Protein-coding gene promoters in Methanocaldococcus (Methanococcus) jannaschii

Jian Zhang, Enhu Li, Gary J. Olsen

Research output: Contribution to journalArticle

Abstract

Although Methanocaldococcus (Methanococcus) jannaschii was the first archaeon to have its genome sequenced, little is known about the promoters of its protein-coding genes. To expand our knowledge, we have experimentally identified 131 promoters for 107 protein-coding genes in this genome by mapping their transcription start sites. Compared to previously identified promoters, more than half of which are from genes for stable RNAs, the protein-coding gene promoters are qualitatively similar in overall sequence pattern, but statistically different at several positions due to greater variation among their sequences. Relative binding affinity for general transcription factors was measured for 12 of these promoters by competition electrophoretic mobility shift assays. These promoters bind the factors less tightly than do most tRNA gene promoters. When a position weight matrix (PWM) was constructed from the protein gene promoters, factor binding affinities correlated with corresponding promoter PWM scores. We show that the PWM based on our data more accurately predicts promoters in the genome and transcription start sites than could be done with the previously available data. We also introduce a PWM logo, which visually displays the implications of observing a given base at a position in a sequence.

Original languageEnglish (US)
Pages (from-to)3588-3601
Number of pages14
JournalNucleic acids research
Volume37
Issue number11
DOIs
StatePublished - Jul 10 2009

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Position-Specific Scoring Matrices
Methanocaldococcus
Transcription Initiation Site
Proteins
General Transcription Factors
Genome
Chromosome Mapping
Archaea
Electrophoretic Mobility Shift Assay
Transfer RNA
Genes
RNA

ASJC Scopus subject areas

  • Genetics

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Protein-coding gene promoters in Methanocaldococcus (Methanococcus) jannaschii. / Zhang, Jian; Li, Enhu; Olsen, Gary J.

In: Nucleic acids research, Vol. 37, No. 11, 10.07.2009, p. 3588-3601.

Research output: Contribution to journalArticle

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