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A whole-genome approach to identifying protein binding sites: promoters in Methanocaldococcus (Methanococcus) jannaschii

Li, Enhu and Reich, Claudia I. and Olsen, Gary J. (2008) A whole-genome approach to identifying protein binding sites: promoters in Methanocaldococcus (Methanococcus) jannaschii. Nucleic Acids Research, 36 (22). pp. 6948-6958. ISSN 0305-1048. doi:10.1093/nar/gkm499.

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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.

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Additional Information:© 2008 The Author(s). This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. Received April 23, 2007. Revised June 6, 2007. Accepted June 7, 2007. We thank Ying Jiang for sharing her estimates of in vivo transcription factor concentrations. We thank Jian Zhang, Ying Jiang and other members of the laboratory for helpful discussions. We thank two anonymous referees for their insightful and helpful critiques. This work was supported by grants from the US Department of Energy (DE-FG02-01ER63201) and NASA (NAG 5-12334) to G.J.O. We thank Dr. Carl R. Woese for his help in supporting E.L. by sharing funds from the Stanley O. Ikenberry Chair, a position that he holds at the University of Illinois. Funding to pay the Open Access publication charges for this article has been waived by Oxford University Press.
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Department of EnergyDE-FG02-01ER63201
NASANAG 5-12334
University of IllinoisUNSPECIFIED
Issue or Number:22
Record Number:CaltechAUTHORS:LIEnar08
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Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:13495
Deposited By: Tony Diaz
Deposited On:07 Aug 2009 23:46
Last Modified:08 Nov 2021 22:38

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