Tandem promoters preceding the gene for the M1 RNA component of Escherichia coli ribonuclease P.

Motamedi, Haideh; Lee, Younghoon; Schmidt, Francis J.

doi:10.1073/pnas.81.13.3959

Cited by 31 publications

(15 citation statements)

References 26 publications

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“…Multiple promoters control expression of numerous bacterial genes, including the carA (2,28), glnA (30), and Ml RNA (27) genes of E. coli and the spoVG gene of B. subtilis (17). Tandem promoters differ in their spacing, strength, and activity under various enrivonmental or physiological conditions.…”

Section: Discussionmentioning

confidence: 99%

Streptococcus pyogenes type 12 M protein gene regulation by upstream sequences

et al. 1987

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A partial nucleotide sequence that included 1,693 base pairs of the M12 (emml2) gene of group A streptococci (strain CS24) and adjacent upstream DNA was determined. Type 12 M protein-specific mRNA of strain CS24 is transcribed from two promoters (P, and P3) (35) it has been shown that the switch from high to low levels of M-protein expression occurs at high frequency and is reversible, which are characteristics of phase variation described for other bacterial species (7,26). In addition to phase variation of M-protein expression (35), streptococci also exhibit both antigenic variation (more than 70 strains with antigenically distinct M proteins have been described) and size variation of this protein (11). The mechanisms that control phase and antigenic variation and the relationship between them is not understood. Although the nature of M protein as an antiphagocytic molecule has been demonstrated, a role for the M-state in the survival of the organism has not been identified. Phase variation has been postulated to be a virulence factor that controls the expression of the type 1 pilus of Escherichia coli (6, 7) and the pilus of Neisseria gonorrhoeae (26 report results of a study of the role of upstream neighboring sequences in the regulation of expression of the emmi2 gene of strain CS24 in E. coli, describe the physical relationship between the deletion in strain CS64 and the 5' end of the emml2 gene, and study the transcriptional activity of the emml2 gene by Northern and primer extension analyses. We found that transcription of the emml2 gene in strain CS64 is diminished by more than 100-fold and that the deletion is more than 400 bases upstream from the transcription start sites of the emml2 gene. MATERIALS AND METHODSBacterial strains, plasmids, bacteriophage, and media. M type 12 group A streptococcal strain CS24 and variant CS64 have been described previously (3,39). Liquid cultures of group A streptococci were grown in Todd-Hewitt broth supplemented with 1% Neopeptone (Difco Laboratories, Detroit, Mich.) for 15 to 18 h at 37°C. E. coli JM83, JM103, and JM110, carrying constructs of plasmids pUC19 and pUC18, were propagated in L broth or on L agar containing ampicillin (30 ,ug/ml) and 5-bromo-4-chloro-3-indolyl-P-Dgalactoside (0.03%) at 37°C. All plasmids used and constructed in this study are listed in Fig. 1

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Section: Discussionmentioning

confidence: 99%

Streptococcus pyogenes type 12 M protein gene regulation by upstream sequences

et al. 1987

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“…The promoter region of the rnpB gene coding for M1 RNA contains three regions of homology to the E. coli consensus promoter sequence (5). In vitro and in vivo transcriptions arise from the nearest promoter, P-1, almost exclusively (6), even though transcripts can originate from the upstream promoters (5).…”

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“…In vitro and in vivo transcriptions arise from the nearest promoter, P-1, almost exclusively (6), even though transcripts can originate from the upstream promoters (5). The 3Ј-flanking region of the rnpB gene contains a repeated DNA sequence of 113 base pairs.…”

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Mutational Analysis of RNA Structures and Sequences Postulated to Affect 3′ Processing of M1 RNA, the RNA Component of Escherichia coli RNase P

Kim

Park

et al. 1996

Journal of Biological Chemistry

104

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When the rnpB gene encoding M1 RNA, the RNA component of Escherichia coli RNase P, is transcribed, the primary M1 RNA transcript (pM1 RNA) is produced and subsequently processed at the 3 end to generate the mature M1 RNA. To study features of pM1 RNA thought to be involved in RNA processing, systematic mutations were introduced in sequence elements and secondary structures surrounding the processing site using p23 RNA, a truncated pM1 RNA transcribed from the internally deleted rnpB gene, as a model substrate and the processing of its mutant derivatives was analyzed in vivo and in vitro. Neither the alteration of two bases forming the processing site nor the disruption of secondary structures surrounding the site significantly affected the processing efficiency although the secondary structures were required for maintaining RNA stability. In contrast, mutations at the rne-dependent site, GAUUU, immediately 3 to the processing site inhibited the processing and the extent of the inhibition varied with the altered sequences. Furthermore, the processing of the mutants of the rne-dependent site as well as wild-type p23 RNA was inhibited in an E. coli rne ts strain at the nonpermissive temperature.Ribonuclease P (RNase P) is a processing enzyme that catalyzes the endonucleolytic removal of 5Ј leader sequences from precursors of tRNAs to generate the mature 5Ј ends of tRNAs (1). In Escherichia coli, RNase P is composed of the RNA subunit (M1 RNA, 377 nucleotides) and the protein subunit (C5 protein, 119 amino acid residues) (2-4).The promoter region of the rnpB gene coding for M1 RNA contains three regions of homology to the E. coli consensus promoter sequence (5). In vitro and in vivo transcriptions arise from the nearest promoter, P-1, almost exclusively (6), even though transcripts can originate from the upstream promoters (5). The 3Ј-flanking region of the rnpB gene contains a repeated DNA sequence of 113 base pairs. This sequence, which includes both the 3Ј terminal 24 nucleotides of the M1 RNA coding sequence and the region for transcription termination, is repeated almost 3.5 times (7). The region for transcription termination contains a stem and loop structure characteristic of structures found near regions of -independent transcription termination (8), and functions in a -independent fashion in vitro (9). In vivo studies using the galactokinase transcription fusion plasmids (10) indicate that more than 94% of transcription is terminated at the first terminator, T1, in the first repeating unit. Therefore, the RNA product initiated from P-1 and terminated at T1 should be a major primary transcript of the rnpB gene from which mature M1 RNA is derived. This transcript, termed pM1 RNA (primary transcript), carries extra stretches of 36 nucleotides containing a termination stem and loop at the 3Ј end of M1 RNA which are removed by a processing event. pM1 RNA of 413 nucleotides is processed to form mature M1 RNA in vitro by an S30 extract (9). On the other hand, a 40% ammonium sulfate precipitate of S200 extract from...

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“…Nucleotide sequence analysis of this fragment (Fig. 3) revealed both that the sequence from positions 2387 to 3181 was identical to the sequence that included the rnpB gene reported by Motamedi et al (8), with the exception of a few nucleotides in the 5' flanking region, and that positions 3056 to 3820 were identical to the 3'-terminal repeated region of rnpB reported by Reed and Altman (10). Thus, we confirmed that the rnpB gene is located at 3,337 kb on Kohara's physical map with a counterclockwise orientation (Fig.…”

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confidence: 93%

“…In (8). It is noteworthy that ORF 2 exhibits partial homology, in terms of predicted amino acids, to gntZ (which affects the utilization of gluconate) of Bacillus subtilis (5) and gnd (which encodes 6-phosphogluconate dehydrogenase) of E. coli (9) (24.8% identical with respect to 195 N-terminal amino acids and 23.2% identical with respect to 202 N-terminal amino acids, respectively).…”

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Precise mapping of the rnpB gene encoding the RNA component of RNase P in Escherichia coli K-12

Komine

Inokuchi

1991

J Bacteriol

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Cell 50: [495][496][497][498][499][500][501][502][503][504][505][506][507][508] 1987), multiple copies of chromosomal sequence are found at 68 and at 64 to 65 min (M. Umeda and E. Ohtsubo, J. Mol. Biol. 213:229-237, 1990). We have determined that the rnpB gene (previously mapped at 70 min [B. J. Bachmann, Microbiol. Rev. 54:130-197, 1990]) is located within these segments of repeated sequences as five separate copies, together with tdcA, B, C, and R (mapped at 68 min [Bachmann, 1990]) and six unidentified open reading frames. Since close linkage of rnpB and tdc is found in various strains of E. coli K-12, the rnpB gene should be mapped at 68 min rather than 70 min.In Kohara's library derived from Escherichia coli K-12 W3110 (6), a chromosomal duplication which is assumed to be mediated by IS5 has been identified: at 64 to 65 min, a 12.5-kb segment flanked by IS5 is tandemly repeated three times, and at 68 min, the same segment is repeated 1.7 times (15) (Fig. 1A). Comparisons of the restriction maps of these regions in W3110 and those in other strains revealed that this duplication is characteristic of W3110 and that the multiple copies are derived from a segment at 68 min (3,15).Prior to the present study, we made an exhaustive survey of tRNA genes in E. coli by analyzing the tRNAs produced upon infection of each lambda clone in Kohara's library ("miniset," 476 clones) (7). In addition to tRNAs, some small stable RNAs were detected, and these RNAs included some unidentified RNAs. Clones 479, 480, 501, and 502 (at 64 to 65 min) and 514, 515, and 516 (at 68 min), which correspond to the multicopy regions mentioned above, produced stable RNAs of about 400 nucleotides ( Fig. 2) which we have now identified.A candidate for these RNAs was Ml RNA (the RNA component of RNase P), even though the rnpB gene which encodes Ml RNA has been mapped at 70 min (2). We examined the complementation activity of these phage clones in E. coli ts709, an rnpB temperature-sensitive mutant (11). Lambda bacteriophages 479, 480, 501, 502, 514, 515, and 516 were cross-streaked against strain ts709, which had been lysogenized with wild-type phage to provide products of the cI gene, and incubated at the restrictive temperature (42°C). All of the seven X clones were able to complement the rnpB709(Ts) mutation (data not shown). On the other hand, no phage clone corresponding to the 70-min region produced any stable RNA and complemented the rnpB709(Ts) mutation (data not shown). It therefore seemed likely that the rnpB gene is located at 68 min rather than at 70 min, and in strain W3110, the segment containing the rnpB gene was repeated, conserving functional genes.To determine the exact location of the rnpB gene, we constructed plasmids that carried various restriction fragments of phage 515 DNA, which corresponds to the region presumed to be the original segment of the chromosome. Among these plasmids, one carrying an EcoRV 4.4-kb fragment appeared to complement the rnpB709(Ts) mutation * Corresponding author.(data not shown). Nucleotide seque...

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Tandem promoters preceding the gene for the M1 RNA component of Escherichia coli ribonuclease P.

Cited by 31 publications

References 26 publications

Streptococcus pyogenes type 12 M protein gene regulation by upstream sequences

Streptococcus pyogenes type 12 M protein gene regulation by upstream sequences

Mutational Analysis of RNA Structures and Sequences Postulated to Affect 3′ Processing of M1 RNA, the RNA Component of Escherichia coli RNase P

Precise mapping of the rnpB gene encoding the RNA component of RNase P in Escherichia coli K-12

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