1
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Minnick MF. Functional Roles and Genomic Impact of Miniature Inverted-Repeat Transposable Elements (MITEs) in Prokaryotes. Genes (Basel) 2024; 15:328. [PMID: 38540387 PMCID: PMC10969869 DOI: 10.3390/genes15030328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 02/27/2024] [Accepted: 03/01/2024] [Indexed: 06/14/2024] Open
Abstract
Prokaryotic genomes are dynamic tapestries that are strongly influenced by mobile genetic elements (MGEs), including transposons (Tn's), plasmids, and bacteriophages. Of these, miniature inverted-repeat transposable elements (MITEs) are undoubtedly the least studied MGEs in bacteria and archaea. This review explores the diversity and distribution of MITEs in prokaryotes and describes what is known about their functional roles in the host and involvement in genomic plasticity and evolution.
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Affiliation(s)
- Michael F Minnick
- Program in Cellular, Molecular and Microbial Biology, Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
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2
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Fackler JR, Dworjan M, Gazi KS, Grogan DW. Diversity of SIRV-like Viruses from a North American Population. Viruses 2022; 14:v14071439. [PMID: 35891419 PMCID: PMC9319562 DOI: 10.3390/v14071439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 06/21/2022] [Accepted: 06/23/2022] [Indexed: 02/04/2023] Open
Abstract
A small subset of acidic hot springs sampled in Yellowstone National Park yielded rod-shaped viruses which lysed liquid host cultures and formed clear plaques on lawns of host cells. Three isolates chosen for detailed analysis were found to be genetically related to previously described isolates of the Sulfolobus islandicus rod-shaped virus (SIRV), but distinct from them and from each other. Functional stability of the new isolates was assessed in a series of inactivation experiments. UV-C radiation inactivated one of the isolates somewhat faster than bacteriophage λ, suggesting that encapsidation in the SIRV-like virion did not confer unusual protection of the DNA from UV damage. With respect to high temperature, the new isolates were extremely, but not equally, stable. Several chemical treatments were found to inactivate the virions and, in some cases, to reveal apparent differences in virion stability among the isolates. Screening a larger set of isolates identified greater variation of these stability properties but found few correlations among the resulting profiles. The majority of host cells infected by the new isolates were killed, but survivors exhibited heritable resistance, which could not be attributed to CRISPR spacer acquisition or the loss of the pilus-related genes identified by earlier studies. Virus-resistant host variants arose at high frequency and most were resistant to multiple viral strains; conversely, resistant host clones generated virus-sensitive variants, also at high frequency. Virus-resistant cells lacked the ability of virus-sensitive cells to bind virions in liquid suspensions. Rapid interconversion of sensitive and resistant forms of a host strain suggests the operation of a yet-unidentified mechanism that acts to allow both the lytic virus and its host to propagate in highly localized natural populations, whereas variation of virion-stability phenotypes among the new viral isolates suggests that multiple molecular features contribute to the biological durability of these viruses.
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Affiliation(s)
- Joseph R. Fackler
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221-0006, USA; (J.R.F.); (M.D.); (K.S.G.)
- Adaptive Phage Therapeutics, Gaithersburg, MD 20878, USA
| | - Michael Dworjan
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221-0006, USA; (J.R.F.); (M.D.); (K.S.G.)
| | - Khaled S. Gazi
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221-0006, USA; (J.R.F.); (M.D.); (K.S.G.)
- Department of Biology, Faculty of Science and Arts in Almandaq, Al-Baha University, Almandaq 65756, Saudi Arabia
| | - Dennis W. Grogan
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221-0006, USA; (J.R.F.); (M.D.); (K.S.G.)
- Correspondence:
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3
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Medvedeva S, Brandt D, Cvirkaite-Krupovic V, Liu Y, Severinov K, Ishino S, Ishino Y, Prangishvili D, Kalinowski J, Krupovic M. New insights into the diversity and evolution of the archaeal mobilome from three complete genomes of Saccharolobus shibatae. Environ Microbiol 2021; 23:4612-4630. [PMID: 34190379 DOI: 10.1111/1462-2920.15654] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 06/20/2021] [Accepted: 06/28/2021] [Indexed: 12/16/2022]
Abstract
Saccharolobus (formerly Sulfolobus) shibatae B12, isolated from a hot spring in Beppu, Japan in 1982, is one of the first hyperthermophilic and acidophilic archaeal species to be discovered. It serves as a natural host to the extensively studied spindle-shaped virus SSV1, a prototype of the Fuselloviridae family. Two additional Sa. shibatae strains, BEU9 and S38A, sensitive to viruses of the families Lipothrixviridae and Portogloboviridae, respectively, have been isolated more recently. However, none of the strains has been fully sequenced, limiting their utility for studies on archaeal biology and virus-host interactions. Here, we present the complete genome sequences of all three Sa. shibatae strains and explore the rich diversity of their integrated mobile genetic elements (MGE), including transposable insertion sequences, integrative and conjugative elements, plasmids, and viruses, some of which were also detected in the extrachromosomal form. Analysis of related MGEs in other Sulfolobales species and patterns of CRISPR spacer targeting revealed a complex network of MGE distributions, involving horizontal spread and relatively frequent host switching by MGEs over large phylogenetic distances, involving species of the genera Saccharolobus, Sulfurisphaera and Acidianus. Furthermore, we characterize a remarkable case of a virus-to-plasmid transition, whereby a fusellovirus has lost the genes encoding for the capsid proteins, while retaining the replication module, effectively becoming a plasmid.
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Affiliation(s)
- Sofia Medvedeva
- Archaeal Virology Unit, Institut Pasteur, Paris, 75015, France.,Center of Life Science, Skolkovo Institute of Science and Technology, Moscow, 121205, Russia
| | - David Brandt
- Center for Biotechnology, Universität Bielefeld, Bielefeld, 33615, Germany
| | | | - Ying Liu
- Archaeal Virology Unit, Institut Pasteur, Paris, 75015, France
| | - Konstantin Severinov
- Center of Life Science, Skolkovo Institute of Science and Technology, Moscow, 121205, Russia.,Waksman Institute, Rutgers University, Piscataway, NJ, 08854, USA.,Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182, Russia
| | - Sonoko Ishino
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Yoshizumi Ishino
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - David Prangishvili
- Archaeal Virology Unit, Institut Pasteur, Paris, 75015, France.,Ivane Javakhishvili Tbilisi State University, Tbilisi, 0179, Georgia
| | - Jörn Kalinowski
- Center for Biotechnology, Universität Bielefeld, Bielefeld, 33615, Germany
| | - Mart Krupovic
- Archaeal Virology Unit, Institut Pasteur, Paris, 75015, France
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4
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Blesa A, Sánchez M, Sacristán-Horcajada E, González-de la Fuente S, Peiró R, Berenguer J. Into the Thermus Mobilome: Presence, Diversity and Recent Activities of Insertion Sequences Across Thermus spp. Microorganisms 2019; 7:microorganisms7010025. [PMID: 30669685 PMCID: PMC6352166 DOI: 10.3390/microorganisms7010025] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 01/09/2019] [Accepted: 01/17/2019] [Indexed: 11/28/2022] Open
Abstract
A high level of transposon-mediated genome rearrangement is a common trait among microorganisms isolated from thermal environments, probably contributing to the extraordinary genomic plasticity and horizontal gene transfer (HGT) observed in these habitats. In this work, active and inactive insertion sequences (ISs) spanning the sequenced members of the genus Thermus were characterized, with special emphasis on three T. thermophilus strains: HB27, HB8, and NAR1. A large number of full ISs and fragments derived from different IS families were found, concentrating within megaplasmids present in most isolates. Potentially active ISs were identified through analysis of transposase integrity, and domestication-related transposition events of ISTth7 were identified in laboratory-adapted HB27 derivatives. Many partial copies of ISs appeared throughout the genome, which may serve as specific targets for homologous recombination contributing to genome rearrangement. Moreover, recruitment of IS1000 32 bp segments as spacers for CRISPR sequence was identified, pointing to the adaptability of these elements in the biology of these thermophiles. Further knowledge about the activity and functional diversity of ISs in this genus may contribute to the generation of engineered transposons as new genetic tools, and enrich our understanding of the outstanding plasticity shown by these thermophiles.
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Affiliation(s)
- Alba Blesa
- Department of Biotechnology, Faculty of Experimental Sciences, Universidad Francisco de Vitoria, Madrid 28223, Spain.
| | - Mercedes Sánchez
- Centro de Biología Molecular Severo Ochoa (CBMSO), Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas, Madrid 28049, Spain.
| | - Eva Sacristán-Horcajada
- Centro de Biología Molecular Severo Ochoa (CBMSO), Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas, Madrid 28049, Spain.
| | - Sandra González-de la Fuente
- Centro de Biología Molecular Severo Ochoa (CBMSO), Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas, Madrid 28049, Spain.
| | - Ramón Peiró
- Centro de Biología Molecular Severo Ochoa (CBMSO), Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas, Madrid 28049, Spain.
| | - José Berenguer
- Centro de Biología Molecular Severo Ochoa (CBMSO), Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas, Madrid 28049, Spain.
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5
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Chen W, Mandali S, Hancock SP, Kumar P, Collazo M, Cascio D, Johnson RC. Multiple serine transposase dimers assemble the transposon-end synaptic complex during IS 607-family transposition. eLife 2018; 7:e39611. [PMID: 30289389 PMCID: PMC6188088 DOI: 10.7554/elife.39611] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 09/18/2018] [Indexed: 11/13/2022] Open
Abstract
IS607-family transposons are unusual because they do not have terminal inverted repeats or generate target site duplications. They encode two protein-coding genes, but only tnpA is required for transposition. Our X-ray structures confirm that TnpA is a member of the serine recombinase (SR) family, but the chemically-inactive quaternary structure of the dimer, along with the N-terminal location of the DNA binding domain, are different from other SRs. TnpA dimers from IS1535 cooperatively associate with multiple subterminal repeats, which together with additional nonspecific binding, form a nucleoprotein filament on one transposon end that efficiently captures a second unbound end to generate the paired-end complex (PEC). Formation of the PEC does not require a change in the dimeric structure of the catalytic domain, but remodeling of the C-terminal α-helical region is involved. We posit that the PEC recruits a chemically-active conformer of TnpA to the transposon end to initiate DNA chemistry.
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Affiliation(s)
- Wenyang Chen
- Department of Biological ChemistryDavid Geffen School of Medicine, University of California at Los AngelesLos AngelesUnited States
| | - Sridhar Mandali
- Department of Biological ChemistryDavid Geffen School of Medicine, University of California at Los AngelesLos AngelesUnited States
| | - Stephen P Hancock
- Department of Biological ChemistryDavid Geffen School of Medicine, University of California at Los AngelesLos AngelesUnited States
| | - Pramod Kumar
- Department of Biological ChemistryDavid Geffen School of Medicine, University of California at Los AngelesLos AngelesUnited States
| | - Michael Collazo
- Department of Energy Institute of Genomics and ProteomicsUniversity of California at Los AngelesLos AngelesUnited States
| | - Duilio Cascio
- Department of Energy Institute of Genomics and ProteomicsUniversity of California at Los AngelesLos AngelesUnited States
| | - Reid C Johnson
- Department of Biological ChemistryDavid Geffen School of Medicine, University of California at Los AngelesLos AngelesUnited States
- Molecular Biology InstituteUniversity of California at Los AngelesLos AngelesUnited States
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6
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Anderson RE, Kouris A, Seward CH, Campbell KM, Whitaker RJ. Structured Populations of Sulfolobus acidocaldarius with Susceptibility to Mobile Genetic Elements. Genome Biol Evol 2018. [PMID: 28633403 PMCID: PMC5554439 DOI: 10.1093/gbe/evx104] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The impact of a structured environment on genome evolution can be determined through comparative population genomics of species that live in the same habitat. Recent work comparing three genome sequences of Sulfolobus acidocaldarius suggested that highly structured, extreme, hot spring environments do not limit dispersal of this thermoacidophile, in contrast to other co-occurring Sulfolobus species. Instead, a high level of conservation among these three S. acidocaldarius genomes was hypothesized to result from rapid, global-scale dispersal promoted by low susceptibility to viruses that sets S. acidocaldarius apart from its sister Sulfolobus species. To test this hypothesis, we conducted a comparative analysis of 47 genomes of S. acidocaldarius from spatial and temporal sampling of two hot springs in Yellowstone National Park. While we confirm the low diversity in the core genome, we observe differentiation among S. acidocaldarius populations, likely resulting from low migration among hot spring “islands” in Yellowstone National Park. Patterns of genomic variation indicate that differing geological contexts result in the elimination or preservation of diversity among differentiated populations. We observe multiple deletions associated with a large genomic island rich in glycosyltransferases, differential integrations of the Sulfolobus turreted icosahedral virus, as well as two different plasmid elements. These data demonstrate that neither rapid dispersal nor lack of mobile genetic elements result in low diversity in the S. acidocaldarius genomes. We suggest instead that significant differences in the recent evolutionary history, or the intrinsic evolutionary rates, of sister Sulfolobus species result in the relatively low diversity of the S. acidocaldarius genome.
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Affiliation(s)
- Rika E Anderson
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign.,Biology Department, Carleton College, Northfield, Minnesota
| | - Angela Kouris
- Energy, Bioengineering and Geomicrobiology Group, University of Calgary, Alberta, Canada
| | - Christopher H Seward
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign
| | - Kate M Campbell
- U.S. Geological Survey National Research Program, Boulder, Colorado
| | - Rachel J Whitaker
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign.,Department of Microbiology, University of Illinois at Urbana-Champaign
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7
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How a Genetically Stable Extremophile Evolves: Modes of Genome Diversification in the Archaeon Sulfolobus acidocaldarius. J Bacteriol 2017. [PMID: 28630130 DOI: 10.1128/jb.00177-17] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
In order to analyze in molecular terms how Sulfolobus genomes diverge, damage-induced mutations and natural polymorphisms (PMs) were identified in laboratory constructs and wild-type isolates, respectively, of Sulfolobus acidocaldarius Among wild-type isolates drawn from one local population, pairwise nucleotide divergence averaged 4 × 10-6, which is about 0.15% of the corresponding divergence reported for Sulfolobus islandicus The most variable features of wild-type S. acidocaldarius genomes were homopolymer (mononucleotide) tracts and longer tandem repeats, consistent with the spontaneous mutations that occur under laboratory conditions. Natural isolates, however, also revealed large insertions/deletions and inversions, which did not occur in any of the laboratory-manipulated strains. Several of the large insertions/deletions could be attributed to the integration or excision of mobile genetic elements (MGEs), and each MGE represented a distinct system of site-specific recombination. The mode of recombination associated with one MGE, a provirus related to Sulfolobus turreted icosahedral virus, was also seen in certain chromosomal inversions. Artificially induced mutations, non-MGE insertions/deletions, and small PMs exhibited different distributions over the genome, suggesting that large-scale patterning of Sulfolobus genomes begins early in the divergence process. Unlike induced mutations, natural base pair substitutions occurred in clusters, and one cluster exhibited properties expected of nonreciprocal recombination (gene conversion) between dispersed imperfect repeats. Taken together, the results identify simple replication errors, slipped-strand events promoted by tandem repeats, homologous recombination, and rearrangements promoted by MGEs as the primary sources of genetic variation for this extremely acidophilic archaeon in its geothermal environment.IMPORTANCE The optimal growth temperatures of hyperthermophilic archaea accelerate DNA decomposition, which is expected to make DNA repair especially important for their genetic stability, yet these archaea lack certain broadly conserved types of DNA repair proteins. In this study, the genome of the extreme thermoacidophile Sulfolobus acidocaldarius was found to be remarkably stable, accumulating few mutations in many (though not all) laboratory manipulations and in natural populations. Furthermore, all the genetic processes that were inferred to diversify these genomes also operate in mesophilic bacteria and eukaryotes. This suggests that a common set of mechanisms produces most of the genetic variation in all microorganisms, despite the fundamental differences in physiology, DNA repair systems, and genome structure represented in the three domains of life.
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8
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Xiang X, Huang X, Wang H, Huang L. pTC Plasmids from Sulfolobus Species in the Geothermal Area of Tengchong, China: Genomic Conservation and Naturally-Occurring Variations as a Result of Transposition by Mobile Genetic Elements. Life (Basel) 2015; 5:506-20. [PMID: 25686154 PMCID: PMC4390865 DOI: 10.3390/life5010506] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 02/04/2015] [Indexed: 11/30/2022] Open
Abstract
Plasmids occur frequently in Archaea. A novel plasmid (denoted pTC1) containing typical conjugation functions has been isolated from Sulfolobus tengchongensis RT8-4, a strain obtained from a hot spring in Tengchong, China, and characterized. The plasmid is a circular double-stranded DNA molecule of 20,417 bp. Among a total of 26 predicted pTC1 ORFs, 23 have homologues in other known Sulfolobus conjugative plasmids (CPs). pTC1 resembles other Sulfolobus CPs in genome architecture, and is most highly conserved in the genomic region encoding conjugation functions. However, attempts to demonstrate experimentally the capacity of the plasmid for conjugational transfer were unsuccessful. A survey revealed that pTC1 and its closely related plasmid variants were widespread in the geothermal area of Tengchong. Variations of the plasmids at the target sites for transposition by an insertion sequence (IS) and a miniature inverted-repeat transposable element (MITE) were readily detected. The IS was efficiently inserted into the pTC1 genome, and the inserted sequence was inactivated and degraded more frequently in an imprecise manner than in a precise manner. These results suggest that the host organism has evolved a strategy to maintain a balance between the insertion and elimination of mobile genetic elements to permit genomic plasticity while inhibiting their fast spreading.
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Affiliation(s)
- Xiaoyu Xiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing 100101, China.
| | - Xiaoxing Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing 100101, China.
| | - Haina Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing 100101, China.
| | - Li Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing 100101, China.
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9
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Domingues S, da Silva GJ, Nielsen KM. Integrons: Vehicles and pathways for horizontal dissemination in bacteria. Mob Genet Elements 2014; 2:211-223. [PMID: 23550063 PMCID: PMC3575428 DOI: 10.4161/mge.22967] [Citation(s) in RCA: 106] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Integrons are genetic elements first described at the end of the 1980s. Although most integrons were initially described in human clinical isolates, they have now been identified in many non-clinical environments, such as water and soil. Integrons are present in ≈10% of the sequenced bacterial genomes and are frequently linked to mobile genetic elements (MGEs); particularly the class 1 integrons. Genetic linkage to a diverse set of MGEs facilitates horizontal transfer of class 1 integrons within and between bacterial populations and species. The mechanistic aspects limiting transfer of MGEs will therefore limit the transfer of class 1 integrons. However, horizontal movement due to genes provided in trans and homologous recombination can result in class 1 integron dynamics independent of MGEs. A key determinant for continued dissemination of class 1 integrons is the probability that transferred MGEs will be vertically inherited in the recipient bacterial population. Heritability depends both on genetic stability as well as the fitness costs conferred to the host. Here we review the factors known to govern the dissemination of class 1 integrons in bacteria.
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Affiliation(s)
- Sara Domingues
- Centre of Pharmaceutical Studies; Faculty of Pharmacy; University of Coimbra; Coimbra, Portugal ; Department of Pharmacy; Faculty of Health Sciences; University of Tromsø; Tromsø, Norway
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10
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Unveiling cell surface and type IV secretion proteins responsible for archaeal rudivirus entry. J Virol 2014; 88:10264-8. [PMID: 24965447 DOI: 10.1128/jvi.01495-14] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Sulfolobus mutants resistant to archaeal lytic virus Sulfolobus islandicus rod-shaped virus 2 (SIRV2) were isolated, and mutations were identified in two gene clusters, cluster sso3138 to sso3141 and cluster sso2386 and sso2387, encoding cell surface and type IV secretion proteins, respectively. The involvement of the mutations in the resistance was confirmed by genetic complementation. Blocking of virus entry into the mutants was demonstrated by the lack of early gene transcription, strongly supporting the idea of a role of the proteins in SIRV2 entry.
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11
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Boocock MR, Rice PA. A proposed mechanism for IS607-family serine transposases. Mob DNA 2013; 4:24. [PMID: 24195768 PMCID: PMC4058570 DOI: 10.1186/1759-8753-4-24] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2013] [Accepted: 10/07/2013] [Indexed: 01/26/2023] Open
Abstract
Background The transposases encoded by the IS607 family of mobile elements are unusual serine recombinases with an inverted domain order and minimal specificity for target DNA. Results Structural genomics groups have determined three crystal structures of the catalytic domains of IS607 family transposases. The dimers formed by these catalytic domains are very different from those seen for other serine recombinases and include interactions that usually only occur upon formation of a synaptic tetramer. Conclusions Based on these structures, we propose a model for how IS607-family transposases could form a synaptic tetramer. The model suggests that, unlike other serine recombinases, these enzymes carry out sequence-specific DNA binding and catalysis in trans: the DNA binding and catalytic domains of each subunit are proposed to interact with different DNA duplexes. The model also suggests an explanation for the minimal target DNA specificity.
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Affiliation(s)
| | - Phoebe A Rice
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA.
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12
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Cha M, Wang H, Chung D, Bennetzen JL, Westpheling J. Isolation and bioinformatic analysis of a novel transposable element, ISCbe4, from the hyperthermophilic bacterium, Caldicellulosiruptor bescii. J Ind Microbiol Biotechnol 2013; 40:1443-8. [PMID: 24081709 DOI: 10.1007/s10295-013-1345-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 09/09/2013] [Indexed: 01/22/2023]
Abstract
Caldicellulosiruptor bescii is an anaerobic thermophilic bacterium of special interest for use in the consolidated bioprocessing of plant biomass to biofuels. In the course of experiments to engineer pyruvate metabolism in C. bescii, we isolated a mutant of C. bescii that contained an insertion in the L-lactate dehydrogenase gene (ldh). PCR amplification and sequencing of the ldh gene from this mutant revealed a 1,609-bp insertion that contained a single open reading frame of 479 amino acids (1,440 bp) annotated as a hypothetical protein with unknown function. The ORF is flanked by an 8-base direct repeat sequence. Bioinformatic analysis indicated that this ORF is part of a novel transposable element, ISCbe4, which is only intact in the genus Caldicellulosiruptor, but has ancient relatives that are present in degraded (and previously unrecognized) forms across many bacterial and archaeal clades.
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Affiliation(s)
- Minseok Cha
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA
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13
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Jaubert C, Danioux C, Oberto J, Cortez D, Bize A, Krupovic M, She Q, Forterre P, Prangishvili D, Sezonov G. Genomics and genetics of Sulfolobus islandicus LAL14/1, a model hyperthermophilic archaeon. Open Biol 2013; 3:130010. [PMID: 23594878 PMCID: PMC3718332 DOI: 10.1098/rsob.130010] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The 2 465 177 bp genome of Sulfolobus islandicus LAL14/1, host of the model rudivirus SIRV2, was sequenced. Exhaustive comparative genomic analysis of S. islandicus LAL14/1 and the nine other completely sequenced S. islandicus strains isolated from Iceland, Russia and USA revealed a highly syntenic common core genome of approximately 2 Mb and a long hyperplastic region containing most of the strain-specific genes. In LAL14/1, the latter region is enriched in insertion sequences, CRISPR (clustered regularly interspaced short palindromic repeats), glycosyl transferase genes, toxin-antitoxin genes and MITE (miniature inverted-repeat transposable elements). The tRNA genes of LAL14/1 are preferential targets for the integration of mobile elements but clusters of atypical genes (CAG) are also integrated elsewhere in the genome. LAL14/1 carries five CRISPR loci with 10 per cent of spacers matching perfectly or imperfectly the genomes of archaeal viruses and plasmids found in the Icelandic hot springs. Strikingly, the CRISPR_2 region of LAL14/1 carries an unusually long 1.9 kb spacer interspersed between two repeat regions and displays a high similarity to pING1-like conjugative plasmids. Finally, we have developed a genetic system for S. islandicus LAL14/1 and created ΔpyrEF and ΔCRISPR_1 mutants using double cross-over and pop-in/pop-out approaches, respectively. Thus, LAL14/1 is a promising model to study virus-host interactions and the CRISPR/Cas defence mechanism in Archaea.
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Affiliation(s)
- Carole Jaubert
- Département de Microbiologie, Unité Biologie Moléculaire du Gène chez les Extrêmophiles, Institut Pasteur, Paris, France
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14
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Genomic evidence of rapid, global-scale gene flow in a Sulfolobus species. ISME JOURNAL 2012; 6:1613-6. [PMID: 22418622 DOI: 10.1038/ismej.2012.20] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Local populations of Sulfolobus islandicus diverge genetically with geographical separation, and this has been attributed to restricted transfer of propagules imposed by the unfavorable spatial distribution of acidic geothermal habitat. We tested the generality of genetic divergence with distance in Sulfolobus species by analyzing genomes of Sulfolobus acidocaldarius drawn from three populations separated by more than 8000 km. In sharp contrast to S. islandicus, the geographically diverse S. acidocaldarius genomes proved to be nearly identical. We could not link the difference in genome conservation between the two species to a corresponding difference in genome stability or ecological factors affecting propagule dispersal. The results provide the first evidence that genetic isolation of local populations does not result primarily from properties intrinsic to Sulfolobus and the severe discontinuity of its geothermal habitat, but varies with species, and thus may reflect biotic interactions that act after propagule dispersal.
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Bire S, Rouleux-Bonnin F. Transposable elements as tools for reshaping the genome: it is a huge world after all! Methods Mol Biol 2012; 859:1-28. [PMID: 22367863 DOI: 10.1007/978-1-61779-603-6_1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Transposable elements (TEs) are discrete pieces of DNA that can move from one site to another within genomes and sometime between genomes. They are found in all major branches of life. Because of their wide distribution and considerable diversity, they are a considerable source of genomic variation and as such, they constitute powerful drivers of genome evolution. Moreover, it is becoming clear that the epigenetic regulation of certain genes is derived from defense mechanisms against the activity of ancestral transposable elements. TEs now tend to be viewed as natural molecular tools that can reshape the genome, which challenges the idea that TEs are natural tools used to answer biological questions. In the first part of this chapter, we review the classification and distribution of TEs, and look at how they have contributed to the structural and transcriptional reshaping of genomes. In the second part, we describe methodological innovations that have modified their contribution as molecular tools.
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Affiliation(s)
- Solenne Bire
- GICC, UMR CNRS 6239, Université François Rabelais, UFR des Sciences et Technques, Tours, France
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16
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You XY, Liu C, Wang SY, Jiang CY, Shah SA, Prangishvili D, She Q, Liu SJ, Garrett RA. Genomic analysis of Acidianus hospitalis W1 a host for studying crenarchaeal virus and plasmid life cycles. Extremophiles 2011; 15:487-97. [PMID: 21607549 PMCID: PMC3119797 DOI: 10.1007/s00792-011-0379-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2011] [Accepted: 04/26/2011] [Indexed: 11/29/2022]
Abstract
The Acidianus hospitalis W1 genome consists of a minimally sized chromosome of about 2.13 Mb and a conjugative plasmid pAH1 and it is a host for the model filamentous lipothrixvirus AFV1. The chromosome carries three putative replication origins in conserved genomic regions and two large regions where non-essential genes are clustered. Within these variable regions, a few orphan orfB and other elements of the IS200/607/605 family are concentrated with a novel class of MITE-like repeat elements. There are also 26 highly diverse vapBC antitoxin–toxin gene pairs proposed to facilitate maintenance of local chromosomal regions and to minimise the impact of environmental stress. Complex and partially defective CRISPR/Cas/Cmr immune systems are present and interspersed with five vapBC gene pairs. Remnants of integrated viral genomes and plasmids are located at five intron-less tRNA genes and several non-coding RNA genes are predicted that are conserved in other Sulfolobus genomes. The putative metabolic pathways for sulphur metabolism show some significant differences from those proposed for other Acidianus and Sulfolobus species. The small and relatively stable genome of A. hospitalis W1 renders it a promising candidate for developing the first Acidianus genetic systems.
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Affiliation(s)
- Xiao-Yan You
- State Key Laboratory of Microbial Resources and Center for Environmental Microbiology, Institute of Microbiology, Chinese Academy of Sciences, Bei-Chen-Xi-Lu No. Chao-Yang District, Beijing, People's Republic of China
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17
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Abstract
CRISPR (cluster of regularly interspaced palindromic repeats)/Cas and CRISPR/Cmr systems of Sulfolobus, targeting DNA and RNA respectively of invading viruses or plasmids are complex and diverse. We address their classification and functional diversity, and the wide sequence diversity of RAMP (repeat-associated mysterious protein)-motif containing proteins encoded in Cmr modules. Factors influencing maintenance of partially impaired CRISPR-based systems are discussed. The capacity for whole CRISPR transcripts to be generated despite the uptake of transcription signals within spacer sequences is considered. Targeting of protospacer regions of invading elements by Cas protein-crRNA (CRISPR RNA) complexes exhibit relatively low sequence stringency, but the integrity of protospacer-associated motifs appears to be important. Different mechanisms for circumventing or inactivating the immune systems are presented.
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Genome analyses of Icelandic strains of Sulfolobus islandicus, model organisms for genetic and virus-host interaction studies. J Bacteriol 2011; 193:1672-80. [PMID: 21278296 DOI: 10.1128/jb.01487-10] [Citation(s) in RCA: 119] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The genomes of two Sulfolobus islandicus strains obtained from Icelandic solfataras were sequenced and analyzed. Strain REY15A is a host for a versatile genetic toolbox. It exhibits a genome of minimal size, is stable genetically, and is easy to grow and manipulate. Strain HVE10/4 shows a broad host range for exceptional crenarchaeal viruses and conjugative plasmids and was selected for studying their life cycles and host interactions. The genomes of strains REY15A and HVE10/4 are 2.5 and 2.7 Mb, respectively, and each genome carries a variable region of 0.5 to 0.7 Mb where major differences in gene content and gene order occur. These include gene clusters involved in specific metabolic pathways, multiple copies of VapBC antitoxin-toxin gene pairs, and in strain HVE10/4, a 50-kb region rich in glycosyl transferase genes. The variable region also contains most of the insertion sequence (IS) elements and high proportions of the orphan orfB elements and SMN1 miniature inverted-repeat transposable elements (MITEs), as well as the clustered regular interspaced short palindromic repeat (CRISPR)-based immune systems, which are complex and diverse in both strains, consistent with them having been mobilized both intra- and intercellularly. In contrast, the remainder of the genomes are highly conserved in their protein and RNA gene syntenies, closely resembling those of other S. islandicus and Sulfolobus solfataricus strains, and they exhibit only minor remnants of a few genetic elements, mainly conjugative plasmids, which have integrated at a few tRNA genes lacking introns. This provides a possible rationale for the presence of the introns.
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Abstract
Why infer evolution when you can watch it happen in real time? This is the basic premise of using populations of fast-replicating microorganisms in test tubes to study evolution. The approach, known as experimental evolution, has provided a way of testing many of the key hypotheses that arose from the modern evolutionary synthesis. However, details of the unnatural histories of microorganisms in test tubes can be extrapolated only so far. Potential future directions for the approach include studying microbial evolution for its own sake under the most natural conditions possible in the test tube, and testing some qualitative theories of genome evolution.
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Berkner S, Lipps G. Genetic tools for Sulfolobus spp.: vectors and first applications. Arch Microbiol 2008; 190:217-30. [PMID: 18542925 DOI: 10.1007/s00203-008-0392-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2008] [Revised: 05/14/2008] [Accepted: 05/19/2008] [Indexed: 10/22/2022]
Abstract
Sulfolobus species belong to the best-studied archaeal organisms but have lacked powerful genetic methods. Recently, there has been considerable progress in the field of Sulfolobus genetics. Urgently needed basic genetic tools, such as targeted gene knockout techniques and shuttle vectors are being developed at an increasing pace. For S. solfataricus knockout systems as well as different shuttle vectors are available. For the genetically more stable S. acidocaldarius shuttle vectors have been recently developed. In this review we summarize the currently available genetic tools and methods for the genus Sulfolobus. Different transformation protocols are discussed, as well as all so far developed knockout systems and Sulfolobus-Escherichia coli shuttle vectors are summarized. Special emphasis is put on the important vector components, i.e., selectable markers and Sulfolobus replicons. Additionally, the information gathered on different Sulfolobus strains with respect to their use as recipient strains is reviewed. The advantages and disadvantages of the different systems are discussed and aims for further improvement of genetic systems are identified.
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Affiliation(s)
- Silvia Berkner
- Department of Biochemistry, University of Bayreuth, Universitätsstr. 30, 95447 Bayreuth, Germany
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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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22
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Mutation and reversion frequencies of different Sulfolobus species and strains. Extremophiles 2008; 12:263-70. [PMID: 18176778 DOI: 10.1007/s00792-007-0125-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2007] [Accepted: 11/02/2007] [Indexed: 09/29/2022]
Abstract
We have determined the apparent and actual spontaneous mutation frequencies and rates for different species and strains of the thermoacidophilic crenarchaeote Sulfolobus. The proportion of mutations caused by insertion sequences has also been analyzed. Mutation frequencies for S. islandicus (0.08-0.6 mutations per cell division and 10(7) cells) were below those determined for S. solfataricus and comparable to or lower than those for S. acidocaldarius. The proportion of insertion sequence mutations for the S. islandicus strains REN1H1 (9 out of 230) and HVE10/4 (0 out of 24) was found to be considerably lower than in S. solfataricus P1 and P2 and also low in comparison to other S. islandicus strains. Mutants defective in either the pyrEF genes or the lacS gene have been isolated. Their growth phenotype on selective and non-selective medium was examined and the inactivating mutations in either of the genes were determined. In addition the reversion frequencies for these mutants were measured and found to be in the range of <0.6-1.5 mutations per cell division and 10(8) cells. However, when being subjected to electroporation as a transformation procedure, increased reversion was observed.
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van Passel MWJ, Smillie CS, Ochman H. Gene decay in archaea. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2007; 2:137-43. [PMID: 17350934 PMCID: PMC2686384 DOI: 10.1155/2007/165723] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The gene-dense chromosomes of archaea and bacteria were long thought to be devoid of pseudogenes, but with the massive increase in available genome sequences, whole genome comparisons between closely related species have identified mutations that have rendered numerous genes inactive. Comparative analyses of sequenced archaeal genomes revealed numerous pseudogenes, which can constitute up to 8.6% of the annotated coding sequences in some genomes. The largest proportion of pseudogenes is created by gene truncations, followed by frameshift mutations. Within archaeal genomes, large numbers of pseudogenes contain more than one inactivating mutation, suggesting that pseudogenes are deleted from the genome more slowly in archaea than in bacteria. Although archaea seem to retain pseudogenes longer than do bacteria, most archaeal genomes have unique repertoires of pseudogenes.
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Affiliation(s)
- M W J van Passel
- Department of Biochemistry and Molecular Biophysics, University of Arizona, 1007 East Lowell Street, Tucson, AZ 85721, USA.
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24
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Abstract
Insertion sequences (ISs) can constitute an important component of prokaryotic (bacterial and archaeal) genomes. Over 1,500 individual ISs are included at present in the ISfinder database (www-is.biotoul.fr), and these represent only a small portion of those in the available prokaryotic genome sequences and those that are being discovered in ongoing sequencing projects. In spite of this diversity, the transposition mechanisms of only a few of these ubiquitous mobile genetic elements are known, and these are all restricted to those present in bacteria. This review presents an overview of ISs within the archaeal kingdom. We first provide a general historical summary of the known properties and behaviors of archaeal ISs. We then consider how transposition might be regulated in some cases by small antisense RNAs and by termination codon readthrough. This is followed by an extensive analysis of the IS content in the sequenced archaeal genomes present in the public databases as of June 2006, which provides an overview of their distribution among the major archaeal classes and species. We show that the diversity of archaeal ISs is very great and comparable to that of bacteria. We compare archaeal ISs to known bacterial ISs and find that most are clearly members of families first described for bacteria. Several cases of lateral gene transfer between bacteria and archaea are clearly documented, notably for methanogenic archaea. However, several archaeal ISs do not have bacterial equivalents but can be grouped into Archaea-specific groups or families. In addition to ISs, we identify and list nonautonomous IS-derived elements, such as miniature inverted-repeat transposable elements. Finally, we present a possible scenario for the evolutionary history of ISs in the Archaea.
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Affiliation(s)
- J Filée
- Laboratoire de Microbiologie et Génétique Moléculaires (UMR5100 CNRS), Campus Université Paul Sabatier, 118 Route de Narbonne, F-31062 Toulouse Cedex, France
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25
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Berkner S, Lipps G. An active nonautonomous mobile element in Sulfolobus islandicus REN1H1. J Bacteriol 2007; 189:2145-9. [PMID: 17158679 PMCID: PMC1855697 DOI: 10.1128/jb.01567-06] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2006] [Accepted: 11/26/2006] [Indexed: 11/20/2022] Open
Abstract
In the crenarchaeote Sulfolobus islandicus REN1H1, a mobile element of 321 bp length has been shown to be active. It does not contain terminal inverted repeats and transposes by a replicative mechanism. This newly discovered element has been named SMN1 (for Sulfolobus miniature noninverted repeat transposable element).
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Affiliation(s)
- Silvia Berkner
- Department of Biochemistry, University of Bayreuth, 95440 Bayreuth, Germany
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26
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Markov AV, Zakharov IA. Large and small rearrangements in the evolution of prokaryotic genomes. RUSS J GENET+ 2006. [DOI: 10.1134/s1022795406110123] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Durand P, Mahé F, Valin AS, Nicolas J. Browsing repeats in genomes: Pygram and an application to non-coding region analysis. BMC Bioinformatics 2006; 7:477. [PMID: 17067389 PMCID: PMC1635066 DOI: 10.1186/1471-2105-7-477] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2006] [Accepted: 10/26/2006] [Indexed: 01/06/2023] Open
Abstract
Background A large number of studies on genome sequences have revealed the major role played by repeated sequences in the structure, function, dynamics and evolution of genomes. In-depth repeat analysis requires specialized methods, including visualization techniques, to achieve optimum exploratory power. Results This article presents Pygram, a new visualization application for investigating the organization of repeated sequences in complete genome sequences. The application projects data from a repeat index file on the analysed sequences, and by combining this principle with a query system, is capable of locating repeated sequences with specific properties. In short, Pygram provides an efficient, graphical browser for studying repeats. Implementation of the complete configuration is illustrated in an analysis of CRISPR structures in Archaea genomes and the detection of horizontal transfer between Archaea and Viruses. Conclusion By proposing a new visualization environment to analyse repeated sequences, this application aims to increase the efficiency of laboratories involved in investigating repeat organization in single genomes or across several genomes.
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Affiliation(s)
- Patrick Durand
- IRISA/INRIA, Campus de Beaulieu, 35042 Rennes Cedex, France
| | - Frédéric Mahé
- ECOBIO, CNRS UMR 6553, Campus de Beaulieu, 35042 Rennes Cedex, France
| | - Anne-Sophie Valin
- IRISA/INRIA, Campus de Beaulieu, 35042 Rennes Cedex, France
- Institut Curie, Dept transfert, Quadrilatère historique Hôpital Saint Louis, Porte 13, 1 rue Claude Vellefaux, 75010 Paris, France
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Tachdjian S, Kelly RM. Dynamic metabolic adjustments and genome plasticity are implicated in the heat shock response of the extremely thermoacidophilic archaeon Sulfolobus solfataricus. J Bacteriol 2006; 188:4553-9. [PMID: 16740961 PMCID: PMC1482968 DOI: 10.1128/jb.00080-06] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Approximately one-third of the open reading frames encoded in the Sulfolobus solfataricus genome were differentially expressed within 5 min following an 80 to 90 degrees C temperature shift at pH 4.0. This included many toxin-antitoxin loci and insertion elements, implicating a connection between genome plasticity and metabolic regulation in the early stages of stress response.
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Affiliation(s)
- Sabrina Tachdjian
- Dept. of Chemical and Biomolecular Engineering, North Carolina State University, EB-1, 911 Partners Way, Box 7905, Raleigh, NC 27695-7905, USA
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29
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Redder P, Garrett RA. Mutations and rearrangements in the genome of Sulfolobus solfataricus P2. J Bacteriol 2006; 188:4198-206. [PMID: 16740926 PMCID: PMC1482960 DOI: 10.1128/jb.00061-06] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The genome of Sulfolobus solfataricus P2 carries a larger number of transposable elements than any other sequenced genome from an archaeon or bacterium and, as a consequence, may be particularly susceptible to rearrangement and change. In order to gain more insight into the natures and frequencies of different types of mutation and possible rearrangements that can occur in the genome, the pyrEF locus was examined for mutations that were isolated after selection with 5-fluoroorotic acid. About two-thirds of the 130 mutations resulted from insertions of mobile elements, including insertion sequence (IS) elements and a single nonautonomous mobile element, SM2. For each of these, the element was identified and shown to be present at its original genomic position, consistent with a progressive increase in the copy numbers of the mobile elements. In addition, several base pair substitutions, as well as small deletions, insertions, and a duplication, were observed, and about one-fifth of the mutations occurred elsewhere in the genome, possibly in an orotate transporter gene. One mutant exhibited a 5-kb genomic rearrangement at the pyrEF locus involving a two-step IS element-dependent reaction, and its boundaries were defined using a specially developed "in vitro library" strategy. Moreover, while searching for the donor mobile elements, evidence was found for two major changes that had occurred in the genome of strain P2, one constituting a single deletion of about 4% of the total genome (124 kb), while the other involved the inversion of a 25-kb region. Both were bordered by IS elements and were inferred to have arisen through recombination events. The results underline the caution required in working experimentally with an organism such as S. solfataricus with a continually changing genome.
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Affiliation(s)
- Peter Redder
- Danish Archaea Centre, Institute for Molecular Biology and Physiology, Copenhagen University, Sølvgade 83H, DK-1307 Copenhagen K, Denmark .
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30
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Blount ZD, Grogan DW. New insertion sequences of Sulfolobus: functional properties and implications for genome evolution in hyperthermophilic Archaea. Mol Microbiol 2005. [DOI: 10.1111/j.1365-2958.2005.04537.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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31
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Hot spots for Sulfolobus. Nat Rev Microbiol 2005. [DOI: 10.1038/nrmicro1109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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