Genome organization in Mycoplasma hyopneumoniae: identification of promoter-like sequences
详细信息 查看全文
- 作者：Franciele Maboni Siqueira (1) (2)
Shana de Souto Weber (1)
Amanda Malvessi Cattani (1)
Irene Silveira Schrank (1) (3) - 关键词：Transcriptional units ; Species ; specific matrix promoter ; Transcription initiation ; Genome organization
- 刊名：Molecular Biology Reports
- 出版年：2014
- 出版时间：August 2014
- 年：2014
- 卷：41
- 期：8
- 页码：5395-5402
- 全文大小：453 KB
- 参考文献：1. Ross RF (1992) Mycoplasmal disease. In: Leman AD, Straw BE, Mengeling WL, D’Allaire S, Taylor DJ (eds) Diseases of swine. Iowa State University Press, Ames, p 537-351
2. Minion FC, Lefkowitz EL, Madsen ML, Cleary BJ, Swartzell SM, Mahairas GG (2004) The genome sequence of strain 232, the agent of swine mycoplasmosis. J Bacteriol 186:7123-133 CrossRef
3. Vasconcelos AT, Ferreira HB, Bizarro CV et al (2005) Swine and poultry pathogens: the complete genome sequences of two strains of / Mycoplasma hyopneumoniae and a strain of / Mycoplasma synoviae. J Bacteriol 187:5568-577 CrossRef
4. Liu W, Feng Z, Fang L, Zhou Z, Li Q, Li S, Luo R, Wang L, Chen H et al (2011) Complete genome sequence of / Mycoplasma hyopneumoniae strain 168. J Bacteriol 193:1016-017 CrossRef
5. Siqueira FM, Schrank A, Schrank IS (2011) / Mycoplasma hyopneumoniae transcription unit organization: genome survey and prediction. DNA Res 18:413-22 CrossRef
6. Weber SS, Sant’anna FH, Schrank IS (2012) Unveiling / Mycoplasma hyopneumoniae promoters: sequence definition and genomic distribution. DNA Res 19:103-15 CrossRef
7. Güell M, Noort V, Yus E, Chen WH, Leigh-Bell J, Michalodimitrakis K, Yamada T, Arumugam M, Doerks T et al (2009) Transcriptome complexity in a genome-reduced bacterium. Science 326:1268-271 CrossRef
8. Weiner JIII, Herrmann R, Browning GF (2000) Transcription in / Mycoplasma pneumonia. Nucl Acids Res 28:4488-496 CrossRef
9. Sinoquet C, Demey S, Braun F (2008) Large-scale computational and statistical analyses of high transcription potentialities in 32 prokaryotic genomes. Nucl Acids Res 36:3332-340 CrossRef
10. Rutherford K, Parkhill J, Crook J, Horsnell T, Rice P, Rajandream MA, Barrell B (2000) Artemis: sequence visualization and annotation. Bioinformatics 16:944-45 CrossRef
11. Friis NF (1975) Some recommendations concerning primary isolation of / Mycoplasma / suipneumoniae and / Mycoplasma flocculare a survey. Nordisk Veterinaer Med 27:337-39
12. Madsen ML, Puttamreddy S, Thacker EL, Carruthers MD, Minion FC (2008) Transcriptome changes in / Mycoplasma hyopneumoniae during infection. Infect Immun 76:658-63 CrossRef
13. Moitinho-Silva L, Heineck BL, Reolon LA, Paes JA, Klein CS, Rebelatto R, Schrank IS, Zaha A, Ferreira HB (2011) / Mycoplasma hyopneumoniae type I signal peptidase: expression and evaluation of its diagnostic potential. Vet Microbiol 154:282-91 CrossRef
14. Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2(?delta delta C(T)) method. Methods 25:402-08 CrossRef
15. McGrath PT, Lee H, Zhang L, Iniesta AA, Hottes AK, Tan MH, Hillson NJ, Hu P, Shapiro L, McAdams H (2007) High-throughput identification of transcription start sites conserved promoter motifs and predicted regulons. Nat Biotech 25:584-92 CrossRef
16. Gardner SW, Minion FC (2010) Detection and quantification of intergenic transcription in / Mycoplasma hyopneumoniae. Microbiology 156:2305-315 CrossRef
17. Makita Y, Nakao M, Ogasawara N, Nakai K (2004) DBTBS: database of transcriptional regulation in / Bacillus subtilis and its contribution to comparative genomics. Nucl Acids Res 32:D75–D77 CrossRef - 作者单位：Franciele Maboni Siqueira (1) (2)
Shana de Souto Weber (1)
Amanda Malvessi Cattani (1)
Irene Silveira Schrank (1) (3)
1. Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
2. Programa de Pós-Gradua??o em Ciências Biológicas- Bioquímica, UFRGS, Porto Alegre, Brazil
3. Departamento de Biologia Molecular e Biotecnologia, Instituto de Biociências, UFRGS, Porto Alegre, Brazil - ISSN：1573-4978
文摘
Information related to open reading frame (ORF) organization, transcription regulation and promoter sequence has been available for the Mycoplasma hyopneumoniae 7448 genome, demonstrating that the ORFs are continuously transcribed (cotranscription) in large clusters. A species-specific position-specific scoring matrix was applied to scan for putative promoters upstream of all coding sequences on a genome scale in M. hyopneumoniae. This study consisted of a detailed in silico promoter localization analysis by scanning the position-specific promoters upstream of predicted ORF clusters (OCs) and mCs (monocistronic genes) in the M. hyopneumoniae whole genome; this was combined with experimental data for the promoterless ORFs. Promoter-like sequences were found in 86?% of the OCs (from the OC first gene) and in 85?% of the mCs. A transcription analysis of the promoterless ORF was performed by RT-PCR. This strategy allowed the definition of a specific promoter sequence for all OCs and mCs indicating that all the transcriptional units are preceded by putative promoter sequences (matrix and manually located) and providing evidence for functional gene organization in the M. hyopneumoniae genome. These results shown that the species-specific, position-specific scoring matrix for promoter prediction is effective, further increasing the knowledge of gene organization and transcription initiation in mycoplasmas.