Note_TranscriptionUnitStructure – TranscriptionUnitStructure

WID Note_TranscriptionUnitStructure
Name TranscriptionUnitStructure
Comments The promoter and transcriptional start site for each gene was predicted by Weiner, Hermann, and Browning using a PSS matrix developed by sequencing the 5' ends of several M. pneumoniae transcripts [PUB_0411]. The transcription unit structure was compiled by mapping the reported M. pneumoniae transcription structure to M. genitalium [PUB_0418 Table S5 Suboperons] with three modifications: r/s/tRNAs were assigned to transcription units according to their reference operons [PUB_0418 Table s4] mRNAs not assigned to suboperons because of insufficient evidence where assigned to separate transcription units. The 5 non-homologous genes were were assigned to separate transcription units. These genes occur outside other transcription units. We considered several additional data set when compiling the the transcription unit structure: Primary reports of cotranscribed genes [PUB_0176, PUB_0182, PUB_0186, PUB_0188, PUB_0188, PUB_0244, PUB_0247, PUB_0248, PUB_0249, PUB_0251] OperonDB database of cotranscribed genes [PUB_0250] Conservation of gene order across multiple species Related function of adjacent genes Expression levels as measured by microarrays of adjacent genes [PUB_0569] Strandedness of adjacent genes
  1. Duffy MF, Walker ID, Browning GF. The immunoreactive 116 kDa surface protein of Mycoplasma pneumoniae is encoded in an operon. Microbiology 143 ( Pt 10), 3391-402 (1997). WholeCell: PUB_0176, PubMed: 9353941

  2. Güell M, van Noort V, Yus E, Chen WH, Leigh-Bell J, Michalodimitrakis K, Yamada T, Arumugam M, Doerks T, Kühner S, Rode M, Suyama M, Schmidt S, Gavin AC, Bork P, Serrano L. Transcriptome complexity in a genome-reduced bacterium. Science 326, 1268-71 (2009). WholeCell: PUB_0418, PubMed: 19965477

  3. Huynen M, Snel B, Lathe W 3rd, Bork P. Predicting protein function by genomic context: quantitative evaluation and qualitative inferences. Genome Res 10, 1204-10 (2000). WholeCell: PUB_0251, PubMed: 10958638

  4. Krause DC, Proft T, Hedreyda CT, Hilbert H, Plagens H, Herrmann R. Transposon mutagenesis reinforces the correlation between Mycoplasma pneumoniae cytoskeletal protein HMW2 and cytadherence. J Bacteriol 179, 2668-77 (1997). WholeCell: PUB_0188, PubMed: 9098066

  5. Musatovova O, Dhandayuthapani S, Baseman JB. Transcriptional heat shock response in the smallest known self-replicating cell, Mycoplasma genitalium. J Bacteriol 188, 2845-55 (2006). WholeCell: PUB_0186, PubMed: 16585746

  6. ... 8 more

  7. Muto A, Andachi Y, Yuzawa H, Yamao F, Osawa S. The organization and evolution of transfer RNA genes in Mycoplasma capricolum. Nucleic Acids Res 18, 5037-43 (1990). WholeCell: PUB_0248, PubMed: 1698277

  8. Pertea M, Ayanbule K, Smedinghoff M, Salzberg SL. OperonDB: a comprehensive database of predicted operons in microbial genomes. Nucleic Acids Res 37, D479-82 (2009). WholeCell: PUB_0250, PubMed: 18948284

  9. Peterson JD, Umayam LA, Dickinson T, Hickey EK, White O. The Comprehensive Microbial Resource. Nucleic Acids Res 29, 123-5 (2001). WholeCell: PUB_0182, PubMed: 11125067, URL:

  10. Simoneau P, Wenzel R, Herrmann R, Hu PC. Nucleotide sequence of a tRNA cluster from Mycoplasma pneumoniae. Nucleic Acids Res 18, 2814 (1990). WholeCell: PUB_0247, PubMed: 2111011

  11. Tanaka R, Andachi Y, Muto A. Evolution of tRNAs and tRNA genes in Acholeplasma laidlawii. Nucleic Acids Res 19, 6787-92 (1991). WholeCell: PUB_0249, PubMed: 1722304

  12. Tomii K, Kanehisa M. A comparative analysis of ABC transporters in complete microbial genomes. Genome Res 8, 1048-59 (1998). WholeCell: PUB_0244, PubMed: 9799792

  13. Weiner J 3rd, Herrmann R, Browning GF. Transcription in Mycoplasma pneumoniae. Nucleic Acids Res 28, 4488-96 (2000). WholeCell: PUB_0411, PubMed: 11071937, URL:

  14. Weiner J 3rd, Zimmerman CU, Göhlmann HW, Herrmann R. Transcription profiles of the bacterium Mycoplasma pneumoniae grown at different temperatures. Nucleic Acids Res 31, 6306-20 (2003). WholeCell: PUB_0569, PubMed: 14576319

Created 2012-10-01 15:07:34
Last updated 2012-10-01 15:13:59