19th-banner-rev.gif

Book of Abstracts: Albany 2011

category image Albany 2011
Conversation 17
June 14-18 2011
©Adenine Press (2010)

Promoter Islands: The Novel Elements In Bacterial Genomes

Seventy-eight “promoter islands” (PIs) were delineated in E.coli genome based on high density of potential transcription start points, high ability of RNA polymerase (RNAP) binding and paradoxically low transcription efficiency (1). Among them there are 23 PIs lying inside coding sequences (exemplified in Fig. 1A) or between convergent genes, where promoter activity is not expected. The specific location and high length of genomic regions (≥300bp), containing overlapping transcription signals, distinguish them from clustered promoter-like sites previously found nearby highly expressed genes. In this study we compared chromatin structure for PIs and 181 “single” promoters using published ChIP-on-chip data (2-4) and validated the ability of 16 intragenic PIs + 3 PIs located between convergent genes to form “open” complexes with RNAP in vitro and in vivo.


Fig.1. A: PI associated with genes yigF and yigG. Bars represent transcription start points predicted by PlatProm. Triangles and asterisks indicate positions of transcription bubbles registered in vitro and in vivo, respectively. B: Sites of interaction with RNAP as registered by ChIP-on-chip technique (4) with σ- or β-specific antibodies.

It turned out that PIs more frequently than “single” promoters associate with nucleoide proteins H-NS and Fis. Interaction with RNAP was registered for all PIs (100%) if antibodies against σ subunit were used to collect complexes (Fig. 1B gray bars) and only for 43% of “islands” if precipitation was carried out by β-specific reaction (Fig. 1B black symbols), while complexes with “single” promoters were detected with approximately equal efficiency by these two approaches (~87% and 77%, respectively). These differences assume certain singularity in the chromatin structure within PIs. Functional analysis testified ability of all analyzed PIs to undergo local DNA melting upon interaction with RNAP in vitro and 12 “islands” form transcription bubbles in vivo, thus assuming their ability to start RNA synthesis. However in most cases (75% for analyzed PIs and 75.6% for the total set of 78 PIs) expected products were not found among the sequenced cDNAs (5). For “single” promoters this failure was 2-fold lower (35%). Since other bacterial genomes show approximately the same distribution of PIs, we suppose that they perform evolutionary conserved biological role, not necessarily associated with RNA synthesis.

The research is supported by grants from Russian Foundation for Basic Research (10-04-01218).

References
  1. K. S. Shavkunov, I. S. Masulis, M. N. Tutukina, A. A. Deev, O. N. Ozoline, Nucleic Acids Res., 37, 4919-4931 (2009).
  2. D. C. Grainger, D. Hurd, M. D. Goldberg, S. J. W. Busby, Nucleic Acids Res., 34: 4642 – 4652 (2006).
  3. D. C. Grainger, H. Aiba, D. Hurd, D. F. Browning, S. J. W. Busby, Nucleic Acids Res., 35: 269 – 278 (2007).
  4. N. B. Reppas, J. T. Wade, G. M. Church, K. Struhl. Mol Cell, 24, 747-757 (2006).
  5. J. E. Dornenburg, A. M. DeVita, M. J. Palumbo, J. T. Wade, mBio, 1: e00024-10 (2010).

Konstantin S. Shavkunov
Maria N Tutukina
Irina S. Masulis
Olga N. Ozoline*

Institute of Cell Biophysics, RAS, Pushchino Moscow Region, 142290, Russian Federation

ph: +7-496-773-9140
fax: +7-496-733-05-09

ozoline@icb.psn.ru