← Back to Search
A Whole-genome Approach To Identifying Protein Binding Sites: Promoters In Methanocaldococcus (Methanococcus) Jannaschii
E. Li, C. Reich, G. Olsen
Published 2008 · Biology, Medicine
Save to my Library
Download PDFAnalyze on Scholarcy
We have adapted an electrophoretic mobility shift assay (EMSA) to isolate genomic DNA fragments that bind the archaeal transcription initiation factors TATA-binding protein (TBP) and transcription factor B (TFB) to perform a genome-wide search for promoters. Mobility-shifted fragments were cloned, tested for their ability to compete with known promoter-containing fragments for a limited concentration of transcription factors, and sequenced. We applied the method to search for promoters in the genome of Methanocaldococcus jannaschii. Selection was most efficient for promoters of tRNA genes and genes for several presumed small non-coding RNAs (ncRNA). Protein-coding gene promoters were dramatically underrepresented relative to their frequency in the genome. The repeated isolation of these genomic regions was partially rectified by including a hybridization-based screening. Sequence alignment of the affinity-selected promoters revealed previously identified TATA box, BRE, and the putative initiator element. In addition, the conserved bases immediately upstream and downstream of the BRE and TATA box suggest that the composition and structure of archaeal natural promoters are more complicated.
This paper references
Libraries for genomic SELEX.
B. Singer (1997)
Whole genome PCR: application to the identification of sequences bound by gene regulatory proteins.
K. Kinzler (1989)
In vitro selection of RNA molecules that bind specific ligands
A. Ellington (1990)
Primer extension analysis of RNA.
W. R. Boorstein (1989)
Transcription factor IID in the Archaea: sequences in the Thermococcus celer genome would encode a product closely related to the TATA-binding protein of eukaryotes.
T. Marsh (1994)
A thermostable platform for transcriptional regulation: the DNA‐binding properties of two Lrp homologs from the hyperthermophilic archaeon Methanococcus jannaschii
M. Ouhammouch (2001)
Fitting a Mixture Model By Expectation Maximization To Discover Motifs In Biopolymer
T. Bailey (1994)
The Role of Transcription Factor B in Transcription Initiation and Promoter Clearance in the Archaeon Sulfolobus acidocaldarius *
S. Bell (2000)
Transcription Factor B Contacts Promoter DNA Near the Transcription Start Site of the Archaeal Transcription Initiation Complex*
M. Renfrow (2004)
Colony hybridization: a method for the isolation of cloned DNAs that contain a specific gene.
M. Grunstein (1975)
Orientation of the transcription preinitiation complex in archaea.
S. Bell (1999)
Transcription in archaea: similarity to that in eucarya.
D. Langer (1995)
Activator-induced conformational change in general transcription factor TFIIB
S. Roberts (1994)
Topography of the Euryarchaeal Transcription Initiation Complex*
M. S. Bartlett (2004)
CRITICA: coding region identification tool invoking comparative analysis.
J. H. Badger (1999)
Noncoding RNA genes identified in AT-rich hyperthermophiles
R. Klein (2002)
Sizing and mapping of early adenovirus mRNAs by gel electrophoresis of S1 endonuclease-digested hybrids
A. Berk (1977)
The 2.1-A crystal structure of an archaeal preinitiation complex: TATA-box-binding protein/transcription factor (II)B core/TATA-box.
P. F. Kosa (1997)
Prediction of probable genes by Fourier analysis of genomic sequences
S. Tiwari (1997)
Specific SR protein-dependent splicing substrates identified through genomic SELEX.
Soyoun Kim (2003)
Control regions of an archaeal gene. A TATA box and an initiator element promote cell-free transcription of the tRNA(Val) gene of Methanococcus vannielii.
W. Hausner (1991)
Similar subunit architecture of archaeal and eukaryal RNA polymerases.
A. Best (2001)
GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions.
J. Besemer (2001)
Sequence-specific DNA binding by the S. shibatae TFIIB homolog, TFB, and its effect on promoter strength.
S. Qureshi (1998)
The structural basis for the oriented assembly of a TBP/TFB/promoter complex.
O. Littlefield (1999)
Transcription signals for stable RNA genes in Methanococcus.
G. Wich (1986)
Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals.
A. Huerta (2003)
A Fully Recombinant System for Activator-dependent Archaeal Transcription*
M. Ouhammouch (2004)
Searching for RNA genes using base-composition statistics.
Peter Schattner (2002)
Identification of 86 candidates for small non-messenger RNAs from the archaeon Archaeoglobus fulgidus
Thean-Hock Tang (2002)
Basal and regulated transcription in archaea.
J. Soppa (2001)
DNAse footprinting: a simple method for the detection of protein-DNA binding specificity.
D. Galas (1978)
Interactions of Escherichia coli RNA with bacteriophage MS2 coat protein: genomic SELEX.
T. Shtatland (2000)
The Effects of Transcription Regulating Genes PDR1, pdr1-3 and PDR3 in Pleiotropic Drug Resistance
A. Nawrocki (2001)
A general method of isolating high molecular weight DNA from methanogenic archaea (archaebacteria).
K. Jarrell (1992)
Finding Functional Features in Saccharomyces Genomes by Phylogenetic Footprinting
P. Cliften (2003)
Systematic search for the Cra‐binding promoters using genomic SELEX system
T. Shimada (2005)
Prediction of transcription regulatory sites in Archaea by a comparative genomic approach.
M. Gelfand (2000)
New core promoter element in RNA polymerase II-dependent transcription: sequence-specific DNA binding by transcription factor IIB.
T. Lagrange (1998)
Structural Modifications of Methanococcus Jannaschii Flagellin Proteins Revealed by Proteome Analysis
C. Giometti (2001)
Transcription and translation in Archaea: a mosaic of eukaryal and bacterial features.
S. Bell (1998)
Sequence-specific DNA binding by the S. shibatae TFIIB homolog, TFB, and its effect on promoter
S. A. Qureshi (1998)
Tandem promoters in the gene for ribosomal protein S20.
G. Mackie (1983)
Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase.
C. Tuerk (1990)
Archaeal Genomics: An Overview
G. Olsen (1997)
Recent advances in computational promoter analysis in understanding the transcriptional regulatory network.
Ping Qiu (2003)
Transcriptional regulation in Archaea.
J. Leigh (1999)
Sequence logos: a new way to display consensus sequences.
T. Schneider (1990)
Two Transcription Factors Related with the Eucaryal Transcription Factors TATA-binding Protein and Transcription Factor IIB Direct Promoter Recognition by an Archaeal RNA Polymerase*
W. Hausner (1996)
Structural basis of preinitiation complex assembly on human Pol II promoters
F. T. Tsai (2000)
Microbial gene identification using interpolated Markov models.
S. Salzberg (1998)
A Genomewide Search for Ribozymes Reveals an HDV-Like Sequence in the Human CPEB3 Gene
K. Salehi-Ashtiani (2006)
An archaebacterial promoter element for stable RNA genes with homology to the TATA box of higher eukaryotes
M. Thomm (1988)
Evidence for similar subunit architectures between archaeal and eukaryal RNA polymerases
A. A. Best (2001)
Complete Genome Sequence of the Methanogenic Archaeon, Methanococcus jannaschii
Carol J Bult (1996)
Complete genome sequence of the methanogenic archaeon
C J Bult (1996)
Archaeal basal transcription factor: DNA protein pnteractions
G. M. Colón Gonzalez (2001)
Promoter recognition and discrimination by EσS RNA polymerase
T. Gaál (2001)
Bias and artifacts in multitemplate polymerase chain reactions (PCR).
T. Kanagawa (2003)
Molecular cloning of the transcription factor TFIIB homolog from Sulfolobus shibatae.
S. Qureshi (1995)
This paper is referenced by
Regulation of expression of copper responsive genes in Sulfolobus solfataricus
V. Martínez (2010)
Protein-coding gene promoters in Methanocaldococcus (Methanococcus) jannaschii
Jian Zhang (2009)
A global analysis of transcription reveals two modes of Spt4/5 recruitment to archaeal RNA polymerase
Katherine Smollett (2017)
Bypassing the Need for the Transcriptional Activator EarA through a Spontaneous Deletion in the BRE Portion of the fla Operon Promoter in Methanococcus maripaludis
Y. Ding (2017)
Data integration methods for systems-level investigation of gene functional association networks
Matthew T. Weirauch (2009)
Transcription initiation factor TBP: old friend new questions.
Kevin Kramm (2019)