Lack of conservation of bacterial type promoters in plastids of Streptophyta

Biology Direct

Volumn 5, Issue , 2010, Pages

  Lyubetsky, Vassily A ^a   Rubanov, Lev I ^a   Seliverstov, Alexandr V ^a  

^a INSTITUTE FOR INFORMATION TRANSMISSION PROBLEMS   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA (MICROORGANISMS); STREPTOPHYTA;

ARCHAEAL PROTEIN;

ARTICLE; GENETICS; GREEN ALGA; PLASTID; PROMOTER REGION;

ALGAE, GREEN; ARCHAEAL PROTEINS; PLASTIDS; PROMOTER REGIONS, GENETIC;

EID: 77951958863     PISSN: None     EISSN: 17456150     Source Type: Journal    
DOI: 10.1186/1745-6150-5-34     Document Type: Article

References (24)

1. Singer M, Berg P. Genes and Genomes 1991, Blackwell Scientific Publications Ltd. Oxford.
2. Collado-Vides J, Salgado H, Morett E, Gama-Castro S, Jiménez-Jacinto V, Martínez-Flores I, Medina-Rivera A, Muñiz-Rascado L, Peralta-Gil M, Santos-Zavaleta A. Bioinformatics resources for the study of gene regulation in bacteria. J Bacteriol 2009, 191(1):23-31. 10.1128/JB.01017-08, 2612416, 18978060.
3. Swiatecka-Hagenbruch M, Liere K, Borner T. High diversity of plastidial promoters in Arabidopsis thaliana. Mol Genet Genomics 2007, 277:725-734. 10.1007/s00438-007-0222-4, 17333279.
4. Hoffer PH, Christopher DA. Structure and blue-light-responsive transcription of a chloroplast psbD promoter from Arabidopsis thaliana. Plant Physiol 1997, 115:213-222. 10.1104/pp.115.1.213, 158477, 9306699.
5. Seliverstov AV, Lysenko EA, Lyubetsky VA. Rapid evolution of promoters for the plastome gene ndhF in flowering plants. Russian Journal of Plant Physiology 2009, 56(6):837-844.
6. Finding of multi-box regulatory signal in the set of unaligned sequences. , http://lab6.iitp.ru/en/twobox/
7. A tree-based method of sequence alignment. , http://lab6.iitp.ru/en/treeal/
8. Favorov AV, Gelfand MS, Gerasimova AV, Ravcheev DA, Mironov AA, Makeev V. A Gibbs sampler for identification of symmetrically structured, spaced DNA motifs with improved estimation of the signal length. Bioinformatics 2005, 21(10):2240-5. 10.1093/bioinformatics/bti336, 15728117.
9. Danilova LV, Gorbunov K, Gelfand MS, Liubetskiǐ (Lyubetsky) VA. Algorithms for isolating regulatory signals in DNA sequences. Mol Biol (Mosk) 2001, 35(6):987-95. [Article in Russian]., 10.1023/A:1013282101105, 11771146.
10. Danilova LV, Lyubetsky VA, Gelfand MS. An algorithm for identification of regulatory signals in unaligned DNA sequences, its testing and parallel implementation. In Silico Biol 2003, 3(1-2):33-47.
11. Rubanov L, Seliverstov A, Lyubetsky V. Multiple alignment based on species tree. Abstracts of the Sixth International Conference on Bioinformatics of Genome Regulation and Structure, BGRS'2008: 22-28 June 2008; Novosibirsk 2008, 212.
12. Homann A, Link G. DNA-binding and transcription characteristics of three cloned sigma factors from mustard (Sinapis alba L.) suggest overlapping and distinct roles in plastid gene expression. Eur J Biochem 2003, 270(6):1288-300. 10.1046/j.1432-1033.2003.03494.x, 12631287.
13. Gruissem W, Zurawski G. Analysis of promoter regions for the spinach chloroplast rbcL, atpB and psbA genes. The EMBO Journal 1985, 4(13A):3375-3383. 554673, 2868888.
14. Crooks GE, Hon G, Chandonia JM, Brenner SE. WebLogo: A sequence logo generator. Genome Research 2004, 14:1188-1190. 10.1101/gr.849004, 419797, 15173120.
15. Westhoff P, Herrmann RG. Complex RNA maturation in chloroplasts. The psbB operon from spinach. Eur J Biochem 1988, 171:551-564. 10.1111/j.1432-1033.1988.tb13824.x, 2831053.
16. Fey V, Wagner R, Braütigam K, Wirtz M, Hell R, Dietzmann A, Leister D, Oelmüller R, Pfannschmidt T. Retrograde plastid redox signals in the expression of nuclear genes for chloroplast proteins of Arabidopsis thaliana. The Journal of Biological Chemistry 2005, 280:5318-5328. Additions and Corrections, ibid, 280(17): 17572, 10.1074/jbc.M406358200, 15561727.
17. Nagashima A, Hanaoka M, Motohashi R, Seki M, Shinozaki K, Kanamaru K, Takahashi H, Tanaka K. DNA microarray analysis of plastid gene expression in Arabidopsis mutant deficient in a plastid transcription factor sigma, SIG2. Biosci Biotechnol Biochem 2004, 68(3):694-704. 10.1271/bbb.68.694, 15056905.
18. Rogers MB, Gilson PR, Su V, McFadden GI, Keeling PJ. The complete chloroplast genome of the chlorarachniophyte Bigelowiella natans: evidence for independent origins of Chlorarachniophyte and Euglenid secondary endosymbionts. Mol Biol Evol 2007, 24(1):54-62. 10.1093/molbev/msl129, 16990439.
19. Lemieux C, Otis C, Turmel M. A clade uniting the green algae Mesostigma viride and Chlorokybus atmophyticus represents the deepest branch of the Streptophyta in chloroplast genome-based phylogenies. BMC Biology 2007, 5(2):1-17. 1797197, 17222327.
20. Li S, Nosenko T, Hackett JD, Bhattacharya D. Phylogenomic analysis identifies red algal genes of endosymbiotic origin in the Chromalveolates. Mol Biol Evol 2006, 23(3):663-674. 10.1093/molbev/msj075, 16357039.
21. Lysenko EA. Plant sigma factors and their role in plastid transcription. Plant Cell Rep 2007, 26:845-859. 10.1007/s00299-007-0318-7, 17356883.
22. Swiatecka-Hagenbruch M, Emanuel C, Hedtke B, Liere K, Borner T. Impaired function of the phage-type RNA polymerase RpoTp in transcription of chloroplast genes is compensated by a second phage-type RNA polymerase. Nucleic Acids Research 2008, 36(3):785-792. 10.1093/nar/gkm1111, 2241911, 18084023.
23. Wickett NJ, Zhang Y, Hansen SK, Roper JM, Kuehl JV, Plock SA, Wolf PG, Depamphilis CW, Boore JL, Goffinet B. Functional Gene Losses Occur with Minimal Size Reduction in the Plastid Genome of the Parasitic Liverwort Aneura mirabilis. Mol Biol Evol 2008, 25(2):393-401. 10.1093/molbev/msm267, 18056074.
24. Seliverstov AV, Lyubetsky VA. Translation regulation of intron containing genes in chloroplasts. Journal of Bioinformatics and Computational Biology 2006, 4(4):783-793. 10.1142/S0219720006002235, 17007067.