A global analysis of adaptive evolution of operons in cyanobacteria

Antonie van Leeuwenhoek, International Journal of General and Molecular Microbiology

Volumn 103, Issue 2, 2013, Pages 331-346

  Memon, Danish ^a,b,d   Singh, Abhay K ^c   Pakrasi, Himadri B ^c   Wangikar, Pramod P ^a  

^a INDIAN INSTITUTE OF TECHNOLOGY BOMBAY   (India)

^b UNIVERSITY OF PUNE   (India)

^c WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^d UNIVERSITY OF MANCHESTER   (United Kingdom)

Author keywords

Blue green algae; Comparative genomics; Gene packing; Genome context; Phylogenetic distance

Indexed keywords

RNA 16S;

ACCURACY; ARTICLE; BACILLUS SUBTILIS; BACTERIAL GENOME; BACTERIAL STRAIN; BACTERIUM; CLADISTICS; CONTROLLED STUDY; CYANOBACTERIUM; ESCHERICHIA COLI; EVOLUTIONARY ADAPTATION; GENE CLUSTER; GENETIC ALGORITHM; GENETIC CONSERVATION; GENETIC DISTANCE; GENETIC SIMILARITY; GENETIC TRAIT; GENETIC VARIABILITY; NONHUMAN; OPERON; PHYLOGENETIC TREE; PRIORITY JOURNAL; PROCESS OPTIMIZATION; PROKARYOTE; QUALITATIVE ANALYSIS; QUANTITATIVE ANALYSIS; RECEIVER OPERATING CHARACTERISTIC; SYNECHOCOCCUS ELONGATUS; SYNECHOCYSTIS; TRICHODESMIUM ERYTHRAEUM;

BIOLOGICAL EVOLUTION; CYANOBACTERIA; EVOLUTION, MOLECULAR; OPERON;

CHLOROPHYTA; CYANOBACTERIA; PROKARYOTA; SYNECHOCYSTIS SP. PCC 6803;

EID: 84878864757     PISSN: 00036072     EISSN: 15729699     Source Type: Journal    
DOI: 10.1007/s10482-012-9813-0     Document Type: Article

References (68)

1. Agervald A, Stensjo K, Holmqvist M, Lindblad P (2008) Transcription of the extended hyp-operon in Nostoc sp. strain PCC 7120. BMC Microbiol 8:69
2. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucl Acids Res 25:3389-3402
3. Bergman NH, Passalacqua KD, Hanna PC, Qin ZS (2007) Operon prediction for sequenced bacterial genomes without experimental information. Appl Environ Microbiol 73(3):846-854
4. Bockhorst J, Craven M, Page D, Shavlik J, Glasner J (2003a) A Bayesian network approach to operon prediction. Bioinformatics 19(10):1227-1235
5. Bockhorst J, Qiu Y, Glasner J, Liu M, Blattner F, Craven M (2003b) Predicting bacterial transcription units using sequence and expression data. Bioinformatics 19(Suppl 1):i34-i43
6. Brouwer RW, Kuipers OP, van Hijum SA (2008) The relative value of operon predictions. Brief Bioinform 9(5):367-375
7. Chen X, Su Z, Dam P, Palenik B, Xu Y, Jiang T (2004a) Operon prediction by comparative genomics: an application to the Synechococcus sp WH8102 genome. Nucl Acids Res 32(7):2147-2157
8. Chen X, Su Z, Xu Y, Jiang T (2004b) Computational prediction of operons in Synechococcus sp. WH8102. Genome Inform 15(2):211-222
9. Dam P, Olman V, Harris K, Su Z, Xu Y (2007) Operon prediction using both genome-specific and general genomic information. Nucl Acids Res 35(1):288-298
10. Dandekar T, Snel B, Huynen M, Bork P (1998) Conservation of gene order: a fingerprint of proteins that physically interact. Trends Biochem Sci 23(9):324-328
11. de Daruvar A, Collado-Vides J, Valencia A (2002) Analysis of the cellular functions of Escherichia coli operons and their conservation in Bacillus subtilis. J Mol Evol 55(2):211-221
12. de Hoon MJ, Makita Y, Nakai K, Miyano S (2005) Prediction of transcriptional terminators in Bacillus subtilis and related species. PLoS Comput Biol 1(3):e25
13. Dehal PS, Joachimiak MP, Price MN, Bates JT, Baumohl JK, Chivian D, Friedland GD, Huang KH, Keller K, Novichkov PS, Dubchak IL, Alm EJ, Arkin AP (2010) MicrobesOnline: an integrated portal for comparative and functional genomics. Nucl Acids Res 38(Database issue):D396-D400
14. Dufresne A, Garczarek L, Partensky F (2005) Accelerated evolution associated with genome reduction in a free-living prokaryote. Genome Biol 6(2):R14
15. Edwards MT, Rison SC, Stoker NG, Wernisch L (2005) A universally applicable method of operon map prediction on minimally annotated genomes using conserved genomic context. Nucl Acids Res 33(10):3253-3262
16. Ermolaeva MD, White O, Salzberg SL (2001) Prediction of operons in microbial genomes. Nucl Acids Res 29(5):1216-1221
17. Felsenstein J (1996) Inferring phylogenies from protein sequences by parsimony, distance, and likelihood methods. Methods Enzymol 266:418-427
18. Felsenstein J (2008) Comparative methods with sampling error and within-species variation: contrasts revisited and revised. Am Nat 171(6):713-725
19. Galperin MY, Koonin EV (2000) Who's your neighbor? New computational approaches for functional genomics. Nat Biotechnol 18(6):609-613
20. Gupta RS (2009) Protein signatures (molecular synapomorphies) that are distinctive characteristics of the major cyanobacterial clades. Int J Syst Evol Microbiol 59(Pt 10):2510-2526
21. Gupta RS, Mathews DW (2010) Signature proteins for the major clades of cyanobacteria. BMC Evol Biol 10:24
22. Honda D, Yokota A, Sugiyama J (1999) Detection of seven major evolutionary lineages in cyanobacteria based on the 16S rRNA gene sequence analysis with new sequences of five marine Synechococcus strains. J Mol Evol 48(6):723-739
23. Huynen M, Snel B, Lathe W, Bork P (2000) Exploitation of gene context. Curr Opin Struct Biol 10(3):366-370
24. Itoh T, Takemoto K, Mori H, Gojobori T (1999) Evolutionary instability of operon structures disclosed by sequence comparisons of complete microbial genomes. Mol Biol Evol 16(3):332-346
25. Jacob F, Monod J (1961a) Genetic regulatory mechanisms in the synthesis of proteins. J Mol Biol 3:318-356
26. Jacob F, Monod J (1961b) On the regulation of gene activity. Cold Spring Harb Symp Quant Biol 26:193-211
27. Jacob E, Sasikumar R, Nair KN (2005) A fuzzy guided genetic algorithm for operon prediction. Bioinformatics 21(8):1403-1407
28. Janga SC, Lamboy WF, Huerta AM, Moreno-Hagelsieb G (2006) The distinctive signatures of promoter regions and operon junctions across prokaryotes. Nucl Acids Res 34(14):3980-3987
29. Johnson ZI, Zinser ER, Coe A, McNulty NP, Woodward EM, Chisholm SW (2006) Niche partitioning among Prochlorococcus ecotypes along ocean-scale environmental gradients. Science 311(5768):1737-1740
30. Kanehisa M, Goto S, Kawashima S, Nakaya A (2002) The KEGG databases at GenomeNet. Nucl Acids Res 30:42-46
31. Kazakov AE, Cipriano MJ, Novichkov PS, Minovitsky S, Vinogradov DV, Arkin A, Mironov AA, Gelfand MS, Dubchak I (2007) RegTransBase - a database of regulatory sequences and interactions in a wide range of prokaryotic genomes. Nucl Acids Res 35(Database issue):D407-D412
32. Kettler GC, Martiny AC, Huang K, Zucker J, Coleman ML, Rodrigue S, Chen F, Lapidus A, Ferriera S, Johnson J, Steglich C, Church GM, Richardson P, Chisholm SW (2007) Patterns and implications of gene gain and loss in the evolution of Prochlorococcus. PLoS Genet 3(12):e231
33. Lawrence JG (2003) Gene organization: selection, selfishness, and serendipity. Annu Rev Microbiol 57:419-440
34. Lawrence JG, Roth JR (1996) Selfish operons: horizontal transfer may drive the evolution of gene clusters. Genetics 143(4):1843-1860
35. Mao F, Dam P, Chou J, Olman V, Xu Y (2009) DOOR: a database for prokaryotic operons. Nucl Acids Res 37(Database issue):D459-D463
36. Marcotte EM (2000) Computational genetics: finding protein function by nonhomology methods. Curr Opin Struct Biol 10(3):359-365
37. Merino-Puerto V, Mariscal V, Mullineaux CW, Herrero A, Flores E (2010) Fra proteins influencing filament integrity, diazotrophy and localization of septal protein SepJ in the heterocyst-forming cyanobacterium Anabaena sp. Mol Microbiol 75(5):1159-1170
38. Moreno-Hagelsieb G, Collado-Vides J (2002) A powerful non-homology method for the prediction of operons in prokaryotes. Bioinformatics 18(Suppl 1):S329-S336
39. Mulkidjanian AY, Koonin EV, Makarova KS, Mekhedov SL, Sorokin A, Wolf YI, Dufresne A, Partensky F, Burd H, Kaznadzey D, Haselkorn R, Galperin MY (2006) The cyanobacterial genome core and the origin of photosynthesis. Proc Natl Acad Sci USA 103(35):13126-13131
40. Nakamura Y, Kaneko T, Hirosawa M, Miyajima N, Tabata S (1998) CyanoBase, a www database containing the complete nucleotide sequence of the genome of Synechocystis sp. strain PCC6803. Nucl Acids Res 26(1):63-67
41. Nakao M, Okamoto S, Kohara M, Fujishiro T, Fujisawa T, Sato S, Tabata S, Kaneko T, Nakamura Y (2010) CyanoBase: the cyanobacteria genome database update 2010. Nucl Acids Res 38(Database issue):D379-D381
42. Ogata H, Goto S, Sato K, Fujibuchi W, Bono H, Kanehisa M (1999) KEGG: Kyoto encyclopedia of genes and genomes. Nucl Acids Res 27(1):29-34
43. Okuda S, Yoshizawa AC (2011) ODB: a database for operon organizations, 2011 update. Nucl Acids Res 39(Database issue):D552-D555
44. Okuda S, Katayama T, Kawashima S, Goto S, Kanehisa M (2006) ODB: a database of operons accumulating known operons across multiple genomes. Nucl Acids Res 34(Database issue):D358-D362
45. Overbeek R, Fonstein M, D'Souza M, Pusch GD, Maltsev N (1999) The use of gene clusters to infer functional coupling. Proc Natl Acad Sci USA 96(6):2896-2901
46. Price MN, Huang KH, Alm EJ, Arkin AP (2005a) A novel method for accurate operon predictions in all sequenced prokaryotes. Nucl Acids Res 33(3):880-892
47. Price MN, Huang KH, Arkin AP, Alm EJ (2005b) Operon formation is driven by co-regulation and not by horizontal gene transfer. Genome Res 15(6):809-819
48. Price MN, Arkin AP, Alm EJ (2006) The life-cycle of operons. PLoS Genet 2(6):e96
49. Quackenbush J (2002) Microarray data normalization and transformation. Nat Genet 32(Suppl):496-501
50. Rippka R, Deruelles J, Waterbury JB, Herdman M, Stanier RY (1979) Generic assignments, strain histories and properties of pure cultures of cyanobacteria. J Gen Microbiol 111(MAR):1-61
51. Rocap G, Larimer FW, Lamerdin J, Malfatti S, Chain P, Ahlgren NA, Arellano A, Coleman M, Hauser L, Hess WR, Johnson ZI, Land M, Lindell D, Post AF, Regala W, Shah M, Shaw SL, Steglich C, Sullivan MB, Ting CS, Tolonen A, Webb EA, Zinser ER, Chisholm SW (2003) Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation. Nature 424(6952):1042-1047
52. Rocha EP (2008) The organization of the bacterial genome. Annu Rev Genet 42:211-233
53. Rogozin IB, Makarova KS, Murvai J, Czabarka E, Wolf YI, Tatusov RL, Szekely LA, Koonin EV (2002a) Connected gene neighborhoods in prokaryotic genomes. Nucl Acids Res 30(10):2212-2223
54. Rogozin IB, Makarova KS, Natale DA, Spiridonov AN, Tatusov RL, Wolf YI, Yin J, Koonin EV (2002b) Congruent evolution of different classes of non-coding DNA in prokaryotic genomes. Nucl Acids Res 30(19):4264-4271
55. Sabatti C, Rohlin L, Oh MK, Liao JC (2002) Co-expression pattern from DNA microarray experiments as a tool for operon prediction. Nucl Acids Res 30(13):2886-2893
56. Salgado H, Moreno-Hagelsieb G, Smith TF, Collado-Vides J (2000) Operons in Escherichia coli: genomic analyses and predictions. Proc Natl Acad Sci USA 97(12):6652-6657
57. Salgado H, Gama-Castro S, Peralta-Gil M, Diaz-Peredo E, Sanchez-Solano F, Santos-Zavaleta A, Martinez-Flores I, Jimenez-Jacinto V, Bonavides-Martinez C, Segura-Salazar J, Martinez-Antonio A, Collado-Vides J (2006) RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions. Nucl Acids Res 34:D394-D397
58. Sanchez-Baracaldo P, Hayes PK, Blank CE (2005) Morphological and habitat evolution in the cyanobacteria using a compartmentalization approach. Geobiology 3(3):145-165
59. Singh AK, Elvitigala T, Cameron JC, Ghosh BK, Bhattacharyya-Pakrasi M, Pakrasi HB (2010) Integrative analysis of large scale expression profiles reveals core transcriptional response and coordination between multiple cellular processes in a cyanobacterium. BMC Syst Biol 4:105
60. Sivashankari S, Shanmughavel P (2006) Functional annotation of hypothetical proteins - a review. Bioinformation 1(8):335-338
61. Snel B, Bork P, Huynen MA (2002) The identification of functional modules from the genomic association of genes. Proc Natl Acad Sci USA 99(9):5890-5895
62. Steglich C, Futschik M, Rector T, Steen R, Chisholm SW (2006) Genome-wide analysis of light sensing in Prochlorococcus. J Bacteriol 188(22):7796-7806
63. Sun J, Xu J, Liu Z, Liu Q, Zhao A, Shi T, Li Y (2005) Refined phylogenetic profiles method for predicting protein-protein interactions. Bioinformatics 21(16):3409-3415
64. Swingley WD, Blankenship RE, Raymond J (2008) Integrating markov clustering and molecular phylogenetics to reconstruct the cyanobacterial species tree from conserved protein families. Mol Biol Evol 25(4):643-654
65. Vijayan V, Jain IH, O'Shea EK (2011) A high resolution map of a cyanobacterial transcriptome. Genome Biol 12(5):R47
66. von Mering C, Huynen M, Jaeggi D, Schmidt S, Bork P, Snel B (2003) STRING: a database of predicted functional associations between proteins. Nucl Acids Res 31(1):258-261
67. Zhang GQ, Cao ZW, Luo QM, Cai YD, Li YX (2006) Operon prediction based on SVM. Comput Biol Chem 30(3):233-240
68. Zheng Y, Szustakowski JD, Fortnow L, Roberts RJ, Kasif S (2002) Computational identification of operons in microbial genomes. Genome Res 12(8):1221-1230