Transcription Machinery and Regulation in E. coli

Jin, Ding Jun

Abstract

Regulation of transcription is a key step in controlling gene expression in all cells. The basic structure and function of RNA polymerase (RNAP) and RNAP-associated proteins are conserved throughout evolution. The sophisticated genetics and advanced biochemistry make E. coli an ideal model system. The overall research goal of my lab is to study the transcription machinery and the influence of transcription factors on gene expression and regulation. Currently, we focus on: (i) RNAP of E. coli and the RNAP-associated proteins RapA and SspA; and (ii) the mechanism of the global change in the transcription pattern associated with nutrient starvation known as the stringent response.

Funding Agency

• Agency: National Institute of Health (NIH)
• Institute: Division of Basic Sciences - NCI (NCI)
• Type: Intramural Research (Z01)
• Project #: 1Z01BC010632-01
• Application #: 7064512
• Study Section: (GRCB)
• Support Year: 1
• Fiscal Year: 2004

Institution

• Name: Basic Sciences
• Country: United States

Publications

Shaw, Gary; Gan, Jianhua; Zhou, Yan Ning et al. (2008) Structure of RapA, a Swi2/Snf2 protein that recycles RNA polymerase during transcription. Structure 16:1417-27

Durfee, Tim; Hansen, Anne-Marie; Zhi, Huijun et al. (2008) Transcription profiling of the stringent response in Escherichia coli. J Bacteriol 190:1084-96

Wickstrum, Jason R; Skredenske, Jeff M; Kolin, Ana et al. (2007) Transcription activation by the DNA-binding domain of the AraC family protein RhaS in the absence of its effector-binding domain. J Bacteriol 189:4984-93

Norris, Vic; den Blaauwen, Tanneke; Cabin-Flaman, Armelle et al. (2007) Functional taxonomy of bacterial hyperstructures. Microbiol Mol Biol Rev 71:230-53

Cabrera, Julio E; Jin, Ding J (2006) Active transcription of rRNA operons is a driving force for the distribution of RNA polymerase in bacteria: effect of extrachromosomal copies of rrnB on the in vivo localization of RNA polymerase. J Bacteriol 188:4007-14

Jin, Ding Jun; Cabrera, Julio E (2006) Coupling the distribution of RNA polymerase to global gene regulation and the dynamic structure of the bacterial nucleoid in Escherichia coli. J Struct Biol 156:284-91

Hansen, Anne-Marie; Gu, Yijun; Li, Mi et al. (2005) Structural basis for the function of stringent starvation protein a as a transcription factor. J Biol Chem 280:17380-91

Hansen, Anne-Marie; Qiu, Yu; Yeh, Norman et al. (2005) SspA is required for acid resistance in stationary phase by downregulation of H-NS in Escherichia coli. Mol Microbiol 56:719-34

Liu, Mingzhu; Durfee, Tim; Cabrera, Julio E et al. (2005) Global transcriptional programs reveal a carbon source foraging strategy by Escherichia coli. J Biol Chem 280:15921-7

Xu, Ming; Zhou, Yan Ning; Goldstein, Beth P et al. (2005) Cross-resistance of Escherichia coli RNA polymerases conferring rifampin resistance to different antibiotics. J Bacteriol 187:2783-92