Genome Research

Home Help [Feedback] [For Subscribers] [Archive] [Search] [Contents]
QUICK SEARCH:   [advanced]


     

Published online before print August 1, 2002
Genome Research, DOI: 10.1101/gr.200601
October 15, 2001, 10.1101/gr.200601
This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow All Versions of this Article:
GR-2006Rv1
11/11/1842
12/8/1221    most recent
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Right arrow Citation Map
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrow reprints & permissions
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Zheng, Y.
Right arrow Articles by Kasif, S.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Zheng, Y.
Right arrow Articles by Kasif, S.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us   Add to Digg   Add to Reddit   Add to Technorati  
What's this?

Vol. 12, Issue 8, 1221-1230, August 2002

LETTER
Computational Identification of Operons in Microbial Genomes

Yu Zheng,1 Joseph D. Szustakowski,2 Lance Fortnow,3 Richard J. Roberts,4 and Simon Kasif1,2,5

1 Bioinformatics Graduate Program, Boston University, Boston, Massachusetts 02215, USA; 2 Biomedical Engineering Department, Boston University, Boston, Massachusetts 02215, USA; 3 NEC Research Institute, Inc., Princeton, New Jersey 08540, USA; 4 New England BioLabs, Beverly, Massachusetts 01915, USA

By applying graph representations to biochemical pathways, a new computational pipeline is proposed to find potential operons in microbial genomes. The algorithm relies on the fact that enzyme genes in operons tend to catalyze successive reactions in metabolic pathways. We applied this algorithm to 42 microbial genomes to identify putative operon structures. The predicted operons from Escherichia coli were compared with a selected metabolism-related operon dataset from the RegulonDB database, yielding a prediction sensitivity (89%) and specificity (87%) relative to this dataset. Several examples of detected operons are given and analyzed. Modular gene cluster transfer and operon fusion are observed. A further use of predicted operon data to assign function to putative genes was suggested and, as an example, a previous putative gene (MJ1604) from Methanococcus jannaschii is now annotated as a phosphofructokinase, which was regarded previously as a missing enzyme in this organism. GC content changes in the operon region and nonoperon region were examined. The results reveal a clear GC content transition at the boundaries of putative operons. We looked further into the conservation of operons across genomes. A trp operon alignment is analyzed in depth to show gene loss and rearrangement in different organisms during operon evolution.

5 Corresponding author.

12:1221-1230 ©2002 by Cold Spring Harbor Laboratory Press  ISSN 1088-9051/02 $5.00
Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us   Add to Digg Digg   Add to Reddit Reddit   Add to Technorati Technorati    What's this?


This article has been cited by other articles:


Home page
 Brief BioinformHome page
R. W. W. Brouwer, O. P. Kuipers, and S. A. F. T. v. Hijum
The relative value of operon predictions
Brief Bioinform, April 17, 2008; (2008) bbn019v1.
[Abstract] [Full Text] [PDF]

Home page
 Brief BioinformHome page
M. Brilli, R. Fani, and P. Lio
Current trends in the bioinformatic sequence analysis of metabolic pathways in prokaryotes
Brief Bioinform, January 1, 2008; 9(1): 34 - 45.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
S. Charaniya, S. Mehra, W. Lian, K. P. Jayapal, G. Karypis, and W.-S. Hu
Transcriptome dynamics-based operon prediction and verification in Streptomyces coelicolor
Nucleic Acids Res., December 18, 2007; 35(21): 7222 - 7236.
[Abstract] [Full Text] [PDF]

Home page
 Genome Res.Home page
Y. Nakatani, H. Takeda, Y. Kohara, and S. Morishita
Reconstruction of the vertebrate ancestral genome reveals dynamic genome reorganization in early vertebrates
Genome Res., September 1, 2007; 17(9): 1254 - 1265.
[Abstract] [Full Text] [PDF]

Home page
 Genome Res.Home page
S. Yellaboina, K. Goyal, and S. C. Mande
Inferring genome-wide functional linkages in E. coli by combining improved genome context methods: Comparison with high-throughput experimental data
Genome Res., April 1, 2007; 17(4): 527 - 535.
[Abstract] [Full Text] [PDF]

Home page
 Appl. Environ. Microbiol.Home page
N. H. Bergman, K. D. Passalacqua, P. C. Hanna, and Z. S. Qin
Operon Prediction for Sequenced Bacterial Genomes without Experimental Information
Appl. Envir. Microbiol., February 1, 2007; 73(3): 846 - 854.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
T. T. Tran, P. Dam, Z. Su, F. L. Poole II, M. W. W. Adams, G. T. Zhou, and Y. Xu
Operon prediction in Pyrococcus furiosus
Nucleic Acids Res., January 12, 2007; 35(1): 11 - 20.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
P. Dam, V. Olman, K. Harris, Z. Su, and Y. Xu
Operon prediction using both genome-specific and general genomic information
Nucleic Acids Res., January 12, 2007; 35(1): 288 - 298.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
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]

Home page
 Mol Biol EvolHome page
E. P. C. Rocha
Inference and Analysis of the Relative Stability of Bacterial Chromosomes
Mol. Biol. Evol., March 1, 2006; 23(3): 513 - 522.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
S. Okuda, T. Katayama, S. Kawashima, S. Goto, and M. Kanehisa
ODB: a database of operons accumulating known operons across multiple genomes
Nucleic Acids Res., January 1, 2006; 34(suppl_1): D358 - D362.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
F. Boyer, A. Morgat, L. Labarre, J. Pothier, and A. Viari
Syntons, metabolons and interactons: an exact graph-theoretical approach for exploring neighbourhood between genomic and functional data
Bioinformatics, December 1, 2005; 21(23): 4209 - 4215.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
M. Nei
Selectionism and Neutralism in Molecular Evolution
Mol. Biol. Evol., December 1, 2005; 22(12): 2318 - 2342.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
K. S. Makarova, Y. I. Wolf, S. L. Mekhedov, B. G. Mirkin, and E. V. Koonin
Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell
Nucleic Acids Res., August 16, 2005; 33(14): 4626 - 4638.
[Abstract] [Full Text] [PDF]

Home page
 Int. J. Syst. Evol. Microbiol.Home page
K. R. Sakharkar, M. K. Sakharkar, C. Verma, and V. T. K. Chow
Comparative study of overlapping genes in bacteria, with special reference to Rickettsia prowazekii and Rickettsia conorii
Int J Syst Evol Microbiol, May 1, 2005; 55(3): 1205 - 1209.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
E. Jacob, R. Sasikumar, and K. N. R. Nair
A fuzzy guided genetic algorithm for operon prediction
Bioinformatics, April 15, 2005; 21(8): 1403 - 1407.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
M. N. Price, K. H. Huang, E. J. Alm, and A. P. Arkin
A novel method for accurate operon predictions in all sequenced prokaryotes
Nucleic Acids Res., February 8, 2005; 33(3): 880 - 892.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
L. Wang, J. D. Trawick, R. Yamamoto, and C. Zamudio
Genome-wide operon prediction in Staphylococcus aureus
Nucleic Acids Res., July 13, 2004; 32(12): 3689 - 3702.
[Abstract] [Full Text] [PDF]

Home page
 Genome Res.Home page
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]

Home page
 Mol Biol EvolHome page
R. Friedman and A. L. Hughes
Two Patterns of Genome Organization in Mammals: the Chromosomal Distribution of Duplicate Genes in Human and Mouse
Mol. Biol. Evol., June 1, 2004; 21(6): 1008 - 1013.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
A. Christoffels, E. G. L. Koh, J.-m. Chia, S. Brenner, S. Aparicio, and B. Venkatesh
Fugu Genome Analysis Provides Evidence for a Whole-Genome Duplication Early During the Evolution of Ray-Finned Fishes
Mol. Biol. Evol., June 1, 2004; 21(6): 1146 - 1151.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
X. Chen, Z. Su, P. Dam, B. Palenik, Y. Xu, and T. Jiang
Operon prediction by comparative genomics: an application to the Synechococcus sp. WH8102 genome
Nucleic Acids Res., April 19, 2004; 32(7): 2147 - 2157.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
U. Karaoz, T. M. Murali, S. Letovsky, Y. Zheng, C. Ding, C. R. Cantor, and S. Kasif
Whole-genome annotation by using evidence integration in functional-linkage networks
PNAS, March 2, 2004; 101(9): 2888 - 2893.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
K. M. Teshima and H. Innan
The Effect of Gene Conversion on the Divergence Between Duplicated Genes
Genetics, March 1, 2004; 166(3): 1553 - 1560.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
K. Vandepoele, W. De Vos, J. S. Taylor, A. Meyer, and Y. Van de Peer
Major events in the genome evolution of vertebrates: Paranome age and size differ considerably between ray-finned fishes and land vertebrates
PNAS, February 10, 2004; 101(6): 1638 - 1643.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
H. Salgado, S. Gama-Castro, A. Martinez-Antonio, E. Diaz-Peredo, F. Sanchez-Solano, M. Peralta-Gil, D. Garcia-Alonso, V. Jimenez-Jacinto, A. Santos-Zavaleta, C. Bonavides-Martinez, et al.
RegulonDB (version 4.0): transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12
Nucleic Acids Res., January 1, 2004; 32(90001): D303 - 306.
[Abstract] [Full Text] [PDF]

Home page
 Genome Res.Home page
A. J. Poustka, D. Groth, S. Hennig, S. Thamm, A. Cameron, A. Beck, R. Reinhardt, R. Herwig, G. Panopoulou, and H. Lehrach
Generation, Annotation, Evolutionary Analysis, and Database Integration of 20,000 Unique Sea Urchin EST Clusters
Genome Res., December 1, 2003; 13(12): 2736 - 2746.
[Abstract] [Full Text] [PDF]

Home page
 Microbiol. Mol. Biol. Rev.Home page
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]

Home page
 Mol Biol EvolHome page
L. David, S. Blum, M. W. Feldman, U. Lavi, and J. Hillel
Recent Duplication of the Common Carp (Cyprinus carpio L.) Genome as Revealed by Analyses of Microsatellite Loci
Mol. Biol. Evol., September 1, 2003; 20(9): 1425 - 1434.
[Abstract] [Full Text] [PDF]

Home page
 Genome Res.Home page
G. Panopoulou, S. Hennig, D. Groth, A. Krause, A. J. Poustka, R. Herwig, M. Vingron, and H. Lehrach
New Evidence for Genome-Wide Duplications at the Origin of Vertebrates Using an Amphioxus Gene Set and Completed Animal Genomes
Genome Res., June 1, 2003; 13(6): 1056 - 1066.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
A. L. Hughes and R. Friedman
Genome-Wide Survey for Genes Horizontally Transferred from Cellular Organisms to Baculoviruses
Mol. Biol. Evol., June 1, 2003; 20(6): 979 - 987.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
A. P. Spicer, A. Joo, and R. A. Bowling Jr.
A Hyaluronan Binding Link Protein Gene Family Whose Members Are Physically Linked Adjacent to Chrondroitin Sulfate Proteoglycan Core Protein Genes: THE MISSING LINKS
J. Biol. Chem., May 30, 2003; 278(23): 21083 - 21091.
[Abstract] [Full Text] [PDF]

Home page
 Genome Res.Home page
A. L. Hughes and R. Friedman
Parallel Evolution by Gene Duplication in the Genomes of Two Unicellular Fungi
Genome Res., May 1, 2003; 13(5): 794 - 799.
[Abstract] [Full Text] [PDF]

Home page
 Genome Res.Home page
Y. Wu, X. Wang, X. Liu, and Y. Wang
Data-Mining Approaches Reveal Hidden Families of Proteases in the Genome of Malaria Parasite
Genome Res., April 1, 2003; 13(4): 601 - 616.
[Abstract] [Full Text] [PDF]

Home page
 Genome Res.Home page
J. S. Taylor, I. Braasch, T. Frickey, A. Meyer, and Y. Van de Peer
Genome Duplication, a Trait Shared by 22,000 Species of Ray-Finned Fish
Genome Res., March 1, 2003; 13(3): 382 - 390.
[Abstract] [Full Text] [PDF]

Home page
 Genome Res.Home page
A. Courseaux, F. Richard, J. Grosgeorge, C. Ortola, A. Viale, C. Turc-Carel, B. Dutrillaux, P. Gaudray, and J.-L. Nahon
Segmental Duplications in Euchromatic Regions of Human Chromosome 5: A Source of Evolutionary Instability and Transcriptional Innovation
Genome Res., March 1, 2003; 13(3): 369 - 381.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
R. Friedman and A. L. Hughes
The Temporal Distribution of Gene Duplication Events in a Set of Highly Conserved Human Gene Families
Mol. Biol. Evol., January 1, 2003; 20(1): 154 - 161.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
Y. Lin, A. Khokhlatchev, D. Figeys, and J. Avruch
Death-associated Protein 4 Binds MST1 and Augments MST1-induced Apoptosis
J. Biol. Chem., December 6, 2002; 277(50): 47991 - 48001.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
N. Sankar, J. Machado, P. Abdulla, A. J. Hilliker, and I. R. Coe
Comparative genomic analysis of equilibrative nucleoside transporters suggests conserved protein structure despite limited sequence identity
Nucleic Acids Res., October 15, 2002; 30(20): 4339 - 4350.
[Abstract] [Full Text] [PDF]


Home Help [Feedback] [For Subscribers] [Archive] [Search] [Contents]
Genes Dev. Learn. Mem.
Protein Science RNA Genome Res.