|
|
|
|||||||
|
|||||||||
J. Biol. Chem., Vol. 277, Issue 50, 48949-48959, December 13, 2002
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
From the Vitamin B1 in its
active form thiamin pyrophosphate is an essential coenzyme that is
synthesized by coupling of pyrimidine (hydroxymethylpyrimidine; HMP)
and thiazole (hydroxyethylthiazole) moieties in bacteria. Using
comparative analysis of genes, operons, and regulatory elements, we
describe the thiamin biosynthetic pathway in available bacterial
genomes. The previously detected thiamin-regulatory element,
thi box (Miranda-Rios, J., Navarro, M., and Soberon, M. (2001) Proc. Natl. Acad. Sci. U. S. A. 98, 9736-9741),
was extended, resulting in a new, highly conserved RNA secondary
structure, the THI element, which is widely distributed in
eubacteria and also occurs in some archaea. Search for THI elements and analysis of operon structures identified a large number of
new candidate thiamin-regulated genes, mostly transporters, in various
prokaryotic organisms. In particular, we assign the thiamin transporter
function to yuaJ in the
Bacillus/Clostridium group and the HMP
transporter function to an ABC transporter thiXYZ in some
proteobacteria and firmicutes. By analogy to the model of regulation of
the riboflavin biosynthesis, we suggest thiamin-mediated regulation
based on formation of alternative RNA structures involving the
THI element. Either transcriptional or translational
attenuation mechanism may operate in different taxonomic groups,
dependent on the existence of putative hairpins that either act as
transcriptional terminators or sequester translation initiation sites.
Based on analysis of co-occurrence of the thiamin biosynthetic genes in complete genomes, we predict that eubacteria, archaea, and eukaryota have different pathways for the HMP and hydroxyethylthiazole biosynthesis.
Comparative Genomics of Thiamin Biosynthesis in
Procaryotes
NEW GENES AND REGULATORY MECHANISMS*,
§,
, and
State Scientific Center GosNIIGenetika,
Moscow 113545, Russia, ¶ Institute for Problems of Information
Transmission, Moscow 101447, Russia, and Integrated Genomics,
Moscow, P.O. Pox 348, Moscow 117333, Russia
*
This study was partially supported by INTAS Grant
99-1476 and Howard Hughes Medical Institute Grant 55000309.The costs of publication of this
article were defrayed in part by the
payment of page charges. The article
must therefore be hereby marked
"advertisement" in
accordance with 18 U.S.C. Section
1734 solely to indicate this fact.
The on-line version of this article (available at
http://www.jbc.org) contains one figure and one table.
§
To whom correspondence should be addressed: State Scientific Center
GosNIIGenetika, Moscow 113545, Russia. Fax: 7-095-315-05-01; E-mail:
rodionov@genetika.ru.
Copyright © 2002 by The American Society for Biochemistry and Molecular Biology, Inc.
CiteULike 
Complore 
Connotea 
Del.icio.us 
Digg 
Reddit 
Technorati What's this?
This article has been cited by other articles:
|
|
 |
|
  K. Schauer, J. Stolz, S. Scherer, and T. M. Fuchs Both Thiamine Uptake and Biosynthesis of Thiamine Precursors Are Required for Intracellular Replication of Listeria monocytogenes J. Bacteriol., April 1, 2009; 191(7): 2218 - 2227. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. A. Rodionov, P. Hebbeln, A. Eudes, J. ter Beek, I. A. Rodionova, G. B. Erkens, D. J. Slotboom, M. S. Gelfand, A. L. Osterman, A. D. Hanson, et al. A Novel Class of Modular Transporters for Vitamins in Prokaryotes J. Bacteriol., January 1, 2009; 191(1): 42 - 51. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Eudes, G. B. Erkens, D. J. Slotboom, D. A. Rodionov, V. Naponelli, and A. D. Hanson Identification of Genes Encoding the Folate- and Thiamine-Binding Membrane Proteins in Firmicutes J. Bacteriol., November 15, 2008; 190(22): 7591 - 7594. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. L. Davidson, E. Dassa, C. Orelle, and J. Chen Structure, Function, and Evolution of Bacterial ATP-Binding Cassette Systems Microbiol. Mol. Biol. Rev., June 1, 2008; 72(2): 317 - 364. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
I. Anderson, J. Rodriguez, D. Susanti, I. Porat, C. Reich, L. E. Ulrich, J. G. Elkins, K. Mavromatis, A. Lykidis, E. Kim, et al. Genome Sequence of Thermofilum pendens Reveals an Exceptional Loss of Biosynthetic Pathways without Genome Reduction J. Bacteriol., April 15, 2008; 190(8): 2957 - 2965. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. M. Meyer, A. Roth, S. M. Chervin, G. A. Garcia, and R. R. Breaker Confirmation of a second natural preQ1 aptamer class in Streptococcaceae bacteria RNA, April 1, 2008; 14(4): 685 - 695. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. Vogl, C. M. Klein, A. F. Batke, M. E. Schweingruber, and J. Stolz Characterization of Thi9, a Novel Thiamine (Vitamin B1) Transporter from Schizosaccharomyces pombe J. Biol. Chem., March 21, 2008; 283(12): 7379 - 7389. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 P. R Kensche, V. van Noort, B. E Dutilh, and M. A Huynen Practical and theoretical advances in predicting the function of a protein by its phylogenetic distribution J R Soc Interface, February 6, 2008; 5(19): 151 - 170. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. Bocobza, A. Adato, T. Mandel, M. Shapira, E. Nudler, and A. Aharoni Riboswitch-dependent gene regulation and its evolution in the plant kingdom Genes & Dev., November 15, 2007; 21(22): 2874 - 2879. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 W. Martin and M. J Russell On the origin of biochemistry at an alkaline hydrothermal vent Phil Trans R Soc B, October 29, 2007; 362(1486): 1887 - 1926. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. N. Kim, A. Roth, and R. R. Breaker Guanine riboswitch variants from Mesoplasma florum selectively recognize 2'-deoxyguanosine PNAS, October 9, 2007; 104(41): 16092 - 16097. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. Rentmeister, G. Mayer, N. Kuhn, and M. Famulok Conformational changes in the expression domain of the Escherichia coli thiM riboswitch Nucleic Acids Res., June 28, 2007; 35(11): 3713 - 3722. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. Welz and R. R. Breaker Ligand binding and gene control characteristics of tandem riboswitches in Bacillus anthracis RNA, April 1, 2007; 13(4): 573 - 582. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. T. Fuchs, F. J. Grundy, and T. M. Henkin S-adenosylmethionine directly inhibits binding of 30S ribosomal subunits to the SMK box translational riboswitch RNA PNAS, March 20, 2007; 104(12): 4876 - 4880. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. Krause, A. C. McHardy, T. W. Nattkemper, A. Puhler, J. Stoye, and F. Meyer GISMO--gene identification using a support vector machine for ORF classification Nucleic Acids Res., January 28, 2007; 35(2): 540 - 549. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. H. Link, L. Guo, and R. R. Breaker Examination of the structural and functional versatility of glmS ribozymes by using in vitro selection Nucleic Acids Res., October 18, 2006; 34(17): 4968 - 4975. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. Karunakaran, K. Ebert, S. Harvey, M. E. Leonard, V. Ramachandran, and P. S. Poole Thiamine Is Synthesized by a Salvage Pathway in Rhizobium leguminosarum bv. viciae Strain 3841. J. Bacteriol., September 1, 2006; 188(18): 6661 - 6668. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
V. Spirin, M. S. Gelfand, A. A. Mironov, and L. A. Mirny A metabolic network in the evolutionary context: Multiscale structure and modularity PNAS, June 6, 2006; 103(23): 8774 - 8779. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Wels, C. Francke, R. Kerkhoven, M. Kleerebezem, and R. J. Siezen Predicting cis-acting elements of Lactobacillus plantarum by comparative genomics with different taxonomic subgroups Nucleic Acids Res., April 13, 2006; 34(7): 1947 - 1958. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. Schyns, S. Potot, Y. Geng, T. M. Barbosa, A. Henriques, and J. B. Perkins Isolation and Characterization of New Thiamine-Deregulated Mutants of Bacillus subtilis J. Bacteriol., December 1, 2005; 187(23): 8127 - 8136. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 B. Teusink, F. H. J. van Enckevort, C. Francke, A. Wiersma, A. Wegkamp, E. J. Smid, and R. J. Siezen In Silico Reconstruction of the Metabolic Pathways of Lactobacillus plantarum: Comparing Predictions of Nutrient Requirements with Those from Growth Experiments Appl. Envir. Microbiol., November 1, 2005; 71(11): 7253 - 7262. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. Overbeek, T. Begley, R. M. Butler, J. V. Choudhuri, H.-Y. Chuang, M. Cohoon, V. de Crecy-Lagard, N. Diaz, T. Disz, R. Edwards, et al. The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes Nucleic Acids Res., October 7, 2005; 33(17): 5691 - 5702. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Tsubouchi, R. Mineki, H. Taka, N. Kaga, K. Murayama, C. Nishiyama, H. Yamane, T. Kuzuyama, and M. Nishiyama Leader Peptide-mediated Transcriptional Attenuation of Lysine Biosynthetic Gene Cluster in Thermus thermophilus J. Biol. Chem., May 6, 2005; 280(18): 18511 - 18516. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. H. Havgaard, R. B. Lyngso, G. D. Stormo, and J. Gorodkin Pairwise local structural alignment of RNA sequences with sequence similarity less than 40% Bioinformatics, May 1, 2005; 21(9): 1815 - 1824. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. C. Martinez-Gomez, M. Robers, and D. M. Downs Mutational Analysis of ThiH, a Member of the Radical S-Adenosylmethionine (AdoMet) Protein Superfamily J. Biol. Chem., September 24, 2004; 279(39): 40505 - 40510. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 W. B.L. Alkema, B. Lenhard, and W. W. Wasserman Regulog Analysis: Detection of Conserved Regulatory Networks Across Bacteria: Application to Staphylococcus aureus Genome Res., July 1, 2004; 14(7): 1362 - 1373. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. E. Barrick, K. A. Corbino, W. C. Winkler, A. Nahvi, M. Mandal, J. Collins, M. Lee, A. Roth, N. Sudarsan, I. Jona, et al. New RNA motifs suggest an expanded scope for riboswitches in bacterial genetic control PNAS, April 27, 2004; 101(17): 6421 - 6426. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Nahvi, J. E. Barrick, and R. R. Breaker Coenzyme B12 riboswitches are widespread genetic control elements in prokaryotes Nucleic Acids Res., January 2, 2004; 32(1): 143 - 150. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. A. Rodionov, A. G. Vitreschak, A. A. Mironov, and M. S. Gelfand Regulation of lysine biosynthesis and transport genes in bacteria: yet another RNA riboswitch? Nucleic Acids Res., December 1, 2003; 31(23): 6748 - 6757. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Vogel, V. Bartels, T. H. Tang, G. Churakov, J. G. Slagter-Jager, A. Huttenhofer, and E. G. H. Wagner RNomics in Escherichia coli detects new sRNA species and indicates parallel transcriptional output in bacteria Nucleic Acids Res., November 15, 2003; 31(22): 6435 - 6443. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. Barash Deleterious mutation prediction in the secondary structure of RNAs Nucleic Acids Res., November 15, 2003; 31(22): 6578 - 6584. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. A. Rodionov, A. G. Vitreschak, A. A. Mironov, and M. S. Gelfand Comparative Genomics of the Vitamin B12 Metabolism and Regulation in Prokaryotes J. Biol. Chem., October 17, 2003; 278(42): 41148 - 41159. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. G. VITRESCHAK, D. A. RODIONOV, A. A. MIRONOV, and M. S. GELFAND Regulation of the vitamin B12 metabolism and transport in bacteria by a conserved RNA structural element RNA, September 1, 2003; 9(9): 1084 - 1097. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. SUDARSAN, J. E. BARRICK, and R. R. BREAKER Metabolite-binding RNA domains are present in the genes of eukaryotes RNA, June 1, 2003; 9(6): 644 - 647. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
V. Epshtein, A. S. Mironov, and E. Nudler The riboswitch-mediated control of sulfur metabolism in bacteria PNAS, April 29, 2003; 100(9): 5052 - 5056. [Abstract] [Full Text] [PDF]
|
|
| HOME | HELP | FEEDBACK | SUBSCRIPTIONS | ARCHIVE | SEARCH | TABLE OF CONTENTS |
| All ASBMB Journals | Molecular and Cellular Proteomics |
| Journal of Lipid Research | ASBMB Today |