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Hausmann S, Gonzalez D, Geiser J, Valentini M. The DEAD-box RNA helicase RhlE2 is a global regulator of Pseudomonas aeruginosa lifestyle and pathogenesis. Nucleic Acids Res 2021; 49:6925-6940. [PMID: 34151378 PMCID: PMC8266600 DOI: 10.1093/nar/gkab503] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 05/24/2021] [Accepted: 06/01/2021] [Indexed: 12/13/2022] Open
Abstract
RNA helicases perform essential housekeeping and regulatory functions in all domains of life by binding and unwinding RNA molecules. The bacterial RhlE-like DEAD-box RNA helicases are among the least well studied of these enzymes. They are widespread especially among Proteobacteria, whose genomes often encode multiple homologs. The significance of the expansion and diversification of RhlE-like proteins for bacterial fitness has not yet been established. Here, we study the two RhlE homologs present in the opportunistic pathogen Pseudomonas aeruginosa. We show that, in the course of evolution, RhlE1 and RhlE2 have diverged in their biological functions, molecular partners and RNA-dependent enzymatic activities. Whereas RhlE1 is mainly needed for growth in the cold, RhlE2 also acts as global post-transcriptional regulator, affecting the level of hundreds of cellular transcripts indispensable for both environmental adaptation and virulence. The global impact of RhlE2 is mediated by its unique C-terminal extension, which supports the RNA unwinding activity of the N-terminal domain as well as an RNA-dependent interaction with the RNase E endonuclease and the cellular RNA degradation machinery. Overall, our work reveals how the functional and molecular divergence between two homologous RNA helicases can contribute to bacterial fitness and pathogenesis.
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Affiliation(s)
- Stéphane Hausmann
- Department of Microbiology and Molecular Medicine, CMU, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Diego Gonzalez
- Laboratory of Microbiology, Institute of Biology, Faculty of Sciences, University of Neuchâtel, Neuchâtel, Switzerland
| | - Johan Geiser
- Department of Microbiology and Molecular Medicine, CMU, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Martina Valentini
- Department of Microbiology and Molecular Medicine, CMU, Faculty of Medicine, University of Geneva, Geneva, Switzerland
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2
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Lee J, Lee M, Lee K. Trans-acting regulators of ribonuclease activity. J Microbiol 2021; 59:341-359. [PMID: 33779951 DOI: 10.1007/s12275-021-0650-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 12/28/2020] [Accepted: 12/28/2020] [Indexed: 12/16/2022]
Abstract
RNA metabolism needs to be tightly regulated in response to changes in cellular physiology. Ribonucleases (RNases) play an essential role in almost all aspects of RNA metabolism, including processing, degradation, and recycling of RNA molecules. Thus, living systems have evolved to regulate RNase activity at multiple levels, including transcription, post-transcription, post-translation, and cellular localization. In addition, various trans-acting regulators of RNase activity have been discovered in recent years. This review focuses on the physiological roles and underlying mechanisms of trans-acting regulators of RNase activity.
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Affiliation(s)
- Jaejin Lee
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Minho Lee
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea.
| | - Kangseok Lee
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea.
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3
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Lee J, Lee M, Lee K. Trans-acting regulators of ribonuclease activity. J Microbiol 2021:10.1007/s12275-021-0650-3. [PMID: 33565052 DOI: 10.1007/s12275-021-0650-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 12/28/2020] [Accepted: 12/28/2020] [Indexed: 11/29/2022]
Abstract
RNA metabolism needs to be tightly regulated in response to changes in cellular physiology. Ribonucleases (RNases) play an essential role in almost all aspects of RNA metabolism, including processing, degradation, and recycling of RNA molecules. Thus, living systems have evolved to regulate RNase activity at multiple levels, including transcription, post-transcription, post-translation, and cellular localization. In addition, various trans-acting regulators of RNase activity have been discovered in recent years. This review focuses on the physiological roles and underlying mechanisms of trans-acting regulators of RNase activity.
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Affiliation(s)
- Jaejin Lee
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Minho Lee
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea.
| | - Kangseok Lee
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea.
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Both Enolase and the DEAD-Box RNA Helicase CrhB Can Form Complexes with RNase E in Anabaena sp. Strain PCC 7120. Appl Environ Microbiol 2020; 86:AEM.00425-20. [PMID: 32303553 DOI: 10.1128/aem.00425-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 04/14/2020] [Indexed: 11/20/2022] Open
Abstract
At present, little is known about the RNA metabolism driven by the RNA degradosome in cyanobacteria. RNA helicase and enolase are the common components of the RNA degradosome in many bacteria. Here, we provide evidence that both enolase and the DEAD-box RNA helicase CrhB can interact with RNase E in Anabaena (Nostoc) sp. strain PCC 7120 (referred to here as PCC 7120). Furthermore, we found that the C-terminal domains of CrhB and AnaEno (enolase of PCC 7120) are required for the interaction, respectively. Moreover, their recognition motifs for AnaRne (RNase E of PCC 7120) turned out to be located in the N-terminal catalytic domain, which is obviously different from those identified previously in Proteobacteria We also demonstrated in enzyme activity assays that CrhB can induce AnaRne to degrade double-stranded RNA with a 5' tail. Furthermore, we investigated the localization of CrhB and AnaRne by green fluorescent protein (GFP) translation fusion in situ and found that they both localized in the center of the PCC 7120 cytoplasm. This localization pattern is also different from the membrane binding of RNase E and RhlB in Escherichia coli Together with the previous identification of polynucleotide phosphorylase (PNPase) in PCC 7120, our results show that there is an RNA degradosome-like complex with a different assembly mechanism in cyanobacteria.IMPORTANCE In all domains of life, RNA turnover is important for gene regulation and quality control. The process of RNA metabolism is regulated by many RNA-processing enzymes and assistant proteins, where these proteins usually exist as complexes. However, there is little known about the RNA metabolism, as well as about the RNA degradation complex. In the present study, we described an RNA degradosome-like complex in cyanobacteria and revealed an assembly mechanism different from that of E. coli Moreover, CrhB could help RNase E in Anabaena sp. strain PCC 7120 degrade double-stranded RNA with a 5' tail. In addition, CrhB and AnaRne have similar cytoplasm localizations, in contrast to the membrane localization in E. coli.
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Rabuck-Gibbons JN, Popova AM, Greene EM, Cervantes CF, Lyumkis D, Williamson JR. SrmB Rescues Trapped Ribosome Assembly Intermediates. J Mol Biol 2019; 432:978-990. [PMID: 31877323 DOI: 10.1016/j.jmb.2019.12.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 12/03/2019] [Accepted: 12/04/2019] [Indexed: 02/07/2023]
Abstract
RNA helicases play various roles in ribosome biogenesis depending on the ribosome assembly pathway and stress state of the cell. However, it is unclear how most RNA helicases interact with ribosome assembly intermediates or participate in other cell processes to regulate ribosome assembly. SrmB is a DEAD-box helicase that acts early in the ribosome assembly process, although very little is known about its mechanism of action. Here, we use a combined quantitative mass spectrometry/cryo-electron microscopy approach to detail the protein inventory, rRNA modification state, and structures of 40S ribosomal intermediates that form upon SrmB deletion. We show that the binding site of SrmB is unperturbed by SrmB deletion, but the peptidyl transferase center, the uL7/12 stalk, and 30S contact sites all show severe assembly defects. Taking into account existing data on SrmB function and the experiments presented here, we propose several mechanisms by which SrmB could guide assembling particles from kinetic traps to competent subunits during the 50S ribosome assembly process.
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Affiliation(s)
- Jessica N Rabuck-Gibbons
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, 10550 N Torrey Pines Road, La Jolla, CA, 92037, USA; Laboratory of Genetics and Helmsley Center for Genomic Medicine, The Salk Institute for Biological Studies, 10010 N Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Anna M Popova
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, 10550 N Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Emily M Greene
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, 10550 N Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Carla F Cervantes
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, 10550 N Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Dmitry Lyumkis
- Laboratory of Genetics and Helmsley Center for Genomic Medicine, The Salk Institute for Biological Studies, 10010 N Torrey Pines Road, La Jolla, CA, 92037, USA
| | - James R Williamson
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, 10550 N Torrey Pines Road, La Jolla, CA, 92037, USA.
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Seo S, Kim D, Song W, Heo J, Joo M, Lim Y, Yeom JH, Lee K. RraAS1 inhibits the ribonucleolytic activity of RNase ES by interacting with its catalytic domain in Streptomyces coelicolor. J Microbiol 2016; 55:37-43. [PMID: 28035598 DOI: 10.1007/s12275-017-6518-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 12/15/2016] [Accepted: 12/20/2016] [Indexed: 11/26/2022]
Abstract
RraA is a protein inhibitor of RNase E, which degrades and processes numerous RNAs in Escherichia coli. Streptomyces coelicolor also contains homologs of RNase E and RraA, RNase ES and RraAS1/RraAS2, respectively. Here, we report that, unlike other RraA homologs, RraAS1 directly interacts with the catalytic domain of RNase ES to exert its inhibitory effect. We further show that rraAS1 gene deletion in S. coelicolor results in a higher growth rate and increased production of actinorhodin and undecylprodigiosin, compared with the wild-type strain, suggesting that RraAS1-mediated regulation of RNase ES activity contributes to modulating the cellular physiology of S. coelicolor.
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Affiliation(s)
- Sojin Seo
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Daeyoung Kim
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Wooseok Song
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Jihune Heo
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Minju Joo
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Yeri Lim
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Ji-Hyun Yeom
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea.
| | - Kangseok Lee
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea.
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Patel TR, Winzor DJ, Scott DJ. Analytical ultracentrifugation: A versatile tool for the characterisation of macromolecular complexes in solution. Methods 2016; 95:55-61. [DOI: 10.1016/j.ymeth.2015.11.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 11/05/2015] [Accepted: 11/07/2015] [Indexed: 12/25/2022] Open
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Giraud C, Hausmann S, Lemeille S, Prados J, Redder P, Linder P. The C-terminal region of the RNA helicase CshA is required for the interaction with the degradosome and turnover of bulk RNA in the opportunistic pathogen Staphylococcus aureus. RNA Biol 2015; 12:658-74. [PMID: 25997461 PMCID: PMC4615653 DOI: 10.1080/15476286.2015.1035505] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Staphylococcus aureus is a versatile opportunistic pathogen that adapts readily to a variety of different growth conditions. This adaptation requires a rapid regulation of gene expression including the control of mRNA abundance. The CshA DEAD-box RNA helicase was previously shown to be required for efficient turnover of the agr quorum sensing mRNA. Here we show by transcriptome-wide RNA sequencing and microarray analyses that CshA is required for the degradation of bulk mRNA. Moreover a subset of mRNAs is significantly stabilised in absence of CshA. Deletion of the C-terminal extension affects RNA turnover similar to the full deletion of the cshA gene. In accordance with RNA decay data, the C-terminal region of CshA is required for an RNA-independent interaction with components of the RNA degradation machinery. The C-terminal truncation of CshA reduces its ATPase activity and this reduction cannot be compensated at high RNA concentrations. Finally, the deletion of the C-terminal extension does affect growth at low temperatures, but to a significantly lesser degree than the full deletion, indicating that the core of the helicase can assume a partial function and opening the possibility that CshA is involved in different cellular processes.
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Affiliation(s)
- Caroline Giraud
- a Department of Microbiology and Molecular Medicine ; Medical Faculty; University of Geneva ; Michel Servet , Geneva , Switzerland
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Redder P, Hausmann S, Khemici V, Yasrebi H, Linder P. Bacterial versatility requires DEAD-box RNA helicases. FEMS Microbiol Rev 2015; 39:392-412. [PMID: 25907111 DOI: 10.1093/femsre/fuv011] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/04/2015] [Indexed: 11/13/2022] Open
Abstract
RNA helicases of the DEAD-box and DEAH-box families are important players in many processes involving RNA molecules. These proteins can modify RNA secondary structures or intermolecular RNA interactions and modulate RNA-protein complexes. In bacteria, they are known to be involved in ribosome biogenesis, RNA turnover and translation initiation. They thereby play an important role in the adaptation of bacteria to changing environments and to respond to stress conditions.
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Affiliation(s)
- Peter Redder
- Department of Microbiology and Molecular Medicine, CMU, Faculty of Medicine, University of Geneva, 1, rue Michel Servet, CH 1211 Geneva 4, Switzerland
| | - Stéphane Hausmann
- Department of Microbiology and Molecular Medicine, CMU, Faculty of Medicine, University of Geneva, 1, rue Michel Servet, CH 1211 Geneva 4, Switzerland
| | - Vanessa Khemici
- Department of Microbiology and Molecular Medicine, CMU, Faculty of Medicine, University of Geneva, 1, rue Michel Servet, CH 1211 Geneva 4, Switzerland
| | - Haleh Yasrebi
- Department of Microbiology and Molecular Medicine, CMU, Faculty of Medicine, University of Geneva, 1, rue Michel Servet, CH 1211 Geneva 4, Switzerland
| | - Patrick Linder
- Department of Microbiology and Molecular Medicine, CMU, Faculty of Medicine, University of Geneva, 1, rue Michel Servet, CH 1211 Geneva 4, Switzerland
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DeForte S, Reddy KD, Uversky VN. Digested disorder, Quarterly intrinsic disorder digest (October-November-December, 2013). INTRINSICALLY DISORDERED PROTEINS 2015; 3:e984569. [PMID: 28293487 DOI: 10.4161/21690707.2014.984569] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 10/09/2014] [Accepted: 10/10/2014] [Indexed: 11/19/2022]
Abstract
This is the 4th issue of the Digested Disorder series that represents reader's digest of the scientific literature on intrinsically disordered proteins. The only 2 criteria for inclusion in this digest are the publication date (a paper should be published within the covered time frame) and topic (a paper should be dedicated to any aspect of protein intrinsic disorder). The current digest issue covers papers published during the fourth quarter of 2013; i.e. during the period of October, November, and December of 2013. Similar to previous issues, the papers are grouped hierarchically by topics they cover, and for each of the included paper a short description is given on its major findings.
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Affiliation(s)
- Shelly DeForte
- Department of Molecular Medicine; Morsani College of Medicine; University of South Florida; Tampa, FL USA; These authors contributed equally to this work
| | - Krishna D Reddy
- Department of Molecular Medicine; Morsani College of Medicine; University of South Florida; Tampa, FL USA; These authors contributed equally to this work
| | - Vladimir N Uversky
- Department of Molecular Medicine; Morsani College of Medicine; University of South Florida; Tampa, FL USA; USF Health Byrd Alzheimer Research Institute; Morsani College of Medicine; University of South Florida; Tampa, FL USA; Biology Department; Faculty of Science; King Abdulaziz University; Jeddah, Kingdom of Saudi Arabia; Laboratory of Structural Dynamics, Stability, and Folding of Proteins; Institute of Cytology; Russian Academy of Sciences; St. Petersburg, Russia; Institute for Biological Instrumentation; Russian Academy of Sciences; Moscow Region, Russia
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Mazurkewich S, Wang W, Seah SYK. Biochemical and structural analysis of RraA proteins to decipher their relationships with 4-hydroxy-4-methyl-2-oxoglutarate/4-carboxy-4-hydroxy-2-oxoadipate aldolases. Biochemistry 2014; 53:542-53. [PMID: 24359411 DOI: 10.1021/bi401486g] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
4-Hydroxy-4-methyl-2-oxoglutarate (HMG)/4-carboxy-4-hydroxy-2-oxoadipate (CHA) aldolases are class II (divalent metal ion dependent) pyruvate aldolases from the meta cleavage pathways of protocatechuate and gallate. The enzyme from Pseudomonas putida F1 is structurally similar to a group of proteins termed regulators of RNase E activity A (RraA) that bind to the regulatory domain of RNase E and inhibit the ribonuclease activity in certain bacteria. Analysis of homologous RraA-like proteins from varying species revealed that they share sequence conservation within the active site of HMG/CHA aldolase. In particular, the P. putida F1 HMG/CHA aldolase has a D-X20-R-D motif, whereas a G-X20-R-D-X2-E/D motif is observed in the structures of the RraA-like proteins from Thermus thermophilus HB8 (TtRraA) and Saccharomyces cerevisiae S288C (Yer010Cp) that may support metal binding. TtRraA and Yer010Cp were found to contain HMG aldolase and oxaloacetate decarboxylase activities. Similar to the P. putida F1 HMG/CHA aldolase, both TtRraA and Yer010Cp enzymes required divalent metal ions for activity and were competitively inhibited by oxalate, a pyruvate enolate analogue, suggesting a common mechanism among the enzymes. The RraA from Escherichia coli (EcRraA) lacked detectable C-C lyase activity. Upon restoration of the G-X20-R-D-X2-E/D motif, by site-specific mutagenesis, the EcRraA variant was able to catalyze oxaloacetate decarboxylation. Sequence analysis of RraA-like gene products found across all the domains of life revealed conservation of the metal binding motifs that can likely support a divalent metal ion-dependent enzyme reaction either in addition to or in place of the putative RraA function.
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Affiliation(s)
- Scott Mazurkewich
- Department of Molecular and Cellular Biology, University of Guelph , Guelph, Ontario, Canada N1G 5E9
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