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Abstract
Rho is a hexameric bacterial RNA helicase, which became a paradigm of factor-dependent transcription termination. The broadly accepted ("textbook") model posits a series of steps, wherein Rho first binds C-rich Rho utilization (rut) sites on nascent RNA, uses its ATP-dependent translocase activity to catch up with RNA polymerase (RNAP), and either pulls the transcript from the elongation complex or pushes RNAP forward, thus terminating transcription. However, this appealingly simple mechano-chemical model lacks a biological realism and is increasingly at odds with genetic and biochemical data. Here, we summarize recent structural and biochemical studies that have advanced our understanding of molecular details of RNA recognition, termination signaling, and RNAP inactivation in Rho-dependent transcription termination, rebalancing the view in favor of an alternative "allosteric" mechanism. In the revised model, Rho binds RNAP early in elongation assisted by the cofactors NusA and NusG, forming a pre-termination complex (PTC). The formation of PTC allows Rho to continuously sample nascent transcripts for a termination signal, which subsequently traps the elongation complex in an inactive state prior to its dissociation.
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Affiliation(s)
- Zhitai Hao
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Vladimir Svetlov
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Evgeny Nudler
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA.,Howard Hughes Medical Institute, New York University School of Medicine, New York, Ny, USA
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2
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Wiedermannová J, Krásný L. β-CASP proteins removing RNA polymerase from DNA: when a torpedo is needed to shoot a sitting duck. Nucleic Acids Res 2021; 49:10221-10234. [PMID: 34551438 PMCID: PMC8501993 DOI: 10.1093/nar/gkab803] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 09/01/2021] [Accepted: 09/06/2021] [Indexed: 12/12/2022] Open
Abstract
During the first step of gene expression, RNA polymerase (RNAP) engages DNA to transcribe RNA, forming highly stable complexes. These complexes need to be dissociated at the end of transcription units or when RNAP stalls during elongation and becomes an obstacle (‘sitting duck’) to further transcription or replication. In this review, we first outline the mechanisms involved in these processes. Then, we explore in detail the torpedo mechanism whereby a 5′–3′ RNA exonuclease (torpedo) latches itself onto the 5′ end of RNA protruding from RNAP, degrades it and upon contact with RNAP, induces dissociation of the complex. This mechanism, originally described in Eukaryotes and executed by Xrn-type 5′–3′ exonucleases, was recently found in Bacteria and Archaea, mediated by β-CASP family exonucleases. We discuss the mechanistic aspects of this process across the three kingdoms of life and conclude that 5′–3′ exoribonucleases (β-CASP and Xrn families) involved in the ancient torpedo mechanism have emerged at least twice during evolution.
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Affiliation(s)
- Jana Wiedermannová
- Correspondence may also be addressed to Jana Wiedermannová. Tel: +44 191 208 3226; Fax: +44 191 208 3205;
| | - Libor Krásný
- To whom correspondence should be addressed. Tel: +420 241063208;
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3
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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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4
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Said N, Hilal T, Sunday ND, Khatri A, Bürger J, Mielke T, Belogurov GA, Loll B, Sen R, Artsimovitch I, Wahl MC. Steps toward translocation-independent RNA polymerase inactivation by terminator ATPase ρ. Science 2021; 371:eabd1673. [PMID: 33243850 PMCID: PMC7864586 DOI: 10.1126/science.abd1673] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 10/26/2020] [Indexed: 12/31/2022]
Abstract
Factor-dependent transcription termination mechanisms are poorly understood. We determined a series of cryo-electron microscopy structures portraying the hexameric adenosine triphosphatase (ATPase) ρ on a pathway to terminating NusA/NusG-modified elongation complexes. An open ρ ring contacts NusA, NusG, and multiple regions of RNA polymerase, trapping and locally unwinding proximal upstream DNA. NusA wedges into the ρ ring, initially sequestering RNA. Upon deflection of distal upstream DNA over the RNA polymerase zinc-binding domain, NusA rotates underneath one capping ρ subunit, which subsequently captures RNA. After detachment of NusG and clamp opening, RNA polymerase loses its grip on the RNA:DNA hybrid and is inactivated. Our structural and functional analyses suggest that ρ, and other termination factors across life, may use analogous strategies to allosterically trap transcription complexes in a moribund state.
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Affiliation(s)
- Nelly Said
- Laboratory of Structural Biochemistry, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Tarek Hilal
- Research Center of Electron Microscopy and Core Facility BioSupraMol, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Nicholas D Sunday
- Department of Microbiology and Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Ajay Khatri
- Laboratory of Transcription, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
- Graduate Studies, Regional Centre for Biotechnology, Faridabad, Haryana, India
| | - Jörg Bürger
- Microscopy and Cryo-Electron Microscopy Service Group, Max-Planck-Institut für Molekulare Genetik, Berlin, Germany
- Institute of Medical Physics und Biophysics, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Thorsten Mielke
- Microscopy and Cryo-Electron Microscopy Service Group, Max-Planck-Institut für Molekulare Genetik, Berlin, Germany
| | | | - Bernhard Loll
- Laboratory of Structural Biochemistry, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Ranjan Sen
- Laboratory of Transcription, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Irina Artsimovitch
- Department of Microbiology and Center for RNA Biology, The Ohio State University, Columbus, OH, USA.
| | - Markus C Wahl
- Laboratory of Structural Biochemistry, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany.
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin für Materialien und Energie, Berlin, Germany
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5
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Moreau K, Le Dantec A, Mosrin-Huaman C, Bigot Y, Piégu B, Rahmouni AR. Perturbation of mRNP biogenesis reveals a dynamic landscape of the Rrp6-dependent surveillance machinery trafficking along the yeast genome. RNA Biol 2019; 16:879-889. [PMID: 31007122 PMCID: PMC6546349 DOI: 10.1080/15476286.2019.1593745] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Eukaryotic cells have evolved a nuclear quality control (QC) system to monitor the co-transcriptional mRNA processing and packaging reactions that lead to the formation of export-competent ribonucleoprotein particles (mRNPs). Aberrant mRNPs that fail to pass the QC steps are retained in the nucleus and eliminated by the exonuclease activity of Rrp6. It is still unclear how the surveillance system is precisely coordinated both physically and functionally with the transcription machinery to detect the faulty events that may arise at each step of transcript elongation and mRNP formation. To dissect the QC mechanism, we previously implemented a powerful assay based on global perturbation of mRNP biogenesis in yeast by the bacterial Rho helicase. By monitoring model genes, we have shown that the QC process is coordinated by Nrd1, a component of the NNS complex (Nrd1-Nab3-Sen1) involved in termination, processing and decay of ncRNAs which is recruited by the CTD of RNAP II. Here, we have extended our investigations by analyzing the QC behaviour over the whole yeast genome. We performed high-throughput RNA sequencing (RNA-seq) to survey a large collection of mRNPs whose biogenesis is affected by Rho action and which can be rescued upon Rrp6 depletion. This genome-wide perspective was extended by generating high-resolution binding landscapes (ChIP-seq) of QC components along the yeast chromosomes before and after perturbation of mRNP biogenesis. Our results show that perturbation of mRNP biogenesis redistributes the QC components over the genome with a significant hijacking of Nrd1 and Nab3 from genomic loci producing ncRNAs to Rho-affected protein-coding genes, triggering termination and processing defects of ncRNAs.
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Affiliation(s)
- Kévin Moreau
- a Centre de Biophysique Moléculaire , UPR 4301 du CNRS, Orléans , France
| | - Aurélia Le Dantec
- a Centre de Biophysique Moléculaire , UPR 4301 du CNRS, Orléans , France
| | | | - Yves Bigot
- b Physiologie de la Reproduction et des Comportements , UMR 7247 INRA-CNRS, Nouzilly , France
| | - Benoit Piégu
- b Physiologie de la Reproduction et des Comportements , UMR 7247 INRA-CNRS, Nouzilly , France
| | - A Rachid Rahmouni
- a Centre de Biophysique Moléculaire , UPR 4301 du CNRS, Orléans , France
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6
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Ray-Soni A, Bellecourt MJ, Landick R. Mechanisms of Bacterial Transcription Termination: All Good Things Must End. Annu Rev Biochem 2016; 85:319-47. [PMID: 27023849 DOI: 10.1146/annurev-biochem-060815-014844] [Citation(s) in RCA: 227] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Transcript termination is essential for accurate gene expression and the removal of RNA polymerase (RNAP) at the ends of transcription units. In bacteria, two mechanisms are responsible for proper transcript termination: intrinsic termination and Rho-dependent termination. Intrinsic termination is mediated by signals directly encoded within the DNA template and nascent RNA, whereas Rho-dependent termination relies upon the adenosine triphosphate-dependent RNA translocase Rho, which binds nascent RNA and dissociates the elongation complex. Although significant progress has been made in understanding these pathways, fundamental details remain undetermined. Among those that remain unresolved are the existence of an inactivated intermediate in the intrinsic termination pathway, the role of Rho-RNAP interactions in Rho-dependent termination, and the mechanisms by which accessory factors and nucleoid-associated proteins affect termination. We describe current knowledge, discuss key outstanding questions, and highlight the importance of defining the structural rearrangements of RNAP that are involved in the two mechanisms of transcript termination.
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Affiliation(s)
- Ananya Ray-Soni
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706; ,
| | - Michael J Bellecourt
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706; ,
| | - Robert Landick
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706; , .,Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706;
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7
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Poly(A) Signal-Dependent Transcription Termination Occurs through a Conformational Change Mechanism that Does Not Require Cleavage at the Poly(A) Site. Mol Cell 2015; 59:437-48. [PMID: 26166703 DOI: 10.1016/j.molcel.2015.06.008] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2014] [Revised: 04/24/2015] [Accepted: 06/03/2015] [Indexed: 12/18/2022]
Abstract
Transcription termination for genes encoding polyadenylated mRNAs requires a functional poly(A) signal (PAS) in the nascent pre-mRNA. Often called PAS-dependent termination, or PADT, it is widely assumed that the PAS requirement reflects an obligatory poly(A) site cleavage requirement for termination. Cleavage is thought to provide entry for a 5'-to-3' exonuclease that targets RNA polymerase II via the nascent transcript-i.e., the torpedo model. To assess the role of cleavage in PADT, we developed a PADT assay using HeLa nuclear extract. Here we examine the basal mechanism of PADT and show that cleavage at the poly(A) site is not required for PADT. Isolated elongation complexes undergo termination in a PAS-dependent manner when incubated in buffer, in the absence of extract, nucleotides, or cleavage at the poly(A) site. Thus, PADT-proficient complexes undergo a conformational change that triggers termination. PADT is inhibited by α-amanitin, which presumably blocks the required conformational change.
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8
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Porrua O, Libri D. A bacterial-like mechanism for transcription termination by the Sen1p helicase in budding yeast. Nat Struct Mol Biol 2013; 20:884-91. [PMID: 23748379 DOI: 10.1038/nsmb.2592] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Accepted: 04/22/2013] [Indexed: 12/25/2022]
Abstract
Transcription termination is essential to generate functional RNAs and to prevent disruptive polymerase collisions resulting from concurrent transcription. The yeast Sen1p helicase is involved in termination of most noncoding RNAs transcribed by RNA polymerase II (RNAPII). However, the mechanism of termination and the role of this protein have remained enigmatic. Here we address the mechanism of Sen1p-dependent termination by using a highly purified in vitro system. We show that Sen1p is the key enzyme of the termination reaction and reveal features of the termination mechanism. Like the bacterial termination factor Rho, Sen1p recognizes the nascent RNA and hydrolyzes ATP to dissociate the elongation complex. Sen1p-dependent termination is highly specific and, notably, does not require the C-terminal domain of RNAPII. We also show that termination is inhibited by RNA-DNA hybrids. Our results elucidate the role of Sen1p in controlling pervasive transcription.
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Affiliation(s)
- Odil Porrua
- Centre de Génétique Moléculaire, Centre National de la Recherche Scientifique, Gif sur Yvette, France.
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9
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Mischo HE, Proudfoot NJ. Disengaging polymerase: terminating RNA polymerase II transcription in budding yeast. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2012; 1829:174-85. [PMID: 23085255 PMCID: PMC3793857 DOI: 10.1016/j.bbagrm.2012.10.003] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Revised: 10/01/2012] [Accepted: 10/05/2012] [Indexed: 11/29/2022]
Abstract
Termination of transcription by RNA polymerase II requires two distinct processes: The formation of a defined 3′ end of the transcribed RNA, as well as the disengagement of RNA polymerase from its DNA template. Both processes are intimately connected and equally pivotal in the process of functional messenger RNA production. However, research in recent years has elaborated how both processes can additionally be employed to control gene expression in qualitative and quantitative ways. This review embraces these new findings and attempts to paint a broader picture of how this final step in the transcription cycle is of critical importance to many aspects of gene regulation. This article is part of a Special Issue entitled: RNA polymerase II Transcript Elongation.
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Affiliation(s)
- Hannah E Mischo
- Cancer Research UK London Research Institute, Blanche Lane South Mimms, Herts, UK.
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10
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Unravelling the means to an end: RNA polymerase II transcription termination. Nat Rev Mol Cell Biol 2011; 12:283-94. [PMID: 21487437 DOI: 10.1038/nrm3098] [Citation(s) in RCA: 198] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The pervasiveness of RNA synthesis in eukaryotes is largely the result of RNA polymerase II (Pol II)-mediated transcription, and termination of its activity is necessary to partition the genome and maintain the proper expression of neighbouring genes. Despite its ever-increasing biological significance, transcription termination remains one of the least understood processes in gene expression. However, recent mechanistic studies have revealed a striking convergence among several overlapping models of termination, including the poly(A)- and Sen1-dependent pathways, as well as new insights into the specificity of Pol II termination among its diverse gene targets. Broader knowledge of the role of Pol II carboxy-terminal domain phosphorylation in promoting alternative mechanisms of termination has also been gained.
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11
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Mutagenesis-based evidence for an asymmetric configuration of the ring-shaped transcription termination factor Rho. J Mol Biol 2010; 405:497-518. [PMID: 21059356 DOI: 10.1016/j.jmb.2010.11.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2010] [Revised: 09/16/2010] [Accepted: 11/01/2010] [Indexed: 11/20/2022]
Abstract
Transcription termination factor Rho is an ATP-dependent ring-shaped molecular motor that tracks along RNA to dissociate RNA-DNA duplexes and transcription complexes in its path. The Rho hexamer contains two distinct sites for interaction with RNA. The primary binding site is composed of pyrimidine-specific binding clefts that are located in the N-terminal domains and anchor Rho to transcripts at C-rich Rut (Rho utilization) sites. Components of the secondary binding site (SBS) in the C-terminal domains directly couple RNA binding to ATP hydrolysis in order to translocate RNA through the Rho ring. Published crystal structures of RNA-bound Rho display distinct architectures ('trimer-of-dimers' or asymmetric hexamer) and SBS-RNA interaction networks that suggested conflicting models of RNA "handoff" or "escort" by the Rho subunits. To probe the mechanism of mechanochemical transduction in Rho, we have mutated into alanines (or glycines) the residues that make SBS contacts with RNA in the 'trimer-of-dimers' structure supporting the "handoff" model. We find that the resulting single-point mutants have similar RNA binding affinities but exhibit significantly different ATP hydrolysis, transcription termination, and RNA-DNA unwinding activities that are more compatible with the asymmetric Rho structure than with the 'trimer-of-dimers' structure and the resulting "handoff" model. We discuss our findings in connection with specific features of the asymmetric Rho structure yet argue that a simple RNA "escort" model is insufficient to account for all experimental evidence.
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12
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Rabhi M, Rahmouni AR, Boudvillain M. Transcription Termination Factor Rho: A Ring-Shaped RNA Helicase from Bacteria. RNA HELICASES 2010. [DOI: 10.1039/9781849732215-00243] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Makhlouf Rabhi
- Centre de Biophysique Moléculaire (UPR4301) CNRS rue Charles Sadron 45071 Orléans cedex 2 France
- Ecole doctorale Sciences et Technologies, Université d’Orléans France
| | - A. Rachid Rahmouni
- Centre de Biophysique Moléculaire (UPR4301) CNRS rue Charles Sadron 45071 Orléans cedex 2 France
| | - Marc Boudvillain
- Centre de Biophysique Moléculaire (UPR4301) CNRS rue Charles Sadron 45071 Orléans cedex 2 France
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13
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Expression of bacterial Rho factor in yeast identifies new factors involved in the functional interplay between transcription and mRNP biogenesis. Mol Cell Biol 2009; 29:4033-44. [PMID: 19451224 DOI: 10.1128/mcb.00272-09] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
In eukaryotic cells, the nascent pre-mRNA molecule is coated sequentially with a large set of processing and binding proteins that mediate its transformation into an export-competent ribonucleoprotein particle (mRNP) that is ready for translation in the cytoplasm. We have implemented an original assay that monitors the dynamic interplay between transcription and mRNP biogenesis and that allows the screening for new factors linking mRNA synthesis to translation in Saccharomyces cerevisiae. The assay is based on the perturbation of gene expression induced by the bacterial Rho factor, an RNA-dependent helicase/translocase that acts as a competitor at one or several steps of mRNP biogenesis in yeast. We show that the expression of Rho in yeast leads to a dose-dependent growth defect that stems from its action on RNA polymerase II-mediated transcription. Rho expression induces the production of aberrant transcripts that are degraded by the nuclear exosome. A screen for dosage suppressors of the Rho-induced growth defect identified several genes that are involved in the different steps of mRNP biogenesis and export, as well as other genes with both known functions in transcription regulation and unknown functions. Our results provide evidence for an extensive cross talk between transcription, mRNP biogenesis, and export. They also uncover new factors that potentially are involved in these interconnected events.
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14
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Arnoldo A, Curak J, Kittanakom S, Chevelev I, Lee VT, Sahebol-Amri M, Koscik B, Ljuma L, Roy PJ, Bedalov A, Giaever G, Nislow C, Merrill RA, Lory S, Stagljar I. Identification of small molecule inhibitors of Pseudomonas aeruginosa exoenzyme S using a yeast phenotypic screen. PLoS Genet 2008; 4:e1000005. [PMID: 18454192 PMCID: PMC2265467 DOI: 10.1371/journal.pgen.1000005] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2007] [Accepted: 01/17/2008] [Indexed: 11/19/2022] Open
Abstract
Pseudomonas aeruginosa is an opportunistic human pathogen that is a key factor in the mortality of cystic fibrosis patients, and infection represents an increased threat for human health worldwide. Because resistance of Pseudomonas aeruginosa to antibiotics is increasing, new inhibitors of pharmacologically validated targets of this bacterium are needed. Here we demonstrate that a cell-based yeast phenotypic assay, combined with a large-scale inhibitor screen, identified small molecule inhibitors that can suppress the toxicity caused by heterologous expression of selected Pseudomonas aeruginosa ORFs. We identified the first small molecule inhibitor of Exoenzyme S (ExoS), a toxin involved in Type III secretion. We show that this inhibitor, exosin, modulates ExoS ADP-ribosyltransferase activity in vitro, suggesting the inhibition is direct. Moreover, exosin and two of its analogues display a significant protective effect against Pseudomonas infection in vivo. Furthermore, because the assay was performed in yeast, we were able to demonstrate that several yeast homologues of the known human ExoS targets are likely ADP-ribosylated by the toxin. For example, using an in vitro enzymatic assay, we demonstrate that yeast Ras2p is directly modified by ExoS. Lastly, by surveying a collection of yeast deletion mutants, we identified Bmh1p, a yeast homologue of the human FAS, as an ExoS cofactor, revealing that portions of the bacterial toxin mode of action are conserved from yeast to human. Taken together, our integrated cell-based, chemical-genetic approach demonstrates that such screens can augment traditional drug screening approaches and facilitate the discovery of new compounds against a broad range of human pathogens.
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Affiliation(s)
- Anthony Arnoldo
- Terrence Donnelly Centre for Cellular and Biomolecular Research, Department of Biochemistry, University of Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Ontario, Canada
| | - Jasna Curak
- Terrence Donnelly Centre for Cellular and Biomolecular Research, Department of Biochemistry, University of Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Ontario, Canada
| | - Saranya Kittanakom
- Terrence Donnelly Centre for Cellular and Biomolecular Research, Department of Biochemistry, University of Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Ontario, Canada
| | - Igor Chevelev
- Terrence Donnelly Centre for Cellular and Biomolecular Research, Department of Biochemistry, University of Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Ontario, Canada
| | - Vincent T. Lee
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Mehdi Sahebol-Amri
- Terrence Donnelly Centre for Cellular and Biomolecular Research, Department of Biochemistry, University of Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Ontario, Canada
| | - Becky Koscik
- Terrence Donnelly Centre for Cellular and Biomolecular Research, Department of Biochemistry, University of Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Ontario, Canada
| | - Lana Ljuma
- Terrence Donnelly Centre for Cellular and Biomolecular Research, Department of Biochemistry, University of Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Ontario, Canada
| | - Peter J. Roy
- Terrence Donnelly Centre for Cellular and Biomolecular Research, Department of Biochemistry, University of Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Ontario, Canada
| | - Antonio Bedalov
- Clinical Research and Human Biology Divisions, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Guri Giaever
- Terrence Donnelly Centre for Cellular and Biomolecular Research, Department of Biochemistry, University of Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Ontario, Canada
- Department of Pharmaceutical Sciences, University of Toronto, Ontario, Canada
| | - Corey Nislow
- Terrence Donnelly Centre for Cellular and Biomolecular Research, Department of Biochemistry, University of Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Ontario, Canada
- Department of Pharmaceutical Sciences, University of Toronto, Ontario, Canada
| | - Rod A. Merrill
- Department of Molecular and Cellular Biology, University of Guelph, Ontario, Canada
| | - Stephen Lory
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Igor Stagljar
- Terrence Donnelly Centre for Cellular and Biomolecular Research, Department of Biochemistry, University of Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Ontario, Canada
- * E-mail:
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15
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Zhang Z, Gilmour DS. Pcf11 is a termination factor in Drosophila that dismantles the elongation complex by bridging the CTD of RNA polymerase II to the nascent transcript. Mol Cell 2006; 21:65-74. [PMID: 16387654 DOI: 10.1016/j.molcel.2005.11.002] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2005] [Revised: 10/17/2005] [Accepted: 11/02/2005] [Indexed: 10/25/2022]
Abstract
The mechanism by which Pol II terminates transcription in metazoans is not understood. We show that Pcf11 is directly involved in termination in Drosophila. dPcf11 is concentrated at the 3' end of the hsp70 gene in cells, and depletion of dPcf11 with RNAi causes Pol II to readthrough the normal region of termination. dPcf11 also localizes to most transcribed loci on polytene chromosomes. Biochemical analysis reveals that dPcf11 dismantles elongation complexes by a CTD-dependent but nucleotide-independent mechanism and that dPcf11 forms a bridge between the CTD and RNA. This bridge appears to be crucial because an anti-CTD antibody, which also dismantles the elongation complex, is found to bridge the CTD to RNA. dPcf11 was observed to inhibit transcription at low, but not high, nucleotide levels, suggesting that dPcf11 dismantles paused elongation complexes. These results provide a biochemical basis for the dependency of termination on pausing and the CTD in metazoans.
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Affiliation(s)
- Zhiqiang Zhang
- Department of Biochemistry and Molecular Biology, Center for Gene Regulation, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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16
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Banerjee S, Chalissery J, Bandey I, Sen R. Rho-dependent transcription termination: more questions than answers. J Microbiol 2006; 44:11-22. [PMID: 16554712 PMCID: PMC1838574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Escherichia coli protein Rho is required for the factor-dependent transcription termination by an RNA polymerase and is essential for the viability of the cell. It is a homohexameric protein that recognizes and binds preferably to C-rich sites in the transcribed RNA. Once bound to RNA, it utilizes RNA-dependent ATPase activity and subsequently ATPase-dependent helicase activity to unwind RNA-DNA hybrids and release RNA from a transcribing elongation complex. Studies over the past few decades have highlighted Rho as a molecule and have revealed much of its mechanistic properties. The recently solved crystal structure could explain many of its physiological functions in terms of its structure. Despite all these efforts, many of the fundamental questions pertaining to Rho recognition sites, differential ATPase activity in response to different RNAs, translocation of Rho along the nascent transcript, interactions with elongation complex and finally unwinding and release of RNA remain obscure. In the present review we have attempted to summarize "the knowns" and "the unknowns" of the Rho protein revealed by the recent developments in this field. An attempt has also been made to understand the physiology of Rho in the light of its phylogeny.
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Affiliation(s)
| | | | | | - Ranjan Sen
- To whom correspondence should be addressed. (Tel) 91-40-27151344; (Fax) 91-40-27155610 (E-mail)
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Santangelo TJ, Reeve JN. Archaeal RNA polymerase is sensitive to intrinsic termination directed by transcribed and remote sequences. J Mol Biol 2005; 355:196-210. [PMID: 16305799 DOI: 10.1016/j.jmb.2005.10.062] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2005] [Revised: 10/26/2005] [Accepted: 10/26/2005] [Indexed: 11/15/2022]
Abstract
Archaea are prokaryotes with a single DNA-dependent RNA polymerase (RNAP) that is homologous to, and likely resembles the ancestor of all three eukaryotic RNAPs. In vitro studies have confirmed that initiation by archaeal RNAPs resembles the Pol II system, and we report the first detailed in vitro investigation of archaeal transcription termination. Methanothermobacter thermautotrophicus (M.t.) RNAP is susceptible to intrinsic termination at an intergenic sequence that conforms to a bacterial intrinsic terminator, as well as at bona fide bacterial intrinsic terminators. In contrast to bacterial RNAPs, M.t. RNAP also terminated in response to synthetic and natural oligo-T-rich sequences that were not preceded by sequences with any recognizable potential to form a stable RNA hairpin. Both template topology and temperature influenced the position and extent of termination in vitro, and the results argue that transcription of an upstream sequence can alter the termination response of the archaeal RNAP at a remote downstream sequence.
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Affiliation(s)
- Thomas J Santangelo
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA.
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18
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Abstract
Transcription termination in Escherichia coli is controlled by many factors. The sequence of the DNA template, the structure of the transcript, and the actions of auxiliary proteins all play a role in determining the efficiency of the process. Termination is regulated and can be enhanced or suppressed by host and phage proteins. This complex reaction is rapidly yielding to biochemical and structural analysis of the interacting factors. Below we review and attempt to unify into basic principles the remarkable recent progress in understanding transcription termination and anti-termination.
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Affiliation(s)
- Evgeny Nudler
- Department of Biochemistry, NYU Medical Center, New York, NY 10016, USA.
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19
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Abstract
The task of transcribing nuclear genes is shared between three RNA polymerases in eukaryotes: RNA polymerase (pol) I synthesizes the large rRNA, pol II synthesizes mRNA and pol III synthesizes tRNA and 5S rRNA. Although pol II has received most attention, pol I and pol III are together responsible for the bulk of transcriptional activity. This survey will summarise what is known about the process of transcription by pol I and pol III, how it happens and the proteins involved. Attention will be drawn to the similarities between the three nuclear RNA polymerase systems and also to their differences.
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Affiliation(s)
- M R Paule
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA.
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20
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Zhao J, Hyman L, Moore C. Formation of mRNA 3' ends in eukaryotes: mechanism, regulation, and interrelationships with other steps in mRNA synthesis. Microbiol Mol Biol Rev 1999; 63:405-45. [PMID: 10357856 PMCID: PMC98971 DOI: 10.1128/mmbr.63.2.405-445.1999] [Citation(s) in RCA: 808] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Formation of mRNA 3' ends in eukaryotes requires the interaction of transacting factors with cis-acting signal elements on the RNA precursor by two distinct mechanisms, one for the cleavage of most replication-dependent histone transcripts and the other for cleavage and polyadenylation of the majority of eukaryotic mRNAs. Most of the basic factors have now been identified, as well as some of the key protein-protein and RNA-protein interactions. This processing can be regulated by changing the levels or activity of basic factors or by using activators and repressors, many of which are components of the splicing machinery. These regulatory mechanisms act during differentiation, progression through the cell cycle, or viral infections. Recent findings suggest that the association of cleavage/polyadenylation factors with the transcriptional complex via the carboxyl-terminal domain of the RNA polymerase II (Pol II) large subunit is the means by which the cell restricts polyadenylation to Pol II transcripts. The processing of 3' ends is also important for transcription termination downstream of cleavage sites and for assembly of an export-competent mRNA. The progress of the last few years points to a remarkable coordination and cooperativity in the steps leading to the appearance of translatable mRNA in the cytoplasm.
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Affiliation(s)
- J Zhao
- Department of Molecular Biology and Microbiology, School of Medicine, Tufts University, Boston, Massachusetts 02111, USA
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21
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Zhao J, Hyman L, Moore C. Formation of mRNA 3' ends in eukaryotes: mechanism, regulation, and interrelationships with other steps in mRNA synthesis. Microbiol Mol Biol Rev 1999. [PMID: 10357856 DOI: 10.1007/s13146-011-0050-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2023] Open
Abstract
Formation of mRNA 3' ends in eukaryotes requires the interaction of transacting factors with cis-acting signal elements on the RNA precursor by two distinct mechanisms, one for the cleavage of most replication-dependent histone transcripts and the other for cleavage and polyadenylation of the majority of eukaryotic mRNAs. Most of the basic factors have now been identified, as well as some of the key protein-protein and RNA-protein interactions. This processing can be regulated by changing the levels or activity of basic factors or by using activators and repressors, many of which are components of the splicing machinery. These regulatory mechanisms act during differentiation, progression through the cell cycle, or viral infections. Recent findings suggest that the association of cleavage/polyadenylation factors with the transcriptional complex via the carboxyl-terminal domain of the RNA polymerase II (Pol II) large subunit is the means by which the cell restricts polyadenylation to Pol II transcripts. The processing of 3' ends is also important for transcription termination downstream of cleavage sites and for assembly of an export-competent mRNA. The progress of the last few years points to a remarkable coordination and cooperativity in the steps leading to the appearance of translatable mRNA in the cytoplasm.
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Affiliation(s)
- J Zhao
- Department of Molecular Biology and Microbiology, School of Medicine, Tufts University, Boston, Massachusetts 02111, USA
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22
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Dye MJ, Proudfoot NJ. Terminal exon definition occurs cotranscriptionally and promotes termination of RNA polymerase II. Mol Cell 1999; 3:371-8. [PMID: 10198639 DOI: 10.1016/s1097-2765(00)80464-5] [Citation(s) in RCA: 126] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Analysis of nascent transcription from the human epsilon- and beta-globin genes shows that transcriptional termination occurs within 1.5 kb of the poly(A) site and is dependent on the presence of functional poly(A) signals. Even so, transcripts that have not been cleaved at the poly(A) site are detected up to the termination region, suggesting that there is a kinetic lag between transcription over the poly(A) signal and its effect on transcriptional termination. Surprisingly, mutation of the splice acceptor (SA) of the beta-globin IVS2 also abolishes transcriptional termination. Our results emphasize the interconnection of transcription and RNA processing by showing that the enhancement of 3' end processing by the terminal splice acceptor occurs cotranscriptionally.
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Affiliation(s)
- M J Dye
- Sir William Dunn School of Pathology, University of Oxford, United Kingdom
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23
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Abstract
Downstream elements (DSEs) with transcriptional pausing activity play an important role in transcription termination of RNA polymerase II. We have defined two such DSEs in Schizosaccharomyces pombe, one for the ura4 gene and a new one in the 3'-end region of the nmt2 gene. Although these DSEs do not have sequence homology, both are orientation specific and are composed of multiple and redundant sequence elements that work together to achieve full pausing activity. Previous studies on the nmt1 and nmt2 genes revealed that transcription extends several kilobases past the genes' poly(A) sites. We show that the insertion of either DSE immediately downstream of the nmt1 poly(A) site induces more immediate termination. nmt2 termination efficiency can be increased by moving the DSE closer to the poly(A) site. These results suggest that DSEs may be a common feature in yeast genes.
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Affiliation(s)
- A Aranda
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
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