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Ahmad E, Mitra A, Ahmed W, Mahapatra V, Hegde SR, Sala C, Cole ST, Nagaraja V. Rho-dependent transcription termination is the dominant mechanism in Mycobacterium tuberculosis. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194923. [PMID: 36822574 DOI: 10.1016/j.bbagrm.2023.194923] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/31/2023] [Accepted: 02/14/2023] [Indexed: 02/24/2023]
Abstract
Intrinsic and Rho-dependent transcription termination mechanisms regulate gene expression and recycle RNA polymerase in bacteria. Both the modes are well studied in Escherichia coli, and a few other organisms. The understanding of Rho function is limited in most other bacteria including mycobacteria. Here, we highlight the dominance of Rho-dependent termination in mycobacteria and validate Rho as a key regulatory factor. The lower abundance of intrinsic terminators, high cellular levels of Rho, and its genome-wide association with a majority of transcriptionally active genes indicate the pronounced role of Rho-mediated termination in Mycobacterium tuberculosis (Mtb). Rho modulates the termination of RNA synthesis for both protein-coding and stable RNA genes in Mtb. Concordantly, the depletion of Rho in mycobacteria impact its growth and enhances the transcription read-through at 3' ends of the transcription units. We demonstrate that MtbRho is catalytically active in the presence of RNA with varied secondary structures. These properties suggest an evolutionary adaptation of Rho as the efficient and preponderant mode of transcription termination in mycobacteria.
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Affiliation(s)
- Ezaz Ahmad
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru 560012, India
| | - Anirban Mitra
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru 560012, India
| | - Wareed Ahmed
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru 560012, India
| | - Varsha Mahapatra
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru 560012, India
| | - Shubhada R Hegde
- Institute of Bioinformatics and Applied Biotechnology, Bengaluru 560100, India
| | - Claudia Sala
- Monoclonal Antibody Discovery Laboratory, Fondazione Toscana Life Sciences, 53100 Siena, Italy
| | | | - Valakunja Nagaraja
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru 560012, India; Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru 560064, India.
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2
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Villa TG, Abril AG, Sánchez-Pérez A. Mastering the control of the Rho transcription factor for biotechnological applications. Appl Microbiol Biotechnol 2021; 105:4053-4071. [PMID: 33963893 DOI: 10.1007/s00253-021-11326-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/22/2021] [Accepted: 04/27/2021] [Indexed: 12/25/2022]
Abstract
The present review represents an update on the fundamental role played by the Rho factor, which facilitates the process of Rho-dependent transcription termination in the prokaryotic world; it also provides a summary of relevant mutations in the Rho factor and the insights they provide into the functions carried out by this protein. Furthermore, a section is dedicated to the putative future use of Rho (the 'taming' of Rho) to facilitate biotechnological processes and adapt them to different technological contexts. Novel bacterial strains can be designed, containing mutations in the rho gene, that are better suited for different biotechnological applications. This process can obtain novel microbial strains that are adapted to lower temperatures of fermentation, shorter production times, exhibit better nutrient utilization, or display other traits that are beneficial in productive Biotechnology. Additional important issues reviewed here include epistasis, the design of TATA boxes, the role of small RNAs, and the manipulation of clathrin-mediated endocytosis, by some pathogenic bacteria, to invade eukaryotic cells. KEY POINTS: • It is postulated that controlling the action of the prokaryotic Rho factor could generate major biotechnological improvements, such as an increase in bacterial productivity or a reduction of the microbial-specific growth rate. • The review also evaluates the putative impact of epistatic mechanisms on Biotechnology, both as possible responsible for unexpected failures in gene cloning and more important for the genesis of new strains for biotechnological applications • The use of clathrin-coated vesicles by intracellular bacterial microorganisms is included too and proposed as a putative delivery mechanism, for drugs and vaccines.
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Affiliation(s)
- Tomás G Villa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Santiago de Compostela, La Coruña, 15706, Santiago de Compostela, Spain.
| | - Ana G Abril
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Santiago de Compostela, La Coruña, 15706, Santiago de Compostela, Spain.
| | - Angeles Sánchez-Pérez
- Sydney School of Veterinary Science, Faculty of Science, University of Sydney, Sydney, NSW, 2006, Australia.
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3
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Olson KE, Dolan GF, Müller UF. In vivo evolution of a catalytic RNA couples trans-splicing to translation. PLoS One 2014; 9:e86473. [PMID: 24466112 PMCID: PMC3900562 DOI: 10.1371/journal.pone.0086473] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 12/09/2013] [Indexed: 12/17/2022] Open
Abstract
How does a non-coding RNA evolve in cells? To address this question experimentally we evolved a trans-splicing variant of the group I intron ribozyme from Tetrahymena over 21 cycles of evolution in E.coli cells. Sequence variation was introduced during the evolution by mutagenic and recombinative PCR, and increasingly active ribozymes were selected by their repair of an mRNA mediating antibiotic resistance. The most efficient ribozyme contained four clustered mutations that were necessary and sufficient for maximum activity in cells. Surprisingly, these mutations did not increase the trans-splicing activity of the ribozyme. Instead, they appear to have recruited a cellular protein, the transcription termination factor Rho, and facilitated more efficient translation of the ribozyme’s trans-splicing product. In addition, these mutations affected the expression of several other, unrelated genes. These results suggest that during RNA evolution in cells, four mutations can be sufficient to evolve new protein interactions, and four mutations in an RNA molecule can generate a large effect on gene regulation in the cell.
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Affiliation(s)
- Karen E. Olson
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States of America
| | - Gregory F. Dolan
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States of America
| | - Ulrich F. Müller
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States of America
- * E-mail:
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4
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Peters JM, Vangeloff AD, Landick R. Bacterial transcription terminators: the RNA 3'-end chronicles. J Mol Biol 2011; 412:793-813. [PMID: 21439297 PMCID: PMC3622210 DOI: 10.1016/j.jmb.2011.03.036] [Citation(s) in RCA: 232] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2011] [Revised: 03/14/2011] [Accepted: 03/16/2011] [Indexed: 01/01/2023]
Abstract
The process of transcription termination is essential to proper expression of bacterial genes and, in many cases, to the regulation of bacterial gene expression. Two types of bacterial transcriptional terminators are known to control gene expression. Intrinsic terminators dissociate transcription complexes without the assistance of auxiliary factors. Rho-dependent terminators are sites of dissociation mediated by an RNA helicase called Rho. Despite decades of study, the molecular mechanisms of both intrinsic and Rho-dependent termination remain uncertain in key details. Most knowledge is based on the study of a small number of model terminators. The extent of sequence diversity among functional terminators and the extent of mechanistic variation as a function of sequence diversity are largely unknown. In this review, we consider the current state of knowledge about bacterial termination mechanisms and the relationship between terminator sequence and steps in the termination mechanism.
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Affiliation(s)
- Jason M. Peters
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
- Department of Genetics, University of Wisconsin, Madison, WI 53706, USA
| | - Abbey D. Vangeloff
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
| | - Robert Landick
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
- Department of Bacteriology, University of Wisconsin, Madison, WI 53706, USA
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5
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Moyse KA, Knight JS, Richardson JP. Phenotypic characterization of a comprehensive set of bicyclomycin-resistant mutants. BIOCHIMICA ET BIOPHYSICA ACTA 2001; 1520:223-33. [PMID: 11566358 DOI: 10.1016/s0167-4781(01)00271-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A comprehensive set of bicyclomycin-resistant mutants of transcription termination protein Rho has been characterized in Escherichia coli by in vivo and in vitro assays. Several of the mutant Rho proteins have functional defects. Strains with either the L208R or the S266A mutation in the bacterial chromosome have a higher intracellular concentration of the Rho protein than strains containing a wild-type copy of the rho gene. Strains carrying the L187R, L208R or S266A mutations in the chromosome also have a mutant phenotype; a plasmid-located arabinose promoter is constitutively de-repressed in these strains. The L208R and S266A mutant strains also have a rate of growth defect. When the S266A mutation is located on a high-copy plasmid, the mutant grows more slowly than a wild-type strain. In contrast to the majority of the bicyclomycin-resistant mutants, these two mutants show clear phenotypic differences from wild-type cells. These differences are also seen in vitro. In vitro transcription termination by RhoL208R and RhoS266A is defective at the lambda tR1 terminator, but can be enhanced by NusG. These functionally defective Rho mutations have been located near the putative catalytic site on a model of Rho based on the F1-ATPase. This indicates that this region of the Rho molecule is crucial for Rho function. The crucial region overlaps the putative bicyclomycin-binding site, suggesting an explanation for the efficacy of bicyclomycin as an antibiotic.
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Affiliation(s)
- K A Moyse
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
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6
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Pichoff S, Alibaud L, Guédant A, Castanié MP, Bouché JP. An Escherichia coli gene (yaeO) suppresses temperature-sensitive mutations in essential genes by modulating Rho-dependent transcription termination. Mol Microbiol 1998; 29:859-69. [PMID: 9723924 DOI: 10.1046/j.1365-2958.1998.00981.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
An extragenic multicopy suppressor of the cell division inhibition caused by a MalE-MinE fusion protein in Escherichia coli has been mapped and identified as yaeO, one of the two short open reading frames (ORFs) of an operon located at 4.6 min. Overexpressed yaeO also suppressed some temperature-sensitive mutations in division genes ftsA and ftsQ, in chaperone gene groEL and in co-chaperone gene grpE. Gene yaeO, whose expression is regulated by growth rate, codes for a 9 kDa acidic protein with no obvious resemblance to other proteins. Transcription termination protein Rho co-purified with a histidine-tagged derivative of YaeO protein on Ni2+-NTA agarose columns in a manner that suggested direct YaeO-Rho interaction. In vivo, yaeO expression reduced termination at rho-dependent bacteriophage terminator tL1 and at the terminator of autogenously regulated gene rho. The suppression of temperature-sensitive phenotypes was a consequence of anti-termination, as it could be mimicked by a Prho::Tn10 mutation that reduces the expression and activity of gene rho. Our data indicate that the suppression is not caused by overexpression of the mutated genes, but presumably by indirect stabilization of the mutated proteins.
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Affiliation(s)
- S Pichoff
- Laboratoire de Microbiologie et de Génétique Moléculaire du CNRS, Toulouse, France
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7
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Sozhamannan S, Stitt BL. Effects on mRNA degradation by Escherichia coli transcription termination factor Rho and pBR322 copy number control protein Rop. J Mol Biol 1997; 268:689-703. [PMID: 9175854 DOI: 10.1006/jmbi.1997.1004] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Mutants in Escherichia coli transcription termination factor Rho, termed rho(nusD), were previously isolated based on their ability to block the growth of bacteriophage T4. Here we show that rho(nusD) strains have decreased average half-lives for bulk cellular mRNA. Decreased E. coli message lifetimes could be because of increased ribonuclease activity in the rho mutant cells: if a Rho-dependent terminator precedes a ribonuclease gene, weaker termination in the rho mutants could lead to nuclease overexpression. However, inactivation of ribonuclease genes in rho026 cells did not relieve the defective phage growth. Unexpectedly, expression of the pBR322 Rop protein, a structure-specific, sequence-independent RNA-binding protein, in rho(nusD) cells restored the ability of T4 to grow and prolonged cellular message half-life in both the wild-type and the rho026 mutant. These results suggest that it is the RNA-binding ability of Rho rather than its transcription termination function that is important for the inhibition of bacteriophage growth and the shorter bulk mRNA lifetime. We propose that altered interaction of the mutant Rho with mRNA could make the RNA more susceptible to degradation. The inability of the RNA-binding proteins SrmB and DeaD to reverse the rho mutant phenotype when each is overexpressed implies that the required RNA interactions are specific. The results show novel roles for Rho and Rop in mRNA stability.
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Affiliation(s)
- S Sozhamannan
- Department of Biochemistry, Temple University School of Medicine, Philadelphia, PA 19140, USA
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8
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Geiselmann J, Yager TD, Gill SC, Calmettes P, von Hippel PH. Physical properties of the Escherichia coli transcription termination factor rho. 1. Association states and geometry of the rho hexamer. Biochemistry 1992; 31:111-21. [PMID: 1370623 DOI: 10.1021/bi00116a017] [Citation(s) in RCA: 59] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To function as a DNA-RNA helicase in rho-dependent transcript termination, six genetically identical subunits of the Escherichia coli transcription termination protein rho must first assemble into a hexameric complex. To help determine the quaternary structure of this complex, we have studied the association equilibria of the rho protomers. Sedimentation equilibrium, sedimentation velocity, diffusion, X-ray scattering, and neutron-scattering data have been combined to create a "phase diagram" of the association states of this protein as a function of protein concentration and ionic environment. The results show that rho exists predominantly as a hexamer under approximately physiological conditions and that this hexamer is in equilibrium with both lower and higher states of association that may also have physiological relevance. Small-angle X-ray scattering measurements and theoretical calculations indicate that the rho hexamer has a radius of gyration of 50 +/- 3 A. The radius of gyration measured by small-angle neutron scattering in 2H2O is 47 +/- 3 A. These scattering studies also support earlier models of rho as a planar hexagon which have been developed on the basis of electron microscopy. In the following paper in this issue [Geiselmann, J., Seifried, S. E., Yager, T. D., Liang, C., & von Hippel, P. H. (1992)], these results are combined with information on symmetry, subunit interactions, and packing geometry to obtain a model of the quaternary structure of the functional rho hexamer.
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Affiliation(s)
- J Geiselmann
- Institute of Molecular Biology, University of Oregon, Eugene 97403
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9
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Mori H, Imai M, Shigesada K. Mutant rho factors with increased transcription termination activities. II. Identification and functional dissection of amino acid changes. J Mol Biol 1989; 210:39-49. [PMID: 2479757 DOI: 10.1016/0022-2836(89)90289-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We have determined the nucleotide sequences of three mutant rho genes encoding hyperfunctional rho proteins (rho S) together with their parent allele, rho-ts702. These mutant rho factors contain the following amino acid changes as deduced from their sequences: (1) the thermo-labile mutant, rho-ts702, has Thr304 substituting for Ala; (2) rho S-77 and rho S-81, which are selectively altered in the primary polynucleotide binding site, share an identical mutation, Leu3----Phe; (3) rho S-82, which is altered in both the primary and secondary polynucleotide binding sites, carries three amino acid substitutions together, Leu3----Phe, Asp156----Asn and Thr323----Ile. Dissection and functional characterization of each mutation in rho S-82 have revealed that Ile323 alone is responsible for alterations in both the secondary RNA interaction and the terminator selectivity observed with the original mutant, rho S-82. Taken together, these results not only confirm our proposal in the accompanying paper that the primary and secondary RNA binding sites differently contribute in determining the overall efficiency and site-specificity of termination, respectively, but also support the possibility that these binding sites exist as structurally distinct domains in rho protein. In contrast, Asn156 was shown to cause decreased termination efficiency, though it had no influence on RNA interactions. Thus, this amino acid residue appears to be associated with still another rate-determining step of termination, for instance, interactions between rho and RNA polymerase. On the basis of Chou-Fasman secondary structure predictions as well as amino acid sequence comparison with F1-ATPase, we discuss how the proposed domains are structurally and functionally related to the putative ATPase reactive center of rho protein.
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Affiliation(s)
- H Mori
- Department of Biochemistry, Kyoto University, Japan
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10
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Tsurushita N, Shigesada K, Imai M. Mutant rho factors with increased transcription termination activities. I. Functional correlations of the primary and secondary polynucleotide binding sites with the efficiency and site-selectivity of rho-dependent termination. J Mol Biol 1989; 210:23-37. [PMID: 2479756 DOI: 10.1016/0022-2836(89)90288-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We have characterized rho proteins from mutants of Escherichia coli, rho s-81 and rho s-82, which are hyperactive in termination. The two mutant rho proteins are differentially altered both in termination activities and in RNA interactions. rho s-81 generally elicits enhanced termination on various templates such as phage T7 DNA and a DNA restriction fragment containing the trpE intracistronic rho-dependent terminators, either measured as a whole or examined for individual sites. On the other hand, rho s-82 has strikingly different preferences toward individual termination sites, exhibiting overall termination activities higher or lower than normal, depending on templates. From measurements of the rho ATPase activity with T7 RNA and various homoribopolymers as cofactors, both mutant rho proteins are shown to have broadened RNA base specificities in contrast to the stringent requirement for cytosine observed with the wild-type rho. Functional tests on the two kinds of polynucleotide binding sites known for rho have indicated that rho s-81 is mainly altered in the primary site, whereas rho s-82 is simultaneously affected in the secondary binding site as well as the primary site. Thus, we conclude that the primary and secondary sites contribute distinctly in determining the overall efficiency and site-specificity of termination, respectively. Further analysis of detailed termination points at the trpE and lambda tR1 terminators has revealed that major RNA transcripts generated by the wild-type rho and rho s-81 are notably rich in adenine and poor in cytosine for the 3'-terminal five to ten nucleotides, whereas those preferentially terminated by rho s-82 are conversely richer in cytosine than adenine. This finding suggests that rho may recognize the RNA-DNA hybrid region at the 3' end of a nascent transcript in its secondary binding reaction.
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Affiliation(s)
- N Tsurushita
- Department of Biochemistry, Kyoto University, Japan
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11
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Autogenous regulation of the gene for transcription termination factor rho in Escherichia coli: localization and function of its attenuators. J Bacteriol 1986; 166:945-58. [PMID: 2423505 PMCID: PMC215217 DOI: 10.1128/jb.166.3.945-958.1986] [Citation(s) in RCA: 74] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
We present evidence that the expression of rho is regulated by rho-dependent attenuation of transcription. Gene fusion analysis with nested series of deletions of rho indicated that the transcription of rho is attenuated in a rho-dependent manner in the leader region and that neither a read-through transcription from the upstream gene, trxA, nor a modulation of transcription initiation of the rho promoter is involved in the self-control of rho. S1 mapping and Northern hybridization analyses localized at least six transcription attenuation or termination sites in the region ranging from the 3' end of the trxA structural gene to the middle of the rho structural gene. Among them, the most upstream site overlapping the rho promoter sequence was assigned to the terminator for the trxA gene, and the second and third sites, mapping about 80 and 50 nucleotides upstream from the start codon of rho, were suggested to function as the major attenuation sites for regulation of the rho expression. Further, the start points of the trxA and rho RNAs were determined in an in vitro transcription system to be located 111 nucleotides (U) and 255 nucleotides (G) upstream from their respective start codons. These results necessitate revisions of previous predictions on the sites of transcriptional signals in the trxA and rho genes (S. Brown, B. Albrechtsen, S. Pedersen, and P. Klemm, J. Mol. Biol. 162:283-298, 1982; C.-J. Lim, D. Geraghty, and J. A. Fuchs, J. Bacteriol. 163:311-316, 1985; B.J. Wallace and S.R. Kushner, Gene 32:399-408, 1984).
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Barik S, Bhattacharya P, Das A. Autogenous regulation of transcription termination factor Rho. J Mol Biol 1985; 182:495-508. [PMID: 2409290 DOI: 10.1016/0022-2836(85)90236-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We present evidence that the transcription termination factor Rho is autogenously regulated in Escherichia coli. The steady-state level of Rho is increased approximately tenfold in rho mutant cells. In the rho+ revertants, the content of Rho is similar to the wild-type level. A rho-/rho+ merodiploid produces equimolar amounts of the mutant and the wild-type Rho polypeptides, both at a reduced level compared to the mutant. The steady-state level of rho messenger RNA is also increased in a rho mutant. A rho-galK transcriptional fusion produces at least tenfold more galactokinase in a rho- strain than in a rho+ strain. In vitro, in a coupled transcription-translation system, the synthesis of Rho protein is specifically inhibited by wild-type Rho but not by Rho15 mutant protein. Anti-Rho antibody specifically stimulates Rho synthesis in the rho+ extract but not in a rho- extract. We suggest that the autogenous regulation of Rho involves premature transcription termination within the rho gene. Regulation of Rho level may provide the cell a mechanism to modulate the expression of genes which are separated from their promoters by Rho-dependent termination signals.
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13
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Fassler JS, Tessman I, Tessman ES. Lethality of the double mutations rho rep and rho ssb in Escherichia coli. J Bacteriol 1985; 161:609-14. [PMID: 3155723 PMCID: PMC214926 DOI: 10.1128/jb.161.2.609-614.1985] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The similarity of rho mutants to rep and ssb mutants in sensitivity to UV light and in recombination deficiency suggested that the function of the Rho protein might be related to that of Rep and Ssb. In support of that idea, we found that rho rep and rho ssb double mutants are either nonviable, or at best only marginally viable. Viability could be restored by suppressor mutations, one of which mapped either in the rho gene or close to its 5'-end. Rho may thus share a role with Rep and Ssb in replication and the structural maintenance of DNA; a multifunctional Rho protein could account for the diversity of the defects seen in rho mutants, some of which appear to have no relation to the defect in transcription termination.
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14
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Nwankwo DO, Guterman SK. Purification of RNA polymerase and transcription-termination factor Rho from Erwinia carotovora. EUROPEAN JOURNAL OF BIOCHEMISTRY 1985; 146:383-9. [PMID: 2578393 DOI: 10.1111/j.1432-1033.1985.tb08664.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Erwinia carotovora RNA polymerase consists of the holoenzyme structure sigma 2 beta beta' sigma as found in Escherichia coli and other bacteria. E. carotovora RNA polymerase can synthesize RNA using lambda, T7 of T4 DNA as templates; however, it is two times less active on these templates and is more temperature-sensitive than the E. coli enzyme. The alpha subunit of the E.. carotovora enzyme is lower in molecular mass than its E. coli counterpart. The sigma factors from E. coli and E. carotovora are similar in size and in their ability to stimulate RNA synthesis by core enzyme on DNA templates such as T7 DNA. An additional protein of 115 000 Da molecular mass, termed gamma, is found associated with E. carotovora RNA polymerase. The gamma protein is tightly associated with the polymerase subunits as it is not dissociated by gel filtration in buffer containing 0.5 M NaCl. It can be purified by passing the Agarose 1.5 m enzyme through coupled Bio-Rex 70 and DEAE-cellulose columns. The gamma-protein, when present in excess over the sigma subunit, inhibits holoenzyme activity on T7 DNA but not on poly[d(A-T)]and may thus interfere with sigma activity. The gamma protein by itself cannot transcribe T7 DNA or poly[d(A-T)], nor does it stimulate core enzyme activity on T7 DNA. E. carotovora rho has a subunit molecular mass of 48 000 Da and exhibits RNA-dependent phosphohydrolysis of adenosine ribonucleoside triphosphate. E. coli and E. carotovora rho are indistinguishable immunologically, as total fusion of precipitin bands is observed. E. carotovora rho elutes from a phosphocellulose column at a salt concentration of about 0.21 M KCl, compared to that of 0.29 M KCl for E. coli rho. The poly(C)-dependent ATPase activity of E. carotovora rho is more-temperature sensitive and is six to ten times less active than that of E. coli rho. E. carotovora rho is capable of terminating RNA transcripts, as indicated by a decrease in RNA synthesis using lambda or T7 DNA as template and E. carotovora or E. coli polymerase as the transcribing-enzyme.
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15
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Tsurushita N, Hirano M, Shigesada K, Imai M. Isolation and characterization of rho mutants of Escherichia coli with increased transcription termination activities. MOLECULAR & GENERAL GENETICS : MGG 1984; 196:458-64. [PMID: 6094973 DOI: 10.1007/bf00436193] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
A novel type of rho mutants, rhos, with increased transcription termination activities have been isolated. A termination defective rho mutation rho-ts702 (formerly designated nitA702), which causes temperature-sensitive cell growth, was found to be dominant over the wild-type allele in relieving mutational polarity. The rhos mutations were derived as temperature-resistant revertants of rho-ts702 carried by lambda transducing phage. They exhibited dominance over rho-ts702 leading to restoration of polarity. When the rhos mutations were introduced into the Escherichia coli chromosome, they caused increased polarity in the trp and lac operons. The rhos mutants were classified into two groups in terms of their terminator specificity: The first group demonstrated increased termination efficiencies against all terminators tested, whereas the second exhibited various efficiencies, either more than or less than the normal level depending on the terminator. The cellular content of p protein in each rhos strain was significantly lower than that in the rho+ strain. Moreover, in an in vitro transcription system, purified ps proteins showed increased termination activities against the trpE pseudoterminators. These results indicate that the rhos phenotype is due to qualitative alterations, rather than quantitative increases, of the p protein. The reduced content of ps enforces the current notion that the rho gene is autogenously regulated by rho-dependent transcriptional attenuation.
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16
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Shigesada K, Tsurushita N, Matsumoto Y, Imai M. Overproduction of transcription termination factor Rho in Escherichia coli. Gene X 1984; 29:199-209. [PMID: 6092221 DOI: 10.1016/0378-1119(84)90180-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
A plasmid system has been constructed which allows high-level expression of the rho gene of Escherichia coli under the control of the pL promoter and the N-antitermination regulatory system of bacteriophage lambda. The pL-directed synthesis of Rho crucially depends on the lambda N gene product and is promoted most effectively when this product is supplied from the N gene cloned on a separate compatible plasmid with a moderate copy number. The requirement for N can be circumvented partly, but not completely, by deletion of the region preceding the rho structural gene. Attempts were also made to optimize the construction of rho-expression plasmids by adjusting the orientation and location of pL and rho inserts on the pBR322 vector. With optimal conditions, Rho protein is overexpressed 100-fold and can become as much as 10% of the total cellular protein. Using this plasmid system, Rho can be purified with a yield of more than 20 mg from 10 g of induced cells.
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La Farina M, Vitale M. Rho-dependence of the terminator active at the end of the I region of transcription of bacteriophage f1. MOLECULAR & GENERAL GENETICS : MGG 1984; 195:5-9. [PMID: 6092864 DOI: 10.1007/bf00332715] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Infection of rho- Escherichia coli cells with deletion mutant PII of bacteriophage f1 results in a miniphage RNA population composed of transcripts longer than those synthesized in the infection of rho+ cells. This indicates a Rho dependence of the terminator active at the end of the I region of transcription of bacteriophage f1. An estimate of the length of a transcript, which represents a good fraction of the RNA that passes beyond the terminator, indicates that the hairpin structure where synthesis of complementary strand DNA initiates also acts as a fairly efficient Rho-independent terminator.
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Kung H, Bekesi E, Guterman SK, Gray JE, Traub L, Calhoun DH. Autoregulation of the rho gene of Escherichia coli K-12. MOLECULAR & GENERAL GENETICS : MGG 1984; 193:210-3. [PMID: 6363877 DOI: 10.1007/bf00330669] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
It has previously been proposed, based on indirect evidence, that the Rho protein may control the expression of the rho gene. Using an in vitro system for the transcription and translation of the rho gene cloned into plasmid pBR322, we tested this hypothesis directly by monitoring the effect in vitro of excess or limiting Rho protein. The addition of purified Rho protein suppresses Rho synthesis in vitro. The addition of antibody to Rho specifically stimulates Rho synthesis in vitro. The stimulation of Rho factor synthesis by antibody to Rho is reversed by Rho protein. Rho factor purified from a strain with a mutationally altered rho gene (rho-115) does not suppress Rho synthesis in vitro. These results provide convincing evidence that the rho gene is subject to autoregulation.
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Abstract
The bacteriophage f1 intergenic region distal to gene IV encodes a rho-dependent transcription termination signal. Terminator function in vivo and in vitro is dependent upon active Escherichia coli rho protein, although the RNA 3' ends detected in vivo differ from those seen in vitro. The minimal sequence required for terminator function in a heterologous plasmid system encompasses approximately 100 nucleotides distal to gene IV, which can be drawn as a large hairpin structure. The in vivo rho-dependent 3' end occurs within this sequence, while the in vitro rho-dependent 3' ends occur just distal to it. In vivo in a rho mutant host, f1 transcripts pass through the rho-dependent sites and stop within a sequence of high potential secondary structure near the f1 origin of DNA replication. This sequence alone causes transcription termination in the heterologous plasmid system in vivo. In vitro in the absence of rho protein, transcription does not terminate within this sequence. The RNA 3' ends detected in these studies do not occur within A + T-rich sequences.
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Abstract
We have determined the nucleotide sequence of the rho gene which encodes the E. coli K-12 transcription termination factor. The structural gene was located on a cloned 3.6 kilobase BglII-HindIII restriction fragment by the introduction of the insertion element gamma delta and analysis of the recombinant plasmids by restriction analysis and in maxicells. The coding region consists of 1260 nucleotides directing the synthesis of a polypeptide 419 amino acids in length with a calculated molecular weight of 46,094. The deduced amino acid composition, amino-terminal protein sequence and calculated molecular weight are consistent with the data from the analysis of purified rho protein (16). We have shown that the rho genes from E. coli K-12, B and C strains are located on PvuII-HindIII fragments of the same size by hybridization to the rho (K-12) coding sequences.
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Biville F, Blazy B, Guiso N. Transcription termination factor rho of Escherichia coli K-12: some regulatory aspects of its expression and activity. Biochimie 1983; 65:339-44. [PMID: 6311289 DOI: 10.1016/s0300-9084(83)80155-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
A highly sensitive radioimmunological assay of the transcription termination factor (rho) of Escherichia coli K-12 has been developed. This method allows to measure in crude bacterial extracts quantities as low as 1.8 X 10(-15) moles of rho. We studied, under various conditions of growth and in mutants lacking or overproducing the cyclic AMP receptor protein (CAP) or adenylate cyclase, the relationship between the level of rho and its poly(C)-dependent ATPase activity. We showed that neither growth conditions, nor the presence or absence of a functional cAMP-CAP complex affect the synthesis and the enzymatic activity of the rho protein.
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Brown S, Albrechtsen B, Pedersen S, Klemm P. Localization and regulation of the structural gene for transcription-termination factor rho of Escherichia coli. J Mol Biol 1982; 162:283-98. [PMID: 6219230 DOI: 10.1016/0022-2836(82)90527-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Transcription termination factor rho from wild type and rho-111 strains of Salmonella typhimurium. J Biol Chem 1982. [DOI: 10.1016/s0021-9258(18)34962-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Uzan M, Favre R, Gallay E, Caro L. Genetical and structural analysis of a group of lambda ilv and lambda rho transducing phages. MOLECULAR & GENERAL GENETICS : MGG 1981; 182:462-70. [PMID: 6272063 DOI: 10.1007/bf00293936] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Eight lambda ilv C transducing phages generated from E. coli K12 secondary site lysogens have been analysed genetically and physically. Two of them carry, in addition, the rho gene and its promotor region, but not the cya gene. The ilv O 603 mutation has been located between ilv G and ilv E. Electrophoretic analysis of the proteins synthesized by these phages in a system of UV irradiated cells allowed us to assign molecular weights of 55000 and 66000 daltons to the ilv C and the ilv D gene products, respectively, and to show that an ilv G-encoded polypeptide of 60000 daltons is made from an ilv O- but not from an ilv O+ phage. The expression of the ilv G gene is discussed in the light of the recent finding of a promoter-attenuator region lying upstream to ilv G. Finally, we have found that one of the lambda ilv phages does not have the classical structure of a transducing phage.
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Housley PR, Leavitt AD, Whitfield HJ. Genetic analysis of a temperature-sensitive Salmonella typhimurium rho mutant with an altered rho-associated polycytidylate-dependent adenosine triphosphatase activity. J Bacteriol 1981; 147:13-24. [PMID: 6453864 PMCID: PMC216002 DOI: 10.1128/jb.147.1.13-24.1981] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
A conditional-lethal rho mutant of Salmonella typhimurium LT2 has been isolated. The mutation was selected as a suppressor of the polarity of an insertion sequence (IS)2-induced mutation (gal3) carried on an F' plasmid. In addition to suppression of IS2-induced polarity, the rho-111 mutation suppressed nonsense and frameshift polarity. The rho-associated polycytidylic acid-dependent adenosine triphosphatase activity in the mutant strain was elevated 15-fold above that in the parental strain, and the mutant rho protein was thermally unstable. A temperature-resistant revertant of the mutant strain did not suppress polarity and contained normal levels of polycytidylic acid-dependent adenosine triphosphatase, suggesting that the phenotype of the rho-111-bearing strain is the consequence of a single mutation. The rho-111 mutation was located on the S. typhimurium linkage map midway between the ilv and cya loci by phage P22 cotransduction studies. F' plasmid maintenance was not impaired in the mutant strain, and the mutation was recessive to the wild-type allele. The rho-111 mutation did not alter in vivo expression of either the tryptophan or histidine operons.
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Shigesada K, Imai M. Studies on the altered rho factor in nitA mutants of Escherichia coli defective in transcription termination. II. Purification and molecular properties of the mutant rho. J Mol Biol 1978; 120:467-86. [PMID: 148515 DOI: 10.1016/0022-2836(78)90349-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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