Genetics, Vol 143, 1843-1860, Copyright © 1996


INVESTIGATIONS

Selfish Operons: Horizontal Transfer May Drive the Evolution of Gene Clusters

J. G. Lawrence and J. R. Roth
Department of Biology, University of Utah, Salt Lake City, Utah 84112

A model is presented whereby the formation of gene clusters in bacteria is mediated by transfer of DNA within and among taxa. Bacterial operons are typically composed of genes whose products contribute to a single function. If this function is subject to weak selection or to long periods with no selection, the contributing genes may accumulate mutations and be lost by genetic drift. From a cell's perspective, once several genes are lost, the function can be restored only if all missing genes were acquired simultaneously by lateral transfer. The probability of transfer of multiple genes increases when genes are physically proximate. From a gene's perspective, horizontal transfer provides a way to escape evolutionary loss by allowing colonization of organisms lacking the encoded functions. Since organisms bearing clustered genes are more likely to act as successful donors, clustered genes would spread among bacterial genomes. The physical proximity of genes may be considered a selfish property of the operon since it affects the probability of successful horizontal transfer but may provide no physiological benefit to the host. This process predicts a mosaic structure of modern genomes in which ancestral chromosomal material is interspersed with novel, horizontally transferred operons providing peripheral metabolic functions.


This article has been cited by other articles:


Home page
Nucleic Acids ResHome page
Z. Wunderlich and L. A. Mirny
Spatial effects on the speed and reliability of protein-DNA search
Nucleic Acids Res., June 1, 2008; 36(11): 3570 - 3578.
[Abstract] [Full Text] [PDF]


Home page
Proc. Natl. Acad. Sci. USAHome page
A. Kreimer, E. Borenstein, U. Gophna, and E. Ruppin
The evolution of modularity in bacterial metabolic networks
PNAS, May 13, 2008; 105(19): 6976 - 6981.
[Abstract] [Full Text] [PDF]


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
Proc. Natl. Acad. Sci. USAHome page
M. A. Fischbach, C. T. Walsh, and J. Clardy
Chemical Ecology Special Feature: The evolution of gene collectives: How natural selection drives chemical innovation
PNAS, March 25, 2008; 105(12): 4601 - 4608.
[Abstract] [Full Text] [PDF]


Home page
Genome ResHome page
W. Qian and J. Zhang
Evolutionary dynamics of nematode operons: Easy come, slow go
Genome Res., March 1, 2008; 18(3): 412 - 421.
[Abstract] [Full Text] [PDF]


Home page
J. Bacteriol.Home page
P. J. Anderson, J. Lango, C. Carkeet, A. Britten, B. Krautler, B. D. Hammock, and J. R. Roth
One Pathway Can Incorporate either Adenine or Dimethylbenzimidazole as an {alpha}-Axial Ligand of B12 Cofactors in Salmonella enterica
J. Bacteriol., February 15, 2008; 190(4): 1160 - 1171.
[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
J. Bacteriol.Home page
R. Liu and H. Ochman
Origins of Flagellar Gene Operons and Secondary Flagellar Systems
J. Bacteriol., October 1, 2007; 189(19): 7098 - 7104.
[Abstract] [Full Text] [PDF]


Home page
Proc. Natl. Acad. Sci. USAHome page
G. Kolesov, Z. Wunderlich, O. N. Laikova, M. S. Gelfand, and L. A. Mirny
How gene order is influenced by the biophysics of transcription regulation
PNAS, August 28, 2007; 104(35): 13948 - 13953.
[Abstract] [Full Text] [PDF]


Home page
Appl. Environ. Microbiol.Home page
M. Park, Y. Jeon, H. H. Jang, H.-S. Ro, W. Park, E. L. Madsen, and C. O. Jeon
Molecular and Biochemical Characterization of 3-Hydroxybenzoate 6-Hydroxylase from Polaromonas naphthalenivorans CJ2
Appl. Envir. Microbiol., August 15, 2007; 73(16): 5146 - 5152.
[Abstract] [Full Text] [PDF]


Home page
Mol Biol EvolHome page
M. M. Cunneen and P. R. Reeves
The Yersinia kristensenii O11 O-Antigen Gene Cluster was Acquired by Lateral Gene Transfer and Incorporated at a Novel Chromosomal Locus
Mol. Biol. Evol., June 1, 2007; 24(6): 1355 - 1365.
[Abstract] [Full Text] [PDF]


Home page
Appl. Environ. Microbiol.Home page
B. El Yacoubi, A. M. Brunings, Q. Yuan, S. Shankar, and D. W. Gabriel
In Planta Horizontal Transfer of a Major Pathogenicity Effector Gene
Appl. Envir. Microbiol., March 1, 2007; 73(5): 1612 - 1621.
[Abstract] [Full Text] [PDF]


Home page
Mol Biol EvolHome page
K. Homma, S. Fukuchi, Y. Nakamura, T. Gojobori, and K. Nishikawa
Gene Cluster Analysis Method Identifies Horizontally Transferred Genes with High Reliability and Indicates that They Provide the Main Mechanism of Operon Gain in 8 Species of {gamma}-Proteobacteria
Mol. Biol. Evol., March 1, 2007; 24(3): 805 - 813.
[Abstract] [Full Text] [PDF]


Home page
Mol Biol EvolHome page
I. Comas, A. Moya, R. K. Azad, J. G. Lawrence, and F. Gonzalez-Candelas
The Evolutionary Origin of Xanthomonadales Genomes and the Nature of the Horizontal Gene Transfer Process
Mol. Biol. Evol., November 1, 2006; 23(11): 2049 - 2057.
[Abstract] [Full Text] [PDF]


Home page
J. Bacteriol.Home page
K. P. Scott, J. C. Martin, G. Campbell, C.-D. Mayer, and H. J. Flint
Whole-Genome Transcription Profiling Reveals Genes Up-Regulated by Growth on Fucose in the Human Gut Bacterium "Roseburia inulinivorans".
J. Bacteriol., June 1, 2006; 188(12): 4340 - 4349.
[Abstract] [Full Text] [PDF]


Home page
J. Bacteriol.Home page
T. Sakiyama, H. Ueno, H. Homma, O. Numata, and T. Kuwabara
Purification and Characterization of a Hemolysin-Like Protein, Sll1951, a Nontoxic Member of the RTX Protein Family from the Cyanobacterium Synechocystis sp. Strain PCC 6803.
J. Bacteriol., May 1, 2006; 188(10): 3535 - 3542.
[Abstract] [Full Text] [PDF]


Home page
J. Bacteriol.Home page
A. H. Gaspar and H. Ton-That
Assembly of Distinct Pilus Structures on the Surface of Corynebacterium diphtheriae
J. Bacteriol., February 15, 2006; 188(4): 1526 - 1533.
[Abstract] [Full Text] [PDF]


Home page
Appl. Environ. Microbiol.Home page
C. O. Jeon, M. Park, H.-S. Ro, W. Park, and E. L. Madsen
The Naphthalene Catabolic (nag) Genes of Polaromonas naphthalenivorans CJ2: Evolutionary Implications for Two Gene Clusters and Novel Regulatory Control
Appl. Envir. Microbiol., February 1, 2006; 72(2): 1086 - 1095.
[Abstract] [Full Text] [PDF]


Home page
J. Bacteriol.Home page
M. Mussmann, M. Richter, T. Lombardot, A. Meyerdierks, J. Kuever, M. Kube, F. O. Glockner, and R. Amann
Clustered Genes Related to Sulfate Respiration in Uncultured Prokaryotes Support the Theory of Their Concomitant Horizontal Transfer
J. Bacteriol., October 15, 2005; 187(20): 7126 - 7137.
[Abstract] [Full Text] [PDF]


Home page
Genome ResHome page
M. N. Price, K. H. Huang, A. P. Arkin, and E. J. Alm
Operon formation is driven by co-regulation and not by horizontal gene transfer
Genome Res., June 1, 2005; 15(6): 809 - 819.
[Abstract] [Full Text] [PDF]


Home page
Mol Biol EvolHome page
D. M. Stoebel
Lack of Evidence for Horizontal Transfer of the lac Operon into Escherichia coli
Mol. Biol. Evol., March 1, 2005; 22(3): 683 - 690.
[Abstract] [Full Text] [PDF]


Home page
Proc. Natl. Acad. Sci. USAHome page
A. Castillo, L. E. Eguiarte, and V. Souza
A genomic population genetics analysis of the pathogenic enterocyte effacement island in Escherichia coli: The search for the unit of selection
PNAS, February 1, 2005; 102(5): 1542 - 1547.
[Abstract] [Full Text] [PDF]


Home page
J. Bacteriol.Home page
J. E. McKinley and R. D. Magnuson
Characterization of the Phd Repressor-Antitoxin Boundary
J. Bacteriol., January 15, 2005; 187(2): 765 - 770.
[Abstract] [Full Text] [PDF]


Home page
Appl. Environ. Microbiol.Home page
K. A. Page, S. A. Connon, and S. J. Giovannoni
Representative Freshwater Bacterioplankton Isolated from Crater Lake, Oregon
Appl. Envir. Microbiol., November 1, 2004; 70(11): 6542 - 6550.
[Abstract] [Full Text] [PDF]


Home page
Nucleic Acids ResHome page
S. C. Janga and G. Moreno-Hagelsieb
Conservation of adjacency as evidence of paralogous operons
Nucleic Acids Res., October 11, 2004; 32(18): 5392 - 5397.
[Abstract] [Full Text] [PDF]


Home page
J. Bacteriol.Home page
G. Samuel, J.-P. Hogbin, L. Wang, and P. R. Reeves
Relationships of the Escherichia coli O157, O111, and O55 O-Antigen Gene Clusters with Those of Salmonella enterica and Citrobacter freundii, Which Express Identical O Antigens
J. Bacteriol., October 1, 2004; 186(19): 6536 - 6543.
[Abstract] [Full Text] [PDF]


Home page
MicrobiologyHome page
H. Cruz-Ramos, G. M. Cook, G. Wu, M. W. Cleeter, and R. K. Poole
Membrane topology and mutational analysis of Escherichia coli CydDC, an ABC-type cysteine exporter required for cytochrome assembly
Microbiology, October 1, 2004; 150(10): 3415 - 3427.
[Abstract] [Full Text] [PDF]


Home page
Microbiol. Mol. Biol. Rev.Home page
H. Brussow, C. Canchaya, and W.-D. Hardt
Phages and the Evolution of Bacterial Pathogens: from Genomic Rearrangements to Lysogenic Conversion
Microbiol. Mol. Biol. Rev., September 1, 2004; 68(3): 560 - 602.
[Abstract] [Full Text] [PDF]


Home page
J. Bacteriol.Home page
M. J. Franklin, S. A. Douthit, and M. A. McClure
Evidence that the algI/algJ Gene Cassette, Required for O Acetylation of Pseudomonas aeruginosa Alginate, Evolved by Lateral Gene Transfer
J. Bacteriol., July 15, 2004; 186(14): 4759 - 4773.
[Abstract] [Full Text] [PDF]


Home page
Proc. Natl. Acad. Sci. USAHome page
X. Qi, S. Bakht, M. Leggett, C. Maxwell, R. Melton, and A. Osbourn
A gene cluster for secondary metabolism in oat: Implications for the evolution of metabolic diversity in plants
PNAS, May 25, 2004; 101(21): 8233 - 8238.
[Abstract] [Full Text] [PDF]


Home page
J. Bacteriol.Home page
J. A. Smith and R. D. Magnuson
Modular Organization of the Phd Repressor/Antitoxin Protein
J. Bacteriol., May 1, 2004; 186(9): 2692 - 2698.
[Abstract] [Full Text] [PDF]


Home page
Appl. Environ. Microbiol.Home page
A. Buchan, E. L. Neidle, and M. A. Moran
Diverse Organization of Genes of the {beta}-Ketoadipate Pathway in Members of the Marine Roseobacter Lineage
Appl. Envir. Microbiol., March 1, 2004; 70(3): 1658 - 1668.
[Abstract] [Full Text] [PDF]


Home page
Genome ResHome page
B. Snel and M. A. Huynen
Quantifying Modularity in the Evolution of Biomolecular Systems
Genome Res., March 1, 2004; 14(3): 391 - 397.
[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
GeneticsHome page
E. R. Zinser, D. Schneider, M. Blot, and R. Kolter
Bacterial Evolution Through the Selective Loss of Beneficial Genes: Trade-Offs in Expression Involving Two Loci
Genetics, August 1, 2003; 164(4): 1271 - 1277.
[Abstract] [Full Text] [PDF]


Home page
Crit. Rev. Oral Biol. Med.Home page
M. J. Duncan
GENOMICSOF ORAL BACTERIA
Crit. Rev. Oral. Biol. Med., May 1, 2003; 14(3): 175 - 187.
[Abstract] [Full Text] [PDF]


Home page
J. Bacteriol.Home page
W.-L. Deng, A. H. Rehm, A. O. Charkowski, C. M. Rojas, and A. Collmer
Pseudomonas syringae Exchangeable Effector Loci: Sequence Diversity in Representative Pathovars and Virulence Function in P. syringae pv. syringae B728a
J. Bacteriol., April 15, 2003; 185(8): 2592 - 2602.
[Abstract] [Full Text] [PDF]


Home page
J. Bacteriol.Home page
K. Chan, S. Baker, C. C. Kim, C. S. Detweiler, G. Dougan, and S. Falkow
Genomic Comparison of Salmonella enterica Serovars and Salmonella bongori by Use of an S. enterica Serovar Typhimurium DNA Microarray
J. Bacteriol., January 15, 2003; 185(2): 553 - 563.
[Abstract] [Full Text] [PDF]


Home page
Infect. Immun.Home page
A. Perrin, S. Bonacorsi, E. Carbonnelle, D. Talibi, P. Dessen, X. Nassif, and C. Tinsley
Comparative Genomics Identifies the Genetic Islands That Distinguish Neisseria meningitidis, the Agent of Cerebrospinal Meningitis, from Other Neisseria Species
Infect. Immun., December 1, 2002; 70(12): 7063 - 7072.
[Abstract] [Full Text] [PDF]


Home page
Clin. Microbiol. Rev.Home page
J. L. Martinez and F. Baquero
Interactions among Strategies Associated with Bacterial Infection: Pathogenicity, Epidemicity, and Antibiotic Resistance
Clin. Microbiol. Rev., October 1, 2002; 15(4): 647 - 679.
[Abstract] [Full Text] [PDF]


Home page
MicrobiologyHome page
M. L. Kotewicz, B. Li, D. D. Levy, J. E. LeClerc, A. W. Shifflet, and T. A. Cebula
Evolution of multi-gene segments in the mutS-rpoS intergenic region of Salmonella enterica serovar Typhimurium LT2
Microbiology, August 1, 2002; 148(8): 2531 - 2540.
[Abstract] [Full Text] [PDF]


Home page
J. Bacteriol.Home page
L. Wang, S. Huskic, A. Cisterne, D. Rothemund, and P. R. Reeves
The O-Antigen Gene Cluster of Escherichia coli O55:H7 and Identification of a New UDP-GlcNAc C4 Epimerase Gene
J. Bacteriol., May 15, 2002; 184(10): 2620 - 2625.
[Abstract] [Full Text] [PDF]


Home page
Nucleic Acids ResHome page
I. B. Rogozin, K. S. Makarova, J. Murvai, E. Czabarka, Y. I. Wolf, R. L. Tatusov, L. A. Szekely, and E. V. Koonin
Connected gene neighborhoods in prokaryotic genomes
Nucleic Acids Res., May 15, 2002; 30(10): 2212 - 2223.
[Abstract] [Full Text] [PDF]


Home page
Antimicrob. Agents Chemother.Home page
Y.-C. Yeh, K.-C. Chang, J.-C. Yang, C.-T. Fang, and J.-T. Wang
Association of Metronidazole Resistance and Natural Competence in Helicobacter pylori
Antimicrob. Agents Chemother., May 1, 2002; 46(5): 1564 - 1567.
[Abstract] [Full Text] [PDF]


Home page
Mol Biol EvolHome page
V. Koufopanou, M. R. Goddard, and A. Burt
Adaptation for Horizontal Transfer in a Homing Endonuclease
Mol. Biol. Evol., March 1, 2002; 19(3): 239 - 246.
[Abstract] [Full Text] [PDF]


Home page
Proc. Natl. Acad. Sci. USAHome page
J. de Vries and W. Wackernagel
Integration of foreign DNA during natural transformation of Acinetobacter sp. by homology-facilitated illegitimate recombination
PNAS, February 19, 2002; 99(4): 2094 - 2099.
[Abstract] [Full Text] [PDF]


Home page
J. Bacteriol.Home page
R. L. Davies, S. Campbell, and T. S. Whittam
Mosaic Structure and Molecular Evolution of the Leukotoxin Operon (lktCABD) in Mannheimia (Pasteurella) haemolytica, Mannheimia glucosida, and Pasteurella trehalosi
J. Bacteriol., January 1, 2002; 184(1): 266 - 277.
[Abstract] [Full Text] [PDF]


Home page
Genome ResHome page
S. P. Kennedy, W. V. Ng, S. L. Salzberg, L. Hood, and S. DasSarma
Understanding the Adaptation of Halobacterium Species NRC-1 to Its Extreme Environment through Computational Analysis of Its Genome Sequence
Genome Res., October 1, 2001; 11(10): 1641 - 1650.
[Abstract] [Full Text] [PDF]


Home page
J. Bacteriol.Home page
S. Karlin, J. Mrazek, A. Campbell, and D. Kaiser
Characterizations of Highly Expressed Genes of Four Fast-Growing Bacteria
J. Bacteriol., September 1, 2001; 183(17): 5025 - 5040.
[Abstract] [Full Text] [PDF]


Home page
J. Bacteriol.Home page
J. Davis, A. L. Smith, W. R. Hughes, and M. Golomb
Evolution of an Autotransporter: Domain Shuffling and Lateral Transfer from Pathogenic Haemophilus to Neisseria
J. Bacteriol., August 1, 2001; 183(15): 4626 - 4635.
[Abstract] [Full Text] [PDF]


Home page
MicrobiologyHome page
A. Y. Chistoserdov
Cloning, sequencing and mutagenesis of the genes for aromatic amine dehydrogenase from Alcaligenes faecalis and evolution of amine dehydrogenases
Microbiology, August 1, 2001; 147(8): 2195 - 2202.
[Abstract] [Full Text] [PDF]


Home page
Proc. Natl. Acad. Sci. USAHome page
A. E. Murray, D. Lies, G. Li, K. Nealson, J. Zhou, and J. M. Tiedje
DNA/DNA hybridization to microarrays reveals gene-specific differences between closely related microbial genomes
PNAS, August 1, 2001; (2001) 171178898.
[Abstract] [Full Text] [PDF]


Home page
J. Bacteriol.Home page
E. W. Brown, J. E. LeClerc, B. Li, W. L. Payne, and T. A. Cebula
Phylogenetic Evidence for Horizontal Transfer of mutS Alleles among Naturally Occurring Escherichia coli Strains
J. Bacteriol., March 1, 2001; 183(5): 1631 - 1644.
[Abstract] [Full Text]


Home page
GeneticsHome page
A. G. Smulian, T. Sesterhenn, R. Tanaka, and M. T. Cushion
The ste3 Pheromone Receptor Gene of Pneumocystis carinii Is Surrounded by a Cluster of Signal Transduction Genes
Genetics, March 1, 2001; 157(3): 991 - 1002.
[Abstract] [Full Text]


Home page
GeneticsHome page
L. E. Bean, W. H. Dvorachek , Jr., E. L. Braun, A. Errett, G. S. Saenz, M. D. Giles, M. Werner-Washburne, M. A. Nelson, and D. O. Natvig
Analysis of the pdx-1 (snz-1/sno-1) Region of the Neurospora crassa Genome: Correlation of Pyridoxine-Requiring Phenotypes With Mutations in Two Structural Genes
Genetics, March 1, 2001; 157(3): 1067 - 1075.
[Abstract] [Full Text]


Home page
Proc. Natl. Acad. Sci. USAHome page
T. F. Cooper and J. A. Heinemann
Postsegregational killing does not increase plasmid stability but acts to mediate the exclusion of competing plasmids
PNAS, October 26, 2000; (2000) 220077897.
[Abstract] [Full Text]


Home page
J. Bacteriol.Home page
R. Sanchez, M. Roovers, and N. Glansdorff
Organization and Expression of a Thermus thermophilus Arginine Cluster: Presence of Unidentified Open Reading Frames and Absence of a Shine-Dalgarno Sequence
J. Bacteriol., October 15, 2000; 182(20): 5911 - 5915.
[Abstract] [Full Text]


Home page
Nucleic Acids ResHome page
W. Fujibuchi, H. Ogata, H. Matsuda, and M. Kanehisa
Automatic detection of conserved gene clusters in multiple genomes by graph comparison and P-quasi grouping
Nucleic Acids Res., October 15, 2000; 28(20): 4029 - 4036.
[Abstract] [Full Text] [PDF]


Home page
J. Bacteriol.Home page
E. I. Wilding, J. R. Brown, A. P. Bryant, A. F. Chalker, D. J. Holmes, K. A. Ingraham, S. Iordanescu, C. Y. So, M. Rosenberg, and M. N. Gwynn
Identification, Evolution, and Essentiality of the Mevalonate Pathway for Isopentenyl Diphosphate Biosynthesis in Gram-Positive Cocci
J. Bacteriol., August 1, 2000; 182(15): 4319 - 4327.
[Abstract] [Full Text]


Home page
Infect. Immun.Home page
S. R. Klee, X. Nassif, B. Kusecek, P. Merker, J.-L. Beretti, M. Achtman, and C. R. Tinsley
Molecular and Biological Analysis of Eight Genetic Islands That Distinguish Neisseria meningitidis from the Closely Related Pathogen Neisseria gonorrhoeae
Infect. Immun., April 1, 2000; 68(4): 2082 - 2095.
[Abstract] [Full Text] [PDF]


Home page
J. Bacteriol.Home page
D. Parke, D. A. D'Argenio, and L. N. Ornston
Bacteria Are Not What They Eat: That Is Why They Are So Diverse
J. Bacteriol., January 15, 2000; 182(2): 257 - 263.
[Full Text]


Home page
J. Bacteriol.Home page
T. Allen, P. Shen, L. Samsel, R. Liu, L. Lindahl, and J. M. Zengel
Phylogenetic Analysis of L4-Mediated Autogenous Control of the S10 Ribosomal Protein Operon
J. Bacteriol., October 1, 1999; 181(19): 6124 - 6132.
[Abstract] [Full Text]


Home page
GeneticsHome page
R. Milkman, E. A. Raleigh, M. McKane, D. Cryderman, P. Bilodeau, and K. McWeeny
Molecular Evolution of the Escherichia coli Chromosome. V. Recombination Patterns Among Strains of Diverse Origin
Genetics, October 1, 1999; 153(2): 539 - 554.
[Abstract] [Full Text] [PDF]


Home page