Coupling the distribution of RNA polymerase to global gene regulation and the dynamic structure of the bacterial nucleoid in Escherichia coli

2006 ◽  
Vol 156 (2) ◽  
pp. 284-291 ◽  
Author(s):  
Ding Jun Jin ◽  
Julio E. Cabrera
2014 ◽  
Vol 12 (02) ◽  
pp. 1441006 ◽  
Author(s):  
Yuri A. Purtov ◽  
Olga A. Glazunova ◽  
Sergey S. Antipov ◽  
Viktoria O. Pokusaeva ◽  
Eugeny E. Fesenko ◽  
...  

Seventy-eight promoter islands with an extraordinarily high density of potential promoters have been recently found in the genome of Escherichia coli. It has been shown that RNA polymerase binds internal promoters of these islands and produces short oligonucleotides, while the synthesis of normal mRNAs is suppressed. This quenching may be biologically relevant, as most islands are associated with foreign genes, which expression may deplete cellular resources. However, a molecular mechanism of silencing with the participation of these promoter-rich regions remains obscure. It has been demonstrated that all islands interact with histone-like protein H-NS — a specific sentinel of foreign genes. In this study, we demonstrated the inhibitory effect of H-NS using Δhns mutant of Escherichia coli and showed that deletion of dps, encoding another protein of bacterial nucleoid, tended to decrease rather than increase the amount of island-specific transcripts. This observation precluded consideration of promoter islands as sites for targeted heterochromatization only and a computer search for the binding sites of 53 transcription factors (TFs) revealed six proteins, which may specifically regulate their transcriptional output.


1999 ◽  
Vol 65 (12) ◽  
pp. 5386-5393 ◽  
Author(s):  
R. T. Gill ◽  
J. J. Valdes ◽  
W. E. Bentley

ABSTRACT A reverse transcription (RT)-PCR technique was developed to analyze global gene regulation in Escherichia coli. A novel combination of primers designed specifically for the start and stop regions of E. coli genes (based on the findings of Fislage et al. [R. Fislage, M. Berceanu, Y. Humboldt, M. Wendt, and H. Oberender, Nucleic Acids Res. 25:1830–1835, 1997]) was used as an alternative to the poly(T) primers often used in eukaryotic RT-PCR. The validity of the technique was demonstrated by applying it to heat shock analysis. Specifically, RT-PCR-amplified total RNA from heat-shocked and non-heat-shocked cells were hybridized with slot blots of the Kohara set (U. Kohara, K. Akiyama, and K. Isono, Cell 50:495–508, 1987; S. Chuang, D. Daniels, and F. Blattner, J. Bacteriol. 175:2026–2036, 1993). The signals obtained for heat-shocked and control cultures of each clone were compared, and differences in intensity were evaluated by calculating induction ratios. Clones that were considered significantly induced were subsequently mapped by the Southern blot technique in order to determine specific gene upregulation. Also, for several genes, Northern blotting and total RNA dot blotting were performed to confirm that the transcript levels in the original RNA samples were different. This technique extended previously described methods for studying global gene regulation inE. coli by incorporating a PCR amplification step in which global, mRNA-specific primers were used. In addition, the method employed here can be easily extended to study E. coliglobal gene regulation in response to additional environmental stimuli.


1987 ◽  
Vol 262 (9) ◽  
pp. 3940-3943
Author(s):  
M. Yamagishi ◽  
J.R. Cole ◽  
M. Nomura ◽  
F.W. Studier ◽  
J.J. Dunn

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