Mutation to rifampicin resistance at the beginning of the RNA polymerase β subunit gene in Escherichia coli

Lisitsyn, Nicholay A.; Свердлов, Е. Д.; Moiseyeva, Elena P.; Danilevskaya, Olga N.; Nikiforov, Vadim

doi:10.1007/bf00334112

Cited by 83 publications

(51 citation statements)

References 5 publications

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“…coli Rif R mutations are exclusively located in the rpoB gene and affect 25 clustered amino acid residues of the fork domain of the ␤ subunit (48,52,53). All are clustered along the RNA flank of the 9-bp RNA-DNA hybrid region near the active center of RNAP ( Fig.…”

Section: Isolation Of Chromosomal Rpob Rif R Mutants With Altered Elomentioning

confidence: 99%

Isolation and Characterization of RNA Polymerase rpoB Mutations That Alter Transcription Slippage during Elongation in Escherichia coli

Zhou¹,

Lubkowska²,

Hui³

et al. 2013

Journal of Biological Chemistry

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Background:The domains in RNA polymerase involved in elongation slippage are unknown. Results: We isolated E. coli RNA polymerase rpoB mutants with altered transcriptional slippage. Conclusion:The fork domain of RNA polymerase controls slippage. Biochemical analysis of the mutants validates the genetic schemes. Significance: Our work sheds light on the mechanism for maintenance of RNA-DNA register during transcription.

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Section: Isolation Of Chromosomal Rpob Rif R Mutants With Altered Elomentioning

confidence: 99%

Isolation and Characterization of RNA Polymerase rpoB Mutations That Alter Transcription Slippage during Elongation in Escherichia coli

Zhou¹,

Lubkowska²,

Hui³

et al. 2013

Journal of Biological Chemistry

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“…Other features in 6 and ~' are indicated with contrasting patterns and labels. In 13, they are a large deletion found in several chloroplast RNA polymerases (Hudson et al 1988), a sequence resembling one found in the RNase barnase (Shirai and Go 1991), sites of substitutions leading to streptolydigin (Heisler et al 1993;Severinov et al 1993) or rifampicin (Lisitsyn et al 1984;Severinov et al 1993} resistance, location where f3 is divided in Chlamydomonas chloroplasts (Fong and Surzycki 1992), the major site of trypsin cleavage in E. coli RNA polymerase (Borukhov et al 1991), a deletable hinge region in ~ (Glass et al 1986), and sites where primer substrate analogs cross-link to the [3 subunit (Grachev et al 1989). Features noted in ~' are a putative Cys4-Zn 2+ motif conserved in most ~' homologs (Borukhov et al 1991), a sequence similarity to DNA polymerase I (Allison et al 1985), a site where ~' homologs are split in cyanobacteria and chloroplasts (Hudson et al 1988;Xie et al 1989;Igloi et al 1990;Shimada et al 1990;Fong and Surzycki 1992), a region in which Ama-resistance substitutions occur in Pol II ~' subunit homologs (Bartolomei and Corden 1987;Chen et al 1993), a site where the 3' end of the nascent transcript cross-links to ~' (Borukhov et al 1991), a site where an insertion occurs in the rice chloroplast ~' subunit (Shimada et al 1990), and a site where a large deletion occurs in M. leprae fY (Honore et al 1993).…”

Section: All But One Termination-altering Substitution Occurred In Fomentioning

confidence: 99%

Termination-altering amino acid substitutions in the beta' subunit of Escherichia coli RNA polymerase identify regions involved in RNA chain elongation.

Weilbaecher¹,

Hebron²,

Feng³

et al. 1994

Genes Dev.

118

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To identify regions of the largest subunit of RNA polymerase that are potentially involved in transcript elongation and termination, we have characterized amino acid substitutions in the 13' subunit of Escherichia coli RNA polymerase that alter expression of reporter genes preceded by terminators in vivo. Termination-altering substitutions occurred in discrete segments of [3', designated 2, 3a, 3b, 4a, 4b, 4c, and 5, many of which are highly conserved in eukaryotic homologs of 13'. Region 2 substitutions (residues 311-386) are tightly clustered around a short sequence that is similar to a portion of the DNA-binding cleft in E. coli DNA polymerase I. Region 3b (residues 718-798) corresponds to the segment of the largest subunit of RNA polymerase II in which amanitin-resistance substitutions occur. Region 4a substitutions (residues 933-936) occur in a segment thought to contact the transcript 3' end. Region 5 substitutions (residues 1308-1356) are tightly clustered in conserved region H near the carboxyl terminus of [3'. A representative set of mutant RNA polymerases were purified and revealed unexpected variation in percent termination at six different p-independent terminators. Based on the location and properties of these substitutions, we suggest a hypothesis for the relationship of subunits in the transcription complex.[Key Words: rpoC gene; [3' subunit; RNA polymerase; transcriptional termination] Received July 26, 1994; revised version accepted October 13, 1994.Escherichia coli RNA polymerase contains a core of four subunits: 6', 155 kD; [3, 150 kD; and two c~, 43 kD each. These subunits form a scaffold and catalytic center for synthesis of RNA on a double-stranded DNA template that appear to be conserved from bacteria to humans. The two largest subunits, 6' and B in E. coli, display significant sequence similarity to homologous subunits found in all multisubunit RNA polymerases (Allison et al. 1985; Jokerst et al. 1989; Young 1991 and references therein): Each contains eight to nine conserved, colinear segments, although no sequence conservation is evident between f3' and B. However, we currently lack a clear picture of how these conserved primary sequence motifs are positioned in the three-dimensional structure of RNA polymerase.In the transcription elongation complex (for review, see Das 1993;Chamberlin 1994;Chan and Landick 1994), RNA polymerase contacts the DNA over a 25-to ~Present address:

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“…It is important to note that a significant number of mutations listed in the catalogue (see Table S2 in the supplemental material) have not been described in this article (2,45,46,49,66,67,73,78,80,84,88,91,97,108,111,112,124,126,129,130,146,151,157,160,165,167,168,170,177,180,181,186,193,204). For most of them, only in vivo phenotypes have been described and no in vitro characterization has yet been performed.…”

Section: Discussionmentioning

confidence: 99%

“…8B). More specifically, they are found in the protrusion, fork and external 1 and 2 domains of ␤ (14,31,81,82,97,108,120,127,129,130,156,160,174,178,186,201,202,207). Thus, these replacements most probably affect the conformation of the binding pocket and lower its affinity for rifampin.…”

Section: Drug-resistant Rnap Mutantsmentioning

confidence: 99%

Structural Perspective on Mutations Affecting the Function of Multisubunit RNA Polymerases

Trinh

Langelier

Archambault

et al. 2006

Microbiol Mol Biol Rev

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SUMMARY High-resolution crystallographic structures of multisubunit RNA polymerases (RNAPs) have increased our understanding of transcriptional mechanisms. Based on a thorough review of the literature, we have compiled the mutations affecting the function of multisubunit RNA polymerases, many of which having been generated and studied prior to the publication of the first high-resolution structure, and highlighted the positions of the altered amino acids in the structures of both the prokaryotic and eukaryotic enzymes. The observations support many previous hypotheses on the transcriptional process, including the implication of the bridge helix and the trigger loop in the processivity of RNAP, the importance of contacts between the RNAP jaw-lobe module and the downstream DNA in the establishment of a transcription bubble and selection of the transcription start site, the destabilizing effects of ppGpp on the open promoter complex, and the link between RNAP processivity and termination. This study also revealed novel, remarkable features of the RNA polymerase catalytic mechanisms that will require additional investigation, including the putative roles of fork loop 2 in the establishment of a transcription bubble, the trigger loop in start site selection, and the uncharacterized funnel domain in RNAP processivity.

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Mutation to rifampicin resistance at the beginning of the RNA polymerase β subunit gene in Escherichia coli

Cited by 83 publications

References 5 publications

Isolation and Characterization of RNA Polymerase rpoB Mutations That Alter Transcription Slippage during Elongation in Escherichia coli

Isolation and Characterization of RNA Polymerase rpoB Mutations That Alter Transcription Slippage during Elongation in Escherichia coli

Termination-altering amino acid substitutions in the beta' subunit of Escherichia coli RNA polymerase identify regions involved in RNA chain elongation.

Structural Perspective on Mutations Affecting the Function of Multisubunit RNA Polymerases

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