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Treangen TJ, Abraham AL, Touchon M, Rocha EPC. Genesis, effects and fates of repeats in prokaryotic genomes. FEMS Microbiol Rev 2009; 33:539-71. [PMID: 19396957 DOI: 10.1111/j.1574-6976.2009.00169.x] [Citation(s) in RCA: 110] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
DNA repeats are causes and consequences of genome plasticity. Repeats are created by intrachromosomal recombination or horizontal transfer. They are targeted by recombination processes leading to amplifications, deletions and rearrangements of genetic material. The identification and analysis of repeats in nearly 700 genomes of bacteria and archaea is facilitated by the existence of sequence data and adequate bioinformatic tools. These have revealed the immense diversity of repeats in genomes, from those created by selfish elements to the ones used for protection against selfish elements, from those arising from transient gene amplifications to the ones leading to stable duplications. Experimental works have shown that some repeats do not carry any adaptive value, while others allow functional diversification and increased expression. All repeats carry some potential to disorganize and destabilize genomes. Because recombination and selection for repeats vary between genomes, the number and types of repeats are also quite diverse and in line with ecological variables, such as host-dependent associations or population sizes, and with genetic variables, such as the recombination machinery. From an evolutionary point of view, repeats represent both opportunities and problems. We describe how repeats are created and how they can be found in genomes. We then focus on the functional and genomic consequences of repeats that dictate their fate.
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152
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Siguier P, Gagnevin L, Chandler M. The new IS1595 family, its relation to IS1 and the frontier between insertion sequences and transposons. Res Microbiol 2009; 160:232-41. [DOI: 10.1016/j.resmic.2009.02.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2008] [Revised: 02/06/2009] [Accepted: 02/09/2009] [Indexed: 11/30/2022]
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153
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154
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Rocha EPC. Evolutionary patterns in prokaryotic genomes. Curr Opin Microbiol 2008; 11:454-60. [DOI: 10.1016/j.mib.2008.09.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2008] [Revised: 09/08/2008] [Accepted: 09/09/2008] [Indexed: 10/21/2022]
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155
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Abstract
Horizontal gene transfer (HGT) is the stable transfer of genetic material from one organism to another without reproduction or human intervention. Transfer occurs by the passage of donor genetic material across cellular boundaries, followed by heritable incorporation to the genome of the recipient organism. In addition to conjugation, transformation and transduction, other diverse mechanisms of DNA and RNA uptake occur in nature. The genome of almost every organism reveals the footprint of many ancient HGT events. Most commonly, HGT involves the transmission of genes on viruses or mobile genetic elements. HGT first became an issue of public concern in the 1970s through the natural spread of antibiotic resistance genes amongst pathogenic bacteria, and more recently with commercial production of genetically modified (GM) crops. However, the frequency of HGT from plants to other eukaryotes or prokaryotes is extremely low. The frequency of HGT to viruses is potentially greater, but is restricted by stringent selection pressures. In most cases the occurrence of HGT from GM crops to other organisms is expected to be lower than background rates. Therefore, HGT from GM plants poses negligible risks to human health or the environment.
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Affiliation(s)
- Paul Keese
- Office of the Gene Technology Regulator, GPO Box 9848 Canberra, ACT 2601 [corrected] Australia.
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156
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Wagner A, de la Chaux N. Distant horizontal gene transfer is rare for multiple families of prokaryotic insertion sequences. Mol Genet Genomics 2008; 280:397-408. [PMID: 18751731 DOI: 10.1007/s00438-008-0373-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2008] [Accepted: 08/11/2008] [Indexed: 10/21/2022]
Abstract
Horizontal gene transfer in prokaryotes is rampant on short and intermediate evolutionary time scales. It poses a fundamental problem to our ability to reconstruct the evolutionary tree of life. Is it also frequent over long evolutionary distances? To address this question, we analyzed the evolution of 2,091 insertion sequences from all 20 major families in 438 completely sequenced prokaryotic genomes. Specifically, we mapped insertion sequence occurrence on a 16S rDNA tree of the genomes we analyzed, and we also constructed phylogenetic trees of the insertion sequence transposase coding sequences. We found only 30 cases of likely horizontal transfer among distantly related prokaryotic clades. Most of these horizontal transfer events are ancient. Only seven events are recent. Almost all of these transfer events occur between pairs of human pathogens or commensals. If true also for other, non-mobile DNA, the rarity of distant horizontal transfer increases the odds of reliable phylogenetic inference from sequence data.
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Affiliation(s)
- Andreas Wagner
- Department of Biochemistry, University of Zurich, Bldg. Y27, Winterthurerstrasse 190, 8057, Zurich, Switzerland.
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157
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Kube M, Schneider B, Kuhl H, Dandekar T, Heitmann K, Migdoll AM, Reinhardt R, Seemüller E. The linear chromosome of the plant-pathogenic mycoplasma 'Candidatus Phytoplasma mali'. BMC Genomics 2008; 9:306. [PMID: 18582369 PMCID: PMC2459194 DOI: 10.1186/1471-2164-9-306] [Citation(s) in RCA: 132] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2008] [Accepted: 06/26/2008] [Indexed: 11/28/2022] Open
Abstract
Background Phytoplasmas are insect-transmitted, uncultivable bacterial plant pathogens that cause diseases in hundreds of economically important plants. They represent a monophyletic group within the class Mollicutes (trivial name mycoplasmas) and are characterized by a small genome with a low GC content, and the lack of a firm cell wall. All mycoplasmas, including strains of 'Candidatus (Ca.) Phytoplasma asteris' and 'Ca. P. australiense', examined so far have circular chromosomes, as is the case for almost all walled bacteria. Results Our work has shown that 'Ca. Phytoplasma mali', the causative agent of apple proliferation disease, has a linear chromosome. Linear chromosomes were also identified in the closely related provisional species 'Ca. P. pyri' and 'Ca. P. prunorum'. The chromosome of 'Ca. P. mali' strain AT is 601,943 bp in size and has a GC content of 21.4%. The chromosome is further characterized by large terminal inverted repeats and covalently closed hairpin ends. Analysis of the protein-coding genes revealed that glycolysis, the major energy-yielding pathway supposed for 'Ca. P. asteris', is incomplete in 'Ca. P. mali'. Due to the apparent lack of other metabolic pathways present in mycoplasmas, it is proposed that maltose and malate are utilized as carbon and energy sources. However, complete ATP-yielding pathways were not identified. 'Ca. P. mali' also differs from 'Ca. P. asteris' by a smaller genome, a lower GC content, a lower number of paralogous genes, fewer insertions of potential mobile DNA elements, and a strongly reduced number of ABC transporters for amino acids. In contrast, 'Ca. P. mali' has an extended set of genes for homologous recombination, excision repair and SOS response than 'Ca. P. asteris'. Conclusion The small linear chromosome with large terminal inverted repeats and covalently closed hairpin ends, the extremely low GC content and the limited metabolic capabilities reflect unique features of 'Ca. P. mali', not only within phytoplasmas, but all mycoplasmas. It is expected that the genome information obtained here will contribute to a better understanding of the reduced metabolism of phytoplasmas, their fastidious nutrition requirements that prevented axenic cultivation, and the mechanisms involved in pathogenicity.
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Affiliation(s)
- Michael Kube
- Max Planck Institute for Molecular Genetics, Ihnestr, 63, D-14195 Berlin, Germany.
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158
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Cordaux R, Pichon S, Ling A, Pérez P, Delaunay C, Vavre F, Bouchon D, Grève P. Intense transpositional activity of insertion sequences in an ancient obligate endosymbiont. Mol Biol Evol 2008; 25:1889-96. [PMID: 18562339 PMCID: PMC2515875 DOI: 10.1093/molbev/msn134] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The streamlined genomes of ancient obligate endosymbionts generally lack transposable elements, such as insertion sequences (IS). Yet, the genome of Wolbachia, one of the most abundant bacterial endosymbionts on Earth, is littered with IS. Such a paradox raises the question as to why there are so many ISs in the genome of this ancient endosymbiont. To address this question, we investigated IS transpositional activity in the unculturable Wolbachia by tracking the evolutionary dynamics and history of ISWpi1 elements. We show that 1) ISWpi1 is widespread in Wolbachia, being present in at least 55% of the 40 sampled strains, 2) ISWpi1 copies exhibit virtually identical nucleotide sequences both within and among Wolbachia genomes and possess an intact transposase gene, 3) individual ISWpi1 copies are differentially inserted among Wolbachia genomes, and 4) ISWpi1 occurs at variable copy numbers among Wolbachia genomes. Collectively, our results provide compelling evidence for intense ISWpi1 transpositional activity and frequent ISWpi1 horizontal transmission among strains during recent Wolbachia evolution. Thus, the genomes of ancient obligate endosymbionts can carry high loads of functional and transpositionally active transposable elements. Our results also indicate that Wolbachia genomes have experienced multiple and temporally distinct ISWpi1 invasions during their evolutionary history. Such recurrent exposition to new IS invasions may explain, at least partly, the unusually high density of transposable elements found in the genomes of Wolbachia endosymbionts.
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Affiliation(s)
- Richard Cordaux
- CNRS UMR 6556 Ecologie, Evolution, Symbiose, Université de Poitiers, Poitiers, France.
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159
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Larionov S, Loskutov A, Ryadchenko E. Chromosome evolution with naked eye: palindromic context of the life origin. CHAOS (WOODBURY, N.Y.) 2008; 18:013105. [PMID: 18377056 DOI: 10.1063/1.2826631] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Based on the representation of the DNA sequence as a two-dimensional (2D) plane walk, we consider the problem of identification and comparison of functional and structural organizations of chromosomes of different organisms. According to the characteristic design of 2D walks we identify telomere sites, palindromes of various sizes and complexity, areas of ribosomal RNA, transposons, as well as diverse satellite sequences. As an interesting result of the application of the 2D walk method, a new duplicated gigantic palindrome in the X human chromosome is detected. A schematic mechanism leading to the formation of such a duplicated palindrome is proposed. Analysis of a large number of the different genomes shows that some chromosomes (or their fragments) of various species appear as imperfect gigantic palindromes, which are disintegrated by many inversions and the mutation drift on different scales. A spread occurrence of these types of sequences in the numerous chromosomes allows us to develop a new insight of some accepted points of the genome evolution in the prebiotic phase.
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Affiliation(s)
- Sergei Larionov
- Physics Faculty, Moscow State University, Moscow 119899, Russia
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160
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Zhou F, Olman V, Xu Y. Insertion Sequences show diverse recent activities in Cyanobacteria and Archaea. BMC Genomics 2008; 9:36. [PMID: 18218090 PMCID: PMC2246112 DOI: 10.1186/1471-2164-9-36] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2007] [Accepted: 01/24/2008] [Indexed: 11/11/2022] Open
Abstract
Background Mobile genetic elements (MGEs) play an essential role in genome rearrangement and evolution, and are widely used as an important genetic tool. Results In this article, we present genetic maps of recently active Insertion Sequence (IS) elements, the simplest form of MGEs, for all sequenced cyanobacteria and archaea, predicted based on the previously identified ~1,500 IS elements. Our predicted IS maps are consistent with the NCBI annotations of the IS elements. By linking the predicted IS elements to various characteristics of the organisms under study and the organism's living conditions, we found that (a) the activities of IS elements heavily depend on the environments where the host organisms live; (b) the number of recently active IS elements in a genome tends to increase with the genome size; (c) the flanking regions of the recently active IS elements are significantly enriched with genes encoding DNA binding factors, transporters and enzymes; and (d) IS movements show no tendency to disrupt operonic structures. Conclusion This is the first genome-scale maps of IS elements with detailed structural information on the sequence level. These genetic maps of recently active IS elements and the several interesting observations would help to improve our understanding of how IS elements proliferate and how they are involved in the evolution of the host genomes.
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Affiliation(s)
- Fengfeng Zhou
- Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA.
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161
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De Palmenaer D, Siguier P, Mahillon J. IS4 family goes genomic. BMC Evol Biol 2008; 8:18. [PMID: 18215304 PMCID: PMC2266710 DOI: 10.1186/1471-2148-8-18] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2007] [Accepted: 01/23/2008] [Indexed: 01/29/2023] Open
Abstract
Background Insertion sequences (ISs) are small, mobile DNA entities able to expand in prokaryotic genomes and trigger important rearrangements. To understand their role in evolution, accurate IS taxonomy is essential. The IS4 family is composed of ~70 elements and, like some other families, displays extremely elevated levels of internal divergence impeding its classification. The increasing availability of complete genome sequences provides a valuable source for the discovery of additional IS4 elements. In this study, this genomic database was used to update the structural and functional definition of the IS4 family. Results A total of 227 IS4-related sequences were collected among more than 500 sequenced bacterial and archaeal genomes, representing more than a three fold increase of the initial inventory. A clear division into seven coherent subgroups was discovered as well as three emerging families, which displayed distinct structural and functional properties. The IS4 family was sporadically present in 17 % of analyzed genomes, with most of them displaying single or a small number of IS4 elements. Significant expansions were detected only in some pathogens as well as among certain extremophiles, suggesting the probable involvement of some elements in bacterial and archaeal adaptation and/or evolution. Finally, it should be noted that some IS4 subgroups and two emerging families occurred preferentially in specific phyla or exclusively inside a specific genus. Conclusion The present taxonomic update of IS4 and emerging families will facilitate the classification of future elements as they arise from ongoing genome sequencing. Their narrow genomic impact and the existence of both IS-poor and IS-rich thriving prokaryotes suggested that these families, and probably ISs in general, are occasionally used as a tool for genome flexibility and evolution, rather than just representing self sustaining DNA entities.
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Affiliation(s)
- Daniel De Palmenaer
- Laboratoire de microbiologie alimentaire et environnementale, Université catholique de Louvain, Croix du Sud 2/12, B-1348 Louvain-la-Neuve, Belgium.
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162
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Cordaux R. ISWpi1 from Wolbachia pipientis defines a novel group of insertion sequences within the IS5 family. Gene 2007; 409:20-7. [PMID: 18155858 DOI: 10.1016/j.gene.2007.10.035] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2007] [Revised: 10/30/2007] [Accepted: 10/30/2007] [Indexed: 11/18/2022]
Abstract
Insertion sequences are transposable elements that can represent substantial proportions of prokaryotic genomes and play a substantial role in shaping host genome evolution. As such, evaluating and understanding insertion sequence diversity is an important task to fulfill, because it is expected to yield new insight into the evolution of bacterial transposable elements and contribute to improve genome annotations. Here, I characterized an insertion sequence, termed ISWpi1, for which the taxonomic distribution appears to be restricted to the obligate intracellular alpha-Proteobacterium Wolbachia pipientis. ISWpi1 exhibits approximately 46% identity at the amino acid level with members of the IS1031 group of insertion sequences from the IS5 family. However, the IS1031 group is characterized by a transposase gene encoded by a single open reading frame, whereas the ISWpi1 transposase gene consists of two overlapping open reading frames presumably translated as a single protein via programmed translational frameshifting. Such structure suggests that ISWpi1 may instead be related to the IS427 group of insertion sequences from the IS5 family. Altogether, these data indicate that ISWpi1 extends the known spectrum of diversity of the IS5 family, and I propose to define a novel group of insertion sequences within the IS5 family typified by ISWpi1. Probable transpositional activity, relevant insertion site preferences and taxonomic specificity make ISWpi1 a promising tool for experimentally manipulating W. pipientis bacteria, especially in light of the increasing interest in developing these bacteria as tools for controlling insect disease vectors and agricultural pests.
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Affiliation(s)
- Richard Cordaux
- Laboratoire de Génétique et Biologie des Populations de Crustacés, CNRS UMR 6556, Université de Poitiers, 40 Avenue du Recteur Pineau, 86022 Poitiers, France.
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163
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Sirand-Pugnet P, Citti C, Barré A, Blanchard A. Evolution of mollicutes: down a bumpy road with twists and turns. Res Microbiol 2007; 158:754-66. [PMID: 18023150 DOI: 10.1016/j.resmic.2007.09.007] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2007] [Revised: 09/03/2007] [Accepted: 09/17/2007] [Indexed: 11/29/2022]
Abstract
Mollicute evolution has been marked by significant changes in genome structure and use of their genetic information. These include a reduction in their genome G+C content and the use by most mollicutes of the UGA universal stop codon as tryptophan. More striking is the size reduction in their genome which, for some species, is now close to the minimal requirement for sustaining cell life. With the growing body of sequence data, a new picture has recently begun to emerge in which the evolution of these simple bacteria cannot be reduced to a race for the smallest genome.
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Affiliation(s)
- Pascal Sirand-Pugnet
- INRA Université Victor Segalen Bordeaux 2, UMR 1090 Génomique Diversité Pouvoir Pathogène, BP 81, 71 avenue Edouard Bourlaux, 33883 Villenave d'Ornon cedex, France
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164
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Abstract
Bacterial insertion sequences (ISs) are the simplest kinds of bacterial mobile DNA. Evolutionary studies need consistent IS annotation across many different genomes. We have developed an open-source software package, IScan, to identify bacterial ISs and their sequence elements—inverted and target direct repeats—in multiple genomes using multiple flexible search parameters. We applied IScan to 438 completely sequenced bacterial genomes and 20 IS families. The resulting data show that ISs within a genome are extremely similar, with a mean synonymous divergence of Ks = 0.033. Our analysis substantially extends previously available information, and suggests that most ISs have entered bacterial genomes recently. By implication, their population persistence may depend on horizontal transfer. We also used IScan's ability to analyze the statistical significance of sequence similarity among many IS inverted repeats. Although the inverted repeats of insertion sequences are evolutionarily highly flexible parts of ISs, we show that this ability can be used to enrich a dataset for ISs that are likely to be functional. Applied to the thousands of genomes that will soon be available, IScan could be used for many purposes, such as mapping the evolutionary history and horizontal transfer patterns of different ISs.
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Affiliation(s)
- Andreas Wagner
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 27-J-54, CH-8057 Zurich, Switzerland.
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