Global mapping of transcription start sites and promoter motifs in the symbiotic a-proteobacterium Sinorhizobium meliloti 1021

被引:122
作者
Schlueter, Jan-Philip [1 ,2 ,3 ]
Reinkensmeier, Jan [4 ]
Barnett, Melanie J. [5 ]
Lang, Claus [5 ]
Krol, Elizaveta [2 ,3 ]
Giegerich, Robert [4 ]
Long, Sharon R. [5 ]
Becker, Anke [2 ,3 ]
机构
[1] Univ Freiburg, Fac Biol, Inst Biol 3, D-79106 Freiburg, Germany
[2] Univ Marburg, LOEWE Ctr Synthet Microbiol SYNMIKRO, Marburg, Germany
[3] Univ Marburg, Dept Biol, Marburg, Germany
[4] Univ Bielefeld, Ctr Biotechnol CeBiTec, D-33615 Bielefeld, Germany
[5] Stanford Univ, Dept Biol, Stanford, CA 94305 USA
来源
BMC GENOMICS | 2013年 / 14卷
基金
美国国家卫生研究院;
关键词
Transcription; RNAseq; Transcription start site; Promoter; Sigma factor; Sinorhizobium meliloti; mRNA; sRNA; Antisense RNA; LEADERLESS MESSENGER-RNAS; GENERAL STRESS-RESPONSE; FUNCTION SIGMA FACTORS; FACTOR-BINDING SITES; ANTISENSE RNA; ESCHERICHIA-COLI; ALPHA-PROTEOBACTERIA; SOLUBLE-RNAS; RIBOSOME BINDING; GENOME;
D O I
10.1186/1471-2164-14-156
中图分类号
Q81 [生物工程学(生物技术)]; Q93 [微生物学];
学科分类号
071005 ; 0836 ; 090102 ; 100705 ;
摘要
Background: Sinorhizobium meliloti is a soil-dwelling a-proteobacterium that possesses a large, tripartite genome and engages in a nitrogen fixing symbiosis with its plant hosts. Although much is known about this important model organism, global characterization of genetic regulatory circuits has been hampered by a lack of information about transcription and promoters. Results: Using an RNAseq approach and RNA populations representing 16 different growth and stress conditions, we comprehensively mapped S. meliloti transcription start sites (TSS). Our work identified 17,001 TSS that we grouped into six categories based on the genomic context of their transcripts: mRNA (4,430 TSS assigned to 2,657 protein-coding genes), leaderless mRNAs (171), putative mRNAs (425), internal sense transcripts (7,650), antisense RNA (3,720), and trans-encoded sRNAs (605). We used this TSS information to identify transcription factor binding sites and putative promoter sequences recognized by seven of the 15 known S. meliloti sigma factors sigma(70), sigma(54), sigma(H1), sigma(H2), sigma(E1), sigma(E2), and sigma(E9)). Altogether, we predicted 2,770 new promoter sequences, including 1,302 located upstream of protein coding genes and 722 located upstream of antisense RNA or trans-encoded sRNA genes. To validate promoter predictions for targets of the general stress response s factor, RpoE2 (sigma(E2)), we identified rpoE2-dependent genes using microarrays and confirmed TSS for a subset of these by 5' RACE mapping. Conclusions: By identifying TSS and promoters on a global scale, our work provides a firm foundation for the continued study of S. meliloti gene expression with relation to gene organization, s factors and other transcription factors, and regulatory RNAs.
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页数:21
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共 104 条
[1]   Deep sequencing-based discovery of the Chlamydia trachomatis transcriptome [J].
Albrecht, Marco ;
Sharma, Cynthia M. ;
Reinhardt, Richard ;
Vogel, Joerg ;
Rudel, Thomas .
NUCLEIC ACIDS RESEARCH, 2010, 38 (03) :868-877
[2]   S-box and T-box riboswitches and antisense RNA control a sulfur metabolic operon of Clostridium acetobutylicum [J].
Andre, Gaelle ;
Even, Sergine ;
Putzer, Harald ;
Burguiere, Pierre ;
Croux, Christian ;
Danchin, Antoine ;
Martin-Verstraete, Isabelle ;
Soutourina, Olga .
NUCLEIC ACIDS RESEARCH, 2008, 36 (18) :5955-5969
[3]  
[Anonymous], 1989, Molecular Cloning: A Laboratory
[4]   Sequence-Based Analysis Uncovers an Abundance of Non-Coding RNA in the Total Transcriptome of Mycobacterium tuberculosis [J].
Arnvig, Kristine B. ;
Comas, Inaki ;
Thomson, Nicholas R. ;
Houghton, Joanna ;
Boshoff, Helena I. ;
Croucher, Nicholas J. ;
Rose, Graham ;
Perkins, Timothy T. ;
Parkhill, Julian ;
Dougan, Gordon ;
Young, Douglas B. .
PLOS PATHOGENS, 2011, 7 (11)
[5]   MEME: discovering and analyzing DNA and protein sequence motifs [J].
Bailey, Timothy L. ;
Williams, Nadya ;
Misleh, Chris ;
Li, Wilfred W. .
NUCLEIC ACIDS RESEARCH, 2006, 34 :W369-W373
[6]   Phosphate Assimilation in Rhizobium (Sinorhizobium) meliloti:: Identification of a pit-like gene [J].
Bardin, SD ;
Voegele, RT ;
Finan, TM .
JOURNAL OF BACTERIOLOGY, 1998, 180 (16) :4219-4226
[7]   Nucleotide sequence and predicted functions of the entire Sinorhizobium meliloti pSymA megaplasmid [J].
Barnett, MJ ;
Fisher, RF ;
Jones, T ;
Komp, C ;
Abola, AP ;
Barloy-Hubler, F ;
Bowser, L ;
Capela, D ;
Galibert, F ;
Gouzy, J ;
Gurjal, M ;
Hong, A ;
Huizar, L ;
Hyman, RW ;
Kahn, D ;
Kahn, ML ;
Kalman, S ;
Keating, DH ;
Palm, C ;
Peck, MC ;
Surzycki, R ;
Wells, DH ;
Yeh, KC ;
Davis, RW ;
Federspiel, NA ;
Long, SR .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2001, 98 (17) :9883-9888
[8]   A dual-genome Symbiosis Chip for coordinate study of signal exchange and development in a prokaryote-host interaction [J].
Barnett, MJ ;
Tolman, CJ ;
Fisher, RF ;
Long, SR .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2004, 101 (47) :16636-16641
[9]  
BARNETT MJ, 2012, J BACTERIOLOGY, V0194
[10]  
Barnett MJ, 1998, GENETICS, V148, P19