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Sato Y, Takebe H, Tominaga K, Yasuda J, Kumagai H, Hirooka H, Yoshida T. A rumen virosphere with implications of contribution to fermentation and methane production, and endemism in cattle breeds and individuals. Appl Environ Microbiol 2024; 90:e0158123. [PMID: 38112444 PMCID: PMC10807420 DOI: 10.1128/aem.01581-23] [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: 09/11/2023] [Accepted: 11/12/2023] [Indexed: 12/21/2023] Open
Abstract
Viruses have a potential to modify the ruminal digestion via infection and cell lysis of prokaryotes, suggesting that viruses are related to animal performance and methane production. This study aimed to elucidate the genome-based diversity of rumen viral communities and the differences in virus structure between individuals and cattle breeds and to understand how viruses influence on the rumen. To these ends, a metagenomic sequencing of virus-like particles in the rumen of 22 Japanese cattle, including Japanese Black (JB, n = 8), Japanese Shorthorn (n = 2), and Japanese Black sires × Holstein dams crossbred steers (F1, n = 12) was conducted. Additionally, the rumen viromes of six JB and six F1 that were fed identical diets and kept in a single barn were compared. A total of 8,232 non-redundant viral genomes (≥5-kb length and ≥50% completeness), including 982 complete genomes, were constructed, and rumen virome exhibited lysogenic signatures. Furthermore, putative hosts of 1,223 viral genomes were predicted using tRNA and clustered regularly interspaced short palindromic repeat (CRISPR)-spacer matching. The genomes included 1 and 10 putative novel complete genomes associated with Fibrobacter and Ruminococcus, respectively, which are the main rumen cellulose-degrading bacteria. Additionally, the hosts of 22 viral genomes, including 2 complete genomes, were predicted as methanogens, such as Methanobrevibacter and Methanomethylophilus. Most rumen viruses were highly rumen and individual specific and related to rumen-specific prokaryotes. Furthermore, the rumen viral community structure was significantly different between JB and F1 steers, indicating that cattle breed is one of the factors influencing the rumen virome composition.IMPORTANCEHere, we investigated the individual and breed differences of the rumen viral community in Japanese cattle. In the process, we reconstructed putative novel complete viral genomes related to rumen fiber-degrading bacteria and methanogen. The finding strongly suggests that rumen viruses contribute to cellulose and hemicellulose digestion and methanogenesis. Notably, this study also found that rumen viruses are highly rumen and individual specific, suggesting that rumen viruses may not be transmitted through environmental exposure. More importantly, we revealed differences of viral communities between JB and F1 cattle, indicating that cattle breed is a factor that influences the establishment of rumen virome. These results suggest the possibility of rumen virus transmission from mother to offspring and its potential to influence beef production traits. These rumen viral genomes and findings provide new insights into the characterizations of the rumen viruses.
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Affiliation(s)
- Yoshiaki Sato
- Department of Agrobiology and Bioresources, School of Agriculture, Utsunomiya University, Tochigi, Japan
| | - Hiroaki Takebe
- Laboratory of Marine Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Kento Tominaga
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, the University of Tokyo, Chiba, Japan
| | - Jumpei Yasuda
- Iwate Agricultural Research Center Animal Industry Research Institute, Iwate, Japan
| | - Hajime Kumagai
- Laboratory of Animal Husbandry Resources, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Hiroyuki Hirooka
- Laboratory of Animal Husbandry Resources, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Takashi Yoshida
- Laboratory of Marine Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
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2
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Nezhadi J, Rezaee MA, Ozma MA, Ganbarov K, Kafil HS. Gut Microbiota Exchange in Domestic Animals and Rural-urban People Axis. Curr Pharm Biotechnol 2024; 25:825-837. [PMID: 37877143 DOI: 10.2174/0113892010261535230920062107] [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: 05/09/2023] [Revised: 08/13/2023] [Accepted: 08/25/2023] [Indexed: 10/26/2023]
Abstract
In recent years, one of the most critical topics in microbiology that can be addressed is microbiome and microbiota. The term microbiome contains both the microbiota and structural elements, metabolites/signal molecules, and the surrounding environmental conditions, and the microbiota consists of all living members forming the microbiome. Among; the intestinal microbiota is one of the most important microbiota, also called the gut microbiota. After colonization, the gut microbiota can have different functions, including resistance to pathogens, maintaining the intestinal epithelium, metabolizing dietary and pharmaceutical compounds, and controlling immune function. Recently, studies have shown that the gut microbiota can prevent the formation of fat in the body. In this study, we examined the gut microbiota in various animals, including dogs, cats, dairy cows, sheep, chickens, horses, and people who live in urban and rural areas. Based on the review of various studies, it has been determined that the population of microbiota in animals and humans is different, and various factors such as the environment, nutrition, and contact with animals can affect the microbiota of people living in urban and rural areas.
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Affiliation(s)
- Javad Nezhadi
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Mahdi Asghari Ozma
- Department of Microbiology, Research Center for Pharmaceutical Nanotechnology, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Khudaverdi Ganbarov
- Department of Microbiology, Research Laboratory of Microbiology and Virology, Baku State University, Baku, Azerbaijan
| | - Hossein Samadi Kafil
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
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3
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Aryee G, Luecke SM, Dahlen CR, Swanson KC, Amat S. Holistic View and Novel Perspective on Ruminal and Extra-Gastrointestinal Methanogens in Cattle. Microorganisms 2023; 11:2746. [PMID: 38004757 PMCID: PMC10673468 DOI: 10.3390/microorganisms11112746] [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: 10/23/2023] [Revised: 11/08/2023] [Accepted: 11/09/2023] [Indexed: 11/26/2023] Open
Abstract
Despite the extensive research conducted on ruminal methanogens and anti-methanogenic intervention strategies over the last 50 years, most of the currently researched enteric methane (CH4) abatement approaches have shown limited efficacy. This is largely because of the complex nature of animal production and the ruminal environment, host genetic variability of CH4 production, and an incomplete understanding of the role of the ruminal microbiome in enteric CH4 emissions. Recent sequencing-based studies suggest the presence of methanogenic archaea in extra-gastrointestinal tract tissues, including respiratory and reproductive tracts of cattle. While these sequencing data require further verification via culture-dependent methods, the consistent identification of methanogens with relatively greater frequency in the airway and urogenital tract of cattle, as well as increasing appreciation of the microbiome-gut-organ axis together highlight the potential interactions between ruminal and extra-gastrointestinal methanogenic communities. Thus, a traditional singular focus on ruminal methanogens may not be sufficient, and a holistic approach which takes into consideration of the transfer of methanogens between ruminal, extra-gastrointestinal, and environmental microbial communities is of necessity to develop more efficient and long-term ruminal CH4 mitigation strategies. In the present review, we provide a holistic survey of the methanogenic archaea present in different anatomical sites of cattle and discuss potential seeding sources of the ruminal methanogens.
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Affiliation(s)
- Godson Aryee
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND 58108, USA; (G.A.); (S.M.L.)
| | - Sarah M. Luecke
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND 58108, USA; (G.A.); (S.M.L.)
| | - Carl R. Dahlen
- Department of Animal Sciences, and Center for Nutrition and Pregnancy, North Dakota State University, Fargo, ND 58102, USA; (C.R.D.); (K.C.S.)
| | - Kendall C. Swanson
- Department of Animal Sciences, and Center for Nutrition and Pregnancy, North Dakota State University, Fargo, ND 58102, USA; (C.R.D.); (K.C.S.)
| | - Samat Amat
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND 58108, USA; (G.A.); (S.M.L.)
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4
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Medvedeva S, Borrel G, Krupovic M, Gribaldo S. A compendium of viruses from methanogenic archaea reveals their diversity and adaptations to the gut environment. Nat Microbiol 2023; 8:2170-2182. [PMID: 37749252 DOI: 10.1038/s41564-023-01485-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 08/30/2023] [Indexed: 09/27/2023]
Abstract
Methanogenic archaea are major producers of methane, a potent greenhouse gas and biofuel, and are widespread in diverse environments, including the animal gut. The ecophysiology of methanogens is likely impacted by viruses, which remain, however, largely uncharacterized. Here we carried out a global investigation of viruses associated with all current diversity of methanogens by assembling an extensive CRISPR database consisting of 156,000 spacers. We report 282 high-quality (pro)viral and 205 virus-like/plasmid sequences assigned to hosts belonging to ten main orders of methanogenic archaea. Viruses of methanogens can be classified into 87 families, underscoring a still largely undiscovered genetic diversity. Viruses infecting gut-associated archaea provide evidence of convergence in adaptation with viruses infecting gut-associated bacteria. These viruses contain a large repertoire of lysin proteins that cleave archaeal pseudomurein and are enriched in glycan-binding domains (Ig-like/Flg_new) and diversity-generating retroelements. The characterization of this vast repertoire of viruses paves the way towards a better understanding of their role in regulating methanogen communities globally, as well as the development of much-needed genetic tools.
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Affiliation(s)
- Sofia Medvedeva
- Institut Pasteur, Université Paris Cité, Unit Evolutionary Biology of the Microbial Cell, Paris, France
| | - Guillaume Borrel
- Institut Pasteur, Université Paris Cité, Unit Evolutionary Biology of the Microbial Cell, Paris, France.
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, Unit Archaeal Virology, Paris, France.
| | - Simonetta Gribaldo
- Institut Pasteur, Université Paris Cité, Unit Evolutionary Biology of the Microbial Cell, Paris, France.
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5
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Gehlert FO, Weidenbach K, Barüske B, Hallack D, Repnik U, Schmitz RA. Newly Established Genetic System for Functional Analysis of MetSV. Int J Mol Sci 2023; 24:11163. [PMID: 37446343 DOI: 10.3390/ijms241311163] [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: 06/09/2023] [Revised: 06/30/2023] [Accepted: 07/04/2023] [Indexed: 07/15/2023] Open
Abstract
The linear chromosome of the Methanosarcina spherical virus with 10,567 bp exhibits 22 ORFs with mostly unknown functions. Annotation using common tools and databases predicted functions for a few genes like the type B DNA polymerase (MetSVORF07) or the small (MetSVORF15) and major (MetSVORF16) capsid proteins. For verification of assigned functions of additional ORFs, biochemical or genetic approaches were found to be essential. Consequently, we established a genetic system for MetSV by cloning its genome into the E. coli plasmid pCR-XL-2. Comparisons of candidate plasmids with the MetSV reference based on Nanopore sequencing revealed several mutations of yet unknown provenance with an impact on protein-coding sequences. Linear MetSV inserts were generated by BamHI restriction, purified and transformed in Methanosarcina mazei by an optimized liposome-mediated transformation protocol. Analysis of resulting MetSV virions by TEM imaging and infection experiments demonstrated no significant differences between plasmid-born viruses and native MetSV particles regarding their morphology or lytic behavior. The functionality of the genetic system was tested by the generation of a ΔMetSVORF09 mutant that was still infectious. Our genetic system of MetSV, the first functional system for a virus of methanoarchaea, now allows us to obtain deeper insights into MetSV protein functions and virus-host interactions.
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Affiliation(s)
- Finn O Gehlert
- Institute for General Microbiology, Christian Albrechts University, 24118 Kiel, Germany
| | - Katrin Weidenbach
- Institute for General Microbiology, Christian Albrechts University, 24118 Kiel, Germany
| | - Brian Barüske
- Institute for General Microbiology, Christian Albrechts University, 24118 Kiel, Germany
| | - Daniela Hallack
- Institute for General Microbiology, Christian Albrechts University, 24118 Kiel, Germany
| | - Urska Repnik
- Central Microscopy, Christian Albrechts University, 24118 Kiel, Germany
| | - Ruth A Schmitz
- Institute for General Microbiology, Christian Albrechts University, 24118 Kiel, Germany
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6
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Shang J, Tang X, Sun Y. PhaTYP: predicting the lifestyle for bacteriophages using BERT. Brief Bioinform 2023; 24:bbac487. [PMID: 36659812 PMCID: PMC9851330 DOI: 10.1093/bib/bbac487] [Citation(s) in RCA: 42] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 10/05/2022] [Accepted: 10/15/2022] [Indexed: 11/24/2022] Open
Abstract
Bacteriophages (or phages), which infect bacteria, have two distinct lifestyles: virulent and temperate. Predicting the lifestyle of phages helps decipher their interactions with their bacterial hosts, aiding phages' applications in fields such as phage therapy. Because experimental methods for annotating the lifestyle of phages cannot keep pace with the fast accumulation of sequenced phages, computational method for predicting phages' lifestyles has become an attractive alternative. Despite some promising results, computational lifestyle prediction remains difficult because of the limited known annotations and the sheer amount of sequenced phage contigs assembled from metagenomic data. In particular, most of the existing tools cannot precisely predict phages' lifestyles for short contigs. In this work, we develop PhaTYP (Phage TYPe prediction tool) to improve the accuracy of lifestyle prediction on short contigs. We design two different training tasks, self-supervised and fine-tuning tasks, to overcome lifestyle prediction difficulties. We rigorously tested and compared PhaTYP with four state-of-the-art methods: DeePhage, PHACTS, PhagePred and BACPHLIP. The experimental results show that PhaTYP outperforms all these methods and achieves more stable performance on short contigs. In addition, we demonstrated the utility of PhaTYP for analyzing the phage lifestyle on human neonates' gut data. This application shows that PhaTYP is a useful means for studying phages in metagenomic data and helps extend our understanding of microbial communities.
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Affiliation(s)
- Jiayu Shang
- Department of Electrical Engineering, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, China SAR
| | - Xubo Tang
- Department of Electrical Engineering, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, China SAR
| | - Yanni Sun
- Department of Electrical Engineering, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, China SAR
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7
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Ngo VQH, Enault F, Midoux C, Mariadassou M, Chapleur O, Mazéas L, Loux V, Bouchez T, Krupovic M, Bize A. Diversity of novel archaeal viruses infecting methanogens discovered through coupling of stable isotope probing and metagenomics. Environ Microbiol 2022; 24:4853-4868. [PMID: 35848130 PMCID: PMC9796341 DOI: 10.1111/1462-2920.16120] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 06/01/2022] [Accepted: 06/29/2022] [Indexed: 01/01/2023]
Abstract
Diversity of viruses infecting non-extremophilic archaea has been grossly understudied. This is particularly the case for viruses infecting methanogenic archaea, key players in the global carbon biogeochemical cycle. Only a dozen of methanogenic archaeal viruses have been isolated so far. In the present study, we implemented an original coupling between stable isotope probing and complementary shotgun metagenomic analyses to identify viruses of methanogens involved in the bioconversion of formate, which was used as the sole carbon source in batch anaerobic digestion microcosms. Under our experimental conditions, the microcosms were dominated by methanogens belonging to the order Methanobacteriales (Methanobacterium and Methanobrevibacter genera). Metagenomic analyses yielded several previously uncharacterized viral genomes, including a complete genome of a head-tailed virus (class Caudoviricetes, proposed family Speroviridae, Methanobacterium host) and several near-complete genomes of spindle-shaped viruses. The two groups of viruses are predicted to infect methanogens of the Methanobacterium and Methanosarcina genera and represent two new virus families. The metagenomics results are in good agreement with the electron microscopy observations, which revealed the dominance of head-tailed virus-like particles and the presence of spindle-shaped particles. The present study significantly expands the knowledge on the viral diversity of viruses of methanogens.
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Affiliation(s)
- Vuong Quoc Hoang Ngo
- Université Paris‐Saclay, INRAE, PRocédés biOtechnologiques au Service de l'EnvironnementAntonyFrance
| | - François Enault
- Université Clermont Auvergne, CNRS, LMGEClermont‐FerrandFrance
| | - Cédric Midoux
- Université Paris‐Saclay, INRAE, PRocédés biOtechnologiques au Service de l'EnvironnementAntonyFrance
- Université Paris‐Saclay, INRAE, MaIAGEJouy‐en‐JosasFrance
- Université Paris‐Saclay, INRAE, BioinfOmics, MIGALE Bioinformatics FacilityJouy‐en‐JosasFrance
| | - Mahendra Mariadassou
- Université Paris‐Saclay, INRAE, MaIAGEJouy‐en‐JosasFrance
- Université Paris‐Saclay, INRAE, BioinfOmics, MIGALE Bioinformatics FacilityJouy‐en‐JosasFrance
| | - Olivier Chapleur
- Université Paris‐Saclay, INRAE, PRocédés biOtechnologiques au Service de l'EnvironnementAntonyFrance
| | - Laurent Mazéas
- Université Paris‐Saclay, INRAE, PRocédés biOtechnologiques au Service de l'EnvironnementAntonyFrance
| | - Valentin Loux
- Université Paris‐Saclay, INRAE, MaIAGEJouy‐en‐JosasFrance
- Université Paris‐Saclay, INRAE, BioinfOmics, MIGALE Bioinformatics FacilityJouy‐en‐JosasFrance
| | - Théodore Bouchez
- Université Paris‐Saclay, INRAE, PRocédés biOtechnologiques au Service de l'EnvironnementAntonyFrance
| | - Mart Krupovic
- Institut Pasteur, Université de Paris, CNRS UMR6047, Archaeal Virology UnitParisFrance
| | - Ariane Bize
- Université Paris‐Saclay, INRAE, PRocédés biOtechnologiques au Service de l'EnvironnementAntonyFrance
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8
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Complete Genome Sequence of Methanofollis aquaemaris BCRC 16166
T
, Isolated from a Marine Aquaculture Fishpond. Microbiol Resour Announc 2022; 11:e0074322. [PMID: 36094213 PMCID: PMC9583781 DOI: 10.1128/mra.00743-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The hydrogenotrophic methanogen Methanofollis aquaemaris BCRC 16166T (= N2F9704T = DSM 14661T) was isolated from a marine aquaculture fishpond near Wang-gong (Taiwan, Republic of China). The genome of strain BCRC 16166T was selected for sequencing in order to provide further information about the species delineation and its infected virus.
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9
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Liu Y, Demina TA, Roux S, Aiewsakun P, Kazlauskas D, Simmonds P, Prangishvili D, Oksanen HM, Krupovic M. Diversity, taxonomy, and evolution of archaeal viruses of the class Caudoviricetes. PLoS Biol 2021; 19:e3001442. [PMID: 34752450 PMCID: PMC8651126 DOI: 10.1371/journal.pbio.3001442] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 12/07/2021] [Accepted: 10/17/2021] [Indexed: 11/19/2022] Open
Abstract
The archaeal tailed viruses (arTV), evolutionarily related to tailed double-stranded DNA (dsDNA) bacteriophages of the class Caudoviricetes, represent the most common isolates infecting halophilic archaea. Only a handful of these viruses have been genomically characterized, limiting our appreciation of their ecological impacts and evolution. Here, we present 37 new genomes of haloarchaeal tailed virus isolates, more than doubling the current number of sequenced arTVs. Analysis of all 63 available complete genomes of arTVs, which we propose to classify into 14 new families and 3 orders, suggests ancient divergence of archaeal and bacterial tailed viruses and points to an extensive sharing of genes involved in DNA metabolism and counterdefense mechanisms, illuminating common strategies of virus-host interactions with tailed bacteriophages. Coupling of the comparative genomics with the host range analysis on a broad panel of haloarchaeal species uncovered 4 distinct groups of viral tail fiber adhesins controlling the host range expansion. The survey of metagenomes using viral hallmark genes suggests that the global architecture of the arTV community is shaped through recurrent transfers between different biomes, including hypersaline, marine, and anoxic environments.
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Affiliation(s)
- Ying Liu
- Institut Pasteur, Université de Paris, Archaeal Virology Unit, Paris, France
| | - Tatiana A. Demina
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Simon Roux
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Pakorn Aiewsakun
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand
- Pornchai Matangkasombut Center for Microbial Genomics, Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Darius Kazlauskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - David Prangishvili
- Institut Pasteur, Université de Paris, Archaeal Virology Unit, Paris, France
- Ivane Javakhishvili Tbilisi State University, Tbilisi, Georgia
| | - Hanna M. Oksanen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Mart Krupovic
- Institut Pasteur, Université de Paris, Archaeal Virology Unit, Paris, France
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10
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Characterization of Blf4, an Archaeal Lytic Virus Targeting a Member of the Methanomicrobiales. Viruses 2021; 13:v13101934. [PMID: 34696364 PMCID: PMC8540584 DOI: 10.3390/v13101934] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 09/14/2021] [Accepted: 09/20/2021] [Indexed: 01/05/2023] Open
Abstract
Today, the number of known viruses infecting methanogenic archaea is limited. Here, we report on a novel lytic virus, designated Blf4, and its host strain Methanoculleus bourgensis E02.3, a methanogenic archaeon belonging to the Methanomicrobiales, both isolated from a commercial biogas plant in Germany. The virus consists of an icosahedral head 60 nm in diameter and a long non-contractile tail of 125 nm in length, which is consistent with the new isolate belonging to the Siphoviridae family. Electron microscopy revealed that Blf4 attaches to the vegetative cells of M. bourgensis E02.3 as well as to cellular appendages. Apart from M. bourgensis E02.3, none of the tested Methanoculleus strains were lysed by Blf4, indicating a narrow host range. The complete 37 kb dsDNA genome of Blf4 contains 63 open reading frames (ORFs), all organized in the same transcriptional direction. For most of the ORFs, potential functions were predicted. In addition, the genome of the host M. bourgensis E02.3 was sequenced and assembled, resulting in a 2.6 Mbp draft genome consisting of nine contigs. All genes required for a hydrogenotrophic lifestyle were predicted. A CRISPR/Cas system (type I-U) was identified with six spacers directed against Blf4, indicating that this defense system might not be very efficient in fending off invading Blf4 virus.
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11
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Xu Q, Qiao Q, Gao Y, Hou J, Hu M, Du Y, Zhao K, Li X. Gut Microbiota and Their Role in Health and Metabolic Disease of Dairy Cow. Front Nutr 2021; 8:701511. [PMID: 34422882 PMCID: PMC8371392 DOI: 10.3389/fnut.2021.701511] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 06/28/2021] [Indexed: 12/12/2022] Open
Abstract
Ruminants are mostly herbivorous animals that employ rumen fermentation for the digestion of feed materials, including dairy cows. Ruminants consume plant fibre as their regular diet, but lack the machinery for their digestion. For this reason, ruminants maintain a symbiotic relation with microorganisms that are capable of producing enzymes to degrade plant polymers. Various species of microflora including bacteria, protozoa, fungi, archaea, and bacteriophages are hosted at distinct concentrations for accomplishing complete digestion. The ingested feed is digested at a defined stratum. The polysaccharic plant fibrils are degraded by cellulolytic bacteria, and the substrate formed is acted upon by other bacteria. This sequential degradative mechanism forms the base of complete digestion as well as harvesting energy from the ingested feed. The composition of microbiota readily gets tuned to the changes in the feed habits of the dairy cow. The overall energy production as well as digestion is decided by the intactness of the resident communal flora. Disturbances in the homogeneity gastrointestinal microflora has severe effects on the digestive system and various other organs. This disharmony in communal relationship also causes various metabolic disorders. The dominance of methanogens sometimes lead to bloating, and high sugar feed culminates in ruminal acidosis. Likewise, disruptive microfloral constitution also ignites reticuloperitonitis, ulcers, diarrhoea, etc. The role of symbiotic microflora in the occurrence and progress of a few important metabolic diseases are discussed in this review. Future studies in multiomics provides platform to determine the physiological and phenotypical upgradation of dairy cow for milk production.
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Affiliation(s)
- Qingbiao Xu
- College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, China
| | - Qinqin Qiao
- College of Information Engineering, Fuyang Normal University, Fuyang, China
| | - Ya Gao
- College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jinxiu Hou
- College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, China
| | - Mingyang Hu
- College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yufeng Du
- College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, China
| | - Ke Zhao
- Institute of Food Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xiang Li
- College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, China.,National Center for International Research on Animal Genetics, Breeding and Reproduction (NCIRAGBR), Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, China
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12
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Okada H, MacTaggart B, Ohya Y, Bi E. The kinetic landscape and interplay of protein networks in cytokinesis. iScience 2021; 24:101917. [PMID: 33392480 PMCID: PMC7773586 DOI: 10.1016/j.isci.2020.101917] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/03/2020] [Accepted: 12/07/2020] [Indexed: 11/08/2022] Open
Abstract
Cytokinesis is executed by protein networks organized into functional modules. Individual proteins within each module have been characterized to various degrees. However, the collective behavior and interplay of the modules remain poorly understood. In this study, we conducted quantitative time-lapse imaging to analyze the accumulation kinetics of more than 20 proteins from different modules of cytokinesis in budding yeast. This analysis has led to a comprehensive picture of the kinetic landscape of cytokinesis, from actomyosin ring (AMR) assembly to cell separation. It revealed that the AMR undergoes biphasic constriction and that the switch between the constriction phases is likely triggered by AMR maturation and primary septum formation. This analysis also provided further insights into the functions of actin filaments and the transglutaminase-like protein Cyk3 in cytokinesis and, in addition, defined Kre6 as the likely enzyme that catalyzes β-1,6-glucan synthesis to drive cell wall maturation during cell growth and division. Cytokinesis is executed by protein modules each with a unique kinetic signature Actomyosin ring constricts in a biphasic manner that is elaborately regulated The transglutaminase-like domain in Cyk3 plays a dual role in cytokinesis Kre6 catalyzes β-1,6-glucan synthesis at the cell surface during growth and division
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Affiliation(s)
- Hiroki Okada
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6058, USA
| | - Brittany MacTaggart
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6058, USA
| | - Yoshikazu Ohya
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba, 277-8562, Japan
| | - Erfei Bi
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6058, USA
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13
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Thiroux S, Dupont S, Nesbø CL, Bienvenu N, Krupovic M, L'Haridon S, Marie D, Forterre P, Godfroy A, Geslin C. The first head-tailed virus, MFTV1, infecting hyperthermophilic methanogenic deep-sea archaea. Environ Microbiol 2020; 23:3614-3626. [PMID: 33022088 DOI: 10.1111/1462-2920.15271] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 08/20/2020] [Accepted: 10/03/2020] [Indexed: 11/27/2022]
Abstract
Deep-sea hydrothermal vents are inhabited by complex communities of microbes and their viruses. Despite the importance of viruses in controlling the diversity, adaptation and evolution of their microbial hosts, to date, only eight bacterial and two archaeal viruses isolated from abyssal ecosystems have been described. Thus, our efforts focused on gaining new insights into viruses associated with deep-sea autotrophic archaea. Here, we provide the first evidence of an infection of hyperthermophilic methanogenic archaea by a head-tailed virus, Methanocaldococcus fervens tailed virus 1 (MFTV1). MFTV1 has an isometric head of 50 nm in diameter and a 150 nm-long non-contractile tail. Virions are released continuously without causing a sudden drop in host growth. MFTV1 infects Methanocaldococcus species and is the first hyperthermophilic head-tailed virus described thus far. The viral genome is a double-stranded linear DNA of 31 kb. Interestingly, our results suggest potential strategies adopted by the plasmid pMEFER01, carried by M. fervens, to spread horizontally in hyperthermophilic methanogens. The data presented here open a new window of understanding on how the abyssal mobilome interacts with hyperthermophilic marine archaea.
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Affiliation(s)
- Sarah Thiroux
- Laboratoire de Microbiologie des Environnements Extrêmes, Univ Brest, CNRS, IFREMER, Plouzané, F-29280, France
| | - Samuel Dupont
- Laboratoire de Microbiologie des Environnements Extrêmes, Univ Brest, CNRS, IFREMER, Plouzané, F-29280, France
| | - Camilla L Nesbø
- Biozone, University of Toronto, Toronto, Ontario, M5S 3E5, Canada.,Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G2R3, 12, Canada
| | - Nadège Bienvenu
- Laboratoire de Microbiologie des Environnements Extrêmes, Univ Brest, CNRS, IFREMER, Plouzané, F-29280, France
| | - Mart Krupovic
- Archaeal Virology Unit, Institut Pasteur, Paris, 75015, France
| | - Stéphane L'Haridon
- Laboratoire de Microbiologie des Environnements Extrêmes, Univ Brest, CNRS, IFREMER, Plouzané, F-29280, France
| | - Dominique Marie
- UPMC Univ Paris 06, INSU-CNRS, UMR 7144, Station Biologique de Roscoff, Sorbonne University, Roscoff, 29680, France
| | - Patrick Forterre
- Archaeal Virology Unit, Institut Pasteur, Paris, 75015, France.,Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS., Gif-sur-Yvette, 91198, France
| | - Anne Godfroy
- Laboratoire de Microbiologie des Environnements Extrêmes, Univ Brest, CNRS, IFREMER, Plouzané, F-29280, France
| | - Claire Geslin
- Laboratoire de Microbiologie des Environnements Extrêmes, Univ Brest, CNRS, IFREMER, Plouzané, F-29280, France
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14
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Baquero DP, Liu Y, Wang F, Egelman EH, Prangishvili D, Krupovic M. Structure and assembly of archaeal viruses. Adv Virus Res 2020; 108:127-164. [PMID: 33837715 DOI: 10.1016/bs.aivir.2020.09.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Viruses of archaea represent one of the most enigmatic parts of the virosphere. Most of the characterized archaeal viruses infect extremophilic hosts and display remarkable diversity of virion morphotypes, many of which have never been observed among bacteriophages or viruses of eukaryotes. However, recent environmental studies have shown that archaeal viruses are widespread also in moderate ecosystems, where they play an important ecological role by influencing the turnover of microbial communities, with a global impact on the carbon and nitrogen cycles. In this review, we summarize recent advances in understanding the molecular details of virion organization and assembly of archaeal viruses. We start by briefly introducing the 20 officially recognized families of archaeal viruses and then outline the similarities and differences of archaeal virus assembly with the morphogenesis pathways used by bacterial and eukaryotic viruses, and discuss the evolutionary implications of these observations. Generally, the assembly of the icosahedral archaeal viruses closely follows the mechanisms employed by evolutionarily related bacterial and eukaryotic viruses with the HK97 fold and double jelly-roll major capsid proteins, emphasizing the overall conservation of these pathways over billions of years of evolution. By contrast, archaea-specific viruses employ unique virion assembly mechanisms. We also highlight some of the molecular adaptations underlying the stability of archaeal viruses in extreme environments. Despite considerable progress during the past few years, the archaeal virosphere continues to represent one of the least studied parts of the global virome, with many molecular features awaiting to be discovered and characterized.
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Affiliation(s)
- Diana P Baquero
- Archaeal Virology Unit, Department of Microbiology, Institut Pasteur, Paris, France; Sorbonne Université, Collège Doctoral, Paris, France
| | - Ying Liu
- Archaeal Virology Unit, Department of Microbiology, Institut Pasteur, Paris, France
| | - Fengbin Wang
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, United States
| | - Edward H Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, United States
| | - David Prangishvili
- Archaeal Virology Unit, Department of Microbiology, Institut Pasteur, Paris, France; Ivane Javakhishvili Tbilisi State University, Tbilisi, Georgia
| | - Mart Krupovic
- Archaeal Virology Unit, Department of Microbiology, Institut Pasteur, Paris, France.
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15
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Methanothermobacter thermautotrophicus strain ΔH as a potential microorganism for bioconversion of CO2 to methane. J CO2 UTIL 2020. [DOI: 10.1016/j.jcou.2020.101210] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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16
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Abstract
The last universal cellular ancestor (LUCA) is the most recent population of organisms from which all cellular life on Earth descends. The reconstruction of the genome and phenotype of the LUCA is a major challenge in evolutionary biology. Given that all life forms are associated with viruses and/or other mobile genetic elements, there is no doubt that the LUCA was a host to viruses. Here, by projecting back in time using the extant distribution of viruses across the two primary domains of life, bacteria and archaea, and tracing the evolutionary histories of some key virus genes, we attempt a reconstruction of the LUCA virome. Even a conservative version of this reconstruction suggests a remarkably complex virome that already included the main groups of extant viruses of bacteria and archaea. We further present evidence of extensive virus evolution antedating the LUCA. The presence of a highly complex virome implies the substantial genomic and pan-genomic complexity of the LUCA itself.
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17
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Rands CM, Brüssow H, Zdobnov EM. Comparative genomics groups phages of Negativicutes and classical Firmicutes despite different Gram-staining properties. Environ Microbiol 2019; 21:3989-4001. [PMID: 31314945 DOI: 10.1111/1462-2920.14746] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 07/02/2019] [Accepted: 07/14/2019] [Indexed: 01/05/2023]
Abstract
Negativicutes are gram-negative bacteria characterized by two cell membranes, but they are phylogenetically a side-branch of gram-positive Firmicutes that contain only a single membrane. We asked whether viruses (phages) infecting Negativicutes were horizontally acquired from gram-negative Proteobacteria, given the shared outer cell structure of their bacterial hosts, or if Negativicute phages co-evolved vertically with their hosts and thus resemble gram-positive Firmicute prophages. We predicted and characterized 485 prophages (mostly Caudovirales) from gram-negative Firmicute genomes plus 2977 prophages from other bacterial clades, and we used virome sequence data from 183 human stool samples to support our predictions. The majority of identified Negativicute prophages were lambdoids closer related to prophages from other Firmicutes than Proteobacteria by sequence relationship and genome organization (position of the lysis module). Only a single Mu-like candidate prophage and no clear P2-like prophages were identified in Negativicutes, both common in Proteobacteria. Given this collective evidence, it is unlikely that Negativicute phages were acquired from Proteobacteria. Sequence-related prophages, which occasionally harboured antibiotic resistance genes, were identified in two distinct Negativicute orders (Veillonellales and Acidaminococcales), possibly suggesting horizontal cross-order phage infection between human gut commensals. Our results reveal ancient genomic signatures of phage and bacteria co-evolution despite horizontal phage mobilization.
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Affiliation(s)
- Chris M Rands
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland.,Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Harald Brüssow
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
| | - Evgeny M Zdobnov
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland.,Swiss Institute of Bioinformatics, Geneva, Switzerland
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18
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Liu Y, Brandt D, Ishino S, Ishino Y, Koonin EV, Kalinowski J, Krupovic M, Prangishvili D. New archaeal viruses discovered by metagenomic analysis of viral communities in enrichment cultures. Environ Microbiol 2019; 21:2002-2014. [PMID: 30451355 PMCID: PMC11128462 DOI: 10.1111/1462-2920.14479] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 11/07/2018] [Accepted: 11/10/2018] [Indexed: 12/20/2022]
Abstract
Viruses infecting hyperthermophilic archaea of the phylum Crenarchaeota display enormous morphological and genetic diversity, and are classified into 12 families. Eight of these families include only one or two species, indicating sparse sampling of the crenarchaeal virus diversity. In an attempt to expand the crenarchaeal virome, we explored virus diversity in the acidic, hot spring Umi Jigoku in Beppu, Japan. Environmental samples were used to establish enrichment cultures under conditions favouring virus replication. The host diversity in the enrichment cultures was restricted to members of the order Sulfolobales. Metagenomic sequencing of the viral communities yielded seven complete or near-complete double-stranded DNA virus genomes. Six of these genomes could be attributed to polyhedral and filamentous viruses that were observed by electron microscopy in the enrichment cultures. Two icosahedral viruses represented species in the family Portogloboviridae. Among the filamentous viruses, two were identified as new species in the families Rudiviridae and Lipothrixviridae, whereas two other formed a group seemingly distinct from the known virus genera. No particle morphotype could be unequivocally assigned to the seventh viral genome, which apparently represents a new virus type. Our results suggest that filamentous viruses are globally distributed and are prevalent virus types in extreme geothermal environments.
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Affiliation(s)
- Ying Liu
- Department of Microbiology, BMGE, Institut Pasteur, Paris 75015, France
| | - David Brandt
- Center for Biotechnology, Universität Bielefeld, Bielefeld 33615, Germany
| | - Sonoko Ishino
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Fukuoka 819-0395, Japan
| | - Yoshizumi Ishino
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Fukuoka 819-0395, Japan
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jörn Kalinowski
- Center for Biotechnology, Universität Bielefeld, Bielefeld 33615, Germany
| | - Mart Krupovic
- Department of Microbiology, BMGE, Institut Pasteur, Paris 75015, France
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19
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Lan W, Yang C. Ruminal methane production: Associated microorganisms and the potential of applying hydrogen-utilizing bacteria for mitigation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 654:1270-1283. [PMID: 30841400 DOI: 10.1016/j.scitotenv.2018.11.180] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 11/12/2018] [Accepted: 11/12/2018] [Indexed: 05/16/2023]
Abstract
Methane emission from ruminants not only causes serious environmental problems, but also represents a significant source of energy loss to animals. The increasing demand for sustainable animal production is driving researchers to explore proper strategies to mitigate ruminal methanogenesis. Since hydrogen is the primary substrate of ruminal methanogenesis, hydrogen metabolism and its associated microbiome in the rumen may closely relate to low- and high-methane phenotypes. Using candidate microbes that can compete with methanogens and redirect hydrogen away from methanogenesis as ruminal methane mitigants are promising avenues for methane mitigation, which can both prevent the adverse effects deriving from chemical additives such as toxicity and resistance, and increase the retention of feed energy. This review describes the ruminal microbial ecosystem and its association with methane production, as well as the effects of interspecies hydrogen transfer on methanogenesis. It provides a scientific perspective on using bacteria that are involved in hydrogen utilization as ruminal modifiers to decrease methanogenesis. This information will be helpful in better understanding the key role of ruminal microbiomes and their relationship with methane production and, therefore, will form the basis of valuable and eco-friendly methane mitigation methods while improving animal productivity.
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Affiliation(s)
- Wei Lan
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China; MoE Key Laboratory of Molecular Animal Nutrition, China
| | - Chunlei Yang
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China; MoE Key Laboratory of Molecular Animal Nutrition, China.
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20
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Characterization of the lytic archaeal virus Drs3 infecting Methanobacterium formicicum. Arch Virol 2018; 164:667-674. [DOI: 10.1007/s00705-018-04120-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 11/19/2018] [Indexed: 01/21/2023]
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21
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Altermann E, Schofield LR, Ronimus RS, Beatty AK, Reilly K. Inhibition of Rumen Methanogens by a Novel Archaeal Lytic Enzyme Displayed on Tailored Bionanoparticles. Front Microbiol 2018; 9:2378. [PMID: 30356700 PMCID: PMC6189367 DOI: 10.3389/fmicb.2018.02378] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 09/18/2018] [Indexed: 11/13/2022] Open
Abstract
Methane is a potent greenhouse gas, 25 times more efficient at trapping heat than carbon dioxide. Ruminant methane emissions contribute almost 30% to anthropogenic sources of global atmospheric methane levels and a reduction in methane emissions would significantly contribute to slowing global temperature rises. Here we demonstrate the use of a lytic enyzme, PeiR, from a methanogen virus that infects Methanobrevibacter ruminantium M1 as an effective agent inhibiting a range of rumen methanogen strains in pure culture. We determined the substrate specificity of soluble PeiR and demonstrated that the enzyme is capable of hydrolysing the pseudomurein cell walls of methanogens. Subsequently, peiR was fused to the polyhydroxyalkanoate (PHA) synthase gene phaC and displayed on the surface of PHA bionanoparticles (BNPs) expressed in Eschericia coli via one-step biosynthesis. These tailored BNPs were capable of lysing not only the original methanogen host strain, but a wide range of other rumen methanogen strains in vitro. Methane production was reduced by up to 97% for 5 days post-inoculation in the in vitro assay. We propose that tailored BNPs carrying anti-methanogen enzymes represent a new class of methane inhibitors. Tailored BNPs can be rapidly developed and may be able to modulate the methanogen community in vivo with the aim to lower ruminant methane emissions without impacting animal productivity.
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Affiliation(s)
- Eric Altermann
- Rumen Microbiology, Animal Science, AgResearch Ltd., Palmerston North, New Zealand.,Riddet Institute, Massey University, Palmerston North, New Zealand
| | - Linley R Schofield
- Rumen Microbiology, Animal Science, AgResearch Ltd., Palmerston North, New Zealand
| | - Ron S Ronimus
- Rumen Microbiology, Animal Science, AgResearch Ltd., Palmerston North, New Zealand
| | - Amy K Beatty
- Soil Biology, Forage Science, AgResearch Ltd., Christchurch, New Zealand
| | - Kerri Reilly
- Rumen Microbiology, Animal Science, AgResearch Ltd., Palmerston North, New Zealand
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22
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Abstract
One of the most prominent features of archaea is the extraordinary diversity of their DNA viruses. Many archaeal viruses differ substantially in morphology from bacterial and eukaryotic viruses and represent unique virus families. The distinct nature of archaeal viruses also extends to the gene composition and architectures of their genomes and the properties of the proteins that they encode. Environmental research has revealed prominent roles of archaeal viruses in influencing microbial communities in ocean ecosystems, and recent metagenomic studies have uncovered new groups of archaeal viruses that infect extremophiles and mesophiles in diverse habitats. In this Review, we summarize recent advances in our understanding of the genomic and morphological diversity of archaeal viruses and the molecular biology of their life cycles and virus-host interactions, including interactions with archaeal CRISPR-Cas systems. We also examine the potential origins and evolution of archaeal viruses and discuss their place in the global virosphere.
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23
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Methanosarcina Spherical Virus, a Novel Archaeal Lytic Virus Targeting Methanosarcina Strains. J Virol 2017; 91:JVI.00955-17. [PMID: 28878086 DOI: 10.1128/jvi.00955-17] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 08/21/2017] [Indexed: 12/21/2022] Open
Abstract
A novel archaeal lytic virus targeting species of the genus Methanosarcina was isolated using Methanosarcina mazei strain Gö1 as the host. Due to its spherical morphology, the virus was designated Methanosarcina spherical virus (MetSV). Molecular analysis demonstrated that MetSV contains double-stranded linear DNA with a genome size of 10,567 bp containing 22 open reading frames (ORFs), all oriented in the same direction. Functions were predicted for some of these ORFs, i.e., such as DNA polymerase, ATPase, and DNA-binding protein as well as envelope (structural) protein. MetSV-derived spacers in CRISPR loci were detected in several published Methanosarcina draft genomes using bioinformatic tools, revealing a potential protospacer-adjacent motif (PAM) motif (TTA/T). Transcription and expression of several predicted viral ORFs were validated by reverse transcription-PCR (RT-PCR), PAGE analysis, and liquid chromatography-mass spectrometry (LC-MS)-based proteomics. Analysis of core lipids by atmospheric pressure chemical ionization (APCI) mass spectrometry showed that MetSV and Methanosarcina mazei both contain archaeol and glycerol dialkyl glycerol tetraether without a cyclopentane moiety (GDGT-0). The MetSV host range is limited to Methanosarcina strains growing as single cells (M. mazei, Methanosarcina barkeri and Methanosarcina soligelidi). In contrast, strains growing as sarcina-like aggregates were apparently protected from infection. Heterogeneity related to morphology phases in M. mazei cultures allowed acquisition of resistance to MetSV after challenge by growing cultures as sarcina-like aggregates. CRISPR/Cas-mediated resistance was excluded since neither of the two CRISPR arrays showed MetSV-derived spacer acquisition. Based on these findings, we propose that changing the morphology from single cells to sarcina-like aggregates upon rearrangement of the envelope structure prevents infection and subsequent lysis by MetSV.IMPORTANCE Methanoarchaea are among the most abundant organisms on the planet since they are present in high numbers in major anaerobic environments. They convert various carbon sources, e.g., acetate, methylamines, or methanol, to methane and carbon dioxide; thus, they have a significant impact on the emission of major greenhouse gases. Today, very little is known about viruses specifically infecting methanoarchaea that most probably impact the abundance of methanoarchaea in microbial consortia. Here, we characterize the first identified Methanosarcina-infecting virus (MetSV) and show a mechanism for acquiring resistance against MetSV. Based on our results, we propose that growth as sarcina-like aggregates prevents infection and subsequent lysis. These findings allow new insights into the virus-host relationship in methanogenic community structures, their dynamics, and their phase heterogeneity. Moreover, the availability of a specific virus provides new possibilities to deepen our knowledge of the defense mechanisms of potential hosts and offers tools for genetic manipulation.
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24
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Ahlgren NA, Chen Y, Needham DM, Parada AE, Sachdeva R, Trinh V, Chen T, Fuhrman JA. Genome and epigenome of a novel marine Thaumarchaeota strain suggest viral infection, phosphorothioation DNA modification and multiple restriction systems. Environ Microbiol 2017; 19:2434-2452. [PMID: 28418097 DOI: 10.1111/1462-2920.13768] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 04/08/2017] [Accepted: 04/11/2017] [Indexed: 11/29/2022]
Abstract
Marine Thaumarchaeota are abundant ammonia-oxidizers but have few representative laboratory-cultured strains. We report the cultivation of Candidatus Nitrosomarinus catalina SPOT01, a novel strain that is less warm-temperature tolerant than other cultivated Thaumarchaeota. Using metagenomic recruitment, strain SPOT01 comprises a major portion of Thaumarchaeota (4-54%) in temperate Pacific waters. Its complete 1.36 Mbp genome possesses several distinguishing features: putative phosphorothioation (PT) DNA modification genes; a region containing probable viral genes; and putative urea utilization genes. The PT modification genes and an adjacent putative restriction enzyme (RE) operon likely form a restriction modification (RM) system for defence from foreign DNA. PacBio sequencing showed >98% methylation at two motifs, and inferred PT guanine modification of 19% of possible TGCA sites. Metagenomic recruitment also reveals the putative virus region and PT modification and RE genes are present in 18-26%, 9-14% and <1.5% of natural populations at 150 m with ≥85% identity to strain SPOT01. The presence of multiple probable RM systems in a highly streamlined genome suggests a surprising importance for defence from foreign DNA for dilute populations that infrequently encounter viruses or other cells. This new strain provides new insights into the ecology, including viral interactions, of this important group of marine microbes.
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Affiliation(s)
- Nathan A Ahlgren
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Yangyang Chen
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, China.,Key Laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - David M Needham
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Alma E Parada
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Rohan Sachdeva
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Vickie Trinh
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Ting Chen
- Bioinformatics Division, TNLIST, Department of Computer Science and Technology, Tsinghua University, Beijing, China
| | - Jed A Fuhrman
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
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25
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Bipartite Network Analysis of the Archaeal Virosphere: Evolutionary Connections between Viruses and Capsidless Mobile Elements. J Virol 2016; 90:11043-11055. [PMID: 27681128 DOI: 10.1128/jvi.01622-16] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 09/19/2016] [Indexed: 11/20/2022] Open
Abstract
Archaea and particularly hyperthermophilic crenarchaea are hosts to many unusual viruses with diverse virion shapes and distinct gene compositions. As is typical of viruses in general, there are no universal genes in the archaeal virosphere. Therefore, to obtain a comprehensive picture of the evolutionary relationships between viruses, network analysis methods are more productive than traditional phylogenetic approaches. Here we present a comprehensive comparative analysis of genomes and proteomes from all currently known taxonomically classified and unclassified, cultivated and uncultivated archaeal viruses. We constructed a bipartite network of archaeal viruses that includes two classes of nodes, the genomes and gene families that connect them. Dissection of this network using formal community detection methods reveals strong modularity, with 10 distinct modules and 3 putative supermodules. However, compared to similar previously analyzed networks of eukaryotic and bacterial viruses, the archaeal virus network is sparsely connected. With the exception of the tailed viruses related to bacteriophages of the order Caudovirales and the families Turriviridae and Sphaerolipoviridae that are linked to a distinct supermodule of eukaryotic and bacterial viruses, there are few connector genes shared by different archaeal virus modules. In contrast, most of these modules include, in addition to viruses, capsidless mobile elements, emphasizing tight evolutionary connections between the two types of entities in archaea. The relative contributions of distinct evolutionary origins, in particular from nonviral elements, and insufficient sampling to the sparsity of the archaeal virus network remain to be determined by further exploration of the archaeal virosphere. IMPORTANCE Viruses infecting archaea are among the most mysterious denizens of the virosphere. Many of these viruses display no genetic or even morphological relationship to viruses of bacteria and eukaryotes, raising questions regarding their origins and position in the global virosphere. Analysis of 5,740 protein sequences from 116 genomes allowed dissection of the archaeal virus network and showed that most groups of archaeal viruses are evolutionarily connected to capsidless mobile genetic elements, including various plasmids and transposons. This finding could reflect actual independent origins of the distinct groups of archaeal viruses from different nonviral elements, providing important insights into the emergence and evolution of the archaeal virome.
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26
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Svirskaitė J, Oksanen HM, Daugelavičius R, Bamford DH. Monitoring Physiological Changes in Haloarchaeal Cell during Virus Release. Viruses 2016; 8:59. [PMID: 26927156 PMCID: PMC4810249 DOI: 10.3390/v8030059] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 02/11/2016] [Accepted: 02/15/2016] [Indexed: 01/14/2023] Open
Abstract
The slow rate of adsorption and non-synchronous release of some archaeal viruses have hindered more thorough analyses of the mechanisms of archaeal virus release. To address this deficit, we utilized four viruses that infect Haloarcula hispanica that represent the four virion morphotypes currently known for halophilic euryarchaeal viruses: (1) icosahedral internal membrane-containing SH1; (2) icosahedral tailed HHTV-1; (3) spindle-shaped His1; and (4) pleomorphic His2. To discern the events occurring as the progeny viruses exit, we monitored culture turbidity, as well as viable cell and progeny virus counts of infected and uninfected cultures. In addition to these traditional metrics, we measured three parameters associated with membrane integrity: the binding of the lipophilic anion phenyldicarbaundecaborane, oxygen consumption, and both intra- and extra-cellular ATP levels.
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Affiliation(s)
- Julija Svirskaitė
- Department of Biosciences, Institute of Biotechnology, University of Helsinki, Viikinkaari 9, 00014 Helsinki, Finland.
| | - Hanna M Oksanen
- Department of Biosciences, Institute of Biotechnology, University of Helsinki, Viikinkaari 9, 00014 Helsinki, Finland.
| | - Rimantas Daugelavičius
- Department of Biochemistry, Vytautas Magnus University, Vileikos g. 8, 44404 Kaunas, Lithuania.
| | - Dennis H Bamford
- Department of Biosciences, Institute of Biotechnology, University of Helsinki, Viikinkaari 9, 00014 Helsinki, Finland.
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Abstract
Many plasmids have been described in Euryarchaeota, one of the three major archaeal phyla, most of them in salt-loving haloarchaea and hyperthermophilic Thermococcales. These plasmids resemble bacterial plasmids in terms of size (from small plasmids encoding only one gene up to large megaplasmids) and replication mechanisms (rolling circle or theta). Some of them are related to viral genomes and form a more or less continuous sequence space including many integrated elements. Plasmids from Euryarchaeota have been useful for designing efficient genetic tools for these microorganisms. In addition, they have also been used to probe the topological state of plasmids in species with or without DNA gyrase and/or reverse gyrase. Plasmids from Euryarchaeota encode both DNA replication proteins recruited from their hosts and novel families of DNA replication proteins. Euryarchaeota form an interesting playground to test evolutionary hypotheses on the origin and evolution of viruses and plasmids, since a robust phylogeny is available for this phylum. Preliminary studies have shown that for different plasmid families, plasmids share a common gene pool and coevolve with their hosts. They are involved in gene transfer, mostly between plasmids and viruses present in closely related species, but rarely between cells from distantly related archaeal lineages. With few exceptions (e.g., plasmids carrying gas vesicle genes), most archaeal plasmids seem to be cryptic. Interestingly, plasmids and viral genomes have been detected in extracellular membrane vesicles produced by Thermococcales, suggesting that these vesicles could be involved in the transfer of viruses and plasmids between cells.
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Biochemical Characterisation of Phage Pseudomurein Endoisopeptidases PeiW and PeiP Using Synthetic Peptides. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2015; 2015:828693. [PMID: 26483615 PMCID: PMC4592898 DOI: 10.1155/2015/828693] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 08/13/2015] [Indexed: 11/18/2022]
Abstract
Pseudomurein endoisopeptidases cause lysis of the cell walls of methanogens by cleaving the isopeptide bond Ala-ε-Lys in the peptide chain of pseudomurein. PeiW and PeiP are two thermostable pseudomurein endoisopeptidases encoded by phage ΨM100 of Methanothermobacter wolfei and phages ΨM1 and ΨM2 of Methanothermobacter marburgensis, respectively. A continuous assay using synthetic peptide substrates was developed and used in the biochemical characterisation of recombinant PeiW and PeiP. The advantages of these synthetic peptide substrates over natural substrates are sensitivity, high purity, and characterisation and the fact that they are more easily obtained than natural substrates. In the presence of a reducing agent, purified PeiW and PeiP each showed similar activity under aerobic and anaerobic conditions. Both enzymes required a divalent metal for activity and showed greater thermostability in the presence of Ca2+. PeiW and PeiP involve a cysteine residue in catalysis and have a monomeric native conformation. The kinetic parameters, KM and kcat, were determined, and the ε-isopeptide bond between alanine and lysine was confirmed as the bond lysed by these enzymes in pseudomurein. The new assay may have wider applications for the general study of peptidases and the identification of specific methanogens susceptible to lysis by specific pseudomurein endoisopeptidases.
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Fernandes CG, Plácido D, Lousa D, Brito JA, Isidro A, Soares CM, Pohl J, Carrondo MA, Archer M, Henriques AO. Structural and Functional Characterization of an Ancient Bacterial Transglutaminase Sheds Light on the Minimal Requirements for Protein Cross-Linking. Biochemistry 2015; 54:5723-34. [PMID: 26322858 DOI: 10.1021/acs.biochem.5b00661] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Transglutaminases are best known for their ability to catalyze protein cross-linking reactions that impart chemical and physical resilience to cellular structures. Here, we report the crystal structure and characterization of Tgl, a transglutaminase from the bacterium Bacillus subtilis. Tgl is produced during sporulation and cross-links the surface of the highly resilient spore. Tgl-like proteins are found only in spore-forming bacteria of the Bacillus and Clostridia classes, indicating an ancient origin. Tgl is a single-domain protein, produced in active form, and the smallest transglutaminase characterized to date. We show that Tgl is structurally similar to bacterial cell wall endopeptidases and has an NlpC/P60 catalytic core, thought to represent the ancestral unit of the cysteine protease fold. We show that Tgl functions through a unique partially redundant catalytic dyad formed by Cys116 and Glu187 or Glu115. Strikingly, the catalytic Cys is insulated within a hydrophobic tunnel that traverses the molecule from side to side. The lack of similarity of Tgl to other transglutaminases together with its small size suggests that an NlpC/P60 catalytic core and insulation of the active site during catalysis may be essential requirements for protein cross-linking.
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Affiliation(s)
| | | | | | | | | | | | - Jan Pohl
- Biotechnology Branch, Centers for Disease Control and Prevention , Atlanta, Georgia 30333, United States
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30
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Abstract
SUMMARY Research on archaeal extrachromosomal genetic elements (ECEs) has progressed rapidly in the past decade. To date, over 60 archaeal viruses and 60 plasmids have been isolated. These archaeal viruses exhibit an exceptional diversity in morphology, with a wide array of shapes, such as spindles, rods, filaments, spheres, head-tails, bottles, and droplets, and some of these new viruses have been classified into one order, 10 families, and 16 genera. Investigation of model archaeal viruses has yielded important insights into mechanisms underlining various steps in the viral life cycle, including infection, DNA replication and transcription, and virion egression. Many of these mechanisms are unprecedented for any known bacterial or eukaryal viruses. Studies of plasmids isolated from different archaeal hosts have also revealed a striking diversity in gene content and innovation in replication strategies. Highly divergent replication proteins are identified in both viral and plasmid genomes. Genomic studies of archaeal ECEs have revealed a modular sequence structure in which modules of DNA sequence are exchangeable within, as well as among, plasmid families and probably also between viruses and plasmids. In particular, it has been suggested that ECE-host interactions have shaped the coevolution of ECEs and their archaeal hosts. Furthermore, archaeal hosts have developed defense systems, including the innate restriction-modification (R-M) system and the adaptive CRISPR (clustered regularly interspaced short palindromic repeats) system, to restrict invasive plasmids and viruses. Together, these interactions permit a delicate balance between ECEs and their hosts, which is vitally important for maintaining an innovative gene reservoir carried by ECEs. In conclusion, while research on archaeal ECEs has just started to unravel the molecular biology of these genetic entities and their interactions with archaeal hosts, it is expected to accelerate in the next decade.
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31
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Stedman KM, DeYoung M, Saha M, Sherman MB, Morais MC. Structural insights into the architecture of the hyperthermophilic Fusellovirus SSV1. Virology 2014; 474:105-9. [PMID: 25463608 DOI: 10.1016/j.virol.2014.10.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 06/17/2014] [Accepted: 10/17/2014] [Indexed: 10/24/2022]
Abstract
The structure and assembly of many icosahedral and helical viruses are well-characterized. However, the molecular basis for the unique spindle-shaped morphology of many viruses that infect Archaea remains unknown. To understand the architecture and assembly of these viruses, the spindle-shaped virus SSV1 was examined using cryo-EM, providing the first 3D-structure of a spindle-shaped virus as well as insight into SSV1 biology, assembly and evolution. Furthermore, a geometric framework underlying the distinct spindle-shaped structure is proposed.
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Affiliation(s)
- Kenneth M Stedman
- Center for Life in Extreme Environments, Biology Department, Portland State University, Portland, OR, USA
| | - Melissa DeYoung
- Center for Life in Extreme Environments, Biology Department, Portland State University, Portland, OR, USA
| | - Mitul Saha
- Sealy Center for Structural Biology and Molecular Biophysics, Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Michael B Sherman
- Sealy Center for Structural Biology and Molecular Biophysics, Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Marc C Morais
- Sealy Center for Structural Biology and Molecular Biophysics, Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA.
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32
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Clokie MR, Millard AD, Letarov AV, Heaphy S. Phages in nature. BACTERIOPHAGE 2014; 1:31-45. [PMID: 21687533 DOI: 10.4161/bact.1.1.14942] [Citation(s) in RCA: 648] [Impact Index Per Article: 64.8] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 10/28/2010] [Revised: 01/17/2011] [Accepted: 01/18/2011] [Indexed: 12/28/2022]
Abstract
Bacteriophages or phages are the most abundant organisms in the biosphere and they are a ubiquitous feature of prokaryotic existence. A bacteriophage is a virus which infects a bacterium. Archaea are also infected by viruses, whether these should be referred to as 'phages' is debatable, but they are included as such in the scope this article. Phages have been of interest to scientists as tools to understand fundamental molecular biology, as vectors of horizontal gene transfer and drivers of bacterial evolution, as sources of diagnostic and genetic tools and as novel therapeutic agents. Unraveling the biology of phages and their relationship with their hosts is key to understanding microbial systems and their exploitation. In this article we describe the roles of phages in different host systems and show how modeling, microscopy, isolation, genomic and metagenomic based approaches have come together to provide unparalleled insights into these small but vital constituents of the microbial world.
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Affiliation(s)
- Martha Rj Clokie
- Department of Infection, Immunity and Inflammation; Medical Sciences Building; University of Leicester; Leicester, UK
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33
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Kadnikov VV, Mardanov AV, Beletsky AV, Karnachuk OV, Ravin NV. Characteristics of the new plasmid, pMTB1, from the metagenome of the microbial community of underground thermal waters of Western Siberia. BIOL BULL+ 2014. [DOI: 10.1134/s1062359014030054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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34
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Kumar S, Choudhury PK, Carro MD, Griffith GW, Dagar SS, Puniya M, Calabro S, Ravella SR, Dhewa T, Upadhyay RC, Sirohi SK, Kundu SS, Wanapat M, Puniya AK. New aspects and strategies for methane mitigation from ruminants. Appl Microbiol Biotechnol 2013; 98:31-44. [DOI: 10.1007/s00253-013-5365-0] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Revised: 10/28/2013] [Accepted: 10/30/2013] [Indexed: 11/29/2022]
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35
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Krupovic M, White MF, Forterre P, Prangishvili D. Postcards from the edge: structural genomics of archaeal viruses. Adv Virus Res 2013; 82:33-62. [PMID: 22420850 DOI: 10.1016/b978-0-12-394621-8.00012-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Ever since their discovery, archaeal viruses have fascinated biologists with their unusual virion morphotypes and their ability to thrive in extreme environments. Attempts to understand the biology of these viruses through genome sequence analysis were not efficient. Genomes of archaeoviruses proved to be terra incognita with only a few genes with predictable functions but uncertain provenance. In order to facilitate functional characterization of archaeal virus proteins, several research groups undertook a structural genomics approach. This chapter summarizes the outcome of these efforts. High-resolution structures of 30 proteins encoded by archaeal viruses have been solved so far. Some of these proteins possess new structural folds, whereas others display previously known topologies, albeit without detectable sequence similarity to their structural homologues. Structures of the major capsid proteins have illuminated intriguing evolutionary connections between viruses infecting hosts from different domains of life and also revealed new structural folds not yet observed in currently known bacterial and eukaryotic viruses. Structural studies, discussed here, have advanced our understanding of the archaeal virosphere and provided precious information on different aspects of biology of archaeal viruses and evolution of viruses in general.
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Affiliation(s)
- Mart Krupovic
- Department of Microbiology, Institut Pasteur, Molecular Biology of the Gene in Extremophiles Unit, Paris, France
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36
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A survey of protein structures from archaeal viruses. Life (Basel) 2013; 3:118-30. [PMID: 25371334 PMCID: PMC4187194 DOI: 10.3390/life3010118] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2012] [Revised: 01/18/2013] [Accepted: 01/21/2013] [Indexed: 11/17/2022] Open
Abstract
Viruses that infect the third domain of life, Archaea, are a newly emerging field of interest. To date, all characterized archaeal viruses infect archaea that thrive in extreme conditions, such as halophilic, hyperthermophilic, and methanogenic environments. Viruses in general, especially those replicating in extreme environments, contain highly mosaic genomes with open reading frames (ORFs) whose sequences are often dissimilar to all other known ORFs. It has been estimated that approximately 85% of virally encoded ORFs do not match known sequences in the nucleic acid databases, and this percentage is even higher for archaeal viruses (typically 90%–100%). This statistic suggests that either virus genomes represent a larger segment of sequence space and/or that viruses encode genes of novel fold and/or function. Because the overall three-dimensional fold of a protein evolves more slowly than its sequence, efforts have been geared toward structural characterization of proteins encoded by archaeal viruses in order to gain insight into their potential functions. In this short review, we provide multiple examples where structural characterization of archaeal viral proteins has indeed provided significant functional and evolutionary insight.
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37
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Abstract
Extremophilic archaea, both hyperthermophiles and halophiles, dominate in habitats where rather harsh conditions are encountered. Like all other organisms, archaeal cells are susceptible to viral infections, and to date, about 100 archaeal viruses have been described. Among them, there are extraordinary virion morphologies as well as the common head-tailed viruses. Although approximately half of the isolated archaeal viruses belong to the latter group, no three-dimensional virion structures of these head-tailed viruses are available. Thus, rigorous comparisons with bacteriophages are not yet warranted. In the present study, we determined the genome sequences of two of such viruses of halophiles and solved their capsid structures by cryo-electron microscopy and three-dimensional image reconstruction. We show that these viruses are inactivated, yet remain intact, at low salinity and that their infectivity is regained when high salinity is restored. This enabled us to determine their three-dimensional capsid structures at low salinity to a ∼10-Å resolution. The genetic and structural data showed that both viruses belong to the same T-number class, but one of them has enlarged its capsid to accommodate a larger genome than typically associated with a T=7 capsid by inserting an additional protein into the capsid lattice.
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Kubota K. CARD-FISH for environmental microorganisms: technical advancement and future applications. Microbes Environ 2012; 28:3-12. [PMID: 23124765 PMCID: PMC4070690 DOI: 10.1264/jsme2.me12107] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Fluorescence in situ hybridization (FISH) has become a standard technique in environmental microbiology. More than 20 years have passed since this technique was first described, and it is currently used for the detection of ribosomal RNA, messenger RNA, and functional genes encoded on chromosomes. This review focuses on the advancement and applications of FISH combined with catalyzed reporter deposition (CARD, also known as tyramide signal amplification or TSA), in the detection of environmental microorganisms. Significant methodological improvements have been made in CARD-FISH technology, including its combination with other techniques and instruments.
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Affiliation(s)
- Kengo Kubota
- Department of Civil and Environmental Engineering, Tohoku University, Miyagi, Japan.
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39
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Archaeal virus with exceptional virion architecture and the largest single-stranded DNA genome. Proc Natl Acad Sci U S A 2012; 109:13386-91. [PMID: 22826255 DOI: 10.1073/pnas.1203668109] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Known viruses build their particles using a restricted number of redundant structural solutions. Here, we describe the Aeropyrum coil-shaped virus (ACV), of the hyperthermophilic archaeon Aeropyrum pernix, with a virion architecture not previously observed in the viral world. The nonenveloped, hollow, cylindrical virion is formed from a coiling fiber, which consists of two intertwining halves of a single circular nucleoprotein. The virus ACV is also exceptional for its genomic properties. It is the only virus with a single-stranded (ss) DNA genome among the known hyperthermophilic archaeal viruses. Moreover, the size of its circular genome, 24,893 nt, is double that of the largest known ssDNA genome, suggesting an efficient solution for keeping ssDNA intact at 90-95 °C, the optimal temperature range of A. pernix growth. The genome content of ACV is in line with its unique morphology and confirms that ACV is not closely related to any known virus.
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40
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Hyman P, Abedon ST. Smaller fleas: viruses of microorganisms. SCIENTIFICA 2012; 2012:734023. [PMID: 24278736 PMCID: PMC3820453 DOI: 10.6064/2012/734023] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2012] [Accepted: 06/20/2012] [Indexed: 05/31/2023]
Abstract
Life forms can be roughly differentiated into those that are microscopic versus those that are not as well as those that are multicellular and those that, instead, are unicellular. Cellular organisms seem generally able to host viruses, and this propensity carries over to those that are both microscopic and less than truly multicellular. These viruses of microorganisms, or VoMs, in fact exist as the world's most abundant somewhat autonomous genetic entities and include the viruses of domain Bacteria (bacteriophages), the viruses of domain Archaea (archaeal viruses), the viruses of protists, the viruses of microscopic fungi such as yeasts (mycoviruses), and even the viruses of other viruses (satellite viruses). In this paper we provide an introduction to the concept of viruses of microorganisms, a.k.a., viruses of microbes. We provide broad discussion particularly of VoM diversity. VoM diversity currently spans, in total, at least three-dozen virus families. This is roughly ten families per category-bacterial, archaeal, fungal, and protist-with some virus families infecting more than one of these microorganism major taxa. Such estimations, however, will vary with further discovery and taxon assignment and also are dependent upon what forms of life one includes among microorganisms.
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Affiliation(s)
- Paul Hyman
- Department of Biology, Ashland University, 401 College Avenue, Ashland, OH 44805, USA
| | - Stephen T. Abedon
- Department of Microbiology, The Ohio State University, 1680 University Dr., Mansfield, OH 44906, USA
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41
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Visweswaran GRR, Dijkstra BW, Kok J. A genetically engineered protein domain binding to bacterial murein, archaeal pseudomurein, and fungal chitin cell wall material. Appl Microbiol Biotechnol 2012; 96:729-37. [PMID: 22262228 PMCID: PMC3466432 DOI: 10.1007/s00253-012-3871-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2011] [Revised: 12/21/2011] [Accepted: 12/23/2011] [Indexed: 11/30/2022]
Abstract
The major murein and pseudomurein cell wall-binding domains, i.e., the Lysin Motif (LysM) (Pfam PF01476) and pseudomurein cell wall-binding (PMB) (Pfam PF09373) motif, respectively, were genetically fused. The fusion protein is capable of binding to both murein- and pseudomurein-containing cell walls. In addition, it also binds to chitin, the major polymer of fungal cell walls. Binding is influenced by pH and occurs at a pH close to the pI of the binding protein. Functional studies on truncated versions of the fusion protein revealed that murein and chitin binding is provided by the LysM domain, while binding to pseudomurein is achieved through the PMB domain.
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Affiliation(s)
- Ganesh Ram R Visweswaran
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747, AG, Groningen, the Netherlands
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42
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Brodt A, Lurie-Weinberger MN, Gophna U. CRISPR loci reveal networks of gene exchange in archaea. Biol Direct 2011; 6:65. [PMID: 22188759 PMCID: PMC3285040 DOI: 10.1186/1745-6150-6-65] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2011] [Accepted: 12/21/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND CRISPR (Clustered, Regularly, Interspaced, Short, Palindromic Repeats) loci provide prokaryotes with an adaptive immunity against viruses and other mobile genetic elements. CRISPR arrays can be transcribed and processed into small crRNA molecules, which are then used by the cell to target the foreign nucleic acid. Since spacers are accumulated by active CRISPR/Cas systems, the sequences of these spacers provide a record of the past "infection history" of the organism. RESULTS Here we analyzed all currently known spacers present in archaeal genomes and identified their source by DNA similarity. While nearly 50% of archaeal spacers matched mobile genetic elements, such as plasmids or viruses, several others matched chromosomal genes of other organisms, primarily other archaea. Thus, networks of gene exchange between archaeal species were revealed by the spacer analysis, including many cases of inter-genus and inter-species gene transfer events. Spacers that recognize viral sequences tend to be located further away from the leader sequence, implying that there exists a selective pressure for their retention. CONCLUSIONS CRISPR spacers provide direct evidence for extensive gene exchange in archaea, especially within genera, and support the current dogma where the primary role of the CRISPR/Cas system is anti-viral and anti-plasmid defense. OPEN PEER REVIEW This article was reviewed by: Profs. W. Ford Doolittle, John van der Oost, Christa Schleper (nominated by board member Prof. J Peter Gogarten).
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Affiliation(s)
- Avital Brodt
- Department of Molecular Microbiology and Biotechnology, George S, Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, 69978, Israel.
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Gorlas A, Koonin EV, Bienvenu N, Prieur D, Geslin C. TPV1, the first virus isolated from the hyperthermophilic genus Thermococcus. Environ Microbiol 2011; 14:503-16. [PMID: 22151304 DOI: 10.1111/j.1462-2920.2011.02662.x] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We describe a novel virus, TPV1 (Thermococcus prieurii virus 1), which was discovered in a hyperthermophilic euryarchaeote isolated from a deep-sea hydrothermal chimney sample collected at a depth of 2700 m at the East Pacific Rise. TPV1 is the first virus isolated and characterized from the hyperthermophilic euryarchaeal genus Thermococcus. TPV1 particles have a lemon-shaped morphology (140 nm × 80 nm) similar to the structures previously reported for Fuselloviruses and for the unclassified virus-like particle PAV1 (Pyrococcus abyssi virus 1). The infection with TPV1 does not cause host lysis and viral replication can be induced by UV irradiation. TPV1 contains a double-stranded circular DNA of 21.5 kb, which is also present in high copy number in a free form in the host cell. The TPV1 genome encompasses 28 predicted genes; the protein sequences encoded in 16 of these genes show no significant similarity to proteins in public databases. Proteins predicted to be involved in genome replication were identified as well as transcriptional regulators. TPV1 encodes also a predicted integrase of the tyrosine recombinase family. The only two genes that are homologous between TPV1 and PAV1 are TPV1-22 and TPV1-23, which encode proteins containing a concanavalin A-like lectin/glucanase domain that might be involved in virus-host recognition.
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Affiliation(s)
- Aurore Gorlas
- Laboratory of Microbiology of Extreme Environments, UMR 6197/CNRS/UBO IUEM, Place Nicolas Copernic, Technopôle Brest Iroise Plouzane, France
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Krupovic M, Prangishvili D, Hendrix RW, Bamford DH. Genomics of bacterial and archaeal viruses: dynamics within the prokaryotic virosphere. Microbiol Mol Biol Rev 2011; 75:610-35. [PMID: 22126996 PMCID: PMC3232739 DOI: 10.1128/mmbr.00011-11] [Citation(s) in RCA: 158] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Prokaryotes, bacteria and archaea, are the most abundant cellular organisms among those sharing the planet Earth with human beings (among others). However, numerous ecological studies have revealed that it is actually prokaryotic viruses that predominate on our planet and outnumber their hosts by at least an order of magnitude. An understanding of how this viral domain is organized and what are the mechanisms governing its evolution is therefore of great interest and importance. The vast majority of characterized prokaryotic viruses belong to the order Caudovirales, double-stranded DNA (dsDNA) bacteriophages with tails. Consequently, these viruses have been studied (and reviewed) extensively from both genomic and functional perspectives. However, albeit numerous, tailed phages represent only a minor fraction of the prokaryotic virus diversity. Therefore, the knowledge which has been generated for this viral system does not offer a comprehensive view of the prokaryotic virosphere. In this review, we discuss all families of bacterial and archaeal viruses that contain more than one characterized member and for which evolutionary conclusions can be attempted by use of comparative genomic analysis. We focus on the molecular mechanisms of their genome evolution as well as on the relationships between different viral groups and plasmids. It becomes clear that evolutionary mechanisms shaping the genomes of prokaryotic viruses vary between different families and depend on the type of the nucleic acid, characteristics of the virion structure, as well as the mode of the life cycle. We also point out that horizontal gene transfer is not equally prevalent in different virus families and is not uniformly unrestricted for diverse viral functions.
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Affiliation(s)
- Mart Krupovic
- Institut Pasteur, Unité Biologie Moléculaire du Gène chez les Extrêmophiles, Département de Microbiologie, 25 rue du Dr. Roux, 75015 Paris, France.
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45
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Murein and pseudomurein cell wall binding domains of bacteria and archaea--a comparative view. Appl Microbiol Biotechnol 2011; 92:921-8. [PMID: 22012341 PMCID: PMC3210951 DOI: 10.1007/s00253-011-3637-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2011] [Revised: 09/29/2011] [Accepted: 10/07/2011] [Indexed: 02/02/2023]
Abstract
The cell wall, a major barrier protecting cells from their environment, is an essential compartment of both bacteria and archaea. It protects the organism from internal turgor pressure and gives a defined shape to the cell. The cell wall serves also as an anchoring surface for various proteins and acts as an adhesion platform for bacteriophages. The walls of bacteria and archaea are mostly composed of murein and pseudomurein, respectively. Cell wall binding domains play a crucial role in the non-covalent attachment of proteins to cell walls. Here, we give an overview of the similarities and differences in the biochemical and functional properties of the two major murein and pseudomurein cell wall binding domains, i.e., the Lysin Motif (LysM) domain (Pfam PF01476) and the pseudomurein binding (PMB) domain (Pfam PF09373) of bacteria and archaea, respectively.
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Reiss K, Kirchner E, Gijzen M, Zocher G, Löffelhardt B, Nürnberger T, Stehle T, Brunner F. Structural and phylogenetic analyses of the GP42 transglutaminase from Phytophthora sojae reveal an evolutionary relationship between oomycetes and marine Vibrio bacteria. J Biol Chem 2011; 286:42585-42593. [PMID: 21994936 DOI: 10.1074/jbc.m111.290544] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Transglutaminases (TGases) are ubiquitous enzymes that catalyze selective cross-linking between protein-bound glutamine and lysine residues; the resulting isopeptide bond confers high resistance to proteolysis. Phytophthora sojae, a pathogen of soybean, secretes a Ca(2+)-dependent TGase (GP42) that is activating defense responses in both host and non-host plants. A GP42 fragment of 13 amino acids, termed Pep-13, was shown to be absolutely indispensable for both TGase and elicitor activity. GP42 does not share significant primary sequence similarity with known TGases from mammals or bacteria. This suggests that GP42 has evolved novel structural and catalytic features to support enzymatic activity. We have solved the crystal structure of the catalytically inactive point mutant GP42 (C290S) at 2.95 Å resolution and identified residues involved in catalysis by mutational analysis. The protein comprises three domains that assemble into an elongated structure. Although GP42 has no structural homolog, its core region displays significant similarity to the catalytic core of the Mac-1 cysteine protease from Group A Streptococcus, a member of the papain-like superfamily of cysteine proteases. Proteins that are taxonomically related to GP42 are only present in plant pathogenic oomycetes belonging to the order of the Peronosporales (e.g. Phytophthora, Hyaloperonospora, and Pythium spp.) and in marine Vibrio bacteria. This suggests that a lateral gene transfer event may have occurred between bacteria and oomycetes. Our results offer a basis to design and use highly specific inhibitors of the GP42-like TGase family that may impair the growth of important oomycete and bacterial pathogens.
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Affiliation(s)
- Kerstin Reiss
- Interfakultäres Institut für Biochemie, Universität Tübingen, 72076 Tübingen, Germany
| | - Eva Kirchner
- Interfakultäres Institut für Biochemie, Universität Tübingen, 72076 Tübingen, Germany
| | - Mark Gijzen
- Agri-Food Canada, London, Ontario N5V 4T3, Canada
| | - Georg Zocher
- Interfakultäres Institut für Biochemie, Universität Tübingen, 72076 Tübingen, Germany
| | - Birgit Löffelhardt
- Zentrum für Molekularbiologie der Pflanzen, Universität Tübingen, 72076 Tübingen, Germany
| | - Thorsten Nürnberger
- Zentrum für Molekularbiologie der Pflanzen, Universität Tübingen, 72076 Tübingen, Germany
| | - Thilo Stehle
- Interfakultäres Institut für Biochemie, Universität Tübingen, 72076 Tübingen, Germany; Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, Tennessee 37232.
| | - Frédéric Brunner
- Zentrum für Molekularbiologie der Pflanzen, Universität Tübingen, 72076 Tübingen, Germany.
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Krupovic M, Bamford DH. Double-stranded DNA viruses: 20 families and only five different architectural principles for virion assembly. Curr Opin Virol 2011; 1:118-24. [PMID: 22440622 DOI: 10.1016/j.coviro.2011.06.001] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2011] [Revised: 05/30/2011] [Accepted: 06/03/2011] [Indexed: 02/03/2023]
Abstract
The number of viral particles in the biosphere is enormous. Virus classification helps to comprehend the virosphere and to understand the relationship between different virus groups. However, the evolutionary reach of the currently employed sequence-based approaches in virus taxonomy is rather limited, producing a fragmented view of the virosphere. As a result, viruses are currently classified into 87 different families. However, studies on virion architectures have unexpectedly revealed that their structural diversity is far more limited. Here we describe structures of the major capsid proteins of double-stranded DNA viruses infecting hosts residing in different domains of life. We note that viruses belonging to 20 different families fall into only five distinct structural groups, suggesting that optimal virus classification approach should equally rely on both sequence and structural information.
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Affiliation(s)
- Mart Krupovic
- Institut Pasteur, Unité Biologie Moléculaire du Gène chez les Extrêmophiles, Department of Microbiology, Paris, France.
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Visweswaran GRR, Dijkstra BW, Kok J. A minimum of three motifs is essential for optimal binding of pseudomurein cell wall-binding domain of Methanothermobacter thermautotrophicus. PLoS One 2011; 6:e21582. [PMID: 21738718 PMCID: PMC3124540 DOI: 10.1371/journal.pone.0021582] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2011] [Accepted: 06/03/2011] [Indexed: 11/18/2022] Open
Abstract
We have biochemically and functionally characterized the pseudomurein cell wall-binding (PMB) domain that is present at the C-terminus of the Surface (S)-layer protein MTH719 from Methanothermobacter thermautotrophicus. Chemical denaturation of the protein with guanidinium hydrochloride occurred at 3.8 M. A PMB-GFP fusion protein not only binds to intact pseudomurein of methanogenic archaea, but also to spheroplasts of lysozyme-treated bacterial cells. This binding is pH dependent. At least two of the three motifs that are present in the domain are necessary for binding. Limited proteolysis revealed a possible cleavage site in the spacing sequence between motifs 1 and 2 of the PMB domain, indicating that the motif region itself is protected from proteases.
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Affiliation(s)
- Ganesh Ram R. Visweswaran
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
- Laboratory of Biophysical Chemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Bauke W. Dijkstra
- Laboratory of Biophysical Chemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Jan Kok
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
- * E-mail:
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A thaumarchaeal provirus testifies for an ancient association of tailed viruses with archaea. Biochem Soc Trans 2011; 39:82-8. [PMID: 21265751 DOI: 10.1042/bst0390082] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Archaeal viruses, or archaeoviruses, display a wide range of virion morphotypes. Whereas the majority of those morphotypes are unique to archaeal viruses, some are more widely distributed across different cellular domains. Tailed double-stranded DNA archaeoviruses are remarkably similar to viruses of the same morphology (order Caudovirales) that infect many bacterial hosts. They have, so far, only been found in one phylum of the archaea, the Euryarchaeota, which has led to controversial hypotheses about their origin. In the present paper, we describe the identification and analysis of a putative provirus present in the genome of a mesophilic thaumarchaeon. We show that the provirus is related to tailed bacterial and euryarchaeal viruses and encodes a full complement of proteins that are required to build a tailed virion. The recently discovered wide distribution of tailed viruses in Euryarchaeota and the identification of a related provirus in Thaumarchaeota, an archaeal phylum which might have branched off before the separation of Crenarchaeota and Euryarchaeota, suggest that an association of these viruses with Archaea might be more ancient than previously anticipated.
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Gonnet M, Erauso G, Prieur D, Le Romancer M. pAMT11, a novel plasmid isolated from a Thermococcus sp. strain closely related to the virus-like integrated element TKV1 of the Thermococcus kodakaraensis genome. Res Microbiol 2010; 162:132-43. [PMID: 21144896 DOI: 10.1016/j.resmic.2010.11.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2010] [Accepted: 10/05/2010] [Indexed: 10/18/2022]
Abstract
A novel extrachromosomal element that we called pAMT11 was discovered in a deep-sea vent isolate belonging to the hyperthermophilic euryarchaeal order Thermococcales. It consists of a double-stranded DNA of 20,534bp which encodes 30 putative open reading frames (ORFs) of which six could be assigned to a putative function on the basis of sequence similarity to known genes or to protein domain families. Most of the ORFs of pAMT1 showed homology and synteny with a genomic island of Thermococcus kodakaraensis KOD1. This region, named TKV1, was previously described as a "virus-like integrated element" and assumed to integrate into the host chromosome by a site-specific recombination mechanism similar to that of Sulfolobus solfataricus virus 1. While most of the genes shared by pAMT11 and TKV1 encode putative membrane proteins presumably involved in virus particle formation, attempts to induce production of virus particles by mitomycin treatment of AMT11 cultures failed, suggesting that pAMT11 may represent the genome of a defective virus or a plasmid. Genomes of mobile elements usually contain two regions: a core of conserved genes mainly involved in replication, maintenance or spreading of the genetic element, and a variable set of accessory genes. Surprisingly, genes presumably implied in the replication process are quite divergent between TKV1 and pAMT11. Indeed, TKV1 possesses a MCM-like protein that may function as a replication initiator, while pAMT11 encodes a putative non-conventional protein distantly related to the Rep protein previously described in a small plasmid of Pyrococcus sp. strain JT1, assumed to replicate by a rolling-circle (RC) mechanism. However, in the case of pAMT11, this mode of plasmid replication could not be experimentally proven and is questionable given the lack of significant similarities with any other members of the RC-Rep superfamily and its unusual large size compared to other RC plasmids.
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Affiliation(s)
- Mathieu Gonnet
- Unité d'Epidémiologie Animale, UR356, INRA centre de Clermont-Ferrand Theix, Route de Theix, 63122 Saint Genès Champanelle, France.
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