372-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 05/10/2023] [Indexed: 05/27/2023] Open
Abstract
BACKGROUND The genus Acidithiobacillus has been widely concerned due to its superior survival and oxidation ability in acid mine drainage (AMD). However, the contribution of insertion sequence (IS) to their biological evolution and environmental adaptation is very limited. ISs are the simplest kinds of mobile genetic elements (MGEs), capable of interrupting genes, operons, or regulating the expression of genes through transposition activity. ISs could be classified into different families with their own members, possessing different copies. RESULTS In this study, the distribution and evolution of ISs, as well as the functions of the genes around ISs in 36 Acidithiobacillus genomes, were analyzed. The results showed that 248 members belonging to 23 IS families with a total of 10,652 copies were identified within the target genomes. The IS families and copy numbers among each species were significantly different, indicating that the IS distribution of Acidithiobacillus were not even. A. ferrooxidans had 166 IS members, which may develop more gene transposition strategies compared with other Acidithiobacillus spp. What's more, A. thiooxidans harbored the most IS copies, suggesting that their ISs were the most active and more likely to transpose. The ISs clustered in the phylogenetic tree approximately according to the family, which were mostly different from the evolutionary trends of their host genomes. Thus, it was suggested that the recent activity of ISs of Acidithiobacillus was not only determined by their genetic characteristics, but related with the environmental pressure. In addition, many ISs especially Tn3 and IS110 families were inserted around the regions whose functions were As/Hg/Cu/Co/Zn/Cd translocation and sulfur oxidation, implying that ISs could improve the adaptive capacities of Acidithiobacillus to the extremely acidic environment by enhancing their resistance to heavy metals and utilization of sulfur. CONCLUSIONS This study provided the genomic evidence for the contribution of IS to evolution and adaptation of Acidithiobacillus, opening novel sights into the genome plasticity of those acidophiles.
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Affiliation(s)
- Shanshan Huang
- School of Minerals Processing and Bioengineering, Central South University, 410083, Changsha, China
| | - Huiying Li
- School of Minerals Processing and Bioengineering, Central South University, 410083, Changsha, China
| | - Liyuan Ma
- Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, School of Environmental Studies, China University of Geosciences, 430074, Wuhan, China.
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, 430074, Wuhan, China.
| | - Rui Liu
- Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, School of Environmental Studies, China University of Geosciences, 430074, Wuhan, China
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, 430074, Wuhan, China
| | - Yiran Li
- School of Minerals Processing and Bioengineering, Central South University, 410083, Changsha, China
| | - Hongmei Wang
- Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, School of Environmental Studies, China University of Geosciences, 430074, Wuhan, China
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, 430074, Wuhan, China
| | - Xiaolu Lu
- Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, School of Environmental Studies, China University of Geosciences, 430074, Wuhan, China
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, 430074, Wuhan, China
| | - Xinping Huang
- Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, School of Environmental Studies, China University of Geosciences, 430074, Wuhan, China
| | - Xinhong Wu
- School of Minerals Processing and Bioengineering, Central South University, 410083, Changsha, China
| | - Xueduan Liu
- School of Minerals Processing and Bioengineering, Central South University, 410083, Changsha, China
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12
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Halter T, Köstlbacher S, Rattei T, Hendrickx F, Manzano-Marín A, Horn M. One to host them all: genomics of the diverse bacterial endosymbionts of the spider Oedothorax gibbosus. Microb Genom 2023; 9:mgen000943. [PMID: 36757767 PMCID: PMC9997750 DOI: 10.1099/mgen.0.000943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023] Open
Abstract
Bacterial endosymbionts of the groups Wolbachia, Cardinium and Rickettsiaceae are well known for their diverse effects on their arthropod hosts, ranging from mutualistic relationships to reproductive phenotypes. Here, we analysed a unique system in which the dwarf spider Oedothorax gibbosus is co-infected with up to five different endosymbionts affiliated with Wolbachia, 'Candidatus Tisiphia' (formerly Torix group Rickettsia), Cardinium and Rhabdochlamydia. Using short-read genome sequencing data, we show that the endosymbionts are heterogeneously distributed among O. gibbosus populations and are frequently found co-infecting spider individuals. To study this intricate host-endosymbiont system on a genome-resolved level, we used long-read sequencing to reconstruct closed genomes of the Wolbachia, 'Ca. Tisiphia' and Cardinium endosymbionts. We provide insights into the ecology and evolution of the endosymbionts and shed light on the interactions with their spider host. We detected high quantities of transposable elements in all endosymbiont genomes and provide evidence that ancestors of the Cardinium, 'Ca. Tisiphia' and Wolbachia endosymbionts have co-infected the same hosts in the past. Our findings contribute to broadening our knowledge about endosymbionts infecting one of the largest animal phyla on Earth and show the usefulness of transposable elements as an evolutionary 'contact-tracing' tool.
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Affiliation(s)
- Tamara Halter
- Centre for Microbiology and Environmental Systems Science, University of Vienna. Djerassiplatz 1, 1030 Vienna, Austria.,Doctoral School in Microbiology and Environmental Science, University of Vienna. Universitätsring 1, 1010 Vienna, Austria
| | - Stephan Köstlbacher
- Centre for Microbiology and Environmental Systems Science, University of Vienna. Djerassiplatz 1, 1030 Vienna, Austria.,Doctoral School in Microbiology and Environmental Science, University of Vienna. Universitätsring 1, 1010 Vienna, Austria.,Current address: Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6700 EH Wageningen, The Netherlands
| | - Thomas Rattei
- Centre for Microbiology and Environmental Systems Science, University of Vienna. Djerassiplatz 1, 1030 Vienna, Austria
| | - Frederik Hendrickx
- OD Taxonomy and Phylogeny, Royal Belgian Institute of Natural Sciences. Rue Vautier/Vautierstraat 29,, 1000 Brussels, Belgium
| | - Alejandro Manzano-Marín
- Centre for Microbiology and Environmental Systems Science, University of Vienna. Djerassiplatz 1, 1030 Vienna, Austria
| | - Matthias Horn
- Centre for Microbiology and Environmental Systems Science, University of Vienna. Djerassiplatz 1, 1030 Vienna, Austria
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13
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Shin E, Noh HS, Ye Q, Lee SJ. Hydrogen peroxide treatment induces the transposition of an insertion sequence in Deinococcus radiopugnans DY59. Front Microbiol 2023; 14:1110084. [PMID: 36937269 PMCID: PMC10017437 DOI: 10.3389/fmicb.2023.1110084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 02/13/2023] [Indexed: 03/06/2023] Open
Abstract
Deinococcus radiopugnans DY59 (formerly Deinococcus swuensis DY59) is a radiation-resistant bacterium isolated from soil. From the 3.5 Mb genomic DNA sequence of strain DY59 (December 2014), 31 insertion sequence (IS) elements of six IS families including IS1, IS4, IS5, IS66, IS630, and IS701 and five unclassified IS elements were detected. Upon induction of oxidative stress with 80 and 100 mM H2O2, the unique ISs of the IS4 family member were actively translocated into a carotenoid biosynthesis gene phytoene desaturase (QR90_10400), resulting in non-pigment phenotypic selection. Therefore, these active transpositions of a specific IS family member were induced by oxidative stress at 80 and 100 mM H2O2. Furthermore, D. radiopugnans DY59 exhibited extremely higher MIC values against H2O2 treatment. To explain this phenomenon, qRT-PCR was conducted to assess the expression levels of catalase and three LysR family regulators. Our findings indicated that the ISDrpg2 and ISDrpg3 elements of the IS4 family were actively transposed into the phytoene desaturase gene by H2O2 treatment via replicative transposition. However, high H2O2 resistance did not originate from H2O2-induced expression of catalase and LysR family regulators.
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14
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Repeat sequences limit the effectiveness of lateral gene transfer and favored the evolution of meiotic sex in early eukaryotes. Proc Natl Acad Sci U S A 2022; 119:e2205041119. [PMID: 35994648 PMCID: PMC9436333 DOI: 10.1073/pnas.2205041119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The transition from prokaryotic lateral gene transfer to eukaryotic meiotic sex is poorly understood. Phylogenetic evidence suggests that it was tightly linked to eukaryogenesis, which involved an unprecedented rise in both genome size and the density of genetic repeats. Expansion of genome size raised the severity of Muller's ratchet, while limiting the effectiveness of lateral gene transfer (LGT) at purging deleterious mutations. In principle, an increase in recombination length combined with higher rates of LGT could solve this problem. Here, we show using a computational model that this solution fails in the presence of genetic repeats prevalent in early eukaryotes. The model demonstrates that dispersed repeat sequences allow ectopic recombination, which leads to the loss of genetic information and curtails the capacity of LGT to prevent mutation accumulation. Increasing recombination length in the presence of repeat sequences exacerbates the problem. Mutational decay can only be resisted with homology along extended sequences of DNA. We conclude that the transition to homologous pairing along linear chromosomes was a key innovation in meiotic sex, which was instrumental in the expansion of eukaryotic genomes and morphological complexity.
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15
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Rodriguez Jimenez A, Guiglielmoni N, Goetghebuer L, Dechamps E, George IF, Flot JF. Comparative genome analysis of Vagococcus fluvialis reveals abundance of mobile genetic elements in sponge-isolated strains. BMC Genomics 2022; 23:618. [PMID: 36008774 PMCID: PMC9413892 DOI: 10.1186/s12864-022-08842-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 07/18/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Vagococcus fluvialis is a species of lactic acid bacteria found both free-living in river and seawater and associated to hosts, such as marine sponges. This species has been greatly understudied, with no complete genome assembly available to date, which is essential for the characterisation of the mobilome. RESULTS We sequenced and assembled de novo the complete genome sequences of five V. fluvialis isolates recovered from marine sponges. Pangenome analysis of the V. fluvialis species (total of 17 genomes) showed a high intraspecific diversity, with 45.5% of orthologous genes found to be strain specific. Despite this diversity, analyses of gene functions clustered all V. fluvialis species together and separated them from other sequenced Vagococcus species. V. fluvialis strains from different habitats were highly similar in terms of functional diversity but the sponge-isolated strains were enriched in several functions related to the marine environment. Furthermore, sponge-isolated strains carried a significantly higher number of mobile genetic elements (MGEs) compared to previously sequenced V. fluvialis strains from other environments. Sponge-isolated strains carried up to 4 circular plasmids each, including a 48-kb conjugative plasmid. Three of the five strains carried an additional circular extrachromosomal sequence, assumed to be an excised prophage as it contained mainly viral genes and lacked plasmid replication genes. Insertion sequences (ISs) were up to five times more abundant in the genomes of sponge-isolated strains compared to the others, including several IS families found exclusively in these genomes. CONCLUSIONS Our findings highlight the dynamics and plasticity of the V. fluvialis genome. The abundance of mobile genetic elements in the genomes of sponge-isolated V. fluvialis strains suggests that the mobilome might be key to understanding the genomic signatures of symbiosis in bacteria.
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Affiliation(s)
- Ana Rodriguez Jimenez
- Ecology of Aquatic Systems, Université libre de Bruxelles (ULB), Brussels, Belgium. .,Evolutionary Biology and Ecology, Université libre de Bruxelles (ULB), Brussels, Belgium.
| | - Nadège Guiglielmoni
- Evolutionary Biology and Ecology, Université libre de Bruxelles (ULB), Brussels, Belgium
| | - Lise Goetghebuer
- Ecology of Aquatic Systems, Université libre de Bruxelles (ULB), Brussels, Belgium
| | - Etienne Dechamps
- Ecology of Aquatic Systems, Université libre de Bruxelles (ULB), Brussels, Belgium
| | - Isabelle F George
- Ecology of Aquatic Systems, Université libre de Bruxelles (ULB), Brussels, Belgium.,Marine Biology, Université libre de Bruxelles (ULB), Brussels, Belgium
| | - Jean-François Flot
- Evolutionary Biology and Ecology, Université libre de Bruxelles (ULB), Brussels, Belgium.,Interuniversity Institute of Bioinformatics in Brussels - (IB)², Brussels, Belgium
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16
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Ambroset C, Peticca A, Tricot A, Tardy F. Genomic features of Mycoplasma bovis subtypes currently circulating in France. BMC Genomics 2022; 23:603. [PMID: 35986252 PMCID: PMC9392320 DOI: 10.1186/s12864-022-08818-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 08/04/2022] [Indexed: 12/04/2022] Open
Abstract
Background Mycoplasma (M.) bovis is a major etiological agent of bovine respiratory disease, which is the most economically costly disease of cattle worldwide. Cattle disease surveillance on M. bovis is increasingly using gene-based techniques, such as multilocus sequence typing (MLST), or genome-based techniques such as core genome MLST that both require only partial genomic data. However, accurate up-to-date surveillance also demands complete, circular genomes that can be used as reference to track the evolution of the different lineages. Yet, in France, two of the main subtypes currently circulating still have no representing genome in public databases. Here, to address this gap, we provide and compare three new complete M. bovis genomes obtained from recent clinical isolates that represent major subtypes circulating in France and Europe. Results Genomes were obtained using a hybrid assembly strategy (Illumina and Nanopore) with fine-tuning of settings and inputs used in the Unicycler assembly pipeline, such as size selection of reads and quality trimming of the FASTQ files. The main characteristics and synteny of the genomes were compared. The three genomes mainly differed by their content in terms of mobile genetic elements, i.e. integrative conjugative elements (ICE) and insertion sequences (IS), a feature that impacts their structure. For instance, strain L15527, representing subtype3 (st3), harbours an exceptionally high number of ICEs, which results in a bigger-sized genome than all those previously described and could be associated with the propensity of st3 to gain and fix mutations through chromosomal transfer mechanisms. In contrast, strain F9160, of st1, is very close to the PG45 type strain isolated in 1961 in the USA, and harbours a huge number of IS. These features may be associated with an evolution towards a host-restricted state or in a “closed” host or environment reservoir until a recent re-emergence. Conclusions Whole-genome comparison of the three French M. bovis subtypes provides valuable resources for future studies combining epidemiology, phylogenetic data, and phylodynamic methods. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08818-9.
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17
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Metagenomic methylation patterns resolve bacterial genomes of unusual size and structural complexity. THE ISME JOURNAL 2022; 16:1921-1931. [PMID: 35459792 PMCID: PMC9296519 DOI: 10.1038/s41396-022-01242-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 04/05/2022] [Accepted: 04/08/2022] [Indexed: 01/01/2023]
Abstract
The plasticity of bacterial and archaeal genomes makes examining their ecological and evolutionary dynamics both exciting and challenging. The same mechanisms that enable rapid genomic change and adaptation confound current approaches for recovering complete genomes from metagenomes. Here, we use strain-specific patterns of DNA methylation to resolve complex bacterial genomes from long-read metagenomic data of a marine microbial consortium, the “pink berries” of the Sippewissett Marsh (USA). Unique combinations of restriction-modification (RM) systems encoded by the bacteria produced distinctive methylation profiles that were used to accurately bin and classify metagenomic sequences. Using this approach, we finished the largest and most complex circularized bacterial genome ever recovered from a metagenome (7.9 Mb with >600 transposons), the finished genome of Thiohalocapsa sp. PB-PSB1 the dominant bacteria in the consortia. From genomes binned by methylation patterns, we identified instances of horizontal gene transfer between sulfur-cycling symbionts (Thiohalocapsa sp. PB-PSB1 and Desulfofustis sp. PB-SRB1), phage infection, and strain-level structural variation. We also linked the methylation patterns of each metagenome-assembled genome with encoded DNA methyltransferases and discovered new RM defense systems, including novel associations of RM systems with RNase toxins.
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18
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Eriksson MC, Mandáková T, McCann J, Temsch EM, Chase MW, Hedrén M, Weiss-Schneeweiss H, Paun O. Repeat dynamics across timescales: a perspective from sibling allotetraploid marsh orchids (Dactylorhiza majalis s.l.). Mol Biol Evol 2022; 39:6651906. [PMID: 35904928 PMCID: PMC9366187 DOI: 10.1093/molbev/msac167] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
To provide insights into the fate of transposable elements (TEs) across timescales in a post-polyploidization context, we comparatively investigate five sibling Dactylorhiza allotetraploids (Orchidaceae) formed independently and sequentially between 500 and 100K generations ago by unidirectional hybridization between diploids D. fuchsii and D. incarnata. Our results first reveal that the paternal D. incarnata genome shows a marked increased content of LTR retrotransposons compared to the maternal species, reflected in its larger genome size and consistent with a previously hypothesized bottleneck. With regard to the allopolyploids, in the youngest D. purpurella both genome size and TE composition appear to be largely additive with respect to parents, whereas for polyploids of intermediate ages we uncover rampant genome expansion on a magnitude of multiple entire genomes of some plants such as Arabidopsis. The oldest allopolyploids in the series are not larger than the intermediate ones. A putative tandem repeat, potentially derived from a non-autonomous miniature inverted-repeat TE (MITE) drives much of the genome dynamics in the allopolyploids. The highly dynamic MITE-like element is found in higher proportions in the maternal diploid, D. fuchsii, but is observed to increase in copy number in both subgenomes of the allopolyploids. Altogether, the fate of repeats appears strongly regulated and therefore predictable across multiple independent allopolyploidization events in this system. Apart from the MITE-like element, we consistently document a mild genomic shock following the allopolyploidizations investigated here, which may be linked to their relatively large genome sizes, possibly associated with strong selection against further genome expansions.
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Affiliation(s)
- Mimmi C Eriksson
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria.,Vienna Graduate School of Population Genetics, Veterinärplatz 1, A-1210 Vienna, Austria
| | - Terezie Mandáková
- Plant Cytogenomics Research Group, CEITEC-Central - European Institute of Technology, Masaryk University, Brno 62500, Czech Republic
| | - Jamie McCann
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
| | - Eva M Temsch
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
| | - Mark W Chase
- Royal Botanic Gardens Kew, London TW9 3AE, United Kingdom.,Department of Environment and Agriculture, Curtin University, Perth, Western Australia, Australia
| | - Mikael Hedrén
- Department of Biology, University of Lund, Sölvegatan 37, SE-223 62 Lund, Sweden
| | - Hanna Weiss-Schneeweiss
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
| | - Ovidiu Paun
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
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19
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How Do Transposable Elements Activate Expression of Transcriptionally Silent Antibiotic Resistance Genes? Int J Mol Sci 2022; 23:ijms23158063. [PMID: 35897639 PMCID: PMC9330008 DOI: 10.3390/ijms23158063] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 07/17/2022] [Accepted: 07/20/2022] [Indexed: 02/06/2023] Open
Abstract
The rapidly emerging phenomenon of antibiotic resistance threatens to substantially reduce the efficacy of available antibacterial therapies. Dissemination of resistance, even between phylogenetically distant bacterial species, is mediated mainly by mobile genetic elements, considered to be natural vectors of horizontal gene transfer. Transposable elements (TEs) play a major role in this process—due to their highly recombinogenic nature they can mobilize adjacent genes and can introduce them into the pool of mobile DNA. Studies investigating this phenomenon usually focus on the genetic load of transposons and the molecular basis of their mobility. However, genes introduced into evolutionarily distant hosts are not necessarily expressed. As a result, bacterial genomes contain a reservoir of transcriptionally silent genetic information that can be activated by various transposon-related recombination events. The TEs themselves along with processes associated with their transposition can introduce promoters into random genomic locations. Thus, similarly to integrons, they have the potential to convert dormant genes into fully functional antibiotic resistance determinants. In this review, we describe the genetic basis of such events and by extension the mechanisms promoting the emergence of new drug-resistant bacterial strains.
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20
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Barker DF. A synergistic arrangement of two unrelated IS elements facilitates adjacent deletion in Micrococcus luteus ATCC49732. FEMS Microbiol Lett 2022; 369:6646518. [DOI: 10.1093/femsle/fnac062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 06/07/2022] [Accepted: 07/15/2022] [Indexed: 11/14/2022] Open
Abstract
Abstract
Mutants of M. luteus strain ATCC49732 lacking the yellow pigment sarcinaxanthin were observed at an unexpectedly high frequency and the molecular basis was investigated. PCR probing revealed complete deletion of the crt biosynthetic operon in 11/14 mutants. Inverse PCR was used to identify a common breakpoint 35 kb downstream from crt precisely at the end of the right inverted repeat (IRR) of a partial ISMlu8 element that lies between two inversely oriented full-length ISMlu2. Three different breakpoints 5′ to crt were found with the sequence CTAG one bp 5′ to each novel junction. Analysis of 35 genomic sites with single ISMlu8 insertions showed that ISMlu8 transposase has high specificity for CTAG, implicating its key role in formation of the Δcrt deletions. No downstream deletion endpoints were observed at an immediately adjacent ISMlu8 with a nearly identical IRR in the same orientation and slightly closer to the crt operon, indicating that access of ISMlu8 transposase to the ISMlu2-flanked ISMlu8 IRR is greatly enhanced by the surrounding inverted repeat arrangement. The association of high frequency genomic rearrangement with this distinctive natural configuration of ISs from two different IS families offers a new insight into IS element evolutionary potential.
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Affiliation(s)
- David F Barker
- Department of Medical Laboratory Science, Bellarmine University , 2001 Newburg Road, Louisville, KY 40205 , USA
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21
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Genetic Characteristics and Enzymatic Activities of Bacillus velezensis KS04AU as a Stable Biocontrol Agent against Phytopathogens. INTERNATIONAL JOURNAL OF PLANT BIOLOGY 2022. [DOI: 10.3390/ijpb13030018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Bacillus velezensis has a broad application in the agricultural and industrial sectors for its biocontrol properties and its potential active secondary metabolites. The defined phenotypic characteristics of a strain vary according to its ecosystem. We report the complete genomic analysis of B. velezensis KS04AU compared to four strains of B. velezensis (SRCM102752, ONU-553, FZB42, and JS25R) and two closely related Bacillus amyloliquefaciens (LL3 and IT-45). A total of 4771 protein coding genes comprises the KS04AU genome, in comparison with 3334 genes core genes found in the six other strains and the remaining 1437 shell genes. Average nucleotide identity of the target strain to the six other strains showed 99.65% to B. velezensis ONU-553, sharing 60 orthologous genes. Secondary metabolite gene cluster analysis of all strains showed that KS04AU has a mersacidin cluster gene, which is absent in the genome of the other strains. PHASTER analysis also showed KS04AU harboring two phages (Aeribacllus AP45 NC_048651 and Paenibacillus_Tripp NC_028930), which were also unique in comparison with the other strains. Analysis on anti-microbial resistance genes showed no difference in the genome of KS04AU to any of the other genomes, with the exception of B. amyloliquefaciens IT-45 which had one unique small multidrug-resistance antibiotic efflux-pump gene (qacJ). The CRISPR-Cas systems in the strains were also compared showing one CRISPR gene found only in KS04AU. Hydrolytic activity, antagonistic activity against phytopathogens (Fusarium oxysporum, Fusarium graminearum, Alternaria alternata and Pseudomonas syringae) and biocontrol against tomato foot and root rot experiments were carried out. B. velezensis KS04AU inhibits the growth of all phytopathogens tested, produces hydrolytic activity, and reduces Fusarium oxysporum f.sp. radicis-lycopersici (Forl) ZUM2407 lesions up to 46.02 ± 0.12%. The obtained results confirm B. velezensis KS04AU as a potential biocontrol strain for plant protection.
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Tempel S, Bedo J, Talla E. From a large-scale genomic analysis of insertion sequences to insights into their regulatory roles in prokaryotes. BMC Genomics 2022; 23:451. [PMID: 35725380 PMCID: PMC9208149 DOI: 10.1186/s12864-022-08678-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 06/07/2022] [Indexed: 12/03/2022] Open
Abstract
Background Insertion sequences (ISs) are mobile repeat sequences and most of them can copy themselves to new host genome locations, leading to genome plasticity and gene regulation in prokaryotes. In this study, we present functional and evolutionary relationships between IS and neighboring genes in a large-scale comparative genomic analysis. Results IS families were located in all prokaryotic phyla, with preferential occurrence of IS3, IS4, IS481, and IS5 families in Alpha-, Beta-, and Gammaproteobacteria, Actinobacteria and Firmicutes as well as in eukaryote host-associated organisms and autotrophic opportunistic pathogens. We defined the concept of the IS-Gene couple (IG), which allowed to highlight the functional and regulatory impacts of an IS on the closest gene. Genes involved in transcriptional regulation and transport activities were found overrepresented in IG. In particular, major facilitator superfamily (MFS) transporters, ATP-binding proteins and transposases raised as favorite neighboring gene functions of IS hotspots. Then, evolutionary conserved IS-Gene sets across taxonomic lineages enabled the classification of IS-gene couples into phylum, class-to-genus, and species syntenic IS-Gene couples. The IS5, IS21, IS4, IS607, IS91, ISL3 and IS200 families displayed two to four times more ISs in the phylum and/or class-to-genus syntenic IGs compared to other IS families. This indicates that those families were probably inserted earlier than others and then subjected to horizontal transfer, transposition and deletion events over time. In phylum syntenic IG category, Betaproteobacteria, Crenarchaeota, Calditrichae, Planctomycetes, Acidithiobacillia and Cyanobacteria phyla act as IS reservoirs for other phyla, and neighboring gene functions are mostly related to transcriptional regulators. Comparison of IS occurrences with predicted regulatory motifs led to ~ 26.5% of motif-containing ISs with 2 motifs per IS in average. These results, concomitantly with short IS-Gene distances, suggest that those ISs would interfere with the expression of neighboring genes and thus form strong candidates for an adaptive pairing. Conclusions All together, our large-scale study provide new insights into the IS genetic context and strongly suggest their regulatory roles. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08678-3.
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Affiliation(s)
- Sebastien Tempel
- Aix Marseille University, CNRS, LCB, Laboratoire de Chimie Bactérienne, 13009, Marseille, France.
| | - Justin Bedo
- Bioinformatics Division, the Walter and Eliza Hall Institute, 1G Royal Parade, Parkville, VIC, 3052, Australia.,School of Computing and Information Systems, the University of Melbourne, Parkville, VIC, 3010, Australia
| | - Emmanuel Talla
- Aix Marseille University, CNRS, LCB, Laboratoire de Chimie Bactérienne, 13009, Marseille, France.
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Fuglsang A. Intragenic codon usage in proteobacteria: Translational selection, IS expansion and genomic shrinkage. Gene 2022; 809:146015. [PMID: 34655721 DOI: 10.1016/j.gene.2021.146015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 08/08/2021] [Accepted: 10/11/2021] [Indexed: 11/16/2022]
Abstract
This manuscript presents a method to systematically study intragenic variations in codon usage using correspondence analysis and the effective number of codons. The method is applied to >1100 proteobacteria. Codon usage biases (measured as inertia) increases with genome size, the same is true for the percentage of inertia explained by the first axis. It is shown that there is often a relaxed or more uniform codon usage near the gene termini. Ithis is not seen n small genomes, notably those of intracellular organisms like Buchnera aphidicola or Rickettsia prowazekii where translational selection plays less of a role. When genes from E. coli, for which translational selection is well described, are split into low, intermediate and high expression, respectively, it is shown that the intragenic codon usage pattern with more uniform usage at termini exist across all three expression groups. Furthermore, the correspondence analysis reveals a unique pattern in Bordetella pertussis due to IS expansion. This study thus shows that translational selection, genome shrinkage and IS expansion result in characteristic patterns in intragenic codon usage.
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inPOSE: A Flexible Toolbox for Chromosomal Cloning and Amplification of Bacterial Transgenes. Microorganisms 2022; 10:microorganisms10020236. [PMID: 35208691 PMCID: PMC8875745 DOI: 10.3390/microorganisms10020236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/14/2022] [Accepted: 01/18/2022] [Indexed: 12/10/2022] Open
Abstract
Cloning the genes and operons encoding heterologous functions in bacterial hosts is now almost exclusively carried out using plasmid vectors. This has multiple drawbacks, including the need for constant selection and variation in copy numbers. The chromosomal integration of transgenes has always offered a viable alternative; however, to date, it has been of limited use due to its tedious nature and often being limited to a single copy. We introduce here a strategy that uses bacterial insertion sequences, which are the simplest autonomous transposable elements to insert and amplify genetic cargo into a bacterial chromosome. Transgene insertion can take place either as transposition or homologous recombination, and copy number amplification is achieved using controlled copy-paste transposition. We display the successful use of IS1 and IS3 for this purpose in Escherichia coli cells using various selection markers. We demonstrate the insertion of selectable genes, an unselectable gene and a five-gene operon in up to two copies in a single step. We continue with the amplification of the inserted cassette to double-digit copy numbers within two rounds of transposase induction and selection. Finally, we analyze the stability of the cloned genetic constructs in the lack of selection and find it to be superior to all investigated plasmid-based systems. Due to the ubiquitous nature of transposable elements, we believe that with proper design, this strategy can be adapted to numerous other bacterial species.
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25
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Leyton-Carcaman B, Abanto M. Beyond to the Stable: Role of the Insertion Sequences as Epidemiological Descriptors in Corynebacterium striatum. Front Microbiol 2022; 13:806576. [PMID: 35126341 PMCID: PMC8811144 DOI: 10.3389/fmicb.2022.806576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 01/04/2022] [Indexed: 11/20/2022] Open
Abstract
In recent years, epidemiological studies of infectious agents have focused mainly on the pathogen and stable components of its genome. The use of these stable components makes it possible to know the evolutionary or epidemiological relationships of the isolates of a particular pathogen. Under this approach, focused on the pathogen, the identification of resistance genes is a complementary stage of a bacterial characterization process or an appendix of its epidemiological characterization, neglecting its genetic components’ acquisition or dispersal mechanisms. Today we know that a large part of antibiotic resistance is associated with mobile elements. Corynebacterium striatum, a bacterium from the normal skin microbiota, is also an opportunistic pathogen. In recent years, reports of infections and nosocomial outbreaks caused by antimicrobial multidrug-resistant C. striatum strains have been increasing worldwide. Despite the different existing mobile genomic elements, there is evidence that acquired resistance genes are coupled to insertion sequences in C. striatum. This perspective article reviews the insertion sequences linked to resistance genes, their relationship to evolutionary lineages, epidemiological characteristics, and the niches the strains inhabit. Finally, we evaluate the potential of the insertion sequences for their application as a descriptor of epidemiological scenarios, allowing us to anticipate the emergence of multidrug-resistant lineages.
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26
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van Dijk B, Bertels F, Stolk L, Takeuchi N, Rainey PB. Transposable elements promote the evolution of genome streamlining. Philos Trans R Soc Lond B Biol Sci 2022; 377:20200477. [PMID: 34839699 PMCID: PMC8628081 DOI: 10.1098/rstb.2020.0477] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Accepted: 08/30/2021] [Indexed: 12/25/2022] Open
Abstract
Eukaryotes and prokaryotes have distinct genome architectures, with marked differences in genome size, the ratio of coding/non-coding DNA, and the abundance of transposable elements (TEs). As TEs replicate independently of their hosts, the proliferation of TEs is thought to have driven genome expansion in eukaryotes. However, prokaryotes also have TEs in intergenic spaces, so why do prokaryotes have small, streamlined genomes? Using an in silico model describing the genomes of single-celled asexual organisms that coevolve with TEs, we show that TEs acquired from the environment by horizontal gene transfer can promote the evolution of genome streamlining. The process depends on local interactions and is underpinned by rock-paper-scissors dynamics in which populations of cells with streamlined genomes beat TEs, which beat non-streamlined genomes, which beat streamlined genomes, in continuous and repeating cycles. Streamlining is maladaptive to individual cells, but improves lineage viability by hindering the proliferation of TEs. Streamlining does not evolve in sexually reproducing populations because recombination partially frees TEs from the deleterious effects they cause. This article is part of the theme issue 'The secret lives of microbial mobile genetic elements'.
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Affiliation(s)
- Bram van Dijk
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Frederic Bertels
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Lianne Stolk
- Theoretical Biology, Department of Biology, Utrecht University, The Netherlands
| | - Nobuto Takeuchi
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Paul B. Rainey
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany
- Laboratory of Biophysics and Evolution, CBI, ESPCI Paris, Université PSL, CNRS, Paris, France
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27
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Rocha EPC, Bikard D. Microbial defenses against mobile genetic elements and viruses: Who defends whom from what? PLoS Biol 2022; 20:e3001514. [PMID: 35025885 PMCID: PMC8791490 DOI: 10.1371/journal.pbio.3001514] [Citation(s) in RCA: 71] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 01/26/2022] [Indexed: 12/27/2022] Open
Abstract
Prokaryotes have numerous mobile genetic elements (MGEs) that mediate horizontal gene transfer (HGT) between cells. These elements can be costly, even deadly, and cells use numerous defense systems to filter, control, or inactivate them. Recent studies have shown that prophages, conjugative elements, their parasites (phage satellites and mobilizable elements), and other poorly described MGEs encode defense systems homologous to those of bacteria. These constitute a significant fraction of the repertoire of cellular defense genes. As components of MGEs, these defense systems have presumably evolved to provide them, not the cell, adaptive functions. While the interests of the host and MGEs are aligned when they face a common threat such as an infection by a virulent phage, defensive functions carried by MGEs might also play more selfish roles to fend off other antagonistic MGEs or to ensure their maintenance in the cell. MGEs are eventually lost from the surviving host genomes by mutational processes and their defense systems can be co-opted when they provide an advantage to the cell. The abundance of defense systems in MGEs thus sheds new light on the role, effect, and fate of the so-called "cellular defense systems," whereby they are not only merely microbial defensive weapons in a 2-partner arms race, but also tools of intragenomic conflict between multiple genetic elements with divergent interests that shape cell fate and gene flow at the population level.
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Affiliation(s)
- Eduardo P. C. Rocha
- Institut Pasteur, Université de Paris, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, France
| | - David Bikard
- Institut Pasteur, Université de Paris, Synthetic Biology, Department of Microbiology, Paris, France
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28
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Baquero F, Martínez JL, F. Lanza V, Rodríguez-Beltrán J, Galán JC, San Millán A, Cantón R, Coque TM. Evolutionary Pathways and Trajectories in Antibiotic Resistance. Clin Microbiol Rev 2021; 34:e0005019. [PMID: 34190572 PMCID: PMC8404696 DOI: 10.1128/cmr.00050-19] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Evolution is the hallmark of life. Descriptions of the evolution of microorganisms have provided a wealth of information, but knowledge regarding "what happened" has precluded a deeper understanding of "how" evolution has proceeded, as in the case of antimicrobial resistance. The difficulty in answering the "how" question lies in the multihierarchical dimensions of evolutionary processes, nested in complex networks, encompassing all units of selection, from genes to communities and ecosystems. At the simplest ontological level (as resistance genes), evolution proceeds by random (mutation and drift) and directional (natural selection) processes; however, sequential pathways of adaptive variation can occasionally be observed, and under fixed circumstances (particular fitness landscapes), evolution is predictable. At the highest level (such as that of plasmids, clones, species, microbiotas), the systems' degrees of freedom increase dramatically, related to the variable dispersal, fragmentation, relatedness, or coalescence of bacterial populations, depending on heterogeneous and changing niches and selective gradients in complex environments. Evolutionary trajectories of antibiotic resistance find their way in these changing landscapes subjected to random variations, becoming highly entropic and therefore unpredictable. However, experimental, phylogenetic, and ecogenetic analyses reveal preferential frequented paths (highways) where antibiotic resistance flows and propagates, allowing some understanding of evolutionary dynamics, modeling and designing interventions. Studies on antibiotic resistance have an applied aspect in improving individual health, One Health, and Global Health, as well as an academic value for understanding evolution. Most importantly, they have a heuristic significance as a model to reduce the negative influence of anthropogenic effects on the environment.
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Affiliation(s)
- F. Baquero
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Network Center for Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - J. L. Martínez
- National Center for Biotechnology (CNB-CSIC), Madrid, Spain
| | - V. F. Lanza
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Network Center for Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
- Central Bioinformatics Unit, Ramón y Cajal Institute for Health Research (IRYCIS), Madrid, Spain
| | - J. Rodríguez-Beltrán
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Network Center for Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - J. C. Galán
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Network Center for Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - A. San Millán
- National Center for Biotechnology (CNB-CSIC), Madrid, Spain
| | - R. Cantón
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Network Center for Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - T. M. Coque
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Network Center for Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
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29
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Brkljacic J, Wittler B, Lindsey BE, Ganeshan VD, Sovic MG, Niehaus J, Ajibola W, Bachle SM, Fehér T, Somers DE. Frequency, composition and mobility of Escherichia coli-derived transposable elements in holdings of plasmid repositories. Microb Biotechnol 2021; 15:455-468. [PMID: 34875147 PMCID: PMC8867978 DOI: 10.1111/1751-7915.13962] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 10/14/2021] [Accepted: 10/19/2021] [Indexed: 11/29/2022] Open
Abstract
By providing the scientific community with uniform and standardized resources of consistent quality, plasmid repositories play an important role in enabling scientific reproducibility. Plasmids containing insertion sequence elements (IS elements) represent a challenge from this perspective, as they can change the plasmid structure and function. In this study, we conducted a systematic analysis of a subset of plasmid stocks distributed by plasmid repositories (The Arabidopsis Biological Resource Center and Addgene) which carry unintended integrations of bacterial mobile genetic elements. The integration of insertion sequences was most often found in, but not limited to, pBR322‐derived vectors, and did not affect the function of the specific plasmids. In certain cases, the entire stock was affected, but the majority of the stocks tested contained a mixture of the wild‐type and the mutated plasmids, suggesting that the acquisition of IS elements likely occurred after the plasmids were acquired by the repositories. However, comparison of the sequencing results of the original samples revealed that some plasmids already carried insertion mutations at the time of donation. While an extensive BLAST analysis of 47 877 plasmids sequenced from the Addgene repository uncovered IS elements in only 1.12%, suggesting that IS contamination is not widespread, further tests showed that plasmid integration of IS elements can propagate in conventional Escherichia coli hosts over a few tens of generations. Use of IS‐free E. coli hosts prevented the emergence of IS insertions as well as that of small indels, suggesting that the use of IS‐free hosts by donors and repositories could help limit unexpected and unwanted IS integrations into plasmids.
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Affiliation(s)
| | | | | | | | - Michael G Sovic
- Center For Applied Plant Sciences, The Ohio State University, Columbus, OH, USA
| | | | - Walliyulahi Ajibola
- Systems and Synthetic Biology Unit, Institute of Biochemistry, Biological Research Centre of the Eötvös Lóránd Research Network, Szeged, Hungary.,Doctoral School in Biology, University of Szeged, Szeged, Hungary
| | | | - Tamás Fehér
- Systems and Synthetic Biology Unit, Institute of Biochemistry, Biological Research Centre of the Eötvös Lóránd Research Network, Szeged, Hungary
| | - David E Somers
- Arabidopsis Biological Resource Center, Columbus, OH, USA.,Center For Applied Plant Sciences, The Ohio State University, Columbus, OH, USA.,Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA
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30
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Ben Amara W, Djebbi S, Ben Lazhar-Ajroud W, Naccache C, Mezghani MK. Insights on mauritiana-like Elements Diversity in Mayetiola destructor and M. hordei (Diptera: Cecidomyiidae). Genome 2021; 65:165-181. [PMID: 34780303 DOI: 10.1139/gen-2021-0020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Mariner-like elements (MLEs) are class II transposons belonging to the Tc1-mariner family, that have successfully invaded many insect genomes. In the current study, the availability of the Hessian fly Mayetiola destructor genome has enabled us to perform in silico analysis of MLEs using as query the previously described mariner element (Desmar1) belonging to mauritiana subfamily. Eighteen mauritiana-like elements were detected and were clustered into three main groups named Desmar1-like, MauCons1 and MauCons2. Subsequently, in vitro analysis was carried out to investigate mauritiana-like elements in M. destructor as well as in Mayetiola hordei using primers designed from TIRs of the previously identified MLEs. PCR amplifications were successful and a total of 12 and 17 mauritiana-like elements were discovered in M. destructor and M. hordei, respectively. Sequence analyses of mauritiana-like elements obtained in silico and in vitro have showed that MauCons1 and MauCons2 elements share low similarity with Desmar1 ranging from 50% to 55% suggesting different groups under mauritiana subfamily have invaded the genomes of M. destructor and M. hordei. These groups are likely inherited by vertical transmission that subsequently underwent different evolutionary histories. This work describes new mauritiana-like elements in M. destructor that are distinct from the previouslydiscovered Desmar1 and provides the first evidence of MLEs belonging to mauritiana subfamily in M. hordei.
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Affiliation(s)
- Wiem Ben Amara
- University of Tunis El Manar Faculty of Sciences of Tunis, 155529, Laboratory of Biochemistry and Biotechnology (LR01ES05), Tunis, Tunisia;
| | - Salma Djebbi
- University of Tunis El Manar Faculty of Sciences of Tunis, 155529, Laboratory of Biochemistry and Biotechnology (LR01ES05), Tunis, Tunisia;
| | - Wafa Ben Lazhar-Ajroud
- University of Tunis El Manar Faculty of Sciences of Tunis, 155529, Laboratory of Biochemistry and Biotechnology (LR01ES05), Tunis, Tunisia;
| | | | - Maha Khemakhem Mezghani
- University of Tunis El Manar Faculty of Sciences of Tunis, 155529, Laboratory of Biochemistry and Biotechnology (LR01ES05), Tunis, Tunisia;
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31
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Ye Q, Lee C, Shin E, Lee SJ. Influence of Redox Imbalances on the Transposition of Insertion Sequences in Deinococcus geothermalis. Antioxidants (Basel) 2021; 10:antiox10101623. [PMID: 34679757 PMCID: PMC8533066 DOI: 10.3390/antiox10101623] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 10/11/2021] [Accepted: 10/13/2021] [Indexed: 01/11/2023] Open
Abstract
The transposition of insertion sequence elements was evaluated among different Deinococcus geothermalis lineages, including the wild-type, a cystine importer-disrupted mutant, a complemented strain, and a cystine importer-overexpressed strain. Cellular growth reached early exponential growth at OD600 2.0 and late exponential growth at OD600 4.0. Exposing the cells to hydrogen peroxide (80–100 mM) resulted in the transposition of insertion sequences (ISs) in genes associated with the carotenoid biosynthesis pathway. Particularly, ISDge7 (an IS5 family member) and ISDge5 (an IS701 family member) from the cystine importer-disrupted mutant were transposed into phytoene desaturase (dgeo_0524) via replicative transposition. Further, the cystine importer-overexpressed strain Δdgeo_1985R showed transposition of both ISDge2 and ISDge5 elements. In contrast, IS transposition was not detected in the complementary strain. Interestingly, a cystine importer-overexpressing strain exhibited streptomycin resistance, indicating that point mutation occurred in the rpsL (dgeo_1873) gene encoding ribosomal protein S12. qRT-PCR analyses were then conducted to evaluate the expression of oxidative stress response genes, IS elements, and low-molecular-weight thiol compounds such as mycothiol and bacillithiol. Nevertheless, the mechanisms that trigger IS transposition in redox imbalance conditions remain unclear. Here, we report that the active transposition of different IS elements was affected by intracellular redox imbalances caused by cystine importer deficiencies or overexpression.
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32
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Prokaryotic and Eukaryotic Horizontal Transfer of Sailor (DD82E), a New Superfamily of IS630-Tc1-Mariner DNA Transposons. BIOLOGY 2021; 10:biology10101005. [PMID: 34681104 PMCID: PMC8533490 DOI: 10.3390/biology10101005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 09/26/2021] [Accepted: 09/28/2021] [Indexed: 12/22/2022]
Abstract
Simple Summary Transposable elements, including DNA transposons, play a significant role in genetic material exchanges between prokaryotes and eukaryotes. Comparative profiling of the evolution pattern of DNA transposons between prokaryotes and eukaryotes may identify potential genetic material exchanges between them and provide insights into the evolutionary history of prokaryotic and eukaryotic genomes. The members of the IS630-Tc1-mariner (ITm) group may represent the most diverse and widely distributed DNA transposons in nature, and the discovery of new members of this group is highly expected based on the increasing availability of genome sequencing data. We discovered a new superfamily (termed Sailor) belonging to the ITm hyperfamily, which differed from the known superfamilies of Tc1/mariner, DDxD/pogo and DD34E/Gambol, regarding phylogenetic position and catalytic domain. Our data revealed that Sailor was distributed in both prokaryotes and eukaryotes and suggested that horizontal transfer (HT) events of Sailor may occur from prokaryotic to eukaryotic genomes. Finally, internal transmissions of Sailor in prokaryotes and eukaryotes were also detected. Abstract Here, a new superfamily of IS630-Tc1-mariner (ITm) DNA transposons, termed Sailor, is identified, that is characterized by a DD82E catalytic domain and is distinct from all previously known superfamilies of the ITm group. Phylogenetic analyses revealed that Sailor forms a monophyletic clade with a more intimate link to the clades of Tc1/mariner and DD34E/Gambol. Sailor was detected in both prokaryotes and eukaryotes and invaded a total of 256 species across six kingdoms. Sailor is present in nine species of bacteria, two species of plantae, four species of protozoa, 23 species of Chromista, 12 species of Fungi and 206 species of animals. Moreover, Sailor is extensively distributed in invertebrates (a total of 206 species from six phyla) but is absent in vertebrates. Sailor transposons are 1.38–6.98 kb in total length and encoded transposases of ~676 aa flanked by TIRs with lengths between 18, 1362 and 4 bp (TATA) target-site duplications. Furthermore, our analysis provided strong evidence of Sailor transmissions from prokaryotes to eukaryotes and internal transmissions in both. These data update the classification of the ITm group and will contribute to the understanding of the evolution of ITm transposons and that of their hosts.
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Lee C, Bae MK, Choi N, Lee SJ, Lee SJ. Genome Plasticity by Insertion Sequences Learned From a Case of Radiation-Resistant Bacterium Deinococcus geothermalis. Bioinform Biol Insights 2021; 15:11779322211037437. [PMID: 34413635 PMCID: PMC8369957 DOI: 10.1177/11779322211037437] [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: 05/17/2021] [Accepted: 07/12/2021] [Indexed: 12/02/2022] Open
Abstract
The genome of the radiation-resistant bacterium Deinococcus geothermalis contains 19 types of insertion sequences (ISs), including 93 total transposases (Tpases) in 73 full-length ISs from the main chromosome and 2 mega plasmids. In this study, 68 ISs from the D. geothermalis genome were extracted to implicate the earlier genome before its mutation by transposition of ISs. The total size of eliminated ISs from genome was 78.85 kb. From these in silico corrections of mutation by the ISs, we have become aware of some bioinformatics factualness as follows: (1) can reassemble the disrupted genes if the exact IS region was eliminated, (2) can configure the schematic clustering of major DDE type Tpases, (3) can determine IS integration order across multiple hot spots, and (4) can compare genetic relativeness by the partial synteny analysis between D. geothermalis and Deinococcus strain S9. Recently, we found that several IS elements actively transferred to other genomic sites under hydrogen peroxide-induced oxidative stress conditions, resulting in the inactivation of functional genes. Therefore, the single species genome’s mobilome study provides significant support to define bacterial genome plasticity and molecular evolution from past and present progressive transposition events.
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Affiliation(s)
- Chanjae Lee
- Department of Biology, Kyung Hee University, Seoul, Korea
| | - Min K Bae
- Department of Biology, Kyung Hee University, Seoul, Korea.,Department of Geography, Kyung Hee University, Seoul, Korea
| | - Nakjun Choi
- Department of Biology, Kyung Hee University, Seoul, Korea.,Department of Life Sciences, Korea University, Seoul, Korea
| | - Su Jeong Lee
- Department of Biology, Kyung Hee University, Seoul, Korea
| | - Sung-Jae Lee
- Department of Biology, Kyung Hee University, Seoul, Korea
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34
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Garber AI, Kupper M, Laetsch DR, Weldon SR, Ladinsky MS, Bjorkman PJ, McCutcheon JP. The Evolution of Interdependence in a Four-Way Mealybug Symbiosis. Genome Biol Evol 2021; 13:evab123. [PMID: 34061185 PMCID: PMC8331144 DOI: 10.1093/gbe/evab123] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2021] [Indexed: 01/03/2023] Open
Abstract
Mealybugs are insects that maintain intracellular bacterial symbionts to supplement their nutrient-poor plant sap diets. Some mealybugs have a single betaproteobacterial endosymbiont, a Candidatus Tremblaya species (hereafter Tremblaya) that alone provides the insect with its required nutrients. Other mealybugs have two nutritional endosymbionts that together provision these same nutrients, where Tremblaya has gained a gammaproteobacterial partner that resides in its cytoplasm. Previous work had established that Pseudococcus longispinus mealybugs maintain not one but two species of gammaproteobacterial endosymbionts along with Tremblaya. Preliminary genomic analyses suggested that these two gammaproteobacterial endosymbionts have large genomes with features consistent with a relatively recent origin as insect endosymbionts, but the patterns of genomic complementarity between members of the symbiosis and their relative cellular locations were unknown. Here, using long-read sequencing and various types of microscopy, we show that the two gammaproteobacterial symbionts of P. longispinus are mixed together within Tremblaya cells, and that their genomes are somewhat reduced in size compared with their closest nonendosymbiotic relatives. Both gammaproteobacterial genomes contain thousands of pseudogenes, consistent with a relatively recent shift from a free-living to an endosymbiotic lifestyle. Biosynthetic pathways of key metabolites are partitioned in complex interdependent patterns among the two gammaproteobacterial genomes, the Tremblaya genome, and horizontally acquired bacterial genes that are encoded on the mealybug nuclear genome. Although these two gammaproteobacterial endosymbionts have been acquired recently in evolutionary time, they have already evolved codependencies with each other, Tremblaya, and their insect host.
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Affiliation(s)
- Arkadiy I Garber
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
- Biodesign Center for Mechanisms of Evolution and School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Maria Kupper
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
- Biodesign Center for Mechanisms of Evolution and School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Dominik R Laetsch
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Stephanie R Weldon
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
| | - Mark S Ladinsky
- Department of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - Pamela J Bjorkman
- Department of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - John P McCutcheon
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
- Biodesign Center for Mechanisms of Evolution and School of Life Sciences, Arizona State University, Tempe, Arizona, USA
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35
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Park HJ, Gokhale CS, Bertels F. How sequence populations persist inside bacterial genomes. Genetics 2021; 217:6151697. [PMID: 33724360 PMCID: PMC8049555 DOI: 10.1093/genetics/iyab027] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 02/04/2021] [Indexed: 01/04/2023] Open
Abstract
Compared to their eukaryotic counterparts, bacterial genomes are small and contain extremely tightly packed genes. Repetitive sequences are rare but not completely absent. One of the most common repeat families is REPINs. REPINs can replicate in the host genome and form populations that persist for millions of years. Here, we model the interactions of these intragenomic sequence populations with the bacterial host. We first confirm well-established results, in the presence and absence of horizontal gene transfer (hgt) sequence populations either expand until they drive the host to extinction or the sequence population gets purged from the genome. We then show that a sequence population can be stably maintained, when each individual sequence provides a benefit that decreases with increasing sequence population size. Maintaining a sequence population of stable size also requires the replication of the sequence population to be costly to the host, otherwise the sequence population size will increase indefinitely. Surprisingly, in regimes with high hgt rates, the benefit conferred by the sequence population does not have to exceed the damage it causes to its host. Our analyses provide a plausible scenario for the persistence of sequence populations in bacterial genomes. We also hypothesize a limited biologically relevant parameter range for the provided benefit, which can be tested in future experiments.
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Affiliation(s)
- Hye Jin Park
- Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Plön, 24306, Germany.,Asia Pacific Center for Theoretical Physics, Pohang, 37673, Korea.,Department of Physics, POSTECH, Pohang, 37673, Korea
| | - Chaitanya S Gokhale
- Research Group for Theoretical Models of Eco-evolutionary Dynamics, Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Plön, 24306, Germany
| | - Frederic Bertels
- Research Group for Microbial Molecular Evolution, Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, 24306, Germany
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Zong W, Gao B, Diaby M, Shen D, Wang S, Wang Y, Sang Y, Chen C, Wang X, Song C. Traveler, a New DD35E Family of Tc1/Mariner Transposons, Invaded Vertebrates Very Recently. Genome Biol Evol 2021; 12:66-76. [PMID: 32068835 PMCID: PMC7093834 DOI: 10.1093/gbe/evaa034] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/13/2020] [Indexed: 02/06/2023] Open
Abstract
The discovery of new members of the Tc1/mariner superfamily of transposons is expected based on the increasing availability of genome sequencing data. Here, we identified a new DD35E family termed Traveler (TR). Phylogenetic analyses of its DDE domain and full-length transposase showed that, although TR formed a monophyletic clade, it exhibited the highest sequence identity and closest phylogenetic relationship with DD34E/Tc1. This family displayed a very restricted taxonomic distribution in the animal kingdom and was only detected in ray-finned fish, anura, and squamata, including 91 vertebrate species. The structural organization of TRs was highly conserved across different classes of animals. Most intact TR transposons had a length of ∼1.5 kb (range 1,072-2,191 bp) and harbored a single open reading frame encoding a transposase of ∼340 aa (range 304-350 aa) flanked by two short-terminal inverted repeats (13-68 bp). Several conserved motifs, including two helix-turn-helix motifs, a GRPR motif, a nuclear localization sequence, and a DDE domain, were also identified in TR transposases. This study also demonstrated the presence of horizontal transfer events of TRs in vertebrates, whereas the average sequence identities and the evolutionary dynamics of TR elements across species and clusters strongly indicated that the TR family invaded the vertebrate lineage very recently and that some of these elements may be currently active, combining the intact TR copies in multiple lineages of vertebrates. These data will contribute to the understanding of the evolutionary history of Tc1/mariner transposons and that of their hosts.
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Affiliation(s)
- Wencheng Zong
- College of Animal Science & Technology, Yangzhou University, Jiangsu, China
| | - Bo Gao
- College of Animal Science & Technology, Yangzhou University, Jiangsu, China
| | - Mohamed Diaby
- College of Animal Science & Technology, Yangzhou University, Jiangsu, China
| | - Dan Shen
- College of Animal Science & Technology, Yangzhou University, Jiangsu, China
| | - Saisai Wang
- College of Animal Science & Technology, Yangzhou University, Jiangsu, China
| | - Yali Wang
- College of Animal Science & Technology, Yangzhou University, Jiangsu, China
| | - Yatong Sang
- College of Animal Science & Technology, Yangzhou University, Jiangsu, China
| | - Cai Chen
- College of Animal Science & Technology, Yangzhou University, Jiangsu, China
| | - Xiaoyan Wang
- College of Animal Science & Technology, Yangzhou University, Jiangsu, China
| | - Chengyi Song
- College of Animal Science & Technology, Yangzhou University, Jiangsu, China
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Insertion-sequence-mediated mutations both promote and constrain evolvability during a long-term experiment with bacteria. Nat Commun 2021; 12:980. [PMID: 33579917 PMCID: PMC7881107 DOI: 10.1038/s41467-021-21210-7] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Accepted: 01/08/2021] [Indexed: 01/26/2023] Open
Abstract
Insertion sequences (IS) are ubiquitous bacterial mobile genetic elements, and the mutations they cause can be deleterious, neutral, or beneficial. The long-term dynamics of IS elements and their effects on bacteria are poorly understood, including whether they are primarily genomic parasites or important drivers of adaptation by natural selection. Here, we investigate the dynamics of IS elements and their contribution to genomic evolution and fitness during a long-term experiment with Escherichia coli. IS elements account for ~35% of the mutations that reached high frequency through 50,000 generations in those populations that retained the ancestral point-mutation rate. In mutator populations, IS-mediated mutations are only half as frequent in absolute numbers. In one population, an exceptionally high ~8-fold increase in IS150 copy number is associated with the beneficial effects of early insertion mutations; however, this expansion later slowed down owing to reduced IS150 activity. This population also achieves the lowest fitness, suggesting that some avenues for further adaptation are precluded by the IS150-mediated mutations. More generally, across all populations, we find that higher IS activity becomes detrimental to adaptation over evolutionary time. Therefore, IS-mediated mutations can both promote and constrain evolvability. Insertion sequences (IS) are common mobile genetic elements in bacteria, but their effects on bacterial evolution are not well understood. Here, Consuegra and colleagues investigate the dynamics and fitness consequences of IS elements in E. coli over 50,000 generations.
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38
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Assessing the Genomic Variability of Gardnerella vaginalis through Comparative Genomic Analyses: Evolutionary and Ecological Implications. Appl Environ Microbiol 2020; 87:AEM.02188-20. [PMID: 33097505 DOI: 10.1128/aem.02188-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 10/06/2020] [Indexed: 01/10/2023] Open
Abstract
Gardnerella vaginalis is described as a common anaerobic vaginal bacterium whose presence may correlate with vaginal dysbiotic conditions. In the current study, we performed phylogenomic analyses of 72 G. vaginalis genome sequences, revealing noteworthy genome differences underlying a polyphyletic organization of this taxon. Particularly, the genomic survey revealed that this species may actually include nine distinct genotypes (GGtype1 to GGtype9). Furthermore, the observed link between sialidase and phylogenomic grouping provided clues of a connection between virulence potential and the evolutionary history of this microbial taxon. Specifically, based on the outcomes of these in silico analyses, GGtype3, GGtype7, GGtype8, and GGtype9 appear to have virulence potential since they exhibited the sialidase gene in their genomes. Notably, the analysis of 34 publicly available vaginal metagenomic samples allowed us to trace the distribution of the nine G. vaginalis genotypes identified in this study among the human population, highlighting how differences in genetic makeup could be related to specific ecological properties. Furthermore, comparative genomic analyses provided details about the G. vaginalis pan- and core genome contents, including putative genetic elements involved in the adaptation to the ecological niche as well as many putative virulence factors. Among these putative virulence factors, particularly noteworthy genes identified were the gene encoding cholesterol-dependent cytolysin (CDC) toxin vaginolysin and genes related to microbial biofilm formation, iron uptake, adhesion to the vaginal epithelium, as well as macrolide antibiotic resistance.IMPORTANCE The identification of nine different genotypes among members of G. vaginalis allowed us to distinguish an uneven distribution of virulence-associated genetic traits within this taxon and thus suggest the potential occurrence of putative pathogen and commensal G. vaginalis strains. These findings, coupled with metagenomics microbial profiling of human vaginal microbiota, permitted us to get insights into the distribution of the genotypes among the human population, highlighting the presence of different structural communities in terms of G. vaginalis genotypes.
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Comparative Pathogenomics of Aeromonas veronii from Pigs in South Africa: Dominance of the Novel ST657 Clone. Microorganisms 2020; 8:microorganisms8122008. [PMID: 33339176 PMCID: PMC7765573 DOI: 10.3390/microorganisms8122008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 12/13/2020] [Accepted: 12/15/2020] [Indexed: 12/13/2022] Open
Abstract
The pathogenomics of carbapenem-resistant Aeromonas veronii (A. veronii) isolates recovered from pigs in KwaZulu-Natal, South Africa, was explored by whole genome sequencing on the Illumina MiSeq platform. Genomic functional annotation revealed a vast array of similar central networks (metabolic, cellular, and biochemical). The pan-genome analysis showed that the isolates formed a total of 4349 orthologous gene clusters, 4296 of which were shared; no unique clusters were observed. All the isolates had similar resistance phenotypes, which corroborated their chromosomally mediated resistome (blaCPHA3 and blaOXA-12) and belonged to a novel sequence type, ST657 (a satellite clone). Isolates in the same sub-clades clustered according to their clonal lineages and host. Mobilome analysis revealed the presence of chromosome-borne insertion sequence families. The estimated pathogenicity score (Pscore ≈ 0.60) indicated their potential pathogenicity in humans. Furthermore, these isolates carried several virulence factors (adherence factors, toxins, and immune evasion), in different permutations and combinations, indicating a differential ability to establish infection. Phylogenomic and metadata analyses revealed a predilection for water environments and aquatic animals, with more recent reports in humans and food animals across geographies, making A. veronii a potential One Health indicator bacterium.
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Wang H, Zhang H, Zhong Z, Sun Y, Wang M, Chen H, Zhou L, Cao L, Lian C, Li C. Molecular analyses of the gill symbiosis of the bathymodiolin mussel Gigantidas platifrons. iScience 2020; 24:101894. [PMID: 33364583 PMCID: PMC7750550 DOI: 10.1016/j.isci.2020.101894] [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: 08/14/2020] [Revised: 10/07/2020] [Accepted: 12/02/2020] [Indexed: 11/29/2022] Open
Abstract
Although the deep-sea bathymodiolin mussels have been intensively studied as a model of animal-bacteria symbiosis, it remains challenging to assess the host-symbiont interactions due to the complexity of the symbiotic tissue-the gill. Using cold-seep mussel Gigantidas platifrons as a model, we isolated the symbiont harboring bacteriocytes and profiled the transcriptomes of the three major parts of the symbiosis-the gill, the bacteriocyte, and the symbiont. This breakdown of the complex symbiotic tissue allowed us to characterize the host-symbiont interactions further. Our data showed that the gill's non-symbiotic parts play crucial roles in maintaining and protecting the symbiosis; the bacteriocytes supply the symbiont with metabolites, control symbiont population, and shelter the symbiont from phage infection; the symbiont dedicates to the methane oxidation and energy production. This study demonstrates that the bathymodiolin symbiosis interacts at the tissue, cellular, and molecular level, maintaining high efficiency and harmonic chemosynthetic micro niche.
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Affiliation(s)
- Hao Wang
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, P. R. China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, P. R. China
| | - Huan Zhang
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, P. R. China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, P. R. China
| | - Zhaoshan Zhong
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, P. R. China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, P. R. China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yan Sun
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, P. R. China.,Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, P. R. China
| | - Minxiao Wang
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, P. R. China.,Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, P. R. China
| | - Hao Chen
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, P. R. China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, P. R. China
| | - Li Zhou
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, P. R. China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, P. R. China
| | - Lei Cao
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, P. R. China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, P. R. China
| | - Chao Lian
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, P. R. China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, P. R. China
| | - Chaolun Li
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, P. R. China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, P. R. China.,Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, P. R. China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,University of Chinese Academy of Sciences, Beijing, China
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41
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Hoff J, Daniel B, Stukenberg D, Thuronyi BW, Waldminghaus T, Fritz G. Vibrio natriegens
: an ultrafast‐growing marine bacterium as emerging synthetic biology chassis. Environ Microbiol 2020; 22:4394-4408. [DOI: 10.1111/1462-2920.15128] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 06/11/2020] [Accepted: 06/12/2020] [Indexed: 12/28/2022]
Affiliation(s)
- Josef Hoff
- School of Molecular Sciences The University of Western Australia Perth Australia
- Center for Synthetic Microbiology Philipps‐Universität Marburg Marburg Germany
| | - Benjamin Daniel
- Center for Synthetic Microbiology Philipps‐Universität Marburg Marburg Germany
- Institute of Microbiology, ETH Zurich Zürich Switzerland
| | - Daniel Stukenberg
- Center for Synthetic Microbiology Philipps‐Universität Marburg Marburg Germany
| | | | - Torsten Waldminghaus
- Centre for Synthetic Biology Technische Universität Darmstadt Darmstadt Germany
- Department of Biology Technische Universität Darmstadt Darmstadt Germany
| | - Georg Fritz
- School of Molecular Sciences The University of Western Australia Perth Australia
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42
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Touchon M, Perrin A, de Sousa JAM, Vangchhia B, Burn S, O’Brien CL, Denamur E, Gordon D, Rocha EPC. Phylogenetic background and habitat drive the genetic diversification of Escherichia coli. PLoS Genet 2020; 16:e1008866. [PMID: 32530914 PMCID: PMC7314097 DOI: 10.1371/journal.pgen.1008866] [Citation(s) in RCA: 99] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 06/24/2020] [Accepted: 05/18/2020] [Indexed: 12/15/2022] Open
Abstract
Escherichia coli is mostly a commensal of birds and mammals, including humans, where it can act as an opportunistic pathogen. It is also found in water and sediments. We investigated the phylogeny, genetic diversification, and habitat-association of 1,294 isolates representative of the phylogenetic diversity of more than 5,000 isolates from the Australian continent. Since many previous studies focused on clinical isolates, we investigated mostly other isolates originating from humans, poultry, wild animals and water. These strains represent the species genetic diversity and reveal widespread associations between phylogroups and isolation sources. The analysis of strains from the same sequence types revealed very rapid change of gene repertoires in the very early stages of divergence, driven by the acquisition of many different types of mobile genetic elements. These elements also lead to rapid variations in genome size, even if few of their genes rise to high frequency in the species. Variations in genome size are associated with phylogroup and isolation sources, but the latter determine the number of MGEs, a marker of recent transfer, suggesting that gene flow reinforces the association of certain genetic backgrounds with specific habitats. After a while, the divergence of gene repertoires becomes linear with phylogenetic distance, presumably reflecting the continuous turnover of mobile element and the occasional acquisition of adaptive genes. Surprisingly, the phylogroups with smallest genomes have the highest rates of gene repertoire diversification and fewer but more diverse mobile genetic elements. This suggests that smaller genomes are associated with higher, not lower, turnover of genetic information. Many of these genomes are from freshwater isolates and have peculiar traits, including a specific capsule, suggesting adaptation to this environment. Altogether, these data contribute to explain why epidemiological clones tend to emerge from specific phylogenetic groups in the presence of pervasive horizontal gene transfer across the species. Previous large scale studies on the evolution of E. coli focused on clinical isolates emphasizing virulence and antibiotic resistance in medically important lineages. Yet, most E. coli strains are either human commensals or not associated with humans at all. Here, we analyzed a large collection of non-clinical isolates of the species to assess the mechanisms of gene repertoire diversification in the light of isolation sources and phylogeny. We show that gene repertoires evolve so rapidly by the high turnover of mobile genetic elements that epidemiologically indistinguishable strains can be phenotypically extremely heterogeneous, illustrating the velocity of bacterial adaptation and the importance of accounting for the information on the whole genome at the epidemiological scale. Phylogeny and habitat shape the genetic diversification of E. coli to similar extents. Surprisingly, freshwater strains seem specifically adapted to this environment, breaking the paradigm that E. coli environmental isolates are systematically fecal contaminations. As a consequence, the evolution of this species is also shaped by environmental habitats, and it may diversify by acquiring genes and mobile elements from environmental bacteria (and not just from gut bacteria). This may facilitate the acquisition of virulence factors and antibiotic resistance in the strains that become pathogenic.
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Affiliation(s)
- Marie Touchon
- Microbial Evolutionary Genomics, Institut Pasteur, CNRS, UMR3525, 25-28 rue Dr Roux, Paris, 75015, France
- * E-mail:
| | - Amandine Perrin
- Microbial Evolutionary Genomics, Institut Pasteur, CNRS, UMR3525, 25-28 rue Dr Roux, Paris, 75015, France
- Sorbonne Université, Collège doctoral, F-75005 Paris, France
| | - Jorge André Moura de Sousa
- Microbial Evolutionary Genomics, Institut Pasteur, CNRS, UMR3525, 25-28 rue Dr Roux, Paris, 75015, France
| | - Belinda Vangchhia
- Ecology and Evolution, Research School of Biology, The Australian National University, Acton, ACT, Australia
- Department of Veterinary Microbiology, College of Veterinary Sciences & Animal Husbandry, Central Agricultural University, Selesih, Aizawl, Mizoram, India
| | - Samantha Burn
- Ecology and Evolution, Research School of Biology, The Australian National University, Acton, ACT, Australia
| | - Claire L. O’Brien
- School of Medicine, University of Wollongong, Northfields Ave Wollongong, Australia
| | - Erick Denamur
- Université de Paris, IAME, UMR 1137, INSERM, Paris, 75018, France
- AP-HP, Laboratoire de Génétique Moléculaire, Hôpital Bichat, 75018, Paris, France
| | - David Gordon
- Ecology and Evolution, Research School of Biology, The Australian National University, Acton, ACT, Australia
| | - Eduardo PC Rocha
- Microbial Evolutionary Genomics, Institut Pasteur, CNRS, UMR3525, 25-28 rue Dr Roux, Paris, 75015, France
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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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Tekedar HC, Kumru S, Blom J, Perkins AD, Griffin MJ, Abdelhamed H, Karsi A, Lawrence ML. Comparative genomics of Aeromonas veronii: Identification of a pathotype impacting aquaculture globally. PLoS One 2019; 14:e0221018. [PMID: 31465454 PMCID: PMC6715197 DOI: 10.1371/journal.pone.0221018] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 07/29/2019] [Indexed: 12/30/2022] Open
Abstract
Aeromonas veronii is a gram-negative species abundant in aquatic environments that causes disease in humans as well as terrestrial and aquatic animals. In the current study, 41 publicly available A. veronii genomes were compared to investigate distribution of putative virulence genes, global dissemination of pathotypes, and potential mechanisms of virulence. The complete genome of A. veronii strain ML09-123 from an outbreak of motile aeromonas septicemia in farm-raised catfish in the southeastern United States was included. Dissemination of A. veronii strain types was discovered in dispersed geographical locations. Isolate ML09-123 is highly similar to Chinese isolate TH0426, suggesting the two strains have a common origin and may represent a pathotype impacting aquaculture in both countries. Virulence of strain ML09-123 in catfish in a dose-dependent manner was confirmed experimentally. Subsystem category disposition showed the majority of genomes exhibit similar distribution of genomic elements. The type I secretion system (T1SS), type II secretion system (T2SS), type 4 pilus (T4P), and flagellum core elements are conserved in all A. veronii genomes, whereas the type III secretion system (T3SS), type V secretion system (T5SS), type VI secretion system (T6SS), and tight adherence (TAD) system demonstrate variable dispersal. Distribution of mobile elements is dependent on host and geographic origin, suggesting this species has undergone considerable genetic exchange. The data presented here lends insight into the genomic variation of A. veronii and identifies a pathotype impacting aquaculture globally.
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Affiliation(s)
- Hasan C. Tekedar
- College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi, United States of America
| | - Salih Kumru
- College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi, United States of America
| | - Jochen Blom
- Bioinformatics & Systems Biology, Justus-Liebig-University Giessen, Giessen, Hesse, Germany
| | - Andy D. Perkins
- Department of Computer Science and Engineering, Mississippi State University, Mississippi State, Mississippi, United States of America
| | - Matt J. Griffin
- College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi, United States of America
- Thad Cochran National Warmwater Aquaculture Center, Stoneville, Mississippi State, United States of America
| | - Hossam Abdelhamed
- College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi, United States of America
| | - Attila Karsi
- College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi, United States of America
| | - Mark L. Lawrence
- College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi, United States of America
- * E-mail:
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45
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Geng P, Leonard SP, Mishler DM, Barrick JE. Synthetic Genome Defenses against Selfish DNA Elements Stabilize Engineered Bacteria against Evolutionary Failure. ACS Synth Biol 2019; 8:521-531. [PMID: 30703321 DOI: 10.1021/acssynbio.8b00426] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Mobile genetic elements drive evolution by disrupting genes and rearranging genomes. Eukaryotes have evolved epigenetic mechanisms, including DNA methylation and RNA interference, that silence mobile elements and thereby preserve the integrity of their genomes. We created an artificial reprogrammable epigenetic system based on CRISPR interference to give engineered bacteria a similar line of defense against transposons and other selfish elements in their genomes. We demonstrate that this CRISPR interference against mobile elements (CRISPRi-ME) approach can be used to simultaneously repress two different transposon families in Escherichia coli, thereby increasing the evolutionary stability of costly protein expression. We further show that silencing a transposon in Acinetobacter baylyi ADP1 reduces mutation rates by a factor of 5, nearly as much as deleting all copies of this element from its genome. By deploying CRISPRi-ME on a broad-host-range vector, we have created a generalizable platform for stabilizing the genomes of engineered bacterial cells for applications in metabolic engineering and synthetic biology.
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Affiliation(s)
- Peng Geng
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Sean P. Leonard
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Dennis M. Mishler
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Jeffrey E. Barrick
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas 78712, United States
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Chua MJ, Campen RL, Wahl L, Grzymski JJ, Mikucki JA. Genomic and physiological characterization and description of Marinobacter gelidimuriae sp. nov., a psychrophilic, moderate halophile from Blood Falls, an antarctic subglacial brine. FEMS Microbiol Ecol 2019; 94:4850642. [PMID: 29444218 DOI: 10.1093/femsec/fiy021] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 02/08/2018] [Indexed: 11/12/2022] Open
Abstract
Antarctic subice environments are diverse, underexplored microbial habitats. Here, we describe the ecophysiology and annotated genome of a Marinobacter strain isolated from a cold, saline, iron-rich subglacial outflow of the Taylor Glacier, Antarctica. This strain (BF04_CF4) grows fastest at neutral pH (range 6-10), is psychrophilic (range: 0°C-20°C), moderately halophilic (range: 0.8%-15% NaCl) and hosts genes encoding potential low temperature and high salt adaptations. The predicted proteome suggests it utilizes fewer charged amino acids than a mesophilic Marinobacter strain. BF04_CF4 has increased concentrations of membrane unsaturated fatty acids including palmitoleic (33%) and oleic (27.5%) acids that may help maintain cell membrane fluidity at low temperatures. The genome encodes proteins for compatible solute biosynthesis and transport, which are known to be important for growth in saline environments. Physiological verification of predicted metabolic functions demonstrate BF04_CF4 is capable of denitrification and may facilitate iron oxidation. Our data indicate that strain BF04_CF4 represents a new Marinobacter species, Marinobacter gelidimuriae sp. nov., that appears well suited for the subglacial environment it was isolated from. Marinobacter species have been isolated from other cold, saline environments in the McMurdo Dry Valleys and permanently cold environments globally suggesting that this lineage is cosmopolitan and ecologically relevant in icy brines.
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Affiliation(s)
- Michelle J Chua
- Department of Microbiology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Richard L Campen
- Department of Microbiology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Lindsay Wahl
- Department of Environmental Studies, Dartmouth College, Hanover, NH, 03755, USA
| | - Joseph J Grzymski
- Division of Earth and Ecosystem Sciences, Desert Research Institute, Reno, NV, 89512, USA
| | - Jill A Mikucki
- Department of Microbiology, University of Tennessee, Knoxville, TN, 37996, USA
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Blesa A, Sánchez M, Sacristán-Horcajada E, González-de la Fuente S, Peiró R, Berenguer J. Into the Thermus Mobilome: Presence, Diversity and Recent Activities of Insertion Sequences Across Thermus spp. Microorganisms 2019; 7:microorganisms7010025. [PMID: 30669685 PMCID: PMC6352166 DOI: 10.3390/microorganisms7010025] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 01/09/2019] [Accepted: 01/17/2019] [Indexed: 11/28/2022] Open
Abstract
A high level of transposon-mediated genome rearrangement is a common trait among microorganisms isolated from thermal environments, probably contributing to the extraordinary genomic plasticity and horizontal gene transfer (HGT) observed in these habitats. In this work, active and inactive insertion sequences (ISs) spanning the sequenced members of the genus Thermus were characterized, with special emphasis on three T. thermophilus strains: HB27, HB8, and NAR1. A large number of full ISs and fragments derived from different IS families were found, concentrating within megaplasmids present in most isolates. Potentially active ISs were identified through analysis of transposase integrity, and domestication-related transposition events of ISTth7 were identified in laboratory-adapted HB27 derivatives. Many partial copies of ISs appeared throughout the genome, which may serve as specific targets for homologous recombination contributing to genome rearrangement. Moreover, recruitment of IS1000 32 bp segments as spacers for CRISPR sequence was identified, pointing to the adaptability of these elements in the biology of these thermophiles. Further knowledge about the activity and functional diversity of ISs in this genus may contribute to the generation of engineered transposons as new genetic tools, and enrich our understanding of the outstanding plasticity shown by these thermophiles.
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Affiliation(s)
- Alba Blesa
- Department of Biotechnology, Faculty of Experimental Sciences, Universidad Francisco de Vitoria, Madrid 28223, Spain.
| | - Mercedes Sánchez
- Centro de Biología Molecular Severo Ochoa (CBMSO), Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas, Madrid 28049, Spain.
| | - Eva Sacristán-Horcajada
- Centro de Biología Molecular Severo Ochoa (CBMSO), Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas, Madrid 28049, Spain.
| | - Sandra González-de la Fuente
- Centro de Biología Molecular Severo Ochoa (CBMSO), Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas, Madrid 28049, Spain.
| | - Ramón Peiró
- Centro de Biología Molecular Severo Ochoa (CBMSO), Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas, Madrid 28049, Spain.
| | - José Berenguer
- Centro de Biología Molecular Severo Ochoa (CBMSO), Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas, Madrid 28049, Spain.
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48
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Guio L, González J. New Insights on the Evolution of Genome Content: Population Dynamics of Transposable Elements in Flies and Humans. Methods Mol Biol 2019; 1910:505-530. [PMID: 31278675 DOI: 10.1007/978-1-4939-9074-0_16] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Understanding the abundance, diversity, and distribution of TEs in genomes is crucial to understand genome structure, function, and evolution. Advances in whole-genome sequencing techniques, as well as in bioinformatics tools, have increased our ability to detect and analyze the transposable element content in genomes. In addition to reference genomes, we now have access to population datasets in which multiple individuals within a species are sequenced. In this chapter, we highlight the recent advances in the study of TE population dynamics focusing on fruit flies and humans, which represent two extremes in terms of TE abundance, diversity, and activity. We review the most recent methodological approaches applied to the study of TE dynamics as well as the new knowledge on host factors involved in the regulation of TE activity. In addition to transposition rates, we also focus on TE deletion rates and on the selective forces that affect the dynamics of TEs in genomes.
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Affiliation(s)
- Lain Guio
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Josefa González
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain.
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49
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Sharma V, Mobeen F, Prakash T. Exploration of Survival Traits, Probiotic Determinants, Host Interactions, and Functional Evolution of Bifidobacterial Genomes Using Comparative Genomics. Genes (Basel) 2018; 9:genes9100477. [PMID: 30275399 PMCID: PMC6210967 DOI: 10.3390/genes9100477] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Accepted: 09/10/2018] [Indexed: 12/15/2022] Open
Abstract
Members of the genus Bifidobacterium are found in a wide-range of habitats and are used as important probiotics. Thus, exploration of their functional traits at the genus level is of utmost significance. Besides, this genus has been demonstrated to exhibit an open pan-genome based on the limited number of genomes used in earlier studies. However, the number of genomes is a crucial factor for pan-genome calculations. We have analyzed the pan-genome of a comparatively larger dataset of 215 members of the genus Bifidobacterium belonging to different habitats, which revealed an open nature. The pan-genome for the 56 probiotic and human-gut strains of this genus, was also found to be open. The accessory- and unique-components of this pan-genome were found to be under the operation of Darwinian selection pressure. Further, their genome-size variation was predicted to be attributed to the abundance of certain functions carried by genomic islands, which are facilitated by insertion elements and prophages. In silico functional and host-microbe interaction analyses of their core-genome revealed significant genomic factors for niche-specific adaptations and probiotic traits. The core survival traits include stress tolerance, biofilm formation, nutrient transport, and Sec-secretion system, whereas the core probiotic traits are imparted by the factors involved in carbohydrate- and protein-metabolism and host-immunomodulations.
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Affiliation(s)
- Vikas Sharma
- School of Basic Sciences, Indian Institute of Technology Mandi, Kamand, Mandi, Himachal Pradesh 175005, India.
| | - Fauzul Mobeen
- School of Basic Sciences, Indian Institute of Technology Mandi, Kamand, Mandi, Himachal Pradesh 175005, India.
| | - Tulika Prakash
- School of Basic Sciences, Indian Institute of Technology Mandi, Kamand, Mandi, Himachal Pradesh 175005, India.
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50
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Scott KM, Williams J, Porter CMB, Russel S, Harmer TL, Paul JH, Antonen KM, Bridges MK, Camper GJ, Campla CK, Casella LG, Chase E, Conrad JW, Cruz MC, Dunlap DS, Duran L, Fahsbender EM, Goldsmith DB, Keeley RF, Kondoff MR, Kussy BI, Lane MK, Lawler S, Leigh BA, Lewis C, Lostal LM, Marking D, Mancera PA, McClenthan EC, McIntyre EA, Mine JA, Modi S, Moore BD, Morgan WA, Nelson KM, Nguyen KN, Ogburn N, Parrino DG, Pedapudi AD, Pelham RP, Preece AM, Rampersad EA, Richardson JC, Rodgers CM, Schaffer BL, Sheridan NE, Solone MR, Staley ZR, Tabuchi M, Waide RJ, Wanjugi PW, Young S, Clum A, Daum C, Huntemann M, Ivanova N, Kyrpides N, Mikhailova N, Palaniappan K, Pillay M, Reddy TBK, Shapiro N, Stamatis D, Varghese N, Woyke T, Boden R, Freyermuth SK, Kerfeld CA. Genomes of ubiquitous marine and hypersaline Hydrogenovibrio, Thiomicrorhabdus and Thiomicrospira spp. encode a diversity of mechanisms to sustain chemolithoautotrophy in heterogeneous environments. Environ Microbiol 2018. [PMID: 29521452 DOI: 10.1111/1462-2920.14090] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Chemolithoautotrophic bacteria from the genera Hydrogenovibrio, Thiomicrorhabdus and Thiomicrospira are common, sometimes dominant, isolates from sulfidic habitats including hydrothermal vents, soda and salt lakes and marine sediments. Their genome sequences confirm their membership in a deeply branching clade of the Gammaproteobacteria. Several adaptations to heterogeneous habitats are apparent. Their genomes include large numbers of genes for sensing and responding to their environment (EAL- and GGDEF-domain proteins and methyl-accepting chemotaxis proteins) despite their small sizes (2.1-3.1 Mbp). An array of sulfur-oxidizing complexes are encoded, likely to facilitate these organisms' use of multiple forms of reduced sulfur as electron donors. Hydrogenase genes are present in some taxa, including group 1d and 2b hydrogenases in Hydrogenovibrio marinus and H. thermophilus MA2-6, acquired via horizontal gene transfer. In addition to high-affinity cbb3 cytochrome c oxidase, some also encode cytochrome bd-type quinol oxidase or ba3 -type cytochrome c oxidase, which could facilitate growth under different oxygen tensions, or maintain redox balance. Carboxysome operons are present in most, with genes downstream encoding transporters from four evolutionarily distinct families, which may act with the carboxysomes to form CO2 concentrating mechanisms. These adaptations to habitat variability likely contribute to the cosmopolitan distribution of these organisms.
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Affiliation(s)
- Kathleen M Scott
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - John Williams
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Cody M B Porter
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Sydney Russel
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Tara L Harmer
- Biology Program, Stockton University, Galloway, NJ, USA
| | - John H Paul
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Kirsten M Antonen
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Megan K Bridges
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Gary J Camper
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Christie K Campla
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Leila G Casella
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Eva Chase
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - James W Conrad
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Mercedez C Cruz
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Darren S Dunlap
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Laura Duran
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Elizabeth M Fahsbender
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Dawn B Goldsmith
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Ryan F Keeley
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Matthew R Kondoff
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Breanna I Kussy
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Marannda K Lane
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Stephanie Lawler
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Brittany A Leigh
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Courtney Lewis
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Lygia M Lostal
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Devon Marking
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Paola A Mancera
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Evan C McClenthan
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Emily A McIntyre
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Jessica A Mine
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Swapnil Modi
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Brittney D Moore
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - William A Morgan
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Kaleigh M Nelson
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Kimmy N Nguyen
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Nicholas Ogburn
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - David G Parrino
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Anangamanjari D Pedapudi
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Rebecca P Pelham
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Amanda M Preece
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Elizabeth A Rampersad
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Jason C Richardson
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Christina M Rodgers
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Brent L Schaffer
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Nancy E Sheridan
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Michael R Solone
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Zachery R Staley
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Maki Tabuchi
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Ramond J Waide
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Pauline W Wanjugi
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Suzanne Young
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Alicia Clum
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Chris Daum
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Marcel Huntemann
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Natalia Ivanova
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Nikos Kyrpides
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | | | | | - Manoj Pillay
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - T B K Reddy
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Nicole Shapiro
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | | | - Neha Varghese
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Tanja Woyke
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Rich Boden
- School of Biological & Marine Sciences, University of Plymouth, Drake Circus, Plymouth, UK.,Sustainable Earth Institute, University of Plymouth, Drake Circus, Plymouth, UK
| | | | - Cheryl A Kerfeld
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, USA.,Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA.,MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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