201
|
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: 2.7] [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.
Collapse
Affiliation(s)
- Peter Redder
- Danish Archaea Centre, Institute for Molecular Biology and Physiology, Copenhagen University, Sølvgade 83H, DK-1307 Copenhagen K, Denmark .
| | | |
Collapse
|
202
|
Jung J, Lee S. Identification and characterization of Thermoplasma acidophilum glyceraldehyde dehydrogenase: a new class of NADP+-specific aldehyde dehydrogenase. Biochem J 2006; 397:131-8. [PMID: 16566751 PMCID: PMC1479753 DOI: 10.1042/bj20051763] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2005] [Revised: 03/13/2006] [Accepted: 03/27/2006] [Indexed: 01/03/2023]
Abstract
Thermoacidophilic archaea such as Thermoplasma acidophilum and Sulfolobus solfataricus are known to metabolize D-glucose via the nED (non-phosphorylated Entner-Doudoroff) pathway. In the present study, we identified and characterized a glyceraldehyde dehydrogenase involved in the downstream portion of the nED pathway. This glyceraldehyde dehydrogenase was purified from T. acidophilum cell extracts by sequential chromatography on DEAE-Sepharose, Q-Sepharose, Phenyl-Sepharose and Affi-Gel Blue columns. SDS/PAGE of the purified enzyme showed a molecular mass of approx. 53 kDa, whereas the molecular mass of the native protein was 215 kDa, indicating that glyceraldehyde dehydrogenase is a tetrameric protein. By MALDI-TOF-MS (matrix-assisted laser-desorption ionization-time-of-flight MS) peptide fingerprinting of the purified protein, it was found that the gene product of Ta0809 in the T. acidophilum genome database corresponds to the purified glyceraldehyde dehydrogenase. The native enzyme showed the highest activity towards glyceraldehyde, but no activity towards aliphatic or aromatic aldehydes, and no activity when NAD+ was substituted for NADP+. Analysis of the amino acid sequence and enzyme inhibition studies indicated that this glyceraldehyde dehydrogenase belongs to the ALDH (aldehyde dehydrogenase) superfamily. BLAST searches showed that homologues of the Ta0809 protein are not present in the Sulfolobus genome. Possible differences between T. acidophilum (Euryarchaeota) and S. solfataricus (Crenarchaeaota) in terms of the glycolytic pathway are thus expected.
Collapse
Affiliation(s)
- Jin Hwa Jung
- *Department of Chemical Engineering, Pohang University of Science and Technology, San 31, Hyoja-Dong, Pohang 790-784, Korea
| | - Sun Bok Lee
- *Department of Chemical Engineering, Pohang University of Science and Technology, San 31, Hyoja-Dong, Pohang 790-784, Korea
- †Division of Molecular and Life Sciences, Pohang University of Science and Technology, San 31, Hyoja-Dong, Pohang 790-784, Korea
| |
Collapse
|
203
|
Barry RC, Young MJ, Stedman KM, Dratz EA. Proteomic mapping of the hyperthermophilic and acidophilic archaeonSulfolobus solfataricus P2. Electrophoresis 2006; 27:2970-83. [PMID: 16721906 DOI: 10.1002/elps.200500851] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
A proteomic map of Sulfolobus solfataricus P2, an archaeon that grows optimally at 80 degrees C and pH 3.2, was developed using high-resolution 2-DE and peptide mass fingerprinting. A total of 867 protein spots (659 aqueous Tris-soluble spots and 208 aqueous Tris-insoluble) were mapped over IPG 3-10, 4-7, and 6-11, with second-dimensional gels made of 8-18% polyacrylamide. Three hundred and twenty-four different gene products were represented by the 867 spots, with 274 gene products being identified in the Tris-soluble fractions and 100 gene products in the Tris-insoluble portion. Fifty gene products were found on gels from both fractions. Additionally, an average of 1.50 +/- 0.12 isoforms/protein was identified. This mapping study confirmed the expression of proteins involved in numerous metabolic, transport, energy production, nucleic acid replication, translation, and transcription pathways. Of particular interest, phosphoenolpyruvate carboxykinase (SSO2537) was detected even though the pathway for gluconeogenesis is unknown for this archaeon. Tris-soluble fractions contained many cytosolic proteins while Tris-insoluble fractions contained many membrane-associated proteins, including ABC transporters and an ATP synthase. This study provides an optimized 2-DE approach for investigating the biochemical pathways and post-translational modifications employed by Sulfolobus to survive in its extreme environment.
Collapse
Affiliation(s)
- Richard C Barry
- Biological Monitoring and Modeling, Pacific NW National Laboratory, Richland, WA, USA
| | | | | | | |
Collapse
|
204
|
Yoshinari S, Itoh T, Hallam SJ, DeLong EF, Yokobori SI, Yamagishi A, Oshima T, Kita K, Watanabe YI. Archaeal pre-mRNA splicing: a connection to hetero-oligomeric splicing endonuclease. Biochem Biophys Res Commun 2006; 346:1024-32. [PMID: 16781672 DOI: 10.1016/j.bbrc.2006.06.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2006] [Accepted: 06/02/2006] [Indexed: 10/24/2022]
Abstract
Eukaryotic Cbf5 is a protein subunit of the small nucleolar RNA-protein complex. Previously, we identified, in archaeal homologs of cbf5 of the crenarchaea, Aeropyrum pernix, Sulfolobus solfataricus, and Sulfolobus tokodaii, the first examples of introns of archaeal protein-coding genes. Here, we report the immunological detection of Cbf5 protein of S. tokodaii, the product of the spliced cbf5 mRNA. The hetero-oligomeric splicing endonuclease activity from recombinant S. tokodaii subunits cleaved at the exon-intron boundaries of cbf5 pre-mRNA fragments,suggesting that synthesis of full-length Cbf5 protein requires this activity. Database searches and PCR screens identified additional cbf5 introns in some, but not all sequenced crenarchaeal genomes. The predicted secondary structures of exon-intron boundaries of many of the newly identified intron-containing cbf5 pre-mRNAs contained relaxed forms of the bulge-helix-bulge motif similar to that of S. tokodaii. These observations are consistent with previous reports indicating that subunit composition of the splicing endonuclease contributes to substrate specificity.
Collapse
Affiliation(s)
- Shigeo Yoshinari
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | | | | | | | | | | | | | | | | |
Collapse
|
205
|
Podar M, Reysenbach AL. New opportunities revealed by biotechnological explorations of extremophiles. Curr Opin Biotechnol 2006; 17:250-5. [PMID: 16701993 DOI: 10.1016/j.copbio.2006.05.002] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2006] [Revised: 04/25/2006] [Accepted: 05/04/2006] [Indexed: 11/16/2022]
Abstract
Over the past few decades the extremes at which life thrives has continued to challenge our understanding of biochemistry, biology and evolution. As more new extremophiles are brought into laboratory culture, they have provided a multitude of potential applications for biotechnology. More recently, innovative culturing approaches, environmental genome sequencing and whole genome sequencing have provided new opportunities for the biotechnological exploration of extremophiles.
Collapse
|
206
|
Nishimasu H, Fushinobu S, Shoun H, Wakagi T. Identification and characterization of an ATP-dependent hexokinase with broad substrate specificity from the hyperthermophilic archaeon Sulfolobus tokodaii. J Bacteriol 2006; 188:2014-9. [PMID: 16484213 PMCID: PMC1426560 DOI: 10.1128/jb.188.5.2014-2019.2006] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
As a new member of the glucose-phosphorylating enzymes, the ATP-dependent hexokinase from the hyperthermophilic crenarchaeon Sulfolobus tokodaii was purified, identified, and characterized. Our results revealed that the enzyme differs from other known enzymes in primary structure and its broad substrate specificity for both phosphoryl donors and acceptors.
Collapse
Affiliation(s)
- Hiroshi Nishimasu
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | | | | | | |
Collapse
|
207
|
Brouns SJJ, Smits N, Wu H, Snijders APL, Wright PC, de Vos WM, van der Oost J. Identification of a novel alpha-galactosidase from the hyperthermophilic archaeon Sulfolobus solfataricus. J Bacteriol 2006; 188:2392-9. [PMID: 16547025 PMCID: PMC1428385 DOI: 10.1128/jb.188.7.2392-2399.2006] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Sulfolobus solfataricus is an aerobic crenarchaeon that thrives in acidic volcanic pools. In this study, we have purified and characterized a thermostable alpha-galactosidase from cell extracts of S. solfataricus P2 grown on the trisaccharide raffinose. The enzyme, designated GalS, is highly specific for alpha-linked galactosides, which are optimally hydrolyzed at pH 5 and 90 degrees C. The protein consists of 74.7-kDa subunits and has been identified as the gene product of open reading frame Sso3127. Its primary sequence is most related to plant enzymes of glycoside hydrolase family 36, which are involved in the synthesis and degradation of raffinose and stachyose. Both the galS gene from S. solfataricus P2 and an orthologous gene from Sulfolobus tokodaii have been cloned and functionally expressed in Escherichia coli, and their activity was confirmed. At present, these Sulfolobus enzymes not only constitute a distinct type of thermostable alpha-galactosidases within glycoside hydrolase clan D but also represent the first members from the Archaea.
Collapse
Affiliation(s)
- Stan J J Brouns
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Hesselink van Suchtelenweg 4, 6703 CT Wageningen, The Netherlands.
| | | | | | | | | | | | | |
Collapse
|
208
|
Lipps G. Plasmids and viruses of the thermoacidophilic crenarchaeote Sulfolobus. Extremophiles 2006; 10:17-28. [PMID: 16397749 DOI: 10.1007/s00792-005-0492-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2005] [Accepted: 07/15/2005] [Indexed: 11/28/2022]
Abstract
The crenarchaeote Sulfolobus spp. is a host for a remarkably large spectrum of viruses and plasmids. The genetic elements characterized so far indicate a large degree of novelty in terms of morphology (viruses) and in terms of genome content (plasmids and viruses). The viruses and conjugative plasmids encode a great number of conserved proteins of unknown function due to the lack of sequence similarity to functionally characterized proteins. These apparently essential proteins remain to be studied and should help to understand the physiology and genetics of the respective genetic elements as well as the host. Sulfolobus is one of the best-studied archaeons and could develop into an important model organism of the crenarchaea and the archaea.
Collapse
Affiliation(s)
- Georg Lipps
- Institute of Biochemistry, University of Bayreuth, Universitätstrasse 30, 95440, Bayreuth, Germany.
| |
Collapse
|
209
|
van der Oost J, Walther J, Brouns SJJ, van de Werken HJG, Snijders APL, Wright PC, Andersson A, Bernander R, de Vos WM. 9 Functional Genomics of the Thermo-Acidophilic Archaeon Sulfolobus solfataricus. METHODS IN MICROBIOLOGY 2006. [DOI: 10.1016/s0580-9517(08)70012-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
210
|
Kill K, Binnewies TT, Sicheritz-Pontén T, Willenbrock H, Hallin PF, Wassenaar TM, Ussery DW. Genome update: sigma factors in 240 bacterial genomes. MICROBIOLOGY-SGM 2005; 151:3147-3150. [PMID: 16207898 DOI: 10.1099/mic.0.28339-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Kristoffer Kill
- Center for Biological Sequence Analysis, BioCentrum-DTU, Building 208, The Technical University of Denmark, DK-2800 Kgs Lyngby, Denmark
| | - Tim T Binnewies
- Center for Biological Sequence Analysis, BioCentrum-DTU, Building 208, The Technical University of Denmark, DK-2800 Kgs Lyngby, Denmark
| | - Thomas Sicheritz-Pontén
- Center for Biological Sequence Analysis, BioCentrum-DTU, Building 208, The Technical University of Denmark, DK-2800 Kgs Lyngby, Denmark
| | - Hanni Willenbrock
- Center for Biological Sequence Analysis, BioCentrum-DTU, Building 208, The Technical University of Denmark, DK-2800 Kgs Lyngby, Denmark
| | - Peter F Hallin
- Center for Biological Sequence Analysis, BioCentrum-DTU, Building 208, The Technical University of Denmark, DK-2800 Kgs Lyngby, Denmark
| | - Trudy M Wassenaar
- Center for Biological Sequence Analysis, BioCentrum-DTU, Building 208, The Technical University of Denmark, DK-2800 Kgs Lyngby, Denmark
| | - David W Ussery
- Center for Biological Sequence Analysis, BioCentrum-DTU, Building 208, The Technical University of Denmark, DK-2800 Kgs Lyngby, Denmark
| |
Collapse
|
211
|
Roberts JA, White MF. DNA end-directed and processive nuclease activities of the archaeal XPF enzyme. Nucleic Acids Res 2005; 33:6662-70. [PMID: 16314325 PMCID: PMC1298930 DOI: 10.1093/nar/gki974] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The XPF/Mus81 family of structure-specific nucleases cleaves branched or nicked DNA substrates and are implicated in a wide range of DNA repair and recombination processes. The structure of the crenarchaeal XPF bound to a DNA duplex has revealed a plausible mechanism for DNA binding, involving DNA distortion into upstream and downstream duplexes engaged by the two helix–hairpin–helix domains that form a dimeric structure at the C-terminus of the enzyme. A flexible linker joins these to the dimeric nuclease domain, and a C-terminal motif interacts with the sliding clamp, which is essential for the activity of the enzyme. Here, we demonstrate the importance of the downstream duplex in directing the endonuclease activity of crenarchaeal XPF, which is similar to that of Mus81-Eme1, and suggest a mechanistic basis for this control. Furthermore, our data reveal that the enzyme can digest a nicked DNA strand processively over at least 60 nt in a 3′–5′ direction and can remove varied types of DNA lesions and blocked DNA termini. This in vitro activity suggests a potential role for crenarchaeal XPF in a variety of repair processes for which there are no clear pathways in archaea.
Collapse
Affiliation(s)
| | - Malcolm F. White
- To whom correspondence should be addressed. Tel: +44 1334 463432; Fax +44 1334 462595;
| |
Collapse
|
212
|
Bartlett MS. Determinants of transcription initiation by archaeal RNA polymerase. Curr Opin Microbiol 2005; 8:677-84. [PMID: 16249119 DOI: 10.1016/j.mib.2005.10.016] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2005] [Accepted: 10/13/2005] [Indexed: 12/27/2022]
Abstract
Transcription in Archaea is catalyzed by an RNA polymerase that is most similar to eukaryotic RNA polymerases both in subunit composition and in transcription initiation factor requirements. Recent studies on archaeal transcription in diverse members of this domain have contributed new details concerning the functions of promoters and transcription factors in guiding initiation by RNA polymerase, and phylogenetic arguments have allowed modeling of archaeal transcription initiation complexes by comparison with recently described models of eukaryotic and bacterial transcription initiation complexes. Important new advances in reconstitution of archaeal transcription complexes from fully recombinant components is permitting testing of hypotheses derived from and informed by these structural models, and will help bring the study of archaeal transcription to the levels of understanding currently enjoyed by bacterial and eukaryotic RNA polymerase II transcription.
Collapse
Affiliation(s)
- Michael S Bartlett
- Department of Biology, Portland State University, SB2 Room 246, 1719 SW 10th Avenue, Portland, OR 97201, USA.
| |
Collapse
|
213
|
Kurosawa N, Grogan DW. Homologous recombination of exogenous DNA with the Sulfolobus acidocaldarius genome: properties and uses. FEMS Microbiol Lett 2005; 253:141-9. [PMID: 16243457 DOI: 10.1016/j.femsle.2005.09.031] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2005] [Revised: 09/17/2005] [Accepted: 09/21/2005] [Indexed: 10/25/2022] Open
Abstract
In order to quantify recombination between exogenous DNA and the Sulfolobus acidocaldarius chromosome, we electroporated pyrE (uracil-auxtotrophic) recipient strains with functional pyrE sequences and counted Pyr+ transformants by direct plating. Certain culture and post-electroporation conditions increased the yield of Pyr+ recombinants from non-replicating pyrE plasmid, whereas cognate methylation of SuaI restriction sites in the plasmid decreased it. Recombination of linear DNAs with the S. acidocaldarius genome was proportional to the length of a limiting overlap, but even synthetic oligonucleotides produced reasonable numbers of recombinants with appropriate recipient strains. To investigate uses of this latter property, we electroporated an 18-bp pyrE deletion mutant with mixtures of synthetic oligonucleotides altering glycine-55 of the orotate phosphoribosyl transferase encoded by pyrE. Pyr+ transformants were recovered in which this codon was converted to each of the alternatives encoded by the oligonucleotide mixtures, thereby identifying five amino acid substitutions tolerated at this position of the thermostable enzyme.
Collapse
Affiliation(s)
- Norio Kurosawa
- Department of Environmental Engineering for Symbiosis, Soka University, Hachioji, Tokyo 192-8577, Japan
| | | |
Collapse
|
214
|
Affiliation(s)
- Michael Y Galperin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
| |
Collapse
|