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Reva ON, La Cono V, Crisafi F, Smedile F, Mudaliyar M, Ghosal D, Giuliano L, Krupovic M, Yakimov MM. Interplay of intracellular and trans-cellular DNA methylation in natural archaeal consortia. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13258. [PMID: 38589217 PMCID: PMC11001535 DOI: 10.1111/1758-2229.13258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 03/15/2024] [Indexed: 04/10/2024]
Abstract
DNA methylation serves a variety of functions across all life domains. In this study, we investigated archaeal methylomics within a tripartite xylanolytic halophilic consortium. This consortium includes Haloferax lucertense SVX82, Halorhabdus sp. SVX81, and an ectosymbiotic Candidatus Nanohalococcus occultus SVXNc, a nano-sized archaeon from the DPANN superphylum. We utilized PacBio SMRT and Illumina cDNA sequencing to analyse samples from consortia of different compositions for methylomics and transcriptomics. Endogenous cTAG methylation, typical of Haloferax, was accompanied in this strain by methylation at four other motifs, including GDGcHC methylation, which is specific to the ectosymbiont. Our analysis of the distribution of methylated and unmethylated motifs suggests that autochthonous cTAG methylation may influence gene regulation. The frequency of GRAGAaG methylation increased in highly expressed genes, while CcTTG and GTCGaGG methylation could be linked to restriction-modification (RM) activity. Generally, the RM activity might have been reduced during the evolution of this archaeon to balance the protection of cells from intruders, the reduction of DNA damage due to self-restriction in stressful environments, and the benefits of DNA exchange under extreme conditions. Our methylomics, transcriptomics and complementary electron cryotomography (cryo-ET) data suggest that the nanohaloarchaeon exports its methyltransferase to methylate the Haloferax genome, unveiling a new aspect of the interaction between the symbiont and its host.
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Affiliation(s)
- Oleg N. Reva
- Department of Biochemistry, Genetics and Microbiology, Centre for Bioinformatics and Computational BiologyUniversity of PretoriaPretoriaSouth Africa
| | - Violetta La Cono
- Extreme Microbiology, Biotechnology and Astrobiology GroupInstitute of Polar Sciences, ISP‐CNRMessinaItaly
| | - Francesca Crisafi
- Extreme Microbiology, Biotechnology and Astrobiology GroupInstitute of Polar Sciences, ISP‐CNRMessinaItaly
| | - Francesco Smedile
- Extreme Microbiology, Biotechnology and Astrobiology GroupInstitute of Polar Sciences, ISP‐CNRMessinaItaly
| | - Manasi Mudaliyar
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology InstituteThe University of MelbourneMelbourneVictoriaAustralia
- ARC Centre for Cryo‐electron Microscopy of Membrane Proteins, Bio21 Molecular Science and Biotechnology InstituteUniversity of MelbourneParkvilleVictoriaAustralia
| | - Debnath Ghosal
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology InstituteThe University of MelbourneMelbourneVictoriaAustralia
- ARC Centre for Cryo‐electron Microscopy of Membrane Proteins, Bio21 Molecular Science and Biotechnology InstituteUniversity of MelbourneParkvilleVictoriaAustralia
| | | | - Mart Krupovic
- Istitut Pasteur, Archaeal Virology UnitUniversité Paris CitéParisFrance
| | - Michail M. Yakimov
- Extreme Microbiology, Biotechnology and Astrobiology GroupInstitute of Polar Sciences, ISP‐CNRMessinaItaly
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van Overbeek LS, van Doorn J, Wichers JH, van Amerongen A, van Roermund HJW, Willemsen PTJ. The arable ecosystem as battleground for emergence of new human pathogens. Front Microbiol 2014; 5:104. [PMID: 24688484 PMCID: PMC3960585 DOI: 10.3389/fmicb.2014.00104] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Accepted: 02/27/2014] [Indexed: 01/10/2023] Open
Abstract
Disease incidences related to Escherichia coli and Salmonella enterica infections by consumption of (fresh) vegetables, sprouts, and occasionally fruits made clear that these pathogens are not only transmitted to humans via the "classical" routes of meat, eggs, and dairy products, but also can be transmitted to humans via plants or products derived from plants. Nowadays, it is of major concern that these human pathogens, especially the ones belonging to the taxonomical family of Enterobacteriaceae, become adapted to environmental habitats without losing their virulence to humans. Adaptation to the plant environment would lead to longer persistence in plants, increasing their chances on transmission to humans via consumption of plant-derived food. One of the mechanisms of adaptation to the plant environment in human pathogens, proposed in this paper, is horizontal transfer of genes from different microbial communities present in the arable ecosystem, like the ones originating from soil, animal digestive track systems (manure), water and plants themselves. Genes that would confer better adaptation to the phytosphere might be genes involved in plant colonization, stress resistance and nutrient acquisition and utilization. Because human pathogenic enterics often were prone to genetic exchanges via phages and conjugative plasmids, it was postulated that these genetic elements may be hold key responsible for horizontal gene transfers between human pathogens and indigenous microbes in agroproduction systems. In analogy to zoonosis, we coin the term phytonosis for a human pathogen that is transmitted via plants and not exclusively via animals.
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Affiliation(s)
- Leonard S van Overbeek
- Plant Research International, Wageningen University and Research Centre Wageningen, Netherlands
| | - Joop van Doorn
- Applied Plant Research, Wageningen University and Research Centre Lisse, Netherlands
| | - Jan H Wichers
- Food and Biobased Research, Wageningen University and Research Centre Wageningen, Netherlands
| | - Aart van Amerongen
- Food and Biobased Research, Wageningen University and Research Centre Wageningen, Netherlands
| | - Herman J W van Roermund
- Central Veterinary Institute, Wageningen University and Research Centre Lelystad, Netherlands
| | - Peter T J Willemsen
- Central Veterinary Institute, Wageningen University and Research Centre Lelystad, Netherlands
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Xiong D, Xiao F, Liu L, Hu K, Tan Y, He S, Gao X. Towards a better detection of horizontally transferred genes by combining unusual properties effectively. PLoS One 2012; 7:e43126. [PMID: 22905214 PMCID: PMC3419211 DOI: 10.1371/journal.pone.0043126] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2012] [Accepted: 07/16/2012] [Indexed: 02/01/2023] Open
Abstract
Background Horizontal gene transfer (HGT) is one of the major mechanisms contributing to microbial genome diversification. A number of computational methods for finding horizontally transferred genes have been proposed in the past decades; however none of them has provided a reliable detector yet. In existing parametric approaches, only one single compositional property can participate in the detection process, or the results obtained through each single property are just simply combined. It’s known that different properties may mean different information, so the single property can’t sufficiently contain the information encoded by gene sequences. In addition, the class imbalance problem in the datasets, which also results in great errors for the gene detection, hasn’t been considered by the published methods. Here we developed an effective classifier system (Hgtident) that used support vector machine (SVM) by combining unusual properties effectively for HGT detection. Results Our approach Hgtident includes the introduction of more representative datasets, optimization of SVM model, feature selection, handling of imbalance problem in the datasets and extensive performance evaluation via systematic cross-validation methods. Through feature selection, we found that JS-DN and JS-CB have higher discriminating power for HGT detection, while GC1–GC3 and k-mer (k = 1, 2, …, 7) make the least contribution. Extensive experiments indicated the new classifier could reduce Mean error dramatically, and also improve Recall by a certain level. For the testing genomes, compared with the existing popular multiple-threshold approach, on average, our Recall and Mean error was respectively improved by 2.81% and reduced by 26.32%, which means that numerous false positives were identified correctly. Conclusions Hgtident introduced here is an effective approach for better detecting HGT. Combining multiple features of HGT is also essential for a wider range of HGT events detection.
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Affiliation(s)
- Dapeng Xiong
- Key Laboratory of Intelligent Computing & Information Processing of Ministry of Education, Xiangtan University, Xiangtan, Hunan, People’s Republic of China
| | - Fen Xiao
- Key Laboratory of Intelligent Computing & Information Processing of Ministry of Education, Xiangtan University, Xiangtan, Hunan, People’s Republic of China
| | - Li Liu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Kai Hu
- Key Laboratory of Intelligent Computing & Information Processing of Ministry of Education, Xiangtan University, Xiangtan, Hunan, People’s Republic of China
| | - Yanping Tan
- Key Laboratory of Intelligent Computing & Information Processing of Ministry of Education, Xiangtan University, Xiangtan, Hunan, People’s Republic of China
| | - Shunmin He
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, People’s Republic of China
- * E-mail: (SH); (XG)
| | - Xieping Gao
- Key Laboratory of Intelligent Computing & Information Processing of Ministry of Education, Xiangtan University, Xiangtan, Hunan, People’s Republic of China
- * E-mail: (SH); (XG)
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Bokhari H, Anwar M, Mirza HB, Gillevet PM. Evidences of lateral gene transfer between archaea and pathogenic bacteria. Bioinformation 2011; 6:293-6. [PMID: 21769188 PMCID: PMC3134775 DOI: 10.6026/97320630006293] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2011] [Accepted: 06/27/2011] [Indexed: 11/23/2022] Open
Abstract
Acquisition of new genetic material through horizontal gene transfer has been shown to be an important feature in the evolution of many pathogenic bacteria. Changes in the genetic repertoire, occurring through gene acquisition and deletion, are the major events underlying the emergence and evolution of bacterial pathogens. However, horizontal gene transfer across the domains i.e. archaea and bacteria is not so common. In this context, we explore events of horizontal gene transfer between archaea and bacteria. In order to determine whether the acquisition of archaeal genes by lateral gene transfer is an important feature in the evolutionary history of the pathogenic bacteria, we have developed a scheme of stepwise eliminations that identifies archaeal-like genes in various bacterial genomes. We report the presence of 9 genes of archaeal origin in the genomes of various bacteria, a subset of which is also unique to the pathogenic members and are not found in respective non-pathogenic counterparts. We believe that these genes, having been retained in the respective genomes through selective advantage, have key functions in the organism's biology and may play a role in pathogenesis.
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Affiliation(s)
- Habib Bokhari
- Department of Biosciences, COMSATS Institute of Information Technology, Chakshahzad Campus, Park road Islamabad, Pakistan
| | - Maryam Anwar
- Department of Biosciences, COMSATS Institute of Information Technology, Chakshahzad Campus, Park road Islamabad, Pakistan
| | - Hasan Bilal Mirza
- Centre for Advanced Studies in Telecommunication (CAST), COMSATS Institute of Information Technology, Chakshahzad Campus, Park road Islamabad, Pakistan
| | - Patrick Martin Gillevet
- Department of Environmental Sciences and Policy, George Mason University, Manassas, Virginia, USA
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Abstract
Although Archaea inhabit the human body and possess some characteristics of pathogens, there is a notable lack of pathogenic archaeal species identified to date. We hypothesize that the scarcity of disease-causing Archaea is due, in part, to mutually-exclusive phage and virus populations infecting Bacteria and Archaea, coupled with an association of bacterial virulence factors with phages or mobile elements. The ability of bacterial phages to infect Bacteria and then use them as a vehicle to infect eukaryotes may be difficult for archaeal viruses to evolve independently. Differences in extracellular structures between Bacteria and Archaea would make adsorption of bacterial phage particles onto Archaea (i.e. horizontal transfer of virulence) exceedingly hard. If phage and virus populations are indeed exclusive to their respective host Domains, this has important implications for both the evolution of pathogens and approaches to infectious disease control.
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Affiliation(s)
- Erin E Gill
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
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6
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Abstract
The carotenoids constitute the most widespread class of pigments in nature. Most previous work has concentrated on the identification and characterization of their chemical physical properties and bioavailability. In recent years, significant amounts of research have been conducted in an attempt to analyze the genes and the molecular regulation of the genes involved in the biosynthesis of carotenoids. However, it is important not to lose sight of the early evolution of carotenoid biosynthesis. One of the major obstacles in understanding the evolution of the respective enzymes and their patterns of selection is a lack of a well-supported phylogenic analysis. In the present research, a major long-term objective was to provide a clearer picture of the evolutionary history of genes, together with an evaluation of the patterns of selection in algae. These phylogenies will be important in studies characterizing the evolution of algae. The gene sequences of the enzymes involved in the major steps of the carotenoid biosynthetic pathway in algae (cyanobacteria, rhofophyta, chlorophyta) have been analyzed. Phylogenetic relationships among protein-coding DNA sequences were reconstructed by neighbor-joining (NJ) analysis for the respective carotenoid biosynthetic pathway genes (crt) in algae. The analysis also contains an estimation of the rate of nonsynonymous nucleotide substitutions per nonsynonymous site (d(N)), synonymous nucleotide substitution per synonymous site (d(S)), and the ratio of nonsynonmous (d(N)/d(S)) for the test of selection patterns. The phylogenetic trees show that the taxa of some genera have a closer evolutionary relationship with other genera in some gene sequences, which suggests a common ancient origin and that lateral gene transfer has occurred among unrelated genera. The d(N) values of crt genes in the early pathway are relatively low, while those of the following steps are slightly higher, while the d(N) values of crt genes in chlorophyta are higher than those in cyanobacteria. Most of the d(N)/d(S) values exceed 1. The phylogenetic analysis revealed that lateral gene transfer may have taken place across algal genomes and the d(N) values suggest that most of the early crt genes are well conserved compared to the later crt genes. Furthermore, d(N) values also revealed that the crt genes of chlorophyta are more evolutionary than cyanobacteria. The amino acids' changes are mostly adaptive evolution under the influence of positive diversity selection.
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Affiliation(s)
- Qian Chen
- College of Food and Bioengineering, South China University of Technology, Guangzhou, People's Republic of China
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Podell S, Gaasterland T. DarkHorse: a method for genome-wide prediction of horizontal gene transfer. Genome Biol 2007; 8:R16. [PMID: 17274820 PMCID: PMC1852411 DOI: 10.1186/gb-2007-8-2-r16] [Citation(s) in RCA: 123] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2006] [Revised: 11/09/2006] [Accepted: 02/02/2007] [Indexed: 12/14/2022] Open
Abstract
DarkHorse is a new approach to rapid, genome-wide identification and ranking of horizontal transfer candidate proteins. A new approach to rapid, genome-wide identification and ranking of horizontal transfer candidate proteins is presented. The method is quantitative, reproducible, and computationally undemanding. It can be combined with genomic signature and/or phylogenetic tree-building procedures to improve accuracy and efficiency. The method is also useful for retrospective assessments of horizontal transfer prediction reliability, recognizing orthologous sequences that may have been previously overlooked or unavailable. These features are demonstrated in bacterial, archaeal, and eukaryotic examples.
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Affiliation(s)
- Sheila Podell
- Scripps Genome Center, Scripps Institution of Oceanography, University of California at San Diego, Gilman Drive, La Jolla, CA 92093-0202, USA
| | - Terry Gaasterland
- Scripps Genome Center, Scripps Institution of Oceanography, University of California at San Diego, Gilman Drive, La Jolla, CA 92093-0202, USA
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8
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McGowan E. Comment on "antibiotic resistance genes as emerging contaminants: studies in northern Colorado". ENVIRONMENTAL SCIENCE & TECHNOLOGY 2007; 41:2651-2. [PMID: 17438829 DOI: 10.1021/es0680156] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
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9
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Shepard JRE, Danin-Poleg Y, Kashi Y, Walt DR. Array-based binary analysis for bacterial typing. Anal Chem 2007; 77:319-26. [PMID: 15623311 DOI: 10.1021/ac0488006] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An allele-specific oligonucleotide microarray was developed for rapid typing of pathogens based on analysis of genomic variations. Using a panel of Escherichia coli strains as a model system, selected loci were sequenced to uncover differences, such as single- or multiple-nucleotide polymorphisms as well as insertion/deletions (indels). While typical genomic profiling experiments employ specific sequences targeted to genomic DNA unique to a single strain or virulent gene, the present array is designed to type bacteria based on a patterned signature response across multiple loci. In the signature concept, all strains are interrogated by hybridizing their amplified DNA to an array containing multiple probe sequences. Allele-specific oligonucleotide probe sequences targeting each of these variable regions were synthesized and included in a custom fiber-optic array. For each locus, a set of specific probe sequences is selected, such that hybridization gives a binary signal/no signal response to each of the probes. Using this strategy for multiple loci, many pathogens or microorganisms could be classified using a limited number of probes. Because of the advantages of the fiber-optic array platform over other array formats, including sensitivity and speed, the platform described in this paper is capable of supporting a high-throughput diagnostic strategy.
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Affiliation(s)
- Jason R E Shepard
- Department of Chemistry, Tufts University, 62 Talbot Avenue, Medford, MA 02155, USA
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Wiezer A, Merkl R. A comparative categorization of gene flux in diverse microbial species. Genomics 2006; 86:462-75. [PMID: 16026964 DOI: 10.1016/j.ygeno.2005.05.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2004] [Revised: 05/25/2005] [Accepted: 05/25/2005] [Indexed: 12/18/2022]
Abstract
Microbial genomes harbor genomic islands (GIs), genes presumably acquired via horizontal gene transfer (HGT). We compared GIs of hyperthermophilic, thermophilic, mesophilic, and pathogenic/nonpathogenic species and of small and large genomes. The COG database was used to characterize gene-encoded functions. Putative donors were determined to quantify gene flux between superkingdoms. In hyperthermophiles, more than 10% of the genes were on average acquired across the superkingdom border. For thermophiles and particularly mesophiles, we identified a nearly unidirectional export from bacteria to archaea. Additionally, we analyzed GI composition for Escherichia, and pairs of Listeria, Rhizobiales, Methanosarcinaceae, and Thermus thermophilus/Deinococcus radiodurans. For Escherichia and Listeria, the composition of GIs in pathogenic and nonpathogenic species did not differ significantly with respect to encoded COG classes. The analysis of related genomes showed that the composition of GIs cannot be explained with trends of gene content known to depend on genome size.
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Affiliation(s)
- Arnim Wiezer
- Göttingen Genomics Laboratory, Grisebachstrasse 8, D-37077 Göttingen, Germany
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Saunders NFW, Goodchild A, Raftery M, Guilhaus M, Curmi PMG, Cavicchioli R. Predicted roles for hypothetical proteins in the low-temperature expressed proteome of the Antarctic archaeon Methanococcoides burtonii. J Proteome Res 2005; 4:464-72. [PMID: 15822923 DOI: 10.1021/pr049797+] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Using liquid chromatography-mass spectrometry, 528 proteins were identified that are expressed during growth at 4 degrees C in the cold adapted archaeon, Methanococcoides burtonii. Of those, 135 were annotated previously as unique or conserved hypothetical proteins. We have performed a comprehensive, integrated analysis of the latter proteins using threading, InterProScan, predicted subcellular localization and visualization of conserved gene context across multiple prokaryotic genomes. Functional information was obtained for 55 proteins, providing new insight into the physiology of M. burtonii. Many of the proteins were predicted to be involved in DNA/RNA binding or modification and cell signaling, suggesting a complex, uncharacterized regulatory network controlling cellular processes during growth at low-temperature. Novel enzymatic functions were predicted for several proteins, including a putative candidate gene for the posttranslational modification of the key methanogenesis enzyme coenzyme M methyl reductase. A bacterial-like CRISPR locus was identified as a strong candidate for archaeal-bacterial lateral gene transfer. Gene context analysis proved a valuable augmentation to the other predictive methods in several cases, by revealing conserved gene associations and annotations in other microbial genomes. Our results underscore the importance of addressing the "hypothetical protein problem" for a complete understanding of cell physiology.
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Affiliation(s)
- Neil F W Saunders
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, 2052, NSW, Australia
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12
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Gophna U, Charlebois RL, Doolittle WF. Have archaeal genes contributed to bacterial virulence? Trends Microbiol 2004; 12:213-9. [PMID: 15120140 DOI: 10.1016/j.tim.2004.03.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Uri Gophna
- Genome Atlantic and Department of Biochemistry and Molecular Biology, Dalhousie University, 5850 College Street, Halifax, Nova Scotia B3H 1X5, Canada.
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