|
Vol. 12, Issue 5, 689-700, May 2002
A Complete Sequence of the T. tengcongensis Genome
Qiyu
Bao,1,5
Yuqing
Tian,2,5
Wei
Li,3,5
Zuyuan
Xu,1
Zhenyu
Xuan,3
Songnian
Hu,1
Wei
Dong,1
Jian
Yang,3
Yanjiong
Chen,1
Yanfen
Xue,2
Yi
Xu,2
Xiaoqin
Lai,2
Li
Huang,2
Xiuzhu
Dong,2
Yanhe
Ma,2
Lunjiang
Ling,3
Huarong
Tan,2,6
Runsheng
Chen,3,6
Jian
Wang,1
Jun
Yu,1,4 and
Huanming
Yang1,6
1 Beijing Genomics Institute/Genomics and Bioinformatics
Center, Institute of Genetics and Developmental Biology, Chinese
Academy of Sciences (CAS), Beijing 100101, China; 2 Institute
of Microbiology, CAS, Beijing 100080, China; 3 Institute of
Biophysics, CAS, Beijing 100101, China; 4 Genome Center,
University of Washington, Seattle, Washington 98195, USA
Thermoanaerobacter tengcongensis is a rod-shaped,
gram-negative, anaerobic eubacterium that was isolated from a
freshwater hot spring in Tengchong, China. Using a whole-genome-shotgun
method, we sequenced its 2,689,445-bp genome from an isolate,
MB4T (Genbank accession no. AE008691). The genome encodes
2588 predicted coding sequences (CDS). Among them, 1764 (68.2%) are classified according to homology to other documented proteins, and the
rest, 824 CDS (31.8%), are functionally unknown. One of the
interesting features of the T. tengcongensis genome is that 86.7% of its genes are encoded on the leading strand of DNA
replication. Based on protein sequence similarity, the T. tengcongensis genome is most similar to that of Bacillus
halodurans, a mesophilic eubacterium, among all fully sequenced
prokaryotic genomes up to date. Computational analysis on genes
involved in basic metabolic pathways supports the experimental
discovery that T. tengcongensis metabolizes sugars as
principal energy and carbon source and utilizes thiosulfate and element
sulfur, but not sulfate, as electron acceptors. T. tengcongensis, as a gram-negative rod by empirical definitions (such as staining), shares many genes that are characteristics of
gram-positive bacteria whereas it is missing molecular
components unique to gram-negative bacteria. A strong correlation
between the G + C content of tDNA and rDNA genes and the optimal
growth temperature is found among the sequenced thermophiles. It is
concluded that thermophiles are a biologically and phylogenetically
divergent group of prokaryotes that have converged to sustain extreme
environmental conditions over evolutionary timescale.
[Supplemental material is available online at
http://www.genome.org.]
5
These authors contributed equally to this work.
6
Corresponding authors.
12:689-700 ©2002 by Cold Spring Harbor Laboratory Press ISSN 1088-9051/02 $5.00
 CiteULike  Connotea  Del.icio.us  Digg  Reddit  Technorati What's this?
This article has been cited by other articles:
|
|
|
|
 
I. D. WAGNER and J. WIEGEL
Diversity of Thermophilic Anaerobes
Ann. N.Y. Acad. Sci.,
March 1, 2008;
1125(1):
1 - 43.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
A. L. VANFOSSEN, D. L. LEWIS, J. D. NICHOLS, and R. M. KELLY
Polysaccharide Degradation and Synthesis by Extremely Thermophilic Anaerobes
Ann. N.Y. Acad. Sci.,
March 1, 2008;
1125(1):
322 - 337.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
T. Kosaka, S. Kato, T. Shimoyama, S. Ishii, T. Abe, and K. Watanabe
The genome of Pelotomaculum thermopropionicum reveals niche-associated evolution in anaerobic microbiota
Genome Res.,
March 1, 2008;
18(3):
442 - 448.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
H. Pei, J. Liu, J. Li, A. Guo, J. Zhou, and H. Xiang
Mechanism for the TtDnaA-Tt-oriC cooperative interaction at high temperature and duplex opening at an unusual AT-rich region in Thermoanaerobacter tengcongensis
Nucleic Acids Res.,
May 14, 2007;
35(9):
3087 - 3099.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
S. Forman, A. G. Bobrov, O. Kirillina, S. K. Craig, J. Abney, J. D. Fetherston, and R. D. Perry
Identification of critical amino acid residues in the plague biofilm Hms proteins.
Microbiology,
November 1, 2006;
152(Pt 11):
3399 - 3410.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
R. M. de Lorimier, Y. Tian, and H. W. Hellinga
Binding and signaling of surface-immobilized reagentless fluorescent biosensors derived from periplasmic binding proteins
Protein Sci.,
August 1, 2006;
15(8):
1936 - 1944.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
H. Nonaka, G. Keresztes, Y. Shinoda, Y. Ikenaga, M. Abe, K. Naito, K. Inatomi, K. Furukawa, M. Inui, and H. Yukawa
Complete Genome Sequence of the Dehalorespiring Bacterium Desulfitobacterium hafniense Y51 and Comparison with Dehalococcoides ethenogenes 195
J. Bacteriol.,
March 15, 2006;
188(6):
2262 - 2274.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
G. A. Soukup
Core requirements for glmS ribozyme self-cleavage reveal a putative pseudoknot structure
Nucleic Acids Res.,
February 7, 2006;
34(3):
968 - 975.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
R. D. Barabote and M. H. Saier Jr.
Comparative Genomic Analyses of the Bacterial Phosphotransferase System
Microbiol. Mol. Biol. Rev.,
December 1, 2005;
69(4):
608 - 634.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
S. B. Conners, C. I. Montero, D. A. Comfort, K. R. Shockley, M. R. Johnson, S. R. Chhabra, and R. M. Kelly
An Expression-Driven Approach to the Prediction of Carbohydrate Transport and Utilization Regulons in the Hyperthermophilic Bacterium Thermotoga maritima
J. Bacteriol.,
November 1, 2005;
187(21):
7267 - 7282.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
L. An, W. Tang, T. A. Ranalli, H.-J. Kim, J. Wytiaz, and H. Kong
Characterization of a Thermostable UvrD Helicase and Its Participation in Helicase-dependent Amplification
J. Biol. Chem.,
August 12, 2005;
280(32):
28952 - 28958.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
S. Shen, M. Mascarenhas, R. Morgan, K. Rahn, and M. A. Karmali
Identification of Four Fimbria-Encoding Genomic Islands That Are Highly Specific for Verocytotoxin-Producing Escherichia coli Serotype O157 Strains
J. Clin. Microbiol.,
August 1, 2005;
43(8):
3840 - 3850.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
P. Guo, L. Zhang, Z. Qi, R. Chen, and G. Jing
Expression in Escherichia coli, Purification and Characterization of Thermoanaerobacter tengcongensis Ribosome Recycling Factor
J. Biochem.,
July 1, 2005;
138(1):
89 - 94.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
C.-H. Chiu, P. Tang, C. Chu, S. Hu, Q. Bao, J. Yu, Y.-Y. Chou, H.-S. Wang, and Y.-S. Lee
The genome sequence of Salmonella enterica serovar Choleraesuis, a highly invasive and resistant zoonotic pathogen
Nucleic Acids Res.,
March 21, 2005;
33(5):
1690 - 1698.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
E. J. Deeds, H. Hennessey, and E. I. Shakhnovich
Prokaryotic phylogenies inferred from protein structural domains
Genome Res.,
March 1, 2005;
15(3):
393 - 402.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
H. Takami, Y. Takaki, G.-J. Chee, S. Nishi, S. Shimamura, H. Suzuki, S. Matsui, and I. Uchiyama
Thermoadaptation trait revealed by the genome sequence of thermophilic Geobacillus kaustophilus
Nucleic Acids Res.,
December 1, 2004;
32(21):
6292 - 6303.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
K. Ueda, A. Yamashita, J. Ishikawa, M. Shimada, T.-o Watsuji, K. Morimura, H. Ikeda, M. Hattori, and T. Beppu
Genome sequence of Symbiobacterium thermophilum, an uncultivable bacterium that depends on microbial commensalism
Nucleic Acids Res.,
September 21, 2004;
32(16):
4937 - 4944.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
K. Kimura, L.-S. P. Tran, and Y. Itoh
Roles and regulation of the glutamate racemase isogenes, racE and yrpC, in Bacillus subtilis
Microbiology,
September 1, 2004;
150(9):
2911 - 2920.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
B. Soboh, D. Linder, and R. Hedderich
A multisubunit membrane-bound [NiFe] hydrogenase and an NADH-dependent Fe-only hydrogenase in the fermenting bacterium Thermoanaerobacter tengcongensis
Microbiology,
July 1, 2004;
150(7):
2451 - 2463.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
S. G. Acinas, L. A. Marcelino, V. Klepac-Ceraj, and M. F. Polz
Divergence and Redundancy of 16S rRNA Sequences in Genomes with Multiple rrn Operons
J. Bacteriol.,
May 1, 2004;
186(9):
2629 - 2635.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
T. L. Bannam, P. A. Johanesen, C. L. Salvado, S. J. A. Pidot, K. A. Farrow, and J. I. Rood
The Clostridium perfringens TetA(P) efflux protein contains a functional variant of the Motif A region found in major facilitator superfamily transport proteins
Microbiology,
January 1, 2004;
150(1):
127 - 134.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
K. Jim, K. Parmar, M. Singh, and S. Tavazoie
A Cross-Genomic Approach for Systematic Mapping of Phenotypic Traits to Genes
Genome Res.,
January 1, 2004;
14(1):
109 - 115.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
S. Tojo, M. Matsunaga, T. Matsumoto, C.-M. Kang, H. Yamaguchi, K. Asai, Y. Sadaie, K.-i. Yoshida, and Y. Fujita
Organization and Expression of the Bacillus subtilis sigY Operon
J. Biochem.,
December 1, 2003;
134(6):
935 - 946.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
E. P. C. Rocha and A. Danchin
Gene essentiality determines chromosome organisation in bacteria
Nucleic Acids Res.,
November 15, 2003;
31(22):
6570 - 6577.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
J. Nishi, J. Sheikh, K. Mizuguchi, B. Luisi, V. Burland, A. Boutin, D. J. Rose, F. R. Blattner, and J. P. Nataro
The Export of Coat Protein from Enteroaggregative Escherichia coli by a Specific ATP-binding Cassette Transporter System
J. Biol. Chem.,
November 14, 2003;
278(46):
45680 - 45689.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
G. Xie, N. O. Keyhani, C. A. Bonner, and R. A. Jensen
Ancient Origin of the Tryptophan Operon and the Dynamics of Evolutionary Change
Microbiol. Mol. Biol. Rev.,
September 1, 2003;
67(3):
303 - 342.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
T. M. Salmassi and J. R. Leadbetter
Analysis of genes of tetrahydrofolate-dependent metabolism from cultivated spirochaetes and the gut community of the termite Zootermopsis angusticollis
Microbiology,
September 1, 2003;
149(9):
2529 - 2537.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
J. L. England, B. E. Shakhnovich, and E. I. Shakhnovich
Natural selection of more designable folds: A mechanism for thermophilic adaptation
PNAS,
July 22, 2003;
100(15):
8727 - 8731.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
C.-H. Baek, S. K. Farrand, K.-E. Lee, D.-K. Park, J. K. Lee, and K.-S. Kim
Convergent Evolution of Amadori Opine Catabolic Systems in Plasmids of Agrobacterium tumefaciens
J. Bacteriol.,
January 15, 2003;
185(2):
513 - 524.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
W. J. Cho, W. J. Yoon, C. H. Moon, S. J. Cha, H. Song, H. R. Cho, S. J. Jang, D. K. Chung, C. S. Jeong, and J. W. Park
Molecular Cloning of a Novel Chaperone-like Protein Induced by Rhabdovirus Infection with Sequence Similarity to the Bacterial Extracellular Solute-binding Protein Family 5
J. Biol. Chem.,
October 25, 2002;
277(44):
41489 - 41496.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
![[Feedback]](/icons/banner/feedbackACT.gif){kind=icon}
![[For Subscribers]](/icons/banner/subscriberACT.gif){kind=icon}
![[Archive]](/icons/banner/archiveACT.gif){kind=icon}
![[Search]](/icons/banner/searchACT.gif){kind=icon}
![[Contents]](/icons/banner/tocACT.gif){kind=icon}
