Heterogeneity of the Principal Sigma Factor in Escherichia Coli: the RpoS Gene Product, Sigma 38, is a Second Principal Sigma Factor of RNA Polymerase in Stationary-phase Escherichia Coli

Overview

Journal Proc Natl Acad Sci U S A

Specialty Science

Date 1993 Apr 15

PMID 8475100

Citations 136

Authors

K Tanaka

Y Takayanagi

N Fujita

A Ishihama

H Takahashi

Affiliations

Soon will be listed here.

Abstract

The rpoS gene of Escherichia coli encodes a putative RNA polymerase sigma factor that is considered to be the central regulator of gene expression in stationary phase. The gene product (sigma 38) was overproduced using the cloned rpoS gene and purified to homogeneity. Reconstituted RNA polymerase holoenzyme (E sigma 38) was found to recognize in vitro a number of typical sigma 70-type promoters, including the lacUV5 and trp promoters. Some, however, were recognized exclusively or preferentially by E sigma 70, whereas at least one, fic, was favored by E sigma 38. Thus E. coli promoters can be classified into three groups: the first group is recognized by E sigma 70 and E sigma 38, but the second and third groups are recognized substantially by either E sigma 70 or E sigma 38 alone. In contrast to other minor sigma factors, sigma 38 shares a set of amino acid sequences common among the principal sigma factors of eubacteria and is therefore a member of the RpoD-related protein family. The intracellular level of sigma 38 was demonstrated to increase in vivo upon entry into stationary phase. These results together indicate that sigma 38 is a second principal sigma factor in stationary-phase E. coli.

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References

Iwakura Y, Ito K, Ishihama A . Biosynthesis of RNA polymerase in Escherichia coli. I. Control of RNA polymerase content at various growth rates. Mol Gen Genet. 1974; 133(1):1-23. DOI: 10.1007/BF00268673. View

Nomura T, Fujita N, Ishihama A . Promoter selectivity of Escherichia coli RNA polymerase: alteration by fMet-tRNAfMet. Nucleic Acids Res. 1986; 14(17):6857-70. PMC: 311704. DOI: 10.1093/nar/14.17.6857. View

Helmann J, CHAMBERLIN M . Structure and function of bacterial sigma factors. Annu Rev Biochem. 1988; 57:839-72. DOI: 10.1146/annurev.bi.57.070188.004203. View

Tanaka K, Shiina T, Takahashi H . Multiple principal sigma factor homologs in eubacteria: identification of the "rpoD box". Science. 1988; 242(4881):1040-2. DOI: 10.1126/science.3194753. View

Kawamukai M, Matsuda H, Fujii W, Utsumi R, Komano T . Nucleotide sequences of fic and fic-1 genes involved in cell filamentation induced by cyclic AMP in Escherichia coli. J Bacteriol. 1989; 171(8):4525-9. PMC: 210239. DOI: 10.1128/jb.171.8.4525-4529.1989. View

Ishihama A . Promoter selectivity of prokaryotic RNA polymerases. Trends Genet. 1988; 4(10):282-6. DOI: 10.1016/0168-9525(88)90170-9. View

Tran P, Bannor T, Doktor S, Nichols B . Chromosomal organization and expression of Escherichia coli pabA. J Bacteriol. 1990; 172(1):397-410. PMC: 208445. DOI: 10.1128/jb.172.1.397-410.1990. View

Mulvey M, Loewen P . Nucleotide sequence of katF of Escherichia coli suggests KatF protein is a novel sigma transcription factor. Nucleic Acids Res. 1989; 17(23):9979-91. PMC: 335226. DOI: 10.1093/nar/17.23.9979. View

Studier F, Rosenberg A, Dunn J, Dubendorff J . Use of T7 RNA polymerase to direct expression of cloned genes. Methods Enzymol. 1990; 185:60-89. DOI: 10.1016/0076-6879(90)85008-c. View

10.

von Ossowski I, Mulvey M, Leco P, Borys A, Loewen P . Nucleotide sequence of Escherichia coli katE, which encodes catalase HPII. J Bacteriol. 1991; 173(2):514-20. PMC: 207040. DOI: 10.1128/jb.173.2.514-520.1991. View

11.

Lange R . Identification of a central regulator of stationary-phase gene expression in Escherichia coli. Mol Microbiol. 1991; 5(1):49-59. DOI: 10.1111/j.1365-2958.1991.tb01825.x. View

12.

Tanaka K, Takahashi H . Cloning and analysis of the gene (rpoDA) for the principal sigma factor of Pseudomonas aeruginosa. Biochim Biophys Acta. 1991; 1089(1):113-9. DOI: 10.1016/0167-4781(91)90092-z. View

13.

Igarashi K, Ishihama A . Bipartite functional map of the E. coli RNA polymerase alpha subunit: involvement of the C-terminal region in transcription activation by cAMP-CRP. Cell. 1991; 65(6):1015-22. DOI: 10.1016/0092-8674(91)90553-b. View

14.

McCann M, Kidwell J, Matin A . The putative sigma factor KatF has a central role in development of starvation-mediated general resistance in Escherichia coli. J Bacteriol. 1991; 173(13):4188-94. PMC: 208069. DOI: 10.1128/jb.173.13.4188-4194.1991. View

15.

Tanaka K, Shiina T, Takahashi H . Nucleotide sequence of genes hrdA, hrdC, and hrdD from Streptomyces coelicolor A3(2) having similarity to rpoD genes. Mol Gen Genet. 1991; 229(3):334-40. DOI: 10.1007/BF00267453. View

16.

Shiina T, Tanaka K, Takahashi H . Sequence of hrdB, an essential gene encoding sigma-like transcription factor of Streptomyces coelicolor A3(2): homology to principal sigma factors. Gene. 1991; 107(1):145-8. DOI: 10.1016/0378-1119(91)90308-x. View

17.

Ozaki M, Wada A, Fujita N, Ishihama A . Growth phase-dependent modification of RNA polymerase in Escherichia coli. Mol Gen Genet. 1991; 230(1-2):17-23. DOI: 10.1007/BF00290644. View

18.

Siegele D, Kolter R . Life after log. J Bacteriol. 1992; 174(2):345-8. PMC: 205722. DOI: 10.1128/jb.174.2.345-348.1992. View

19.

Vicente M, Kushner S, Garrido T, Aldea M . The role of the 'gearbox' in the transcription of essential genes. Mol Microbiol. 1991; 5(9):2085-91. DOI: 10.1111/j.1365-2958.1991.tb02137.x. View

20.

Ozaki M, Fujita N, Wada A, Ishihama A . Promoter selectivity of the stationary-phase forms of Escherichia coli RNA polymerase and conversion in vitro of the S1 form enzyme into a log-phase enzyme-like form. Nucleic Acids Res. 1992; 20(2):257-61. PMC: 310363. DOI: 10.1093/nar/20.2.257. View