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Taylor AD, Hathaway QA, Kunovac A, Pinti MV, Newman MS, Cook CC, Cramer ER, Starcovic SA, Winters MT, Westemeier-Rice ES, Fink GK, Durr AJ, Rizwan S, Shepherd DL, Robart AR, Martinez I, Hollander JM. Mitochondrial sequencing identifies long noncoding RNA features that promote binding to PNPase. Am J Physiol Cell Physiol 2024; 327:C221-C236. [PMID: 38826135 DOI: 10.1152/ajpcell.00648.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 05/24/2024] [Accepted: 05/24/2024] [Indexed: 06/04/2024]
Abstract
Extranuclear localization of long noncoding RNAs (lncRNAs) is poorly understood. Based on machine learning evaluations, we propose a lncRNA-mitochondrial interaction pathway where polynucleotide phosphorylase (PNPase), through domains that provide specificity for primary sequence and secondary structure, binds nuclear-encoded lncRNAs to facilitate mitochondrial import. Using FVB/NJ mouse and human cardiac tissues, RNA from isolated subcellular compartments (cytoplasmic and mitochondrial) and cross-linked immunoprecipitate (CLIP) with PNPase within the mitochondrion were sequenced on the Illumina HiSeq and MiSeq, respectively. lncRNA sequence and structure were evaluated through supervised [classification and regression trees (CART) and support vector machines (SVM)] machine learning algorithms. In HL-1 cells, quantitative PCR of PNPase CLIP knockout mutants (KH and S1) was performed. In vitro fluorescence assays assessed PNPase RNA binding capacity and verified with PNPase CLIP. One hundred twelve (mouse) and 1,548 (human) lncRNAs were identified in the mitochondrion with Malat1 being the most abundant. Most noncoding RNAs binding PNPase were lncRNAs, including Malat1. lncRNA fragments bound to PNPase compared against randomly generated sequences of similar length showed stratification with SVM and CART algorithms. The lncRNAs bound to PNPase were used to create a criterion for binding, with experimental validation revealing increased binding affinity of RNA designed to bind PNPase compared to control RNA. The binding of lncRNAs to PNPase was decreased through the knockout of RNA binding domains KH and S1. In conclusion, sequence and secondary structural features identified by machine learning enhance the likelihood of nuclear-encoded lncRNAs binding to PNPase and undergoing import into the mitochondrion.NEW & NOTEWORTHY Long noncoding RNAs (lncRNAs) are relatively novel RNAs with increasingly prominent roles in regulating genetic expression, mainly in the nucleus but more recently in regions such as the mitochondrion. This study explores how lncRNAs interact with polynucleotide phosphorylase (PNPase), a protein that regulates RNA import into the mitochondrion. Machine learning identified several RNA structural features that improved lncRNA binding to PNPase, which may be useful in targeting RNA therapeutics to the mitochondrion.
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Affiliation(s)
- Andrew D Taylor
- Division of Exercise Physiology, West Virginia University School of Medicine, Morgantown, West Virginia, United States
- Mitochondria, Metabolism, and Bioenergetics Working Group, West Virginia University School of Medicine, Morgantown, West Virginia, United States
| | - Quincy A Hathaway
- Division of Exercise Physiology, West Virginia University School of Medicine, Morgantown, West Virginia, United States
- Heart and Vascular Institute, West Virginia University, Morgantown, West Virginia, United States
- Department of Medical Education, West Virginia University School of Medicine, Morgantown, West Virginia, United States
| | - Amina Kunovac
- Division of Exercise Physiology, West Virginia University School of Medicine, Morgantown, West Virginia, United States
- Mitochondria, Metabolism, and Bioenergetics Working Group, West Virginia University School of Medicine, Morgantown, West Virginia, United States
| | - Mark V Pinti
- Mitochondria, Metabolism, and Bioenergetics Working Group, West Virginia University School of Medicine, Morgantown, West Virginia, United States
- West Virginia University School of Pharmacy, Morgantown, West Virginia, United States
| | - Mackenzie S Newman
- Department of Physiology and Pharmacology, West Virginia University School of Medicine, Morgantown, West Virginia, United States
| | - Chris C Cook
- Cardiovascular and Thoracic Surgery, West Virginia University School of Medicine, Morgantown, West Virginia, United States
| | - Evan R Cramer
- Department of Biochemistry, West Virginia University School of Medicine, Morgantown, West Virginia, United States
| | - Sarah A Starcovic
- Department of Biochemistry, West Virginia University School of Medicine, Morgantown, West Virginia, United States
| | - Michael T Winters
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University Cancer Institute, School of Medicine, Morgantown, West Virginia, United States
| | - Emily S Westemeier-Rice
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University Cancer Institute, School of Medicine, Morgantown, West Virginia, United States
| | - Garrett K Fink
- Division of Exercise Physiology, West Virginia University School of Medicine, Morgantown, West Virginia, United States
| | - Andrya J Durr
- Division of Exercise Physiology, West Virginia University School of Medicine, Morgantown, West Virginia, United States
- Mitochondria, Metabolism, and Bioenergetics Working Group, West Virginia University School of Medicine, Morgantown, West Virginia, United States
| | - Saira Rizwan
- Division of Exercise Physiology, West Virginia University School of Medicine, Morgantown, West Virginia, United States
- Mitochondria, Metabolism, and Bioenergetics Working Group, West Virginia University School of Medicine, Morgantown, West Virginia, United States
| | - Danielle L Shepherd
- Division of Exercise Physiology, West Virginia University School of Medicine, Morgantown, West Virginia, United States
- Mitochondria, Metabolism, and Bioenergetics Working Group, West Virginia University School of Medicine, Morgantown, West Virginia, United States
| | - Aaron R Robart
- Department of Biochemistry, West Virginia University School of Medicine, Morgantown, West Virginia, United States
| | - Ivan Martinez
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University Cancer Institute, School of Medicine, Morgantown, West Virginia, United States
| | - John M Hollander
- Division of Exercise Physiology, West Virginia University School of Medicine, Morgantown, West Virginia, United States
- Mitochondria, Metabolism, and Bioenergetics Working Group, West Virginia University School of Medicine, Morgantown, West Virginia, United States
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Jaiswal LK, Singh RK, Nayak T, Kakkar A, Kandwal G, Singh VS, Gupta A. A comparative analysis of mycobacterial ribonucleases: Toward a therapeutic novel drug target. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024:105645. [PMID: 39067582 DOI: 10.1016/j.meegid.2024.105645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 06/18/2024] [Accepted: 07/21/2024] [Indexed: 07/30/2024]
Abstract
Bacterial responses to continuously changing environments are addressed through modulation of gene expression at the level of transcription initiation, RNA processing and/or decay. Ribonucleases (RNases) are hydrolytic or phosphorolytic enzymes involved in a majority of RNA metabolism reactions. RNases play a crucial role in RNA degradation, either independently or in collaboration with various trans-acting regulatory factors. The genus Mycobacterium consists of five subgenera: Mycobacteroides, Mycolicibacterium, Mycobacterium, Mycolicibacter and Mycolicibacillus, which include 63 fully sequenced species (pathogenic/non-pathogenic) to date. These include 13 different RNases, among which 5 are exonucleases (RNase PH, PNPase, RNase D, nano-RNases and RNase AS) and 8 are endonucleases (RNase J, RNase H, RNase P, RNase III, RNase BN, RNase Z, RNase G and RNase E), although RNase J and RNase BN were later identified to have exoribonuclease functions also. Here, we provide a detailed comparative insight into the Escherichia coli and mycobacterial RNases with respect to their types, phylogeny, structure, function, regulation and mechanism of action, with the main emphasis on RNase E. Among these 13 different mycobacterial RNases, 10 are essential for cell survival and have diverse structures hence, they are promising drug targets. RNase E is also an essential endonuclease that is abundant in many bacteria, forms an RNA degradosome complex that controls central RNA processing/degradation and has a conserved 5' sensor domain/DNase-I like region in its RNase domain. The essential mycobacterial RNases especially RNase E provide a potential repertoire of drug targets that can be exploited for inhibitor/modulator screening against many deadly mycobacterial diseases.
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Affiliation(s)
- Lav Kumar Jaiswal
- Molecular Microbiology Laboratory, Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi U.P.-221005, India
| | - Rakesh Kumar Singh
- Molecular Microbiology Laboratory, Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi U.P.-221005, India
| | - Tanmayee Nayak
- Molecular Microbiology Laboratory, Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi U.P.-221005, India
| | - Anuja Kakkar
- Molecular Microbiology Laboratory, Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi U.P.-221005, India
| | - Garima Kandwal
- Molecular Microbiology Laboratory, Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi U.P.-221005, India
| | - Vijay Shankar Singh
- Department of Microbiology, School of life Sciences, Sikkim University, Gangtok 737102, Sikkim, India
| | - Ankush Gupta
- Molecular Microbiology Laboratory, Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi U.P.-221005, India.
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3
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Lipońska A, Lee H, Yap MNF. Staphylococcal exoribonuclease YhaM destabilizes ribosomes by targeting the mRNA of a hibernation factor. Nucleic Acids Res 2024:gkae596. [PMID: 38979572 DOI: 10.1093/nar/gkae596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 06/05/2024] [Accepted: 06/26/2024] [Indexed: 07/10/2024] Open
Abstract
The hibernation-promoting factor (Hpf) in Staphylococcus aureus binds to 70S ribosomes and induces the formation of the 100S complex (70S dimer), leading to translational avoidance and occlusion of ribosomes from RNase R-mediated degradation. Here, we show that the 3'-5' exoribonuclease YhaM plays a previously unrecognized role in modulating ribosome stability. Unlike RNase R, which directly degrades the 16S rRNA of ribosomes in S. aureus cells lacking Hpf, YhaM destabilizes ribosomes by indirectly degrading the 3'-hpf mRNA that carries an intrinsic terminator. YhaM adopts an active hexameric assembly and robustly cleaves ssRNA in a manganese-dependent manner. In vivo, YhaM appears to be a low-processive enzyme, trimming the hpf mRNA by only 1 nucleotide. Deletion of yhaM delays cell growth. These findings substantiate the physiological significance of this cryptic enzyme and the protective role of Hpf in ribosome integrity, providing a mechanistic understanding of bacterial ribosome turnover.
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Affiliation(s)
- Anna Lipońska
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, 320 E Superior St, Chicago, IL 60611, USA
| | - Hyun Lee
- Department of Pharmaceutical Sciences, College of Pharmacy and Biophysics Core in Research Resources Center, University of Illinois at Chicago (UIC), 1100 S Ashland Ave, Chicago, IL 60607, USA
| | - Mee-Ngan F Yap
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, 320 E Superior St, Chicago, IL 60611, USA
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4
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Park S, Kim HS, Bang K, Han A, Shin B, Seo M, Kim S, Hwang KY. Structural Insights into the Rrp4 Subunit from the Crystal Structure of the Thermoplasma acidophilum Exosome. Biomolecules 2024; 14:621. [PMID: 38927025 PMCID: PMC11201974 DOI: 10.3390/biom14060621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2024] [Revised: 05/16/2024] [Accepted: 05/23/2024] [Indexed: 06/28/2024] Open
Abstract
The exosome multiprotein complex plays a critical role in RNA processing and degradation. This system governs the regulation of mRNA quality, degradation in the cytoplasm, the processing of short noncoding RNA, and the breakdown of RNA fragments. We determined two crystal structures of exosome components from Thermoplasma acidophilum (Taci): one with a resolution of 2.3 Å that reveals the central components (TaciRrp41 and TaciRrp42), and another with a resolution of 3.5 Å that displays the whole exosome (TaciRrp41, TaciRrp42, and TaciRrp4). The fundamental exosome structure revealed the presence of a heterodimeric complex consisting of TaciRrp41 and TaciRrp42. The structure comprises nine subunits, with TaciRrp41 and TaciRrp42 arranged in a circular configuration, while TaciRrp4 is located at the apex. The RNA degradation capabilities of the TaciRrp4:41:42 complex were verified by RNA degradation assays, consistent with prior findings in other archaeal exosomes. The resemblance between archaeal exosomes and bacterial PNPase suggests a common mechanism for RNA degradation. Despite sharing comparable topologies, the surface charge distributions of TaciRrp4 and other archaea structures are surprisingly distinct. Different RNA breakdown substrates may be responsible for this variation. These newfound structural findings enhance our comprehension of RNA processing and degradation in biological systems.
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Affiliation(s)
- Seonha Park
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea; (S.P.); (H.S.K.); (K.B.); (A.H.); (B.S.); (M.S.)
- Institute of Bioresources, Korea University, Seoul 02841, Republic of Korea
| | - Hyun Sook Kim
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea; (S.P.); (H.S.K.); (K.B.); (A.H.); (B.S.); (M.S.)
| | - Kyuhyeon Bang
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea; (S.P.); (H.S.K.); (K.B.); (A.H.); (B.S.); (M.S.)
| | - Ahreum Han
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea; (S.P.); (H.S.K.); (K.B.); (A.H.); (B.S.); (M.S.)
| | - Byeongmin Shin
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea; (S.P.); (H.S.K.); (K.B.); (A.H.); (B.S.); (M.S.)
| | - Minjeong Seo
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea; (S.P.); (H.S.K.); (K.B.); (A.H.); (B.S.); (M.S.)
| | - Sulhee Kim
- Korea BioDefense Research Institute, Korea University, Seoul 02841, Republic of Korea;
| | - Kwang Yeon Hwang
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea; (S.P.); (H.S.K.); (K.B.); (A.H.); (B.S.); (M.S.)
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5
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Taylor KE, Miller LG, Contreras LM. RNA-binding proteins that preferentially interact with 8-oxoG-modified RNAs: our current understanding. Biochem Soc Trans 2024; 52:111-122. [PMID: 38174726 DOI: 10.1042/bst20230254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 12/18/2023] [Accepted: 12/20/2023] [Indexed: 01/05/2024]
Abstract
Cells encounter a variety of stresses throughout their lifetimes. Oxidative stress can occur via a myriad of factors, including exposure to chemical toxins or UV light. Importantly, these stressors induce chemical changes (e.g. chemical modifications) to biomolecules, such as RNA. Commonly, guanine is oxidized to form 8-oxo-7,8-hydroxyguanine (8-oxoG) and this modification can disrupt a plethora of cellular processes including messenger RNA translation and stability. Polynucleotide phosphorylase (PNPase), heterogeneous nuclear ribonucleoprotein D (HNRPD/Auf1), poly(C)-binding protein (PCBP1/HNRNP E1), and Y-box binding protein 1 (YB-1) have been identified as four RNA-binding proteins that preferentially bind 8-oxoG-modified RNA over unmodified RNA. All four proteins are native to humans and PNPase is additionally found in bacteria. Additionally, under oxidative stress, cell survival declines in mutants that lack PNPase, Auf1, or PCBP1, suggesting they are critical to the oxidative stress response. This mini-review captures the current understanding of the PNPase, HNRPD/Auf1, PCBP1, and YB-1 proteins and the mechanism that has been outlined so far by which they recognize and interact with 8-oxoG-modified RNAs.
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Affiliation(s)
- Kathleen E Taylor
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Lucas G Miller
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Lydia M Contreras
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, USA
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, USA
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6
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Bárria C, Athayde D, Hernandez G, Fonseca L, Casinhas J, Cordeiro TN, Archer M, Arraiano CM, Brito JA, Matos RG. Structure and function of Campylobacter jejuni polynucleotide phosphorylase (PNPase): Insights into the role of this RNase in pathogenicity. Biochimie 2024; 216:56-70. [PMID: 37806617 DOI: 10.1016/j.biochi.2023.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 09/29/2023] [Accepted: 10/06/2023] [Indexed: 10/10/2023]
Abstract
Ribonucleases are in charge of the processing, degradation and quality control of all cellular transcripts, which makes them crucial factors in RNA regulation. This post-transcriptional regulation allows bacteria to promptly react to different stress conditions and growth phase transitions, and also to produce the required virulence factors in pathogenic bacteria. Campylobacter jejuni is the main responsible for human gastroenteritis in the world. In this foodborne pathogen, exoribonuclease PNPase (CjPNP) is essential for low-temperature cell survival, affects the synthesis of proteins involved in virulence and has an important role in swimming, cell adhesion/invasion ability, and chick colonization. Here we report the crystallographic structure of CjPNP, complemented with SAXS, which confirms the characteristic doughnut-shaped trimeric arrangement and evaluates domain arrangement and flexibility. Mutations in highly conserved residues were constructed to access their role in RNA degradation and polymerization. Surprisingly, we found two mutations that altered CjPNP into a protein that is only capable of degrading RNA even in conditions that favour polymerization. These findings will be important to develop new strategies to combat C. jejuni infections.
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Affiliation(s)
- Cátia Bárria
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Avenida da República, 2780-157, Oeiras, Portugal.
| | - Diogo Athayde
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Avenida da República, 2780-157, Oeiras, Portugal.
| | - Guillem Hernandez
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Avenida da República, 2780-157, Oeiras, Portugal.
| | - Leonor Fonseca
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Avenida da República, 2780-157, Oeiras, Portugal.
| | - Jorge Casinhas
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Avenida da República, 2780-157, Oeiras, Portugal.
| | - Tiago N Cordeiro
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Avenida da República, 2780-157, Oeiras, Portugal.
| | - Margarida Archer
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Avenida da República, 2780-157, Oeiras, Portugal.
| | - Cecília M Arraiano
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Avenida da República, 2780-157, Oeiras, Portugal.
| | - José A Brito
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Avenida da República, 2780-157, Oeiras, Portugal.
| | - Rute G Matos
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Avenida da República, 2780-157, Oeiras, Portugal.
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Combes F, Bui TH, Pettersson FJ, Hak S. Rapid and scalable detection of synthetic mRNA byproducts using polynucleotide phosphorylase and polythymidine oligonucleotides. RNA Biol 2024; 21:1-8. [PMID: 38836544 PMCID: PMC11155706 DOI: 10.1080/15476286.2024.2363029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/28/2024] [Indexed: 06/06/2024] Open
Abstract
Production and storage of synthetic mRNA can introduce a variety of byproducts which reduce the overall integrity and functionality of mRNA vaccines and therapeutics. mRNA integrity is therefore designated as a critical quality attribute which must be evaluated with state-of-the-art analytical methods before clinical use. The current study first demonstrates the effect of heat degradation on transcript translatability and then describes a novel enzymatic approach to assess the integrity of conventional mRNA and long self-amplifying mRNA. By first hybridizing oligo-T to the poly(A) tail of intact mRNA and subsequently digesting the unhybridized RNA fragments with a 3'-5' exoribonuclease, individual nucleotides can be selectively released from RNA fragments. The adenosine-based fraction of these nucleotides can then be converted into ATP and detected by luminescence as a sensitive indicator of mRNA byproducts. We developed a polynucleotide phosphorylase (PNPase)-based assay that offers fast and sensitive evaluation of mRNA integrity, regardless of its length, thus presenting a novel and fully scalable alternative to chromatographic-, electrophoresis-, or sequencing-based techniques.
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Affiliation(s)
- Francis Combes
- Department of Biotechnology and Nanomedicine, SINTEF, Trondheim, Norway
| | - Thanh-Huong Bui
- Department of Biotechnology and Nanomedicine, SINTEF, Trondheim, Norway
| | | | - Sjoerd Hak
- Department of Biotechnology and Nanomedicine, SINTEF, Trondheim, Norway
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Khan F, Jeong GJ, Tabassum N, Kim YM. Functional diversity of c-di-GMP receptors in prokaryotic and eukaryotic systems. Cell Commun Signal 2023; 21:259. [PMID: 37749602 PMCID: PMC10519070 DOI: 10.1186/s12964-023-01263-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 08/09/2023] [Indexed: 09/27/2023] Open
Abstract
Cyclic bis-(3', 5')-dimeric guanosine monophosphate (c-di-GMP) is ubiquitous in many bacterial species, where it functions as a nucleotide-based secondary messenger and is a vital regulator of numerous biological processes. Due to its ubiquity, most bacterial species possess a wide range of downstream receptors that has a binding affinity to c-di-GMP and elicit output responses. In eukaryotes, several enzymes and riboswitches operate as receptors that interact with c-di-GMP and transduce cellular or environmental signals. This review examines the functional variety of receptors in prokaryotic and eukaryotic systems that exhibit distinct biological responses after interacting with c-di-GMP. Evolutionary relationships and similarities in distance among the c-di-GMP receptors in various bacterial species were evaluated to understand their specificities. Furthermore, residues of receptors involved in c-di-GMP binding are summarized. This review facilitates the understanding of how distinct receptors from different origins bind c-di-GMP equally well, yet fulfill diverse biological roles at the interspecies, intraspecies, and interkingdom levels. Furthermore, it also highlights c-di-GMP receptors as potential therapeutic targets, particularly those found in pathogenic microorganisms. Video Abstract.
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Affiliation(s)
- Fazlurrahman Khan
- Marine Integrated Biomedical Technology Center, The National Key Research Institutes in Universities, Pukyong National University, Busan, 48513, Republic of Korea.
- Research Center for Marine Integrated Bionics Technology, Pukyong National University, Busan, 48513, Republic of Korea.
| | - Geum-Jae Jeong
- Department of Food Science and Technology, Pukyong National University, Busan, 48513, Republic of Korea
| | - Nazia Tabassum
- Marine Integrated Biomedical Technology Center, The National Key Research Institutes in Universities, Pukyong National University, Busan, 48513, Republic of Korea
- Research Center for Marine Integrated Bionics Technology, Pukyong National University, Busan, 48513, Republic of Korea
| | - Young-Mog Kim
- Marine Integrated Biomedical Technology Center, The National Key Research Institutes in Universities, Pukyong National University, Busan, 48513, Republic of Korea.
- Research Center for Marine Integrated Bionics Technology, Pukyong National University, Busan, 48513, Republic of Korea.
- Department of Food Science and Technology, Pukyong National University, Busan, 48513, Republic of Korea.
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Single-exonuclease nanocircuits reveal the RNA degradation dynamics of PNPase and demonstrate potential for RNA sequencing. Nat Commun 2023; 14:552. [PMID: 36725855 PMCID: PMC9892577 DOI: 10.1038/s41467-023-36278-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 01/23/2023] [Indexed: 02/03/2023] Open
Abstract
The degradation process of RNA is decisive in guaranteeing high-fidelity translation of genetic information in living organisms. However, visualizing the single-base degradation process in real time and deciphering the degradation mechanism at the single-enzyme level remain formidable challenges. Here, we present a reliable in-situ single-PNPase-molecule dynamic electrical detector based on silicon nanowire field-effect transistors with ultra-high temporal resolution. These devices are capable of realizing real-time and label-free monitoring of RNA analog degradation with single-base resolution, including RNA analog binding, single-nucleotide hydrolysis, and single-base movement. We discover a binding event of the enzyme (near the active site) with the nucleoside, offering a further understanding of the RNA degradation mechanism. Relying on systematic analyses of independent reads, approximately 80% accuracy in RNA nucleoside sequencing is achieved in a single testing process. This proof-of-concept sets up a Complementary Metal Oxide Semiconductor (CMOS)-compatible playground for the development of high-throughput detection technologies toward mechanistic exploration and single-molecule sequencing.
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10
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How RNases Shape Mitochondrial Transcriptomes. Int J Mol Sci 2022; 23:ijms23116141. [PMID: 35682820 PMCID: PMC9181182 DOI: 10.3390/ijms23116141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 05/24/2022] [Accepted: 05/25/2022] [Indexed: 11/17/2022] Open
Abstract
Mitochondria are the power houses of eukaryote cells. These endosymbiotic organelles of prokaryote origin are considered as semi-autonomous since they have retained a genome and fully functional gene expression mechanisms. These pathways are particularly interesting because they combine features inherited from the bacterial ancestor of mitochondria with characteristics that appeared during eukaryote evolution. RNA biology is thus particularly diverse in mitochondria. It involves an unexpectedly vast array of factors, some of which being universal to all mitochondria and others being specific from specific eukaryote clades. Among them, ribonucleases are particularly prominent. They play pivotal functions such as the maturation of transcript ends, RNA degradation and surveillance functions that are required to attain the pool of mature RNAs required to synthesize essential mitochondrial proteins such as respiratory chain proteins. Beyond these functions, mitochondrial ribonucleases are also involved in the maintenance and replication of mitochondrial DNA, and even possibly in the biogenesis of mitochondrial ribosomes. The diversity of mitochondrial RNases is reviewed here, showing for instance how in some cases a bacterial-type enzyme was kept in some eukaryotes, while in other clades, eukaryote specific enzymes were recruited for the same function.
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Zhang X, Wang X, Li Q, Chen Y, Zhang X, Wang P, Yuan M, Pei H. [Role of PNPT1 in cardiomyocyte apoptosis induced by oxygen-glucose deprivation]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2022; 42:584-590. [PMID: 35527495 DOI: 10.12122/j.issn.1673-4254.2022.04.15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
OBJECTIVE To explore the effect of inhibiting polyribonucleotide nucleotidyl-transferase 1 (PNPT1) on oxygen-glucose deprivation (OGD)-induced apoptosis of mouse atrial myocytes. METHODS Cultured mouse atrial myocytes (HL-1 cells) with or without OGD were transfected with PNPT1-siRNA or a negative control siRNA (NC-siRNA group), and the cell survival rate was detected using CCK-8 assay. The expression levels of ACTB and TUBA mRNA were detected with qPCR, and the protein expression of PNPT1 was detected with Western blotting. The apoptosis rate of the treated cells was determined with flow cytometry, the mitochondrial membrane potential was detected using JC-1 kit, and the mitochondrial morphology was observed using transmission electron microscope. RESULTS With the extension of OGD time, the protein expression levels of PNPT1 increased progressively in the cytoplasm of HL-1 cells (P < 0.05). Transfection with PNPT1-siRNA significantly reduced PNPT1 expression in HL-1 cells (P < 0.05). Exposure to OGD significantly enhanced degradation of ACTB and TUBA mRNA (P < 0.05) and markedly increased the apoptosis rate of HL-1 cells (P < 0.05), and these changes were significantly inhibited by transfection with PNPT1-siRNA (P < 0.05), which obviously increased mitochondrial membrane potential and improved mitochondrial morphology of HL-1 cells exposed to OGD. CONCLUSION Inhibition of PNPT1 improves mitochondrial damage and reduces degradation of apoptotic-associated mRNAs to alleviate OGD-induced apoptosis of mouse atrial myocyte.
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Affiliation(s)
- X Zhang
- College of Medicine, Southwest Jiaotong University, Chengdu 611756, China.,Department of Cardiology, General Hospital of Western Theater Command, Chengdu 610083, China
| | - X Wang
- Department of Cardiology, General Hospital of Western Theater Command, Chengdu 610083, China
| | - Q Li
- Second Ward of Cadres, General Hospital of Western Theater Command, Chengdu 610083, China
| | - Y Chen
- Department of Cardiology, General Hospital of Western Theater Command, Chengdu 610083, China
| | - X Zhang
- Medical Information Data Office, General Hospital of Western Theater Command, Chengdu 610083, China
| | - P Wang
- Department of Cardiology, General Hospital of Western Theater Command, Chengdu 610083, China
| | - M Yuan
- Medical Center, General Hospital of Western Theater Command, Chengdu 610083, China
| | - H Pei
- College of Medicine, Southwest Jiaotong University, Chengdu 611756, China.,Department of Cardiology, General Hospital of Western Theater Command, Chengdu 610083, China
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12
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Falchi FA, Pizzoccheri R, Briani F. Activity and Function in Human Cells of the Evolutionary Conserved Exonuclease Polynucleotide Phosphorylase. Int J Mol Sci 2022; 23:ijms23031652. [PMID: 35163574 PMCID: PMC8836086 DOI: 10.3390/ijms23031652] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 01/28/2022] [Accepted: 01/28/2022] [Indexed: 02/04/2023] Open
Abstract
Polynucleotide phosphorylase (PNPase) is a phosphorolytic RNA exonuclease highly conserved throughout evolution. Human PNPase (hPNPase) is located in mitochondria and is essential for mitochondrial function and homeostasis. Not surprisingly, mutations in the PNPT1 gene, encoding hPNPase, cause serious diseases. hPNPase has been implicated in a plethora of processes taking place in different cell compartments and involving other proteins, some of which physically interact with hPNPase. This paper reviews hPNPase RNA binding and catalytic activity in relation with the protein structure and in comparison, with the activity of bacterial PNPases. The functions ascribed to hPNPase in different cell compartments are discussed, highlighting the gaps that still need to be filled to understand the physiological role of this ancient protein in human cells.
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13
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Zhang J, Jia K, Huang Y, Wang Y, Liu N, Chen Y, Liu X, Liu X, Zhu Y, Zheng L, Chen H, Liang F, Zhang M, Duan X, Wang H, Lin L, Peng H, Liu Z. Hydrophilic, Clean Graphene for Cell Culture and Cryo-EM Imaging. NANO LETTERS 2021; 21:9587-9593. [PMID: 34734718 DOI: 10.1021/acs.nanolett.1c03344] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The wettability of graphene is critical for numerous applications but is very sensitive to its surface cleanness. Herein, by clarifying the impact of intrinsic contamination, i.e., amorphous carbon, which is formed on the graphene surface during the high-temperature chemical vapor deposition (CVD) process, the hydrophilic nature of clean graphene grown on single-crystal Cu(111) substrate was confirmed by both experimental and theoretical studies, with an average water contact angle of ∼23°. Furthermore, the wettability of as-transferred graphene was proven to be highly dependent on its intrinsic cleanness, because of which the hydrophilic, clean graphene exhibited improved performance when utilized for cell culture and cryoelectron microscopy imaging. This work not only validates the intrinsic hydrophilic nature of graphene but also provides a new insight in developing advanced bioapplications using CVD-grown clean graphene films.
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Affiliation(s)
- Jincan Zhang
- Center for Nanochemistry, Beijing Science and Engineering Center for Nanocarbons, Beijing National Laboratory for Molecular Science, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
- Beijing Graphene Institute, Beijing 100095, P. R. China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, P. R. China
- Department of Engineering, University of Cambridge, Cambridge CB3 0FA, U.K
| | - Kaicheng Jia
- Center for Nanochemistry, Beijing Science and Engineering Center for Nanocarbons, Beijing National Laboratory for Molecular Science, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
- Beijing Graphene Institute, Beijing 100095, P. R. China
| | - Yongfeng Huang
- Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, P. R. China
- Beijing National Laboratory for Condensed Matter Physics and Institute of Physics, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Yanan Wang
- Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, P. R. China
- Beijing National Laboratory for Condensed Matter Physics and Institute of Physics, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Nan Liu
- Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences and Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing 100084, P. R. China
| | - Yanan Chen
- Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences and Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing 100084, P. R. China
| | - Xiaoting Liu
- Center for Nanochemistry, Beijing Science and Engineering Center for Nanocarbons, Beijing National Laboratory for Molecular Science, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
- Beijing Graphene Institute, Beijing 100095, P. R. China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, P. R. China
| | - Xiaojun Liu
- College of Future Technology, Peking University, Beijing 100871, P. R. China
| | - Yeshu Zhu
- Center for Nanochemistry, Beijing Science and Engineering Center for Nanocarbons, Beijing National Laboratory for Molecular Science, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
- Beijing Graphene Institute, Beijing 100095, P. R. China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, P. R. China
| | - Liming Zheng
- Center for Nanochemistry, Beijing Science and Engineering Center for Nanocarbons, Beijing National Laboratory for Molecular Science, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
- Beijing Graphene Institute, Beijing 100095, P. R. China
| | - Heng Chen
- Center for Nanochemistry, Beijing Science and Engineering Center for Nanocarbons, Beijing National Laboratory for Molecular Science, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
- Beijing Graphene Institute, Beijing 100095, P. R. China
| | - Fushun Liang
- Center for Nanochemistry, Beijing Science and Engineering Center for Nanocarbons, Beijing National Laboratory for Molecular Science, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
- Beijing Graphene Institute, Beijing 100095, P. R. China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, P. R. China
| | - Mengqi Zhang
- Beijing Graphene Institute, Beijing 100095, P. R. China
| | - Xiaojie Duan
- College of Future Technology, Peking University, Beijing 100871, P. R. China
| | - Hongwei Wang
- Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences and Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing 100084, P. R. China
| | - Li Lin
- Materials Science and Engineering, National University of Singapore, 119077, Singapore
| | - Hailin Peng
- Center for Nanochemistry, Beijing Science and Engineering Center for Nanocarbons, Beijing National Laboratory for Molecular Science, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
- Beijing Graphene Institute, Beijing 100095, P. R. China
| | - Zhongfan Liu
- Center for Nanochemistry, Beijing Science and Engineering Center for Nanocarbons, Beijing National Laboratory for Molecular Science, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
- Beijing Graphene Institute, Beijing 100095, P. R. China
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14
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Unciuleac MC, Ghosh S, de la Cruz MJ, Goldgur Y, Shuman S. Structure and mechanism of Mycobacterium smegmatis polynucleotide phosphorylase. RNA (NEW YORK, N.Y.) 2021; 27:rna.078822.121. [PMID: 34088850 PMCID: PMC8284320 DOI: 10.1261/rna.078822.121] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Accepted: 06/01/2021] [Indexed: 05/05/2023]
Abstract
Polynucleotide phosphorylase (PNPase) catalyzes stepwise phosphorolysis of the 3'-terminal phosphodiesters of RNA chains to yield nucleoside diphosphate products. In the reverse reaction PNPase acts as a polymerase, using NDPs as substrates to add NMPs to the 3'-OH terminus of RNA chains while expelling inorganic phosphate. The apparent essentiality of PNPase for growth of M. tuberculosis militates for mycobacterial PNPase as a potential drug target. A cryo-EM structure of Mycobacterium smegmatis PNPase (MsmPNPase) reveals a characteristic ring-shaped homotrimer in which each protomer consists of two RNase PH-like domains and an intervening α-helical module on the inferior surface of the ring. The C-terminal KH and S1 domains, which impart RNA specificity to MsmPNPase, are on the opposite face of the core ring and are conformationally mobile. Single particle reconstructions of MsmPNPase in the act of poly(A) synthesis highlight a 3'-terminal (rA)4 oligonucleotide and two magnesium ions in the active site and an adenine nucleobase in the central tunnel. We identify amino acids that engage the 3' segment of the RNA chain (Phe68, Arg105, Arg112, Arg430, Arg431) and the two metal ions (Asp526, Asp532, Gln546, Asp548) and we infer those that bind inorganic phosphate (Thr470, Ser471, His435, Lys534). Alanine mutagenesis pinpointed RNA and phosphate contacts as essential (Arg105, Arg431, Lys534, Thr470+Ser471), important (Arg112, Arg430), or unimportant (Phe68) for PNPase activity. Severe phosphorolysis and polymerase defects accompanying alanine mutations of the enzymic metal ligands suggest a two-metal mechanism of catalysis by MsmPNPase.
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15
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Spanka DT, Reuscher CM, Klug G. Impact of PNPase on the transcriptome of Rhodobacter sphaeroides and its cooperation with RNase III and RNase E. BMC Genomics 2021; 22:106. [PMID: 33549057 PMCID: PMC7866481 DOI: 10.1186/s12864-021-07409-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 01/26/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The polynucleotide phosphorylase (PNPase) is conserved among both Gram-positive and Gram-negative bacteria. As a core part of the Escherichia coli degradosome, PNPase is involved in maintaining proper RNA levels within the bacterial cell. It plays a major role in RNA homeostasis and decay by acting as a 3'-to-5' exoribonuclease. Furthermore, PNPase can catalyze the reverse reaction by elongating RNA molecules in 5'-to-3' end direction which has a destabilizing effect on the prolonged RNA molecule. RNA degradation is often initiated by an endonucleolytic cleavage, followed by exoribonucleolytic decay from the new 3' end. RESULTS The PNPase mutant from the facultative phototrophic Rhodobacter sphaeroides exhibits several phenotypical characteristics, including diminished adaption to low temperature, reduced resistance to organic peroxide induced stress and altered growth behavior. The transcriptome composition differs in the pnp mutant strain, resulting in a decreased abundance of most tRNAs and rRNAs. In addition, PNPase has a major influence on the half-lives of several regulatory sRNAs and can have both a stabilizing or a destabilizing effect. Moreover, we globally identified and compared differential RNA 3' ends in RNA NGS sequencing data obtained from PNPase, RNase E and RNase III mutants for the first time in a Gram-negative organism. The genome wide RNA 3' end analysis revealed that 885 3' ends are degraded by PNPase. A fair percentage of these RNA 3' ends was also identified at the same genomic position in RNase E or RNase III mutant strains. CONCLUSION The PNPase has a major influence on RNA processing and maturation and thus modulates the transcriptome of R. sphaeroides. This includes sRNAs, emphasizing the role of PNPase in cellular homeostasis and its importance in regulatory networks. The global 3' end analysis indicates a sequential RNA processing: 5.9% of all RNase E-dependent and 9.7% of all RNase III-dependent RNA 3' ends are subsequently degraded by PNPase. Moreover, we provide a modular pipeline which greatly facilitates the identification of RNA 5'/3' ends. It is publicly available on GitHub and is distributed under ICS license.
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Affiliation(s)
- Daniel-Timon Spanka
- Institute of Microbiology and Molecular Biology, Justus Liebig University Giessen, IFZ, Giessen, Germany
| | - Carina Maria Reuscher
- Institute of Microbiology and Molecular Biology, Justus Liebig University Giessen, IFZ, Giessen, Germany
| | - Gabriele Klug
- Institute of Microbiology and Molecular Biology, Justus Liebig University Giessen, IFZ, Giessen, Germany.
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16
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Pseudomonas aeruginosa Polynucleotide Phosphorylase Controls Tolerance to Aminoglycoside Antibiotics by Regulating the MexXY Multidrug Efflux Pump. Antimicrob Agents Chemother 2021; 65:AAC.01846-20. [PMID: 33257447 DOI: 10.1128/aac.01846-20] [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: 08/27/2020] [Accepted: 11/18/2020] [Indexed: 01/01/2023] Open
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen that shows high intrinsic resistance to a variety of antibiotics. The MexX-MexY-OprM efflux pump plays an important role in bacterial resistance to aminoglycoside antibiotics. Polynucleotide phosphorylase (PNPase) is a highly conserved exonuclease that plays important roles in RNA processing and the bacterial response to environmental stresses. Previously, we demonstrated that PNPase controls the tolerance to fluoroquinolone antibiotics by influencing the production of pyocin in P. aeruginosa In this study, we found that mutation of the PNPase-encoding gene (pnp) in P. aeruginosa increases bacterial tolerance to aminoglycoside antibiotics. We further demonstrate that the upregulation of the mexXY genes is responsible for the increased tolerance of the pnp mutant. Furthermore, our experimental results revealed that PNPase controls the translation of the armZ mRNA through its 5' untranslated region (UTR). ArmZ had previously been shown to positively regulate the expression of mexXY Therefore, our results revealed a novel role of PNPase in the regulation of armZ and subsequently the MexXY efflux pump.
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17
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Apura P, de Lorenzo V, Arraiano CM, Martínez-García E, Viegas SC. Ribonucleases control distinct traits of Pseudomonas putida lifestyle. Environ Microbiol 2020; 23:174-189. [PMID: 33089610 DOI: 10.1111/1462-2920.15291] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 09/21/2020] [Accepted: 10/19/2020] [Indexed: 11/28/2022]
Abstract
The role of archetypal ribonucleases (RNases) in the physiology and stress endurance of the soil bacterium and metabolic engineering platform Pseudomonas putida KT2440 has been inspected. To this end, variants of this strain lacking each of the most important RNases were constructed. Each mutant lacked either one exoribonuclease (PNPase, RNase R) or one endoribonuclease (RNase E, RNase III, RNase G). The global physiological and metabolic costs of the absence of each of these enzymes were then analysed in terms of growth, motility and morphology. The effects of different oxidative chemicals that mimic the stresses endured by this microorganism in its natural habitats were studied as well. The results highlighted that each ribonuclease is specifically related with different traits of the environmental lifestyle that distinctively characterizes this microorganism. Interestingly, the physiological responses of P. putida to the absence of each enzyme diverged significantly from those known previously in Escherichia coli. This exposed not only species-specific regulatory functions for otherwise known RNase activities but also expanded the panoply of post-transcriptional adaptation devices that P. putida can make use of for facing hostile environments.
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Affiliation(s)
- Patrícia Apura
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Av. da República, EAN, 2780-157, Portugal
| | - Víctor de Lorenzo
- Systems Biology Program, Centro Nacional de Biotecnologia, CSIC, C/Darwin, 3 (Campus de Cantoblanco), Madrid, 28049, Spain
| | - Cecília M Arraiano
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Av. da República, EAN, 2780-157, Portugal
| | - Esteban Martínez-García
- Systems Biology Program, Centro Nacional de Biotecnologia, CSIC, C/Darwin, 3 (Campus de Cantoblanco), Madrid, 28049, Spain
| | - Sandra C Viegas
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Av. da República, EAN, 2780-157, Portugal
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18
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Bhat AS, Kinch LN, Grishin NV. β-Strand-mediated interactions of protein domains. Proteins 2020; 88:1513-1527. [PMID: 32543729 PMCID: PMC8018532 DOI: 10.1002/prot.25970] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 03/10/2020] [Accepted: 06/06/2020] [Indexed: 01/14/2023]
Abstract
Protein domains exist by themselves or in combination with other domains to form complex multidomain proteins. Defining domain boundaries in proteins is essential for understanding their evolution and function but is not trivial. More specifically, partitioning domains that interact by forming a single β-sheet is known to be particularly troublesome for automatic structure-based domain decomposition pipelines. Here, we study edge-to-edge β-strand interactions between domains in a protein chain, to help define the boundaries for some more difficult cases where a single β-sheet spanning over two domains gives an appearance of one. We give a number of examples where β-strands belonging to a single β-sheet do not belong to a single domain and highlight the difficulties of automatic domain parsers on these examples. This work can be used as a baseline for defining domain boundaries in homologous proteins or proteins with similar domain interactions in the future.
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Affiliation(s)
- Archana S. Bhat
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9050
| | - Lisa N. Kinch
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9050
| | - Nick V. Grishin
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9050
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9050
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19
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Quendera AP, Seixas AF, Dos Santos RF, Santos I, Silva JPN, Arraiano CM, Andrade JM. RNA-Binding Proteins Driving the Regulatory Activity of Small Non-coding RNAs in Bacteria. Front Mol Biosci 2020; 7:78. [PMID: 32478092 PMCID: PMC7237705 DOI: 10.3389/fmolb.2020.00078] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 04/06/2020] [Indexed: 12/20/2022] Open
Abstract
Small non-coding RNAs (sRNAs) are critical post-transcriptional regulators of gene expression. Distinct RNA-binding proteins (RBPs) influence the processing, stability and activity of bacterial small RNAs. The vast majority of bacterial sRNAs interact with mRNA targets, affecting mRNA stability and/or its translation rate. The assistance of RNA-binding proteins facilitates and brings accuracy to sRNA-mRNA basepairing and the RNA chaperones Hfq and ProQ are now recognized as the most prominent RNA matchmakers in bacteria. These RBPs exhibit distinct high affinity RNA-binding surfaces, promoting RNA strand interaction between a trans-encoding sRNA and its mRNA target. Nevertheless, some organisms lack ProQ and/or Hfq homologs, suggesting the existence of other RBPs involved in sRNA function. Along this line of thought, the global regulator CsrA was recently shown to facilitate the access of an sRNA to its target mRNA and may represent an additional factor involved in sRNA function. Ribonucleases (RNases) can be considered a class of RNA-binding proteins with nucleolytic activity that are responsible for RNA maturation and/or degradation. Presently RNase E, RNase III, and PNPase appear to be the main players not only in sRNA turnover but also in sRNA processing. Here we review the current knowledge on the most important bacterial RNA-binding proteins affecting sRNA activity and sRNA-mediated networks.
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Affiliation(s)
- Ana P Quendera
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - André F Seixas
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Ricardo F Dos Santos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Inês Santos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - João P N Silva
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Cecília M Arraiano
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - José M Andrade
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
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20
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Viegas SC, Matos RG, Arraiano CM. The Bacterial Counterparts of the Eukaryotic Exosome: An Evolutionary Perspective. Methods Mol Biol 2020; 2062:37-46. [PMID: 31768970 DOI: 10.1007/978-1-4939-9822-7_2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
There are striking similarities between the processes of RNA degradation in bacteria and eukaryotes, which rely on the same basic set of enzymatic activities. In particular, enzymes that catalyze 3'→5' RNA decay share evolutionary relationships across the three domains of life. Over the years, a large body of biochemical and structural data has been generated that elucidated the mechanism of action of these enzymes. In this overview, to trace the evolutionary origins of the multisubunit RNA exosome complex, we compare the structural and functional characteristics of the eukaryotic and prokaryotic exoribonucleolytic activities.
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Affiliation(s)
- Sandra C Viegas
- Instituto de Tecnologia Química e Biológica António Xavier, Oeiras, Portugal.
| | - Rute G Matos
- Instituto de Tecnologia Química e Biológica António Xavier, Oeiras, Portugal
| | - Cecília M Arraiano
- Instituto de Tecnologia Química e Biológica António Xavier, Oeiras, Portugal.
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21
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Bechhofer DH, Deutscher MP. Bacterial ribonucleases and their roles in RNA metabolism. Crit Rev Biochem Mol Biol 2019; 54:242-300. [PMID: 31464530 PMCID: PMC6776250 DOI: 10.1080/10409238.2019.1651816] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 07/22/2019] [Accepted: 07/31/2019] [Indexed: 12/16/2022]
Abstract
Ribonucleases (RNases) are mediators in most reactions of RNA metabolism. In recent years, there has been a surge of new information about RNases and the roles they play in cell physiology. In this review, a detailed description of bacterial RNases is presented, focusing primarily on those from Escherichia coli and Bacillus subtilis, the model Gram-negative and Gram-positive organisms, from which most of our current knowledge has been derived. Information from other organisms is also included, where relevant. In an extensive catalog of the known bacterial RNases, their structure, mechanism of action, physiological roles, genetics, and possible regulation are described. The RNase complement of E. coli and B. subtilis is compared, emphasizing the similarities, but especially the differences, between the two. Included are figures showing the three major RNA metabolic pathways in E. coli and B. subtilis and highlighting specific steps in each of the pathways catalyzed by the different RNases. This compilation of the currently available knowledge about bacterial RNases will be a useful tool for workers in the RNA field and for others interested in learning about this area.
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Affiliation(s)
- David H. Bechhofer
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Murray P. Deutscher
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL, USA
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22
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Cameron TA, Matz LM, De Lay NR. Polynucleotide phosphorylase: Not merely an RNase but a pivotal post-transcriptional regulator. PLoS Genet 2018; 14:e1007654. [PMID: 30307990 PMCID: PMC6181284 DOI: 10.1371/journal.pgen.1007654] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Almost 60 years ago, Severo Ochoa was awarded the Nobel Prize in Physiology or Medicine for his discovery of the enzymatic synthesis of RNA by polynucleotide phosphorylase (PNPase). Although this discovery provided an important tool for deciphering the genetic code, subsequent work revealed that the predominant function of PNPase in bacteria and eukaryotes is catalyzing the reverse reaction, i.e., the release of ribonucleotides from RNA. PNPase has a crucial role in RNA metabolism in bacteria and eukaryotes mainly through its roles in processing and degrading RNAs, but additional functions in RNA metabolism have recently been reported for this enzyme. Here, we discuss these established and noncanonical functions for PNPase and the possibility that the major impact of PNPase on cell physiology is through its unorthodox roles.
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Affiliation(s)
- Todd A. Cameron
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center, Houston, Texas, United States of America
| | - Lisa M. Matz
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center, Houston, Texas, United States of America
| | - Nicholas R. De Lay
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center, Houston, Texas, United States of America
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, University of Texas Health Science Center, Houston, Texas, United States of America
- * E-mail:
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23
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Pobre V, Arraiano CM. Characterizing the Role of Exoribonucleases in the Control of Microbial Gene Expression: Differential RNA-Seq. Methods Enzymol 2018; 612:1-24. [PMID: 30502937 DOI: 10.1016/bs.mie.2018.08.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Differential RNA-Seq is a next-generation technology method to determine the significant transcriptomic differences between two and more samples. With this method it is possible to analyze the total RNA content of different samples making it the best global analysis method currently available to study the roles of exoribonucleases in the cell. These enzymes are responsible for the RNA processing and degradation in the cells and therefore affect the total RNA pool in ways not yet fully understood. In Escherichia coli there are three main degradative exoribonucleases RNase II, RNase R, and PNPase that degrade the RNA from the 3' to the 5'-end. These enzymes have several roles in the cell and even though they are degradative enzymes RNase II and PNPase can also protect some RNAs from degradation and PNPase can also act as an RNA polymerase under some conditions. The multiplicity of roles of these exoribonucleases leads to a very high number of transcripts that are affected by their absence in the cell. With the differential RNA-Seq it is possible to obtain a much deeper understanding of how these enzymes work and regulate the bacterial gene expression. In this chapter we have described a differential RNA-Seq data analysis protocol applied to the study of exoribonucleases. We also included the protocol for experimental validation of the RNA-Seq data using qPCR and motility assays. Although the methods described in this chapter were applied to the study of the exoribonucleases, they can also be used for other differential RNA-Seq studies.
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Affiliation(s)
- Vânia Pobre
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.
| | - Cecília M Arraiano
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.
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24
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Golzarroshan B, Lin CL, Li CL, Yang WZ, Chu LY, Agrawal S, Yuan HS. Crystal structure of dimeric human PNPase reveals why disease-linked mutants suffer from low RNA import and degradation activities. Nucleic Acids Res 2018; 46:8630-8640. [PMID: 30020492 PMCID: PMC6144817 DOI: 10.1093/nar/gky642] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 06/13/2018] [Accepted: 07/16/2018] [Indexed: 11/13/2022] Open
Abstract
Human polynucleotide phosphorylase (PNPase) is an evolutionarily conserved 3'-to-5' exoribonuclease principally located in mitochondria where it is responsible for RNA turnover and import. Mutations in PNPase impair structured RNA transport into mitochondria, resulting in mitochondrial dysfunction and disease. PNPase is a trimeric protein with a doughnut-shaped structure hosting a central channel for single-stranded RNA binding and degradation. Here, we show that the disease-linked human PNPase mutants, Q387R and E475G, form dimers, not trimers, and have significantly lower RNA binding and degradation activities compared to wild-type trimeric PNPase. Moreover, S1 domain-truncated PNPase binds single-stranded RNA but not the stem-loop signature motif of imported structured RNA, suggesting that the S1 domain is responsible for binding structured RNAs. We further determined the crystal structure of dimeric PNPase at a resolution of 2.8 Å and, combined with small-angle X-ray scattering, show that the RNA-binding K homology and S1 domains are relatively inaccessible in the dimeric assembly. Taken together, these results show that mutations at the interface of the trimeric PNPase tend to produce a dimeric protein with destructive RNA-binding surfaces, thus impairing both of its RNA import and degradation activities and leading to mitochondria disorders.
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Affiliation(s)
- Bagher Golzarroshan
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 11529, Republic of China
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan 11529, Republic of China
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan 30013, Republic of China
| | - Chia-Liang Lin
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 11529, Republic of China
| | - Chia-Lung Li
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 11529, Republic of China
| | - Wei-Zen Yang
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 11529, Republic of China
| | - Lee-Ya Chu
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 11529, Republic of China
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan 11529, Republic of China
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan 30013, Republic of China
| | - Sashank Agrawal
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 11529, Republic of China
- Molecular and Cell Biology Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan 11529, Republic of China
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan 11490, Republic of China
| | - Hanna S Yuan
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 11529, Republic of China
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan 11529, Republic of China
- Molecular and Cell Biology Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan 11529, Republic of China
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25
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Walker FC, Chou-Zheng L, Dunkle JA, Hatoum-Aslan A. Molecular determinants for CRISPR RNA maturation in the Cas10-Csm complex and roles for non-Cas nucleases. Nucleic Acids Res 2018; 45:2112-2123. [PMID: 28204542 PMCID: PMC5389561 DOI: 10.1093/nar/gkw891] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 09/01/2016] [Accepted: 09/27/2016] [Indexed: 01/18/2023] Open
Abstract
CRISPR–Cas (Clustered regularly interspaced short palindromic repeats-CRISPR-associated proteins) is a prokaryotic immune system that destroys foreign nucleic acids in a sequence-specific manner using Cas nucleases guided by short RNAs (crRNAs). Staphylococcus epidermidis harbours a Type III-A CRISPR–Cas system that encodes the Cas10–Csm interference complex and crRNAs that are subjected to multiple processing steps. The final step, called maturation, involves a concerted effort between Csm3, a ruler protein in Cas10–Csm that measures six-nucleotide increments, and the activity of a nuclease(s) that remains unknown. Here, we elucidate the contributions of the Cas10–Csm complex toward maturation and explore roles of non-Cas nucleases in this process. Using genetic and biochemical approaches, we show that charged residues in Csm3 facilitate its self-assembly and dictate the extent of maturation cleavage. Additionally, acidic residues in Csm5 are required for efficient maturation, but recombinant Csm5 fails to cleave crRNAs in vitro. However, we detected cellular nucleases that co-purify with Cas10–Csm, and show that Csm5 regulates their activities through distinct mechanisms. Altogether, our results support roles for non-Cas nuclease(s) during crRNA maturation and establish a link between Type III-A CRISPR–Cas immunity and central nucleic acid metabolism.
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Affiliation(s)
- Forrest C Walker
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL 35487, USA
| | - Lucy Chou-Zheng
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL 35487, USA
| | - Jack A Dunkle
- Department of Chemistry, University of Alabama, Tuscaloosa, AL, 35487, USA
| | - Asma Hatoum-Aslan
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL 35487, USA
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26
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Dos Santos RF, Quendera AP, Boavida S, Seixas AF, Arraiano CM, Andrade JM. Major 3'-5' Exoribonucleases in the Metabolism of Coding and Non-coding RNA. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2018; 159:101-155. [PMID: 30340785 DOI: 10.1016/bs.pmbts.2018.07.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
3'-5' exoribonucleases are key enzymes in the degradation of superfluous or aberrant RNAs and in the maturation of precursor RNAs into their functional forms. The major bacterial 3'-5' exoribonucleases responsible for both these activities are PNPase, RNase II and RNase R. These enzymes are of ancient nature with widespread distribution. In eukaryotes, PNPase and RNase II/RNase R enzymes can be found in the cytosol and in mitochondria and chloroplasts; RNase II/RNase R-like enzymes are also found in the nucleus. Humans express one PNPase (PNPT1) and three RNase II/RNase R family members (Dis3, Dis3L and Dis3L2). These enzymes take part in a multitude of RNA surveillance mechanisms that are critical for translation accuracy. Although active against a wide range of both coding and non-coding RNAs, the different 3'-5' exoribonucleases exhibit distinct substrate affinities. The latest studies on these RNA degradative enzymes have contributed to the identification of additional homologue proteins, the uncovering of novel RNA degradation pathways, and to a better comprehension of several disease-related processes and response to stress, amongst many other exciting findings. Here, we provide a comprehensive and up-to-date overview on the function, structure, regulation and substrate preference of the key 3'-5' exoribonucleases involved in RNA metabolism.
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Affiliation(s)
- Ricardo F Dos Santos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Ana P Quendera
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Sofia Boavida
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - André F Seixas
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Cecília M Arraiano
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - José M Andrade
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.
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27
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Orr AA, Gonzalez-Rivera JC, Wilson M, Bhikha PR, Wang D, Contreras LM, Tamamis P. A high-throughput and rapid computational method for screening of RNA post-transcriptional modifications that can be recognized by target proteins. Methods 2018; 143:34-47. [DOI: 10.1016/j.ymeth.2018.01.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 01/14/2018] [Accepted: 01/26/2018] [Indexed: 12/25/2022] Open
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28
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Deng YJ, Feng L, Zhou H, Xiao X, Wang FP, Liu XP. NanoRNase from Aeropyrum pernix shows nuclease activity on ssDNA and ssRNA. DNA Repair (Amst) 2018; 65:54-63. [PMID: 29609115 DOI: 10.1016/j.dnarep.2018.03.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 03/07/2018] [Accepted: 03/23/2018] [Indexed: 01/09/2023]
Abstract
In cells, degrading DNA and RNA by various nucleases is very important. These processes are strictly controlled and regulated to maintain DNA integrity and to mature or recycle various RNAs. NanoRNase (Nrn) is a 3'-exonuclease that specifically degrades nanoRNAs shorter than 5 nucleotides. Several Nrns have been identified and characterized in bacteria, mainly in Firmicutes. Archaea often grow in extreme environments and might be subjected to more damage to DNA/RNA, so DNA repair and recycling of damaged RNA are very important in archaea. There is no report on the identification and characterization of Nrn in archaea. Aeropyrum pernix encodes three potential Nrns: NrnA (Ape1437), NrnB (Ape0124), and an Nrn-like protein Ape2190. Biochemical characterization showed that only Ape0124 could degrade ssDNA and ssRNA from the 3'-end in the presence of Mn2+. Interestingly, unlike bacterial Nrns, Ape0124 prefers ssDNA, including short nanoDNA, and degrades nanoRNA with lower efficiency. The 3'-DNA backbone was found to be required for efficiently hydrolyzing the phosphodiester bonds. In addition, Ape0124 also degrads the 3'-overhang of double-stranded DNA. Interestingly, Ape0124 could hydrolyze pAp into AMP, which is a feature of bacterial NrnA, not NrnB. Our results indicate that Ape0124 is a novel Nrn with a combined substrate profile of bacterial NrnA and NrnB.
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Affiliation(s)
- Yong-Jie Deng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China
| | - Lei Feng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China
| | - Huan Zhou
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, No. 239 Zhangheng Road, Shanghai 201204, China
| | - Xiang Xiao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China; State Key Laboratory of Ocean Engineering, School of Naval Architecture, Ocean and Civil Engineering, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China
| | - Feng-Ping Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China; State Key Laboratory of Ocean Engineering, School of Naval Architecture, Ocean and Civil Engineering, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China
| | - Xi-Peng Liu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China; State Key Laboratory of Ocean Engineering, School of Naval Architecture, Ocean and Civil Engineering, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China.
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29
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Casinhas J, Matos RG, Haddad N, Arraiano CM. Biochemical characterization of Campylobacter jejuni PNPase, an exoribonuclease important for bacterial pathogenicity. Biochimie 2018; 147:70-79. [PMID: 29339148 DOI: 10.1016/j.biochi.2018.01.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 01/11/2018] [Indexed: 10/18/2022]
Abstract
Bacteria need to promptly respond to environmental changes. Ribonucleases (RNases) are key factors in the adaptation to new environments by enabling a rapid adjustment in RNA levels. The exoribonuclease polynucleotide phosphorylase (PNPase) is essential for low-temperature cell survival, affects the synthesis of proteins involved in virulence and has an important role in swimming, cell adhesion/invasion ability, and chick colonization in C. jejuni. However, the mechanism of action of this ribonuclease is not yet known. In this work we have characterized the biochemical activity of C. jejuni PNPase. Our results demonstrate that Cj-PNP is a processive 3' to 5' exoribonuclease that degrades single-stranded RNAs. Its activity is regulated according to the temperature and divalent ions. We have also shown that the KH and S1 domains are important for trimerization, RNA binding, and, consequently, for the activity of Cj-PNP. These findings will be helpful to develop new strategies for fighting against C. jejuni and may be extrapolated to other foodborne pathogens.
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Affiliation(s)
- Jorge Casinhas
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Ava da República, 2780-157, Oeiras, Portugal.
| | - Rute G Matos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Ava da República, 2780-157, Oeiras, Portugal.
| | - Nabila Haddad
- SECALIM, INRA, Oniris, Université Bretagne Loire, 44307, Nantes, France.
| | - Cecília M Arraiano
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Ava da República, 2780-157, Oeiras, Portugal.
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30
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Sikorska N, Zuber H, Gobert A, Lange H, Gagliardi D. RNA degradation by the plant RNA exosome involves both phosphorolytic and hydrolytic activities. Nat Commun 2017; 8:2162. [PMID: 29255150 PMCID: PMC5735172 DOI: 10.1038/s41467-017-02066-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 11/03/2017] [Indexed: 12/21/2022] Open
Abstract
The RNA exosome provides eukaryotic cells with an essential 3'-5' exoribonucleolytic activity, which processes or eliminates many classes of RNAs. Its nine-subunit core (Exo9) is structurally related to prokaryotic phosphorolytic exoribonucleases. Yet, yeast and animal Exo9s have lost the primordial phosphorolytic capacity and rely instead on associated hydrolytic ribonucleases for catalytic activity. Here, we demonstrate that Arabidopsis Exo9 has retained a distributive phosphorolytic activity, which contributes to rRNA maturation processes, the hallmark of exosome function. High-density mapping of 3' extremities of rRNA maturation intermediates reveals the intricate interplay between three exoribonucleolytic activities coordinated by the plant exosome. Interestingly, the analysis of RRP41 protein diversity across eukaryotes suggests that Exo9's intrinsic activity operates throughout the green lineage, and possibly in some earlier-branching non-plant eukaryotes. Our results reveal a remarkable evolutionary variation of this essential RNA degradation machine in eukaryotes.
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Affiliation(s)
- Natalia Sikorska
- IBMP, CNRS, University of Strasbourg, 12 rue du général Zimmer, 67000, Strasbourg, France
| | - Hélène Zuber
- IBMP, CNRS, University of Strasbourg, 12 rue du général Zimmer, 67000, Strasbourg, France
| | - Anthony Gobert
- IBMP, CNRS, University of Strasbourg, 12 rue du général Zimmer, 67000, Strasbourg, France
| | - Heike Lange
- IBMP, CNRS, University of Strasbourg, 12 rue du général Zimmer, 67000, Strasbourg, France
| | - Dominique Gagliardi
- IBMP, CNRS, University of Strasbourg, 12 rue du général Zimmer, 67000, Strasbourg, France.
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31
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Raj R, Mitra S, Gopal B. Characterization of Staphylococcus epidermidis Polynucleotide phosphorylase and its interactions with ribonucleases RNase J1 and RNase J2. Biochem Biophys Res Commun 2017; 495:2078-2084. [PMID: 29242153 DOI: 10.1016/j.bbrc.2017.12.056] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 12/10/2017] [Indexed: 11/16/2022]
Abstract
Polynucleotide phosphorylase catalyzes both 3'-5' exoribonuclease and polyadenylation reactions. The crystal structure of Staphylococcus epidermidis PNPase revealed a bound phosphate in the PH2 domain of each protomer coordinated by three adjacent serine residues. Mutational analysis suggests that phosphate coordination by these serine residues is essential to maintain the catalytic center in an active conformation. We note that PNPase forms a complex with RNase J1 and RNase J2 without substantially altering either exo-ribonuclease or polyadenylation activity of this enzyme. This decoupling of catalytic activity from protein-protein interactions suggests that association of these endo- or exo-ribonucleases with PNPase could be more relevant for cellular localization or concerted targeting of structured RNA for recycling.
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Affiliation(s)
- Rishi Raj
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Sharmistha Mitra
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
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32
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Wang X, Wang C, Wu M, Tian T, Cheng T, Zhang X, Zang J. Enolase binds to RnpA in competition with PNPase in Staphylococcus aureus. FEBS Lett 2017; 591:3523-3535. [PMID: 28960276 DOI: 10.1002/1873-3468.12859] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Revised: 09/01/2017] [Accepted: 09/18/2017] [Indexed: 12/13/2022]
Abstract
The RNA degradosome of the pathogen Staphylococcus aureus regulates the metabolism of RNA, the expression of virulence factors, and the formation of biofilms. It is composed of the RNases J1/J2, RNase Y, CshA, PNPase, Enolase, Pfk, and a newly identified component, RnpA. However, the function and new partners of RnpA in RNA degradosome remain unknown. Here, we identified PNPase and Enolase as two novel partners for RnpA. Further studies revealed that Enolase interacts with RnpA in competition with PNPase. Enzymatic assays showed that RnpA increases Enolase activity but has no effect on PNPase. These findings provide more information about the functional relationship between RnpA and RNA degradosome.
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Affiliation(s)
- Xuejing Wang
- Hefei National Laboratory for Physical Sciences at Microscale CAS Center for Excellence in Biomacromolecules, Collaborative Innovation Center of Chemistry for Life Sciences, and School of Life Sciences, University of Science and Technology of China, Hefei, China.,Key Laboratory of Structural Biology, Chinese Academy of Sciences, Hefei, China
| | - Chengliang Wang
- Hefei National Laboratory for Physical Sciences at Microscale CAS Center for Excellence in Biomacromolecules, Collaborative Innovation Center of Chemistry for Life Sciences, and School of Life Sciences, University of Science and Technology of China, Hefei, China.,Key Laboratory of Structural Biology, Chinese Academy of Sciences, Hefei, China
| | - Minghao Wu
- Hefei National Laboratory for Physical Sciences at Microscale CAS Center for Excellence in Biomacromolecules, Collaborative Innovation Center of Chemistry for Life Sciences, and School of Life Sciences, University of Science and Technology of China, Hefei, China.,Key Laboratory of Structural Biology, Chinese Academy of Sciences, Hefei, China
| | - Tian Tian
- Hefei National Laboratory for Physical Sciences at Microscale CAS Center for Excellence in Biomacromolecules, Collaborative Innovation Center of Chemistry for Life Sciences, and School of Life Sciences, University of Science and Technology of China, Hefei, China.,Key Laboratory of Structural Biology, Chinese Academy of Sciences, Hefei, China
| | - Tianyuan Cheng
- Hefei National Laboratory for Physical Sciences at Microscale CAS Center for Excellence in Biomacromolecules, Collaborative Innovation Center of Chemistry for Life Sciences, and School of Life Sciences, University of Science and Technology of China, Hefei, China.,Key Laboratory of Structural Biology, Chinese Academy of Sciences, Hefei, China
| | - Xuan Zhang
- Hefei National Laboratory for Physical Sciences at Microscale CAS Center for Excellence in Biomacromolecules, Collaborative Innovation Center of Chemistry for Life Sciences, and School of Life Sciences, University of Science and Technology of China, Hefei, China.,Key Laboratory of Structural Biology, Chinese Academy of Sciences, Hefei, China
| | - Jianye Zang
- Hefei National Laboratory for Physical Sciences at Microscale CAS Center for Excellence in Biomacromolecules, Collaborative Innovation Center of Chemistry for Life Sciences, and School of Life Sciences, University of Science and Technology of China, Hefei, China.,Key Laboratory of Structural Biology, Chinese Academy of Sciences, Hefei, China
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33
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Stone CM, Butt LE, Bufton JC, Lourenco DC, Gowers DM, Pickford AR, Cox PA, Vincent HA, Callaghan AJ. Inhibition of homologous phosphorolytic ribonucleases by citrate may represent an evolutionarily conserved communicative link between RNA degradation and central metabolism. Nucleic Acids Res 2017; 45:4655-4666. [PMID: 28334892 PMCID: PMC5416783 DOI: 10.1093/nar/gkx114] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 01/17/2017] [Accepted: 02/14/2017] [Indexed: 12/05/2022] Open
Abstract
Ribonucleases play essential roles in all aspects of RNA metabolism, including the coordination of post-transcriptional gene regulation that allows organisms to respond to internal changes and environmental stimuli. However, as inherently destructive enzymes, their activity must be carefully controlled. Recent research exemplifies the repertoire of regulatory strategies employed by ribonucleases. The activity of the phosphorolytic exoribonuclease, polynucleotide phosphorylase (PNPase), has previously been shown to be modulated by the Krebs cycle metabolite citrate in Escherichia coli. Here, we provide evidence for the existence of citrate-mediated inhibition of ribonucleases in all three domains of life. In silico molecular docking studies predict that citrate will bind not only to bacterial PNPases from E. coli and Streptomyces antibioticus, but also PNPase from human mitochondria and the structurally and functionally related archaeal exosome complex from Sulfolobus solfataricus. Critically, we show experimentally that citrate also inhibits the exoribonuclease activity of bacterial, eukaryotic and archaeal PNPase homologues in vitro. Furthermore, bioinformatics data, showing key citrate-binding motifs conserved across a broad range of PNPase homologues, suggests that this regulatory mechanism may be widespread. Overall, our data highlight a communicative link between ribonuclease activity and central metabolism that may have been conserved through the course of evolution.
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Affiliation(s)
- Carlanne M. Stone
- School of Biological Sciences and Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth, PO1 2DY, UK
| | - Louise E. Butt
- School of Biological Sciences and Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth, PO1 2DY, UK
| | - Joshua C. Bufton
- School of Biological Sciences and Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth, PO1 2DY, UK
| | - Daniel C. Lourenco
- School of Biological Sciences and Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth, PO1 2DY, UK
| | - Darren M. Gowers
- School of Biological Sciences and Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth, PO1 2DY, UK
| | - Andrew R. Pickford
- School of Biological Sciences and Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth, PO1 2DY, UK
| | - Paul A. Cox
- School of Pharmacy and Biomedical Sciences and Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth, PO1 2DT, UK
| | - Helen A. Vincent
- School of Biological Sciences and Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth, PO1 2DY, UK
| | - Anastasia J. Callaghan
- School of Biological Sciences and Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth, PO1 2DY, UK
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34
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Carzaniga T, Sbarufatti G, Briani F, Dehò G. Polynucleotide phosphorylase is implicated in homologous recombination and DNA repair in Escherichia coli. BMC Microbiol 2017; 17:81. [PMID: 28376742 PMCID: PMC5379764 DOI: 10.1186/s12866-017-0980-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 03/25/2017] [Indexed: 11/22/2022] Open
Abstract
Background Polynucleotide phosphorylase (PNPase, encoded by pnp) is generally thought of as an enzyme dedicated to RNA metabolism. The pleiotropic effects of PNPase deficiency is imputed to altered processing and turnover of mRNAs and small RNAs, which in turn leads to aberrant gene expression. However, it has long since been known that this enzyme may also catalyze template-independent polymerization of dNDPs into ssDNA and the reverse phosphorolytic reaction. Recently, PNPase has been implicated in DNA recombination, repair, mutagenesis and resistance to genotoxic agents in diverse bacterial species, raising the possibility that PNPase may directly, rather than through control of gene expression, participate in these processes. Results In this work we present evidence that in Escherichia coli PNPase enhances both homologous recombination upon P1 transduction and error prone DNA repair of double strand breaks induced by zeocin, a radiomimetic agent. Homologous recombination does not require PNPase phosphorolytic activity and is modulated by its RNA binding domains whereas error prone DNA repair of zeocin-induced DNA damage is dependent on PNPase catalytic activity and cannot be suppressed by overexpression of RNase II, the other major enzyme (encoded by rnb) implicated in exonucleolytic RNA degradation. Moreover, E. coli pnp mutants are more sensitive than the wild type to zeocin. This phenotype depends on PNPase phosphorolytic activity and is suppressed by rnb, thus suggesting that zeocin detoxification may largely depend on RNA turnover. Conclusions Our data suggest that PNPase may participate both directly and indirectly through regulation of gene expression to several aspects of DNA metabolism such as recombination, DNA repair and resistance to genotoxic agents.
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Affiliation(s)
- Thomas Carzaniga
- Dipartimento di Bioscienze, Università degli Studi di Milano, via Celoria 26, Milan, 20133, Italy.,Present address: Dipartimento di Biotecnologie mediche e medicina traslazionale, Università degli Studi di Milano, via F.lli Cervi 93, Segrate, MI, 20090, Italy
| | - Giulia Sbarufatti
- Dipartimento di Bioscienze, Università degli Studi di Milano, via Celoria 26, Milan, 20133, Italy.,Present address: Eurofins BioPharma Product Testing Italy, Eurofins Biolab srl, via Bruno Buozzi, 2, Vimodrone, 20090, Italy
| | - Federica Briani
- Dipartimento di Bioscienze, Università degli Studi di Milano, via Celoria 26, Milan, 20133, Italy
| | - Gianni Dehò
- Dipartimento di Bioscienze, Università degli Studi di Milano, via Celoria 26, Milan, 20133, Italy.
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35
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Huen J, Lin CL, Golzarroshan B, Yi WL, Yang WZ, Yuan HS. Structural Insights into a Unique Dimeric DEAD-Box Helicase CshA that Promotes RNA Decay. Structure 2017; 25:469-481. [PMID: 28238534 DOI: 10.1016/j.str.2017.01.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 01/05/2017] [Accepted: 01/29/2017] [Indexed: 11/28/2022]
Abstract
CshA is a dimeric DEAD-box helicase that cooperates with ribonucleases for mRNA turnover. The molecular mechanism for how a dimeric DEAD-box helicase aids in RNA decay remains unknown. Here, we report the crystal structure and small-angle X-ray scattering solution structure of the CshA from Geobacillus stearothermophilus. In contrast to typical monomeric DEAD-box helicases, CshA is exclusively a dimeric protein with the RecA-like domains of each protomer forming a V-shaped structure. We show that the C-terminal domains protruding outward from the tip of the V-shaped structure is critical for mediating strong RNA binding and is crucial for efficient RNA-dependent ATP hydrolysis. We also show that RNA remains bound with CshA during ATP hydrolysis cycles and thus bulk RNAs could be unwound and degraded in a processive manner through cooperation between exoribonucleases and CshA. A dimeric helicase is hence preserved in RNA-degrading machinery for efficient RNA turnover in prokaryotes and eukaryotes.
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Affiliation(s)
- Jennifer Huen
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 11529, ROC
| | - Chia-Liang Lin
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 11529, ROC
| | - Bagher Golzarroshan
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 11529, ROC; Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan 11529, ROC; Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan 30013, ROC
| | - Wan-Li Yi
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 11529, ROC
| | - Wei-Zen Yang
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 11529, ROC
| | - Hanna S Yuan
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 11529, ROC; Graduate Institute of Biochemistry and Molecular Biology, National Taiwan University, Taipei, Taiwan 10048, ROC.
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36
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Puentes B, Balado M, Bermúdez-Crespo J, Osorio CR, Lemos ML. A proteomic analysis of the iron response of Photobacterium damselae subsp. damselae reveals metabolic adaptations to iron levels changes and novel potential virulence factors. Vet Microbiol 2017; 201:257-264. [PMID: 28284618 DOI: 10.1016/j.vetmic.2017.01.040] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 12/13/2016] [Accepted: 01/23/2017] [Indexed: 11/29/2022]
Abstract
Photobacterium damselae subsp. damselae (Pdd) is a marine bacterium that can infect numerous species of marine fish as well as other species including humans. Low iron availability is one of the signs that bacterial pathogens can detect in order to begin colonizing their host, and the reduction of iron levels is a nonspecific host defense strategy that prevents bacterial proliferation. In this work a proteomic approach was used to study the gene expression adaptations of a Pdd strain in response to iron availability. A comparative analysis of induced proteins in both high- and low-iron conditions showed profound cellular metabolic adaptations that result, for instance, in amino acid requirement. It also provided important information about the changes that occur in the energetic metabolism induced by the surrounding iron levels, allowing for the identification of novel potential virulence factors. Among others, genes involved in the synthesis and transport of a vibrioferrin-like siderophore were identified for the first time. In addition to plasmid pPHDD1-encoded Dly and HlyA hemolysins, a pPHDD1-borne operon, which may encode a transferrin receptor, was also found. This operon identification suggests that this virulence plasmid could encode so-far unknown additional virulence factors other than hemolysins.
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Affiliation(s)
- Beatriz Puentes
- Department of Microbiology and Parasitology, Institute of Aquaculture, Universidade de Santiago de Compostela, Campus Sur, Santiago de Compostela 15782, Spain
| | - Miguel Balado
- Department of Microbiology and Parasitology, Institute of Aquaculture, Universidade de Santiago de Compostela, Campus Sur, Santiago de Compostela 15782, Spain
| | - José Bermúdez-Crespo
- Department of Microbiology and Parasitology, Institute of Aquaculture, Universidade de Santiago de Compostela, Campus Sur, Santiago de Compostela 15782, Spain
| | - Carlos R Osorio
- Department of Microbiology and Parasitology, Institute of Aquaculture, Universidade de Santiago de Compostela, Campus Sur, Santiago de Compostela 15782, Spain
| | - Manuel L Lemos
- Department of Microbiology and Parasitology, Institute of Aquaculture, Universidade de Santiago de Compostela, Campus Sur, Santiago de Compostela 15782, Spain.
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37
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CryoEM structure of yeast cytoplasmic exosome complex. Cell Res 2016; 26:822-37. [PMID: 27174052 DOI: 10.1038/cr.2016.56] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 01/26/2016] [Accepted: 03/07/2016] [Indexed: 01/25/2023] Open
Abstract
The eukaryotic multi-subunit RNA exosome complex plays crucial roles in 3'-to-5' RNA processing and decay. Rrp6 and Ski7 are the major cofactors for the nuclear and cytoplasmic exosomes, respectively. In the cytoplasm, Ski7 helps the exosome to target mRNAs for degradation and turnover via a through-core pathway. However, the interaction between Ski7 and the exosome complex has remained unclear. The transaction of RNA substrates within the exosome is also elusive. In this work, we used single-particle cryo-electron microscopy to solve the structures of the Ski7-exosome complex in RNA-free and RNA-bound forms at resolutions of 4.2 Å and 5.8 Å, respectively. These structures reveal that the N-terminal domain of Ski7 adopts a structural arrangement and interacts with the exosome in a similar fashion to the C-terminal domain of nuclear Rrp6. Further structural analysis of exosomes with RNA substrates harboring 3' overhangs of different length suggests a switch mechanism of RNA-induced exosome activation in the through-core pathway of RNA processing.
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38
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Audin MJC, Wurm JP, Cvetkovic MA, Sprangers R. The oligomeric architecture of the archaeal exosome is important for processive and efficient RNA degradation. Nucleic Acids Res 2016; 44:2962-73. [PMID: 26837575 PMCID: PMC4824110 DOI: 10.1093/nar/gkw062] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 01/25/2016] [Indexed: 11/30/2022] Open
Abstract
The exosome plays an important role in RNA degradation and processing. In archaea, three Rrp41:Rrp42 heterodimers assemble into a barrel like structure that contains a narrow RNA entrance pore and a lumen that contains three active sites. Here, we demonstrate that this quaternary structure of the exosome is important for efficient RNA degradation. We find that the entrance pore of the barrel is required for nM substrate affinity. This strong interaction is crucial for processive substrate degradation and prevents premature release of the RNA from the enzyme. Using methyl TROSY NMR techniques, we establish that the 3′ end of the substrate remains highly flexible inside the lumen. As a result, the RNA jumps between the three active sites that all equally participate in substrate degradation. The RNA jumping rate is, however, much faster than the cleavage rate, indicating that not all active site:substrate encounters result in catalysis. Enzymatic turnover therefore benefits from the confinement of the active sites and substrate in the lumen, which ensures that the RNA is at all times bound to one of the active sites. The evolution of the exosome into a hexameric complex and the optimization of its catalytic efficiency were thus likely co-occurring events.
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Affiliation(s)
- Maxime J C Audin
- Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany
| | - Jan Philip Wurm
- Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany
| | - Milos A Cvetkovic
- Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany
| | - Remco Sprangers
- Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany
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39
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Briani F, Carzaniga T, Dehò G. Regulation and functions of bacterial PNPase. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 7:241-58. [PMID: 26750178 DOI: 10.1002/wrna.1328] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 11/23/2015] [Accepted: 11/23/2015] [Indexed: 01/29/2023]
Abstract
Polynucleotide phosphorylase (PNPase) is an exoribonuclease that catalyzes the processive phosphorolytic degradation of RNA from the 3'-end. The enzyme catalyzes also the reverse reaction of polymerization of nucleoside diphosphates that has been implicated in the generation of heteropolymeric tails at the RNA 3'-end. The enzyme is widely conserved and plays a major role in RNA decay in both Gram-negative and Gram-positive bacteria. Moreover, it participates in maturation and quality control of stable RNA. PNPase autoregulates its own expression at post-transcriptional level through a complex mechanism that involves the endoribonuclease RNase III and translation control. The activity of PNPase is modulated in an intricate and still unclear manner by interactions with small molecules and recruitment in different multiprotein complexes. Not surprisingly, given the wide spectrum of PNPase substrates, PNPase-defective mutations in different bacterial species have pleiotropic effects and perturb the execution of genetic programs involving drastic changes in global gene expression such as biofilm formation, growth at suboptimal temperatures, and virulence.
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Affiliation(s)
- Federica Briani
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy
| | - Thomas Carzaniga
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy
| | - Gianni Dehò
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy
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40
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Tseng YT, Chiou NT, Gogiraju R, Lin-Chao S. The Protein Interaction of RNA Helicase B (RhlB) and Polynucleotide Phosphorylase (PNPase) Contributes to the Homeostatic Control of Cysteine in Escherichia coli. J Biol Chem 2015; 290:29953-63. [PMID: 26494621 PMCID: PMC4705995 DOI: 10.1074/jbc.m115.691881] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Indexed: 11/12/2022] Open
Abstract
PNPase, one of the major enzymes with 3′ to 5′ single-stranded RNA degradation and processing activities, can interact with the RNA helicase RhlB independently of RNA degradosome formation in Escherichia coli. Here, we report that loss of interaction between RhlB and PNPase impacts cysteine homeostasis in E. coli. By random mutagenesis, we identified a mutant RhlBP238L that loses 75% of its ability to interact with PNPase but retains normal interaction with RNase E and RNA, in addition to exhibiting normal helicase activity. Applying microarray analyses to an E. coli strain with impaired RNA degradosome formation, we investigated the biological consequences of a weakened interaction between RhlB and PNPase. We found significant increases in 11 of 14 genes involved in cysteine biosynthesis. Subsequent Northern blot analyses showed that the up-regulated transcripts were the result of stabilization of the cysB transcript encoding a transcriptional activator for the cys operons. Furthermore, Northern blots of PNPase or RhlB mutants showed that RhlB-PNPase plays both a catalytic and structural role in regulating cysB degradation. Cells expressing the RhlBP238L mutant exhibited an increase in intracellular cysteine and an enhanced anti-oxidative response. Collectively, this study suggests a mechanism by which bacteria use the PNPase-RhlB exosome-like complex to combat oxidative stress by modulating cysB mRNA degradation.
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Affiliation(s)
- Yi-Ting Tseng
- From the Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan, the Institute of Molecular Medicine, College of Medicine, National Taiwan University, Taipei 10617, Taiwan
| | - Ni-Ting Chiou
- From the Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan, the Institute of Biochemistry & Molecular Biology, National Yang-Ming University, Taipei 11221, Taiwan
| | | | - Sue Lin-Chao
- From the Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan,
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41
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Evguenieva-Hackenberg E, Hou L, Glaeser S, Klug G. Structure and function of the archaeal exosome. WILEY INTERDISCIPLINARY REVIEWS-RNA 2014; 5:623-35. [DOI: 10.1002/wrna.1234] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Revised: 02/28/2014] [Accepted: 03/06/2014] [Indexed: 11/10/2022]
Affiliation(s)
| | - Linlin Hou
- Institute of Microbiology and Molecular Biology; University of Giessen; Giessen Germany
| | - Stefanie Glaeser
- Institute of Applied Microbiology; University of Giessen; Giessen Germany
| | - Gabriele Klug
- Institute of Microbiology and Molecular Biology; University of Giessen; Giessen Germany
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42
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Zhang JY, Deng XM, Li FP, Wang L, Huang QY, Zhang CC, Chen WL. RNase E forms a complex with polynucleotide phosphorylase in cyanobacteria via a cyanobacterial-specific nonapeptide in the noncatalytic region. RNA (NEW YORK, N.Y.) 2014; 20:568-579. [PMID: 24563514 PMCID: PMC3964918 DOI: 10.1261/rna.043513.113] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 01/23/2014] [Indexed: 05/29/2023]
Abstract
RNase E, a central component involved in bacterial RNA metabolism, usually has a highly conserved N-terminal catalytic domain but an extremely divergent C-terminal domain. While the C-terminal domain of RNase E in Escherichia coli recruits other components to form an RNA degradation complex, it is unknown if a similar function can be found for RNase E in other organisms due to the divergent feature of this domain. Here, we provide evidence showing that RNase E forms a complex with another essential ribonuclease-the polynucleotide phosphorylase (PNPase)-in cyanobacteria, a group of ecologically important and phylogenetically ancient organisms. Sequence alignment for all cyanobacterial RNase E proteins revealed several conserved and variable subregions in their noncatalytic domains. One such subregion, an extremely conserved nonapeptide (RRRRRRSSA) located near the very end of RNase E, serves as the PNPase recognition site in both the filamentous cyanobacterium Anabaena PCC7120 and the unicellular cyanobacterium Synechocystis PCC6803. These results indicate that RNase E and PNPase form a ribonuclease complex via a common mechanism in cyanobacteria. The PNPase-recognition motif in cyanobacterial RNase E is distinct from those previously identified in Proteobacteria, implying a mechanism of coevolution for PNPase and RNase E in different organisms.
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Affiliation(s)
- Ju-Yuan Zhang
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xue-Mei Deng
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Feng-Pu Li
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Li Wang
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Qiao-Yun Huang
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Cheng-Cai Zhang
- Aix-Marseille Université and CNRS, Laboratoire de Chimie Bactérienne–UMR7283, 13402 Marseille cedex 20, France
| | - Wen-Li Chen
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
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43
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Januszyk K, Lima CD. The eukaryotic RNA exosome. Curr Opin Struct Biol 2014; 24:132-40. [PMID: 24525139 DOI: 10.1016/j.sbi.2014.01.011] [Citation(s) in RCA: 124] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Revised: 01/15/2014] [Accepted: 01/16/2014] [Indexed: 12/24/2022]
Abstract
The eukaryotic RNA exosome is an essential multi-subunit ribonuclease complex that contributes to the degradation or processing of nearly every class of RNA in both the nucleus and cytoplasm. Its nine-subunit core shares structural similarity to phosphorolytic exoribonucleases such as bacterial PNPase. PNPase and the RNA exosome core feature a central channel that can accommodate single stranded RNA although unlike PNPase, the RNA exosome core is devoid of ribonuclease activity. Instead, the core associates with Rrp44, an endoribonuclease and processive 3'→5' exoribonuclease, and Rrp6, a distributive 3'→5' exoribonuclease. Recent biochemical and structural studies suggest that the exosome core is essential because it coordinates Rrp44 and Rrp6 recruitment, RNA can pass through the central channel, and the association with the core modulates Rrp44 and Rrp6 activities.
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Affiliation(s)
- Kurt Januszyk
- Structural Biology Program, Sloan-Kettering Institute, 1275 York Avenue, NY, USA
| | - Christopher D Lima
- Structural Biology Program, Sloan-Kettering Institute, 1275 York Avenue, NY, USA; Howard Hughes Medical Institute, Structural Biology Program, Sloan-Kettering Institute, 1275 York Avenue, NY, USA.
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44
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Numata S, Nagata M, Mao H, Sekimizu K, Kaito C. CvfA protein and polynucleotide phosphorylase act in an opposing manner to regulate Staphylococcus aureus virulence. J Biol Chem 2014; 289:8420-31. [PMID: 24492613 DOI: 10.1074/jbc.m114.554329] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We previously identified CvfA (SA1129) as a Staphylococcus aureus virulence factor using a silkworm infection model. S. aureus cvfA-deleted mutants exhibit decreased expression of the agr locus encoding a positive regulator of hemolysin genes and decreased hemolysin production. CvfA protein hydrolyzes a 2',3'-cyclic phosphodiester bond at the RNA 3' terminus, producing RNA with a 3'-phosphate (3'-phosphorylated RNA, RNA with a 3'-phosphate). Here, we report that the cvfA-deleted mutant phenotype (decreased agr expression and hemolysin production) was suppressed by disrupting pnpA-encoding polynucleotide phosphorylase (PNPase) with 3'- to 5'-exonuclease activity. The suppression was blocked by introducing a pnpA-encoding PNPase with exonuclease activity but not by a pnpA-encoding mutant PNPase without exonuclease activity. Therefore, loss of PNPase exonuclease activity suppressed the cvfA-deleted mutant phenotype. Purified PNPase efficiently degraded RNA with 2',3'-cyclic phosphate at the 3' terminus (2',3'-cyclic RNA), but it inefficiently degraded 3'-phosphorylated RNA. These findings indicate that 3'-phosphorylated RNA production from 2',3'-cyclic RNA by CvfA prevents RNA degradation by PNPase and contributes to the expression of agr and hemolysin genes. We speculate that in the cvfA-deleted mutant, 2',3'-cyclic RNA is not converted to the 3'-phosphorylated form and is efficiently degraded by PNPase, resulting in the loss of RNA essential for expressing agr and hemolysin genes, whereas in the cvfA/pnpA double-disrupted mutant, 2',3'-cyclic RNA is not degraded by PNPase, leading to hemolysin production. These findings suggest that CvfA and PNPase competitively regulate RNA degradation essential for S. aureus virulence.
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Affiliation(s)
- Shunsuke Numata
- From the Laboratory of Microbiology, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 3-1, 7-chome, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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45
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Li Z, Malla S, Shin B, Li JM. Battle against RNA oxidation: molecular mechanisms for reducing oxidized RNA to protect cells. WILEY INTERDISCIPLINARY REVIEWS-RNA 2013; 5:335-46. [PMID: 24375979 DOI: 10.1002/wrna.1214] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Revised: 09/17/2013] [Accepted: 09/18/2013] [Indexed: 01/08/2023]
Abstract
Oxidation is probably the most common type of damage that occurs in cellular RNA. Oxidized RNA may be dysfunctional and is implicated in the pathogenesis of age-related human diseases. Cellular mechanisms controlling oxidized RNA have begun to be revealed. Currently, a number of ribonucleases and RNA-binding proteins have been shown to reduce oxidized RNA and to protect cells under oxidative stress. Although information about how these factors work is still very limited, we suggest several mechanisms that can be used to minimize oxidized RNA in various organisms.
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Affiliation(s)
- Zhongwei Li
- Department of Biomedical Science, Florida Atlantic University, Boca Raton, FL, USA
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46
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Carzaniga T, Mazzantini E, Nardini M, Regonesi ME, Greco C, Briani F, De Gioia L, Dehò G, Tortora P. A conserved loop in polynucleotide phosphorylase (PNPase) essential for both RNA and ADP/phosphate binding. Biochimie 2013; 97:49-59. [PMID: 24075876 DOI: 10.1016/j.biochi.2013.09.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Accepted: 09/16/2013] [Indexed: 11/27/2022]
Abstract
Polynucleotide phosphorylase (PNPase) reversibly catalyzes RNA phosphorolysis and polymerization of nucleoside diphosphates. Its homotrimeric structure forms a central channel where RNA is accommodated. Each protomer core is formed by two paralogous RNase PH domains: PNPase1, whose function is largely unknown, hosts a conserved FFRR loop interacting with RNA, whereas PNPase2 bears the putative catalytic site, ∼20 Å away from the FFRR loop. To date, little is known regarding PNPase catalytic mechanism. We analyzed the kinetic properties of two Escherichia coli PNPase mutants in the FFRR loop (R79A and R80A), which exhibited a dramatic increase in Km for ADP/Pi binding, but not for poly(A), suggesting that the two residues may be essential for binding ADP and Pi. However, both mutants were severely impaired in shifting RNA electrophoretic mobility, implying that the two arginines contribute also to RNA binding. Additional interactions between RNA and other PNPase domains (such as KH and S1) may preserve the enzymatic activity in R79A and R80A mutants. Inspection of enzyme structure showed that PNPase has evolved a long-range acting hydrogen bonding network that connects the FFRR loop with the catalytic site via the F380 residue. This hypothesis was supported by mutation analysis. Phylogenetic analysis of PNPase domains and RNase PH suggests that such network is a unique feature of PNPase1 domain, which coevolved with the paralogous PNPase2 domain.
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Affiliation(s)
- Thomas Carzaniga
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan 20133, Italy.
| | - Elisa Mazzantini
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano-Bicocca, Milan 20126, Italy.
| | - Marco Nardini
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan 20133, Italy.
| | - Maria Elena Regonesi
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano-Bicocca, Milan 20126, Italy.
| | - Claudio Greco
- Dipartimento di Scienze dell'ambiente e del territorio e di Scienze della terra, Università degli Studi di Milano-Bicocca, Milan 20126, Italy.
| | - Federica Briani
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan 20133, Italy.
| | - Luca De Gioia
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano-Bicocca, Milan 20126, Italy.
| | - Gianni Dehò
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan 20133, Italy.
| | - Paolo Tortora
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano-Bicocca, Milan 20126, Italy.
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47
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Unciuleac MC, Shuman S. Discrimination of RNA from DNA by polynucleotide phosphorylase. Biochemistry 2013; 52:6702-11. [PMID: 23980617 DOI: 10.1021/bi401041v] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Polynucleotide phosphorylase (PNPase) plays synthetic and degradative roles in bacterial RNA metabolism; it is also thought to participate in bacterial DNA transactions. Here we used chimeric polynucleotides, composed of alternating RNA and DNA tracts, to analyze whether and how Mycobacterium smegmatis PNPase discriminates RNA from DNA during the 3'-phosphorolysis reaction. We find that a kinetic block to 3'-phosphorolysis of a DNA tract within an RNA polynucleotide is exerted when resection has progressed to the point that a 3'-monoribonucleotide flanks the impeding DNA segment. The position of the pause one nucleotide before the first deoxynucleotide encountered is independent of DNA tract length. However, the duration of the pause is affected by DNA tract length, being transient for a single deoxynucleotide and durable when two or more consecutive deoxynucleotides are encountered. Substituting manganese for magnesium as the metal cofactor allows PNPase to "nibble" into the DNA tract. A 3'-phosphate group prevents RNA phosphorolysis when the metal cofactor is magnesium. With manganese, PNPase can resect an RNA 3'-phosphate end, albeit 80-fold slower than a 3'-OH. We discuss the findings in light of the available structures of PNPase and the archaeal exosome·RNA·phosphate complex and propose a model for catalysis whereby the metal cofactor interacts with the scissile phosphodiester and the penultimate ribose.
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48
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Hardwick SW, Gubbey T, Hug I, Jenal U, Luisi BF. Crystal structure of Caulobacter crescentus polynucleotide phosphorylase reveals a mechanism of RNA substrate channelling and RNA degradosome assembly. Open Biol 2013; 2:120028. [PMID: 22724061 PMCID: PMC3376730 DOI: 10.1098/rsob.120028] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2012] [Accepted: 03/12/2012] [Indexed: 11/20/2022] Open
Abstract
Polynucleotide phosphorylase (PNPase) is an exoribonuclease that cleaves single-stranded RNA substrates with 3′–5′ directionality and processive behaviour. Its ring-like, trimeric architecture creates a central channel where phosphorolytic active sites reside. One face of the ring is decorated with RNA-binding K-homology (KH) and S1 domains, but exactly how these domains help to direct the 3′ end of single-stranded RNA substrates towards the active sites is an unsolved puzzle. Insight into this process is provided by our crystal structures of RNA-bound and apo Caulobacter crescentus PNPase. In the RNA-free form, the S1 domains adopt a ‘splayed’ conformation that may facilitate capture of RNA substrates. In the RNA-bound structure, the three KH domains collectively close upon the RNA and direct the 3′ end towards a constricted aperture at the entrance of the central channel. The KH domains make non-equivalent interactions with the RNA, and there is a marked asymmetry within the catalytic core of the enzyme. On the basis of these data, we propose that structural non-equivalence, induced upon RNA binding, helps to channel substrate to the active sites through mechanical ratcheting. Structural and biochemical analyses also reveal the basis for PNPase association with RNase E in the multi-enzyme RNA degradosome assembly of the α-proteobacteria.
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Affiliation(s)
- Steven W Hardwick
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK
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Unciuleac MC, Shuman S. Distinctive effects of domain deletions on the manganese-dependent DNA polymerase and DNA phosphorylase activities of Mycobacterium smegmatis polynucleotide phosphorylase. Biochemistry 2013; 52:2967-81. [PMID: 23560592 DOI: 10.1021/bi400281w] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Polynucleotide phosphorylase (PNPase) plays synthetic and degradative roles in bacterial RNA metabolism; it is also suggested to participate in bacterial DNA transactions. Here we characterize and compare the RNA and DNA modifying activities of Mycobacterium smegmatis PNPase. The full-length (763-aa) M. smegmatis PNPase is a homotrimeric enzyme with Mg(2+)•PO(4)-dependent RNA 3'-phosphorylase and Mg(2+)•ADP-dependent RNA polymerase activities. We find that the enzyme is also a Mn(2+)•dADP-dependent DNA polymerase and a Mn(2+)•PO(4)-dependent DNA 3'-phosphorylase. The Mn(2+)•DNA and Mg(2+)•RNA end modifying activities of mycobacterial PNPase are coordinately ablated by mutating the putative manganese ligand Asp526, signifying that both metals likely bind to the same site on PNPase. Deletions of the C-terminal S1 and KH domains of mycobacterial PNPase exert opposite effects on the RNA and DNA modifying activities. Subtracting the S1 domain diminishes RNA phosphorylase and polymerase activity; simultaneous deletion of the S1 and KH domains further cripples the enzyme with respect to RNA substrates. By contrast, the S1 and KH domain deletions enhance the DNA polymerase and phosphorylase activity of mycobacterial PNPase. We observe two distinct modes of nucleic acid binding by mycobacterial PNPase: (i) metal-independent RNA-specific binding via the S1 domain, and (ii) metal-dependent binding to RNA or DNA that is optimal when the S1 domain is deleted. These findings add a new dimension to our understanding of PNPase specificity, whereby the C-terminal modules serve a dual purpose: (i) to help capture an RNA polynucleotide substrate for processive 3' end additions or resections, and (ii) to provide a specificity filter that selects against a DNA polynucleotide substrate.
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Intracellular ribonucleases involved in transcript processing and decay: precision tools for RNA. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2013; 1829:491-513. [PMID: 23545199 DOI: 10.1016/j.bbagrm.2013.03.009] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Revised: 03/19/2013] [Accepted: 03/22/2013] [Indexed: 12/15/2022]
Abstract
In order to adapt to changing environmental conditions and regulate intracellular events such as division, cells are constantly producing new RNAs while discarding old or defective transcripts. These functions require the coordination of numerous ribonucleases that precisely cleave and trim newly made transcripts to produce functional molecules, and rapidly destroy unnecessary cellular RNAs. In recent years our knowledge of the nature, functions and structures of these enzymes in bacteria, archaea and eukaryotes has dramatically expanded. We present here a synthetic overview of the recent development in this dynamic area which has seen the identification of many new endoribonucleases and exoribonucleases. Moreover, the increasing pace at which the structures of these enzymes, or of their catalytic domains, have been solved has provided atomic level detail into their mechanisms of action. Based on sequence conservation and structural data, these proteins have been grouped into families, some of which contain only ribonuclease members, others including a variety of nucleolytic enzymes that act upon DNA and/or RNA. At the other extreme some ribonucleases belong to families of proteins involved in a wide variety of enzymatic reactions. Functional characterization of these fascinating enzymes has provided evidence for the extreme diversity of their biological functions that include, for example, removal of poly(A) tails (deadenylation) or poly(U) tails from eukaryotic RNAs, processing of tRNA and mRNA 3' ends, maturation of rRNAs and destruction of unnecessary mRNAs. This article is part of a Special Issue entitled: RNA Decay mechanisms.
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