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Yeter-Alat H, Belgareh-Touzé N, Le Saux A, Huvelle E, Mokdadi M, Banroques J, Tanner NK. The RNA Helicase Ded1 from Yeast Is Associated with the Signal Recognition Particle and Is Regulated by SRP21. Molecules 2024; 29:2944. [PMID: 38931009 PMCID: PMC11206880 DOI: 10.3390/molecules29122944] [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: 05/22/2024] [Revised: 06/12/2024] [Accepted: 06/18/2024] [Indexed: 06/28/2024] Open
Abstract
The DEAD-box RNA helicase Ded1 is an essential yeast protein involved in translation initiation that belongs to the DDX3 subfamily. The purified Ded1 protein is an ATP-dependent RNA-binding protein and an RNA-dependent ATPase, but it was previously found to lack substrate specificity and enzymatic regulation. Here we demonstrate through yeast genetics, yeast extract pull-down experiments, in situ localization, and in vitro biochemical approaches that Ded1 is associated with, and regulated by, the signal recognition particle (SRP), which is a universally conserved ribonucleoprotein complex required for the co-translational translocation of polypeptides into the endoplasmic reticulum lumen and membrane. Ded1 is physically associated with SRP components in vivo and in vitro. Ded1 is genetically linked with SRP proteins. Finally, the enzymatic activity of Ded1 is inhibited by SRP21 in the presence of SCR1 RNA. We propose a model where Ded1 actively participates in the translocation of proteins during translation. Our results provide a new understanding of the role of Ded1 during translation.
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Affiliation(s)
- Hilal Yeter-Alat
- Expression Génétique Microbienne, UMR8261 CNRS, Université de Paris, 13 rue Pierre et Marie Curie, 75005 Paris, France; (H.Y.-A.); (A.L.S.); (E.H.); (M.M.); (J.B.)
- Expression Génétique Microbienne, Institut de Biologie Physico-Chimique, Paris Sciences et Lettres University, 75005 Paris, France
| | - Naïma Belgareh-Touzé
- Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, UMR8226 CNRS, Sorbonne Université, 13 rue Pierre et Marie Curie, 75005 Paris, France;
| | - Agnès Le Saux
- Expression Génétique Microbienne, UMR8261 CNRS, Université de Paris, 13 rue Pierre et Marie Curie, 75005 Paris, France; (H.Y.-A.); (A.L.S.); (E.H.); (M.M.); (J.B.)
- Expression Génétique Microbienne, Institut de Biologie Physico-Chimique, Paris Sciences et Lettres University, 75005 Paris, France
| | - Emmeline Huvelle
- Expression Génétique Microbienne, UMR8261 CNRS, Université de Paris, 13 rue Pierre et Marie Curie, 75005 Paris, France; (H.Y.-A.); (A.L.S.); (E.H.); (M.M.); (J.B.)
- Expression Génétique Microbienne, Institut de Biologie Physico-Chimique, Paris Sciences et Lettres University, 75005 Paris, France
| | - Molka Mokdadi
- Expression Génétique Microbienne, UMR8261 CNRS, Université de Paris, 13 rue Pierre et Marie Curie, 75005 Paris, France; (H.Y.-A.); (A.L.S.); (E.H.); (M.M.); (J.B.)
- Expression Génétique Microbienne, Institut de Biologie Physico-Chimique, Paris Sciences et Lettres University, 75005 Paris, France
- Laboratory of Molecular Epidemiology and Experimental Pathology, LR16IPT04, Institut Pasteur de Tunis, Université de Tunis El Manar, Tunis 1002, Tunisia
- Institut National des Sciences Appliquées et Technologies, Université de Carthage, Tunis 1080, Tunisia
| | - Josette Banroques
- Expression Génétique Microbienne, UMR8261 CNRS, Université de Paris, 13 rue Pierre et Marie Curie, 75005 Paris, France; (H.Y.-A.); (A.L.S.); (E.H.); (M.M.); (J.B.)
- Expression Génétique Microbienne, Institut de Biologie Physico-Chimique, Paris Sciences et Lettres University, 75005 Paris, France
| | - N. Kyle Tanner
- Expression Génétique Microbienne, UMR8261 CNRS, Université de Paris, 13 rue Pierre et Marie Curie, 75005 Paris, France; (H.Y.-A.); (A.L.S.); (E.H.); (M.M.); (J.B.)
- Expression Génétique Microbienne, Institut de Biologie Physico-Chimique, Paris Sciences et Lettres University, 75005 Paris, France
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2
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Moni BM, Quaye JA, Gadda G. Mutation of a distal gating residue modulates NADH binding in NADH:Quinone oxidoreductase from Pseudomonas aeruginosa PAO1. J Biol Chem 2023; 299:103044. [PMID: 36803963 PMCID: PMC10033279 DOI: 10.1016/j.jbc.2023.103044] [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: 11/01/2022] [Revised: 02/07/2023] [Accepted: 02/11/2023] [Indexed: 02/19/2023] Open
Abstract
Enzymes require flexible regions to adopt multiple conformations during catalysis. The mobile regions of enzymes include gates that modulate the passage of molecules in and out of the enzyme's active site. The enzyme PA1024 from Pseudomonas aeruginosa PA01 is a recently discovered flavin-dependent NADH:quinone oxidoreductase (NQO, EC 1.6.5.9). Q80 in loop 3 (residues 75-86) of NQO is ∼15 Å away from the flavin and creates a gate that seals the active site through a hydrogen bond with Y261 upon NADH binding. In this study, we mutated Q80 to glycine, leucine, or glutamate to investigate the mechanistic significance of distal residue Q80 in NADH binding in the active site of NQO. The UV-visible absorption spectrum reveals that the mutation of Q80 minimally affects the protein microenvironment surrounding the flavin. The anaerobic reductive half-reaction of the NQO-mutants yields a ≥25-fold increase in the Kd value for NADH compared to the WT enzyme. However, we determined that the kred value was similar in the Q80G, Q80L, and wildtype enzymes and only ∼25% smaller in the Q80E enzyme. Steady-state kinetics with NQO-mutants and NQO-WT at varying concentrations of NADH and 1,4-benzoquinone establish a ≤5-fold decrease in the kcat/KNADH value. Moreover, there is no significant difference in the kcat/KBQ (∼1 × 106 M-1s-1) and kcat (∼24 s-1) values in NQO-mutants and NQO-WT. These results are consistent with the distal residue Q80 being mechanistically essential for NADH binding to NQO with minimal effect on the quinone binding to the enzyme and hydride transfer from NADH to flavin.
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Affiliation(s)
- Bilkis Mehrin Moni
- Department of Chemistry, Georgia State University, Atlanta, Georgia, USA
| | - Joanna A Quaye
- Department of Chemistry, Georgia State University, Atlanta, Georgia, USA
| | - Giovanni Gadda
- Department of Chemistry, Georgia State University, Atlanta, Georgia, USA; Department of Biology, Georgia State University, Atlanta, Georgia, USA; The Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia, USA.
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Dumesic PA, Rosenblad MA, Samuelsson T, Nguyen T, Moresco JJ, Yates JR, Madhani HD. Noncanoncial signal recognition particle RNAs in a major eukaryotic phylum revealed by purification of SRP from the human pathogen Cryptococcus neoformans. Nucleic Acids Res 2015; 43:9017-27. [PMID: 26275773 PMCID: PMC4605306 DOI: 10.1093/nar/gkv819] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2015] [Accepted: 08/01/2015] [Indexed: 12/21/2022] Open
Abstract
Despite conservation of the signal recognition particle (SRP) from bacteria to man, computational approaches have failed to identify SRP components from genomes of many lower eukaryotes, raising the possibility that they have been lost or altered in those lineages. We report purification and analysis of SRP in the human pathogen Cryptococcus neoformans, providing the first description of SRP in basidiomycetous yeast. The C. neoformans SRP RNA displays a predicted structure in which the universally conserved helix 8 contains an unprecedented stem-loop insertion. Guided by this sequence, we computationally identified 152 SRP RNAs throughout the phylum Basidiomycota. This analysis revealed additional helix 8 alterations including single and double stem-loop insertions as well as loop diminutions affecting RNA structural elements that are otherwise conserved from bacteria to man. Strikingly, these SRP RNA features in Basidiomycota are accompanied by phylum-specific alterations in the RNA-binding domain of Srp54, the SRP protein subunit that directly interacts with helix 8. Our findings reveal unexpected fungal SRP diversity and suggest coevolution of the two most conserved SRP features-SRP RNA helix 8 and Srp54-in basidiomycetes. Because members of this phylum include important human and plant pathogens, these noncanonical features provide new targets for antifungal compound development.
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Affiliation(s)
- Phillip A Dumesic
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
| | - Magnus A Rosenblad
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, SE-405 30, Sweden
| | - Tore Samuelsson
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, SE-405 30, Sweden
| | - Tiffany Nguyen
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
| | - James J Moresco
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - John R Yates
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Hiten D Madhani
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
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4
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Abstract
The budding yeast Saccharomyces cerevisiae is a powerful model organism for studying fundamental aspects of eukaryotic cell biology. This Primer article presents a brief historical perspective on the emergence of this organism as a premier experimental system over the course of the past century. An overview of the central features of the S. cerevisiae genome, including the nature of its genetic elements and general organization, is also provided. Some of the most common experimental tools and resources available to yeast geneticists are presented in a way designed to engage and challenge undergraduate and graduate students eager to learn more about the experimental amenability of budding yeast. Finally, a discussion of several major discoveries derived from yeast studies highlights the far-reaching impact that the yeast system has had and will continue to have on our understanding of a variety of cellular processes relevant to all eukaryotes, including humans.
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Leung E, Schneider C, Yan F, Mohi-El-Din H, Kudla G, Tuck A, Wlotzka W, Doronina VA, Bartley R, Watkins NJ, Tollervey D, Brown JD. Integrity of SRP RNA is ensured by La and the nuclear RNA quality control machinery. Nucleic Acids Res 2014; 42:10698-710. [PMID: 25159613 PMCID: PMC4176351 DOI: 10.1093/nar/gku761] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The RNA component of signal recognition particle (SRP) is transcribed by RNA polymerase III, and most steps in SRP biogenesis occur in the nucleolus. Here, we examine processing and quality control of the yeast SRP RNA (scR1). In common with other pol III transcripts, scR1 terminates in a U-tract, and mature scR1 retains a U4–5 sequence at its 3′ end. In cells lacking the exonuclease Rex1, scR1 terminates in a longer U5–6 tail that presumably represents the primary transcript. The 3′ U-tract of scR1 is protected from aberrant processing by the La homologue, Lhp1 and overexpressed Lhp1 apparently competes with both the RNA surveillance system and SRP assembly factors. Unexpectedly, the TRAMP and exosome nuclear RNA surveillance complexes are also implicated in protecting the 3′ end of scR1, which accumulates in the nucleolus of cells lacking the activities of these complexes. Misassembled scR1 has a primary degradation pathway in which Rrp6 acts early, followed by TRAMP-stimulated exonuclease degradation by the exosome. We conclude that the RNA surveillance machinery has key roles in both SRP biogenesis and quality control of the RNA, potentially facilitating the decision between these alternative fates.
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Affiliation(s)
- Eileen Leung
- RNA Biology Group and Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Claudia Schneider
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3JR, UK
| | - Fu Yan
- RNA Biology Group and Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Hatem Mohi-El-Din
- RNA Biology Group and Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Grzegorz Kudla
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3JR, UK
| | - Alex Tuck
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3JR, UK
| | - Wiebke Wlotzka
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3JR, UK
| | - Victoria A Doronina
- RNA Biology Group and Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Ralph Bartley
- RNA Biology Group and Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Nicholas J Watkins
- RNA Biology Group and Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - David Tollervey
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3JR, UK
| | - Jeremy D Brown
- RNA Biology Group and Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
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6
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Abstract
The Signal Recognition Particle (SRP) plays a critical role in the sorting of nascent secretory and membrane proteins. Remarkably, this function has been conserved from bacteria, where SRP delivers proteins to the inner membrane, through to eukaryotes, where SRP is required for targeting of proteins to the endoplasmic reticulum. This review focuses on present understanding of SRP structure and function and the relationship between the two. Furthermore, the similarities and differences in the structure, function and cellular role of SRP in bacteria, chloroplasts, fungi and mammals will be stressed.
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Affiliation(s)
- Martin R Pool
- Faculty of Life Sciences, University of Manchester, Manchester, UK.
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Origins and evolution of cotranslational transport to the ER. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2007; 607:52-60. [PMID: 17977458 DOI: 10.1007/978-0-387-74021-8_4] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
All living organisms possess the ability to translocate proteins across biological membranes. This is a fundamental necessity since proteins function in different locations yet are synthesized in one compartment only, the cytosol. Even though different transport systems exist, the pathway that is dominantly used to translocate secretory and membrane proteins is known as the cotranslational transport pathway. It evolved only once and is in its core conserved throughout all kingdoms of life. The process is characterized by a well understood sequence of events: first, an N-terminal signal sequence of a nascent polypeptide is recognized on the ribosome by the signal recognition particle (SRP), then the SRP-ribosome complex is targeted to the membrane via the SRP receptor. Next, the nascent chain is transferred from SRP to the protein conducting channel, through which it is cotranslationally threaded. All the essential components of the system have been identified. Recent structural and biochemical studies have unveiled some of the intricate regulatory circuitry of the process. These studies also shed light on the accessory components unique to eukaryotes, pointing to early events in eukaryotic evolution.
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8
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Tuteja R. Unraveling the components of protein translocation pathway in human malaria parasite Plasmodium falciparum. Arch Biochem Biophys 2007; 467:249-60. [PMID: 17919451 DOI: 10.1016/j.abb.2007.08.031] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2007] [Revised: 08/20/2007] [Accepted: 08/22/2007] [Indexed: 10/22/2022]
Abstract
The targeting and translocation of proteins is an essentially required and conserved process in all the living organisms. This complex process involves multiple steps and requires a variety of factors before the protein reaches its final destination. The major components of translocation machinery are signal recognition particle (SRP) and secretory (Sec) complex. These are composed of highly conserved components. SRP contains SRP RNA and other polypeptides such as SRP9, SRP14, SRP19 and SRP54. Sec complex is composed of Sec61alphabetagamma, Sec62 and Sec63. In this review using bioinformatics approach we have shown that the P. falciparum genome contains the homologues for all of these and other factors such as SRP receptor, and TRAM (translocation associated membrane protein), which are required for post- and co-translational protein translocation. We have also shown the various steps of translocation in a hypothetical model.
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Affiliation(s)
- Renu Tuteja
- Malaria Group, International Centre for Genetic Engineering and Biotechnology, P.O. Box 10504, Aruna Asaf Ali Marg, New Delhi 110067, India
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9
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Zappulla DC, Cech TR. RNA as a flexible scaffold for proteins: yeast telomerase and beyond. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2007; 71:217-24. [PMID: 17381300 DOI: 10.1101/sqb.2006.71.011] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Yeast telomerase, the enzyme that adds a repeated DNA sequence to the ends of the chromosomes, consists of a 1157- nucleotide RNA (TLC1) plus several protein subunits: the telomerase reverse transcriptase Est2p, the regulatory subunit Est1p, the nonhomologous end-joining heterodimer Ku, and the seven Sm proteins involved in ribonucleoprotein (RNP) maturation. The RNA subunit provides the template for telomeric DNA synthesis. In addition, we have reported evidence that it serves as a flexible scaffold to tether the proteins into the complex. More generally, we consider the possibility that RNPs may be considered in three structural categories: (1) those that have specific structures determined in large part by the RNA, including RNase P, other ribozyme-protein complexes, and the ribosome; (2) those that have specific structures determined in large part by proteins, including many small nuclear RNPs (snRNPs) and small nucleolar RNPs (snoRNPs); and (3) flexible scaffolds, with no specific structure of the RNP as a whole, as exemplified by yeast telomerase. Other candidates for flexible scaffold structures are other telomerases, viral IRES (internal ribosome entry site) elements, tmRNA (transfer-messenger RNA), the SRP (signal recognition particle), and Xist and roX1 RNAs that alter chromatin structure to achieve dosage compensation.
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Affiliation(s)
- D C Zappulla
- Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309, USA
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van Nues RW, Brown JD. Distant segments of Saccharomyces cerevisiae scR1 RNA promote assembly and function of the signal recognition particle. J Mol Biol 2007; 368:677-90. [PMID: 17368481 DOI: 10.1016/j.jmb.2007.02.056] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2007] [Accepted: 02/07/2007] [Indexed: 11/19/2022]
Abstract
The conserved signal recognition particle targets ribosomes synthesizing presecretory proteins to the endoplasmic reticulum membrane. Key to the activity of SRP is its ability to bind the ribosome at distant locations, the signal sequence exit and elongation factor-binding sites. These contacts are made by the S and Alu domains of SRP, respectively. We tested earlier secondary structure predictions of the Saccharomyces cerevisiae SRP RNA, scR1, and provide and test a consensus structure. The structure contains four non-conserved insertions, helices 9-12, into the core SRP RNA fold, and an extended helix 7. Using a series of scR1 mutants lacking part or all of these structural elements, we find that they are important for the RNA in both function and assembly of the RNP. About 20% of the RNA, corresponding to the outer regions of these helices, is dispensable for function. Further, we examined the role of several features within the S-domain section of the core, helix 5, and find that its length and flexibility are important for proper SRP function and become essential in the absence of helix 10, 11 and/or 7 regions. Overall, the genetic data indicate that regions of scR1 distant in both primary sequence and secondary structure have interrelated roles in the function of the complex, and possibly mediate communication between Alu and S domains during targeting.
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Affiliation(s)
- Rob W van Nues
- Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
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11
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Gultyaev AP, Roussis A. Identification of conserved secondary structures and expansion segments in enod40 RNAs reveals new enod40 homologues in plants. Nucleic Acids Res 2007; 35:3144-52. [PMID: 17452360 PMCID: PMC1888808 DOI: 10.1093/nar/gkm173] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2006] [Revised: 02/05/2007] [Accepted: 03/06/2007] [Indexed: 11/22/2022] Open
Abstract
enod40 is a plant gene that participates in the regulation of symbiotic interaction between leguminous plants and bacteria or fungi. Furthermore, it has been suggested to play a general role in non-symbiotic plant development. Although enod40 seems to have multiple functions, being present in many land plants, the molecular mechanisms of its activity are unclear; they may be determined though, by short peptides and/or RNA structures encoded in the enod40 genes. We utilized conserved RNA structures in enod40 sequences to search nucleotide sequence databases and identified a number of new enod40 homologues in plant species that belong to known, but also, to yet unknown enod40-containing plant families. RNA secondary structure predictions and comparative sequence analysis of enod40 RNAs allowed us to determine the most conserved structural features, present in all known enod40 genes. Remarkably, the topology and evolution of one of the conserved structural domains are similar to those of the expansion segments found in structural RNAs such as rRNAs, RNase P and SRP RNAs. Surprisingly, the enod40 RNA structural elements are much more stronger conserved than the encoded peptides. This finding suggests that some general functions of enod40 gene could be determined by the encoded RNA structure, whereas short peptides may be responsible for more diverse functions found only in certain plant families.
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Affiliation(s)
- Alexander P. Gultyaev
- Leiden Institute of Biology, Leiden University, Kaiserstraat 63, 2311 GP Leiden, The Netherlands and Agricultural University of Athens, Department of Agricultural Biology and Biotechnology, Iera Odos 75, 118 55 Votanikos, Athens, Greece
| | - Andreas Roussis
- Leiden Institute of Biology, Leiden University, Kaiserstraat 63, 2311 GP Leiden, The Netherlands and Agricultural University of Athens, Department of Agricultural Biology and Biotechnology, Iera Odos 75, 118 55 Votanikos, Athens, Greece
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12
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Cochrane G, Bates K, Apweiler R, Tateno Y, Mashima J, Kosuge T, Mizrachi IK, Schafer S, Fetchko M. Evidence Standards in Experimental and Inferential INSDC Third Party Annotation Data. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2006; 10:105-13. [PMID: 16901214 DOI: 10.1089/omi.2006.10.105] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The Third Party Annotation (TPA) project collects and presents high-quality annotation of nucleotide sequence. Annotation is submitted by researchers who have not themselves generated novel nucleotide sequence. In its first few years, the resource has proven to be popular with submitters from a range of biological research areas. Central to the project is the requirement for high-quality data, resulting from experimental and inferred analysis discussed in peer-reviewed publications. The data are divided into two tiers: those with experimental evidence and those with inferential evidence. Standards for TPA are detailed and illustrated with the aid of case studies.
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Affiliation(s)
- Guy Cochrane
- EMBL Nucleotide Sequence Database, EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom.
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13
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Andersen ES, Rosenblad MA, Larsen N, Westergaard JC, Burks J, Wower IK, Wower J, Gorodkin J, Samuelsson T, Zwieb C. The tmRDB and SRPDB resources. Nucleic Acids Res 2006; 34:D163-8. [PMID: 16381838 PMCID: PMC1347504 DOI: 10.1093/nar/gkj142] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Maintained at the University of Texas Health Science Center at Tyler, Texas, the tmRNA database (tmRDB) is accessible at the URL http://psyche.uthct.edu/dbs/tmRDB/tmRDB.html with mirror sites located at Auburn University, Auburn, Alabama (http://www.ag.auburn.edu/mirror/tmRDB/) and the Royal Veterinary and Agricultural University, Denmark (http://tmrdb.kvl.dk/). The signal recognition particle database (SRPDB) at http://psyche.uthct.edu/dbs/SRPDB/SRPDB.html is mirrored at http://srpdb.kvl.dk/ and the University of Goteborg (http://bio.lundberg.gu.se/dbs/SRPDB/SRPDB.html). The databases assist in investigations of the tmRNP (a ribonucleoprotein complex which liberates stalled bacterial ribosomes) and the SRP (a particle which recognizes signal sequences and directs secretory proteins to cell membranes). The curated tmRNA and SRP RNA alignments consider base pairs supported by comparative sequence analysis. Also shown are alignments of the tmRNA-associated proteins SmpB, ribosomal protein S1, alanyl-tRNA synthetase and Elongation Factor Tu, as well as the SRP proteins SRP9, SRP14, SRP19, SRP21, SRP54 (Ffh), SRP68, SRP72, cpSRP43, Flhf, SRP receptor (alpha) and SRP receptor (beta). All alignments can be easily examined using a new exploratory browser. The databases provide links to high-resolution structures and serve as depositories for structures obtained by molecular modeling.
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Affiliation(s)
| | - Magnus Alm Rosenblad
- Department of Medical Biochemistry, Goteborg UniversityBox 440, SE-405 30 Goteborg, Sweden
- SWEGENE Bioinformatics, Goteborg UniversityBox 413, SE-405 30 Goteborg, Sweden
| | - Niels Larsen
- Danish Genome InstituteGustav Wieds vej 10 C, DK-8000 Aarhus C, Denmark
| | - Jesper Cairo Westergaard
- Department of Natural Sciences, The Royal Veterinary and Agricultural UniversityThorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
| | - Jody Burks
- Department of Animal Sciences, Auburn UniversityAuburn, AL 36849-5415, USA
| | - Iwona K. Wower
- Department of Animal Sciences, Auburn UniversityAuburn, AL 36849-5415, USA
| | - Jacek Wower
- Department of Animal Sciences, Auburn UniversityAuburn, AL 36849-5415, USA
| | - Jan Gorodkin
- Center for Bioinformatics and Division of Genetics, IBHV, The Royal Veterinary and Agricultural UniversityGroennegaardsvej 3, 1870 Frederiksberg C, Denmark
| | - Tore Samuelsson
- Department of Medical Biochemistry, Goteborg UniversityBox 440, SE-405 30 Goteborg, Sweden
| | - Christian Zwieb
- Department of Molecular Biology, The University of Texas Health Science Center at Tyler11937 US Highway 271, Tyler, TX 75708-3154, USA
- To whom correspondence should be addressed. Tel: +1 903 877 7689; Fax: +1 903 877 5731;
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14
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Pohlschröder M, Hartmann E, Hand NJ, Dilks K, Haddad A. DIVERSITY AND EVOLUTION OF PROTEIN TRANSLOCATION. Annu Rev Microbiol 2005; 59:91-111. [PMID: 16153164 DOI: 10.1146/annurev.micro.59.030804.121353] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cells need to translocate proteins into and across hydrophobic membranes in order to interact with the extracellular environment. Although a subset of proteins are thought to spontaneously insert into lipid bilayers, translocation of most transported proteins requires additional cellular components. Such components catalyze efficient lateral transport into or across cellular membranes in prokaryotes and eukaryotes. These include, among others, the conserved YidC/Oxa1/Alb3 proteins as well as components of the Sec and the Tat pathways. Our current knowledge of the function and distribution of these components and their corresponding pathways in organisms of the three domains of life is reviewed. On the basis of this information, the evolution of protein translocation is discussed.
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Affiliation(s)
- Mechthild Pohlschröder
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
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Zwieb C, van Nues RW, Rosenblad MA, Brown JD, Samuelsson T. A nomenclature for all signal recognition particle RNAs. RNA (NEW YORK, N.Y.) 2005; 11:7-13. [PMID: 15611297 PMCID: PMC1370686 DOI: 10.1261/rna.7203605] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The signal recognition particle (SRP) is a cytosolic ribonucleoprotein complex that guides secretory proteins to biological membranes in all organisms. The SRP RNA is at the center of the structure and function of the SRP. The comparison of the growing number of SRP RNA sequences provides a rich source for gaining valuable insight into the composition, assembly, and phylogeny of the SRP. In order to assist in the continuation of these studies, we propose an SRP RNA nomenclature applicable to the three divisions of life.
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Affiliation(s)
- Christian Zwieb
- Department of Molecular Biology, The University of Texas Health Science Center at Tyler, 11937 US Highway 271, Tyler, TX 75708-3154, USA.
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