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72 Nihal Büyükuslu the primary σ factors and has a sequence similarity to the HTH-DNA binding motif (Brennan and Matthews, 1989; Gribskov and Burgess, 1986; Helmann and Chamberlin, 1988; Straiger et al., 1989). A spacer region of variable length and sequence lies between the two subregions. It appears likely that the conserved HTH motif in subregion 4.2 may directly contact the –35 promoter region. Although two mutations, R584C and R588H, in this region of the E. coli σ 70 factor have been implicated in recognition of the –35 promoter sequence, a set of C-truncated σ 70 lacking the –35 recognition domain can activate class II promoters (the pstS and P1gal), indicating that necessary contact or activation sites for the two activators lie at different positions in a segment of σ 70 extending from region 3.2 to the upstream helix within region 4.2 (Kumar et al., 1994; Makino et al., 1993). Further evidence to support this suggestion came from the study by Jin et al., (1995). Using protein-protein photo-crosslinking, they showed that the CRP site for galP1, a class 2 promoter, contacts with amino acids 530-539 of σ 70 region. All RNA polymerase holoenzymes containing σ 70 - related σs appear to function in a similar manner. However, σ 54 (σN), encoded by rpoN, is quite distinct, both structurally and functionally, from the σ 70 family. Among 17 sequenced rpoN genes, there is a high degree of conservation in the protein primary sequence, and three distinct regions can be identified (Merrick et al., 1987). Region I is the N-terminal region is suggested to be α-helical; it is rich in leucine and glutamine residues. Region II varies between 60 to 110 residues in length, with essentially no sequence conservation. The C-terminal region III is highly conserved and contains two motifs; a potential helixturn-helix (HTH) motif and the ‘RpoN box’. σ 54 and σ 70 participate in different transcription mechanisms but bind the same core RNA polymerase (Gralla, 1991). Recent considerations suggest that σ 54 should contain a minimum of two different elements Table 2: The E. coli sigma factors Sigma factor Gene Function for recognition of the –24 and –12 promoter regions. C-terminal deletions near to the HTH motif abolished DNA binding (Sasse-Dwight and Gralla, 1990). Indeed, specific amino acid substitutions in this region showed a similar phenotype (Coppard and Merrick, 1991). Merrick and Chambers (1992) found a specific HTH mutation in K. pneumoniae σN (R363K) suppressed down mutations at position –13 in the glnAp2 promoter, suggesting that the conserved HTH region is involved in recognition of promoter-proximal sequences. Physical studies indicate that amino acids in a region from Asn312 to Arg345 in K. pneumoniae σN, just upstream of the HTH, crosslink to DNA in the presence or absence of core enzyme (Cannon et al., 1994). In contrast to the σ 70 family, activation of Eσ 54 is not dependent on the presence of the C-terminal domain (Lee et al., 1993). Transcription by Eσ 54 appears to be controlled by a mechanism that requires the use of an activator protein and ATP to catalyze formation of open complexes (Popham et al., 1989). Deletions in both region I and region III prevent opencomplex formation. During open-complex formation, region II has been proposed to play a role in triggering conformational changes for DNA melting (Sasse- Dwight and Gralla, 1990). The importance of σ S has been increasingly recognised in recent years. This sigma factor appears only as cells enter the stationary phase of growth. It is responsible for transcription of all of the genes whose products are required during stationary phase (Ishihama, 2000). Two families of σ factors have been characterised in detail. A number of different σ factors belonging to sigma families are presented in Table 2 according to the origin, genetic locus, and presumed function. The ω subunit The ω subunit, encoded rpoZ, is associated with both σ 70 rpoD Housekeeping function σ 54 RpoN (ntrA, glnF) Nitrogen-regulated gene transcription σ 32 RpoH Heat-shock gene transcription σ S RpoS Gene expression in stationary phase cells σ F RpoF Expression of flagellar operons σ FecI fecI Regulates the fec genes for iron dicitrate transport
core and holoenzyme (Burgess, 1969). The omega subunit was for many years considered a curiosity since no function could be ascribed to it. Therefore, the available literature on the ω subunit as regards to its structure and function is rare. The ω subunit is not required for the function of the transcriptional apparatus both in vivo and in vitro. Strain lacking ω, that is, a rpoZ null mutant is viable, suggesting a nonessential nature of the protein or that there might also be a redundancy in function. The only known phenotype ascribed to the rpoZ null mutant is a slower growth time (Mukherjee et al., 1999). However, it is now known that omega is necessary to restore denatured RNA polymerase in vitro to its fully functional form. It may function by binding simultaneously to the N-terminus and C-terminus of the β' subunit. The omega subunit is a part of the Thermus aquaticus enzyme whose structure was recently determined (Murakami et al., 2002). A study by Mukharjee and Chatterji (1999) showed that ω-less holoenzyme has lesser affinity towards the DNA template and external addition of ω destabilizes the open complex for both the wild-type and ω-less enzyme. The ω-less core enzyme interacts with the σ 70 subunit to expose the –35 recognition domain (domain 4·2) unlike that observed in the wild-type interaction. Thus the absence of the ω subunit leads to the formation of an enzyme which has altered DNA binding and σ 70 binding properties. Circular dichroic measurements also indicate a major conformational alteration of both holo and core RNA polymerase in the presence and absence of the ω subunit. References Attey A, Belyaeva T, Savery N, Hoggett J, Fujita N, Ishihama A and Busby S. Interactions between the cyclic AMP receptor protein and the α subunit of RNA polymerase at the E. coli galactose operon P1 promoter. Nucl Acid Res. 22: 4375-4380, 1994. Borukhov S, Lee J and Goldfarb A. Mapping of a contact for the RNA 3' terminus in the largest subunit of RNA polymerase. J Biol Chem. 266: 23932-23935, 1991. Brennan RT and Matthews BW. The helix-turn-helix DNA binding motif. J Biol Chem. 264: 1903-1906, 1989. Burgess RR. Separation and characterization of the subunits of RNA polymerase. J Biol Chem. 244: 2168-2176, 1969. Busby S, West D, Lawes M, Webster C, Ishihama A and Kolb A. Transcription activation by the E. coli cyclic- E. coli RNA polymerase 73 amp protein-receptors bound in tandem at promoters can interact synergistically. J Mol Biol. 241: 341-352, 1994. Büyükuslu N, Trigwell SM, Lim PP, Fujita N, Ishihama A, Ralphs N and Glass RE. Physical mapping of a collection of MaeI-generating mutations in the β gene of E. coli RNA polymerase and the functional effect of internal deletions constructed through their manipulation. Genes and Function 1: 119-129, 1997. Callaci S, Heyduk E and Heyduk T. Conformational changes of E. coli RNA polymerase σ 70 factor induced by binding to the core enzyme. J Biol Chem. 273: 329995-33001, 1998. Callaci S, Heyduk E and Heyduk T. Core RNA polymerase from E. coli induces a major change in the domain arrangement of the σ 70 subunit. Molecular Cell. 3: 229- 238, 1999. Cannon W, Claveriemartin F, Austin S and Buck M. Identification of a DNA-contacting surface in the transcription factor σ 54 . Mol Microbiol. 11: 227-236, 1994. Clerget M, Jin DJ and Weisber RA. A zinc-binding region in the β' subunit of RNA polymerase is involved in antitermination of early transcription of phage HK022. J Mol Biol. 248: 768-780, 1995. Coppard JR and Merrick MJ. Casette mutagenesis implicates a helix-turn-helix motif in promoter recognition by the novel RNA-polymerase σ-factor σ 54 . Mol Microbiol. 5: 1309-1317, 1991. Cromie K, Ahmad K, Malik T, Büyükuslu N and Glass RE. Trans-dominant mutations in the 3'-terminal region of the rpoB gene define highly conserved, essential residues in the β subunit of RNA polymerase: the GEME motif. Genes to Cells. 4: 145-159, 1999. Daniels D, Zuber R and Losick R. Two amino acids in an RNA polymerase σ factor involved in the recognition of adjacent base pairs in the –10 region of a cognate promoter. Proc Nat Acad Sci. USA 87: 8075-8079, 1990. Darst SA, Edwards AM and Kornberg RD. Threedimensional structure of E. coli RNA polymerase holoenzyme determined by electron crystallography. Nature. 340: 730-732, 1989. Dombroski AJ, Walter WA, Record MT, Jr. Siegele DA and Gross CA. Polypeptides containing highly conserved regions of transcription initiation factor sigma 70 exhibit specificity of binding to promoter DNA. Cell. 70: 501- 512, 1992. Dombroski AJ, Walter WA and Gross CA. Amino-terminal amino acids modulate sigma-factor DNA-binding activity. Genes Dev. 7: 2446-2455, 1993. Fukuda R and Ishihama A. Subunits of RNA polymerase in function and structure. V. Maturation in vitro of core enzyme from E. coli. J Mol Biol. 87: 523-540, 1974. Glass RE, Honda A and Ishihama A. Genetic studies on the β subunit of E. coli RNA polymerase. IX The role of the carboxy-terminus in enzyme assembly. Mol Gen Genet.
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Volume contents Volume 2, No. 1 Ded
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Author index Ak›fl N. 91 Aktafl T
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