The origin and evolution of operons: The piecewise building of the proteobacterial histidine operon

Journal of Molecular Evolution

Volumn 60, Issue 3, 2005, Pages 378-390

  Fani, Renato ^a   Brilli, Matteo ^a   Liò, Pietro ^b  

^a Dipto di Biol Animale e Genetica   (Italy)

^b UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

Gene duplicaton; Gene fusion; Operon evolution; Operon origin

Indexed keywords

HISTIDINE;

ARTICLE; BACTERIAL GENE; BIOSYNTHESIS; CAMPYLOBACTER JEJUNI; CONTROLLED STUDY; GENE CLUSTER; NONHUMAN; NUCLEOTIDE SEQUENCE; OPERON; PHYLOGENY; PROMOTER REGION; PROTEOBACTERIA; PURINE METABOLISM;

DATABASES, NUCLEIC ACID; EVOLUTION, MOLECULAR; GENE COMPONENTS; HISTIDINE; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; OPERON; PHYLOGENY; PROTEOBACTERIA; SIGNAL TRANSDUCTION; SPECIES SPECIFICITY;

CAMPYLOBACTER JEJUNI; GAMMAPROTEOBACTERIA; PROTEOBACTERIA;

EID: 18844434690     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-004-0198-1     Document Type: Article

References (34)

1. P Alifano R Fani P Liò A Lazcano M Bazzicalupo MS Carlomagno CB Bruni 1996 Histidine biosynthetic pathway and genes: structure, regulation and evolution Microbiol Rev 60 44 69
2. M Brill R Fani 2004a Molecular evolution of hisB genes J Mol Evol 58 225 237
3. M Brilli R Fani 2004b Origin and evolution of eucaryal HIS7 genes: from metabolons to bifunctional proteins? Gene 339 149 160
4. S Dabizzi S Ammannato R Fani 2001 Expression of horizontally transferred gene clusters: activation by promoter-generating mutations Res Microbiol 152 6 539 549
5. T Dandekar B Snel M Huynen P Bork 1998 Conservation of gene order: a fingerprint of proteins that physically interact Trends Biochem Sci 23 324 328
6. R Fani 2004 Gene duplication and gene loading RV Miller MJ Day Microbial evolution: gene establishment, survival and exchange ASM Press Washington, DC 67 81
7. R Fani P Liò I Chiarelli M Bazzicalupo 1994 The evolution of the histidine biosynthetic genes in prokaryotes: a common ancestor for the hisA and hisF genes J Mol Evol 38 469 495
8. R Fani P Liò A Lazcano 1995 Molecular evolution of the histidine biosynthetic pathway J Mol Evol 41 760 774
9. R Fani E Tamburini E Mori A Lazcano P Liò C Barberio E Casalone D Cavalieri B Perito M Polsinelli 1997 Paralogous histidine biosynthetic genes: evolutionary analysis of the Saccharomyces cerevisiae HIS6 and HIS7 genes Gene 197 9 17
10. R Fani R Gallo S Fancelli E Mori E Tamburini A Lazcano 1998a Heterologous gene expression in an Escherichia coli population under starvation stress conditions J Mol Evol 47 363 368
11. R Fani E Mori E Tamburini A Lazcano 1998b Evolution of the structure and chromosomal distribution of histidine biosynthetic genes Orig Life Evol Biosph 28 4-6 555 570
12. N Glansdorff 1999 On the origin of operons and their possible role in evolution toward thermophily J Mol Evol 49 432 438
13. MA Huynen P Bork 1998 Measuring genome evolution Proc Natl Acad Sci USA 95 5849 5865
14. T Itoh K Takemoto H Mori T Gojobori 1999 Evolutionary instability of operon structures disclosed by sequence comparisons of complete microbial genomes Mol Biol Evol 16 3 332 346
15. AB Kolsto 1997 Dynamic bacterial genome organization Mol Microbiol 24 2 241 248
16. S Kumar K Tamura IB Jakobsen M Nei 2001 MEGA2: molecular evolutionary genetics analysis software Bioinformatics 17 12 1244 1245
17. F Jacob J Monod 1961 Genetic regulatory mechanisms in the synthesis of proteins J Mol Biol 3 318 356
18. F Jacob D Perrin C Sanchez J Monod 1960 L'opèron: groupe de gènes à expression cordonnée par un opératuer CR Acad Sci Paris 250 1727 1730
19. R Jensen 1996 Evolution of metabolic pathways in enteric bacteria FC Neidhart Escherichia coli and Salmonella typhimurium ASM Press Washington, DC 2649 2662
20. A Lazcano GE Fox J Oro' 1992 Life before DNA: the origin and evolution of early Archean cells RP Mortlock The evolution of metabolic function CRC Press Boca Raton 237 339
21. JG Lawrence 1999 Gene transfer, speciation, and the evolution of bacterial genomes Curr Opin Microbiol 2 519 523
22. JG Lawrence JR Roth 1996 Selfish operons: horizontal transfer may drive the evolution of gene clusters Genetics 143 1843 1860
23. P Liò N Goldman J Thorne DT Jones 1998 Combining protein secondary structure prediction and evolutionary inference Bioinformatics 14 726 733
24. WK Mass AJ Clark 1964 Studies on the mechanism of repression of arginine biosynthesis in E.coli II. Dominance of repressibility in hybrids J Mol Biol 8 365 370
25. AR Mushegian EV Koonin 1996 Gene order is not conserved in bacterial evolution Trends Genet 12 289 290
26. B Snel P Bork M Huynen 2000 Genome evolution: Gene fusion versus gene fission Trends Genet 16 9 11
27. Tamames J (2001) Evolution of gene order conservation in prokaryotes. Genome Biol 2(6) RESEARCH0020
28. JD Thompson DG Higgins TJ Gibson 1994 CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice Nucleic Acids Res 22 22 4673 4680
29. Z Yang 1997 PAML: a program package for phylogenetic analysis by maximum likelihood Comput Appl Biosci 13 5 555 556
30. G Xie NO Keyhani CA Bonner RA Jensen 2003 Ancient origin of the tryptophan operon and the dynamics of evolutionary change Microbiol Mol Biol Rev 67 303 342
31. H Watanabe H Mori T Itoh T Gojobori 1997 Genome plasticity as a paradigm for eubacteria evolution J Mol Evol 44 557 564
32. S Whelan N Goldman 2001 A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach Mol Biol Evol 18 691 699
33. S Whelan P Liò N Goldman 2001 Molecular phylogenetics: state-of-art methods for looking into the past Trends Genet 17 262 272
34. C Woese 1998 The universal ancestor Proc Natl Acad Sci USA 95 6854 6859