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Denks K, Vogt A, Sachelaru I, Petriman NA, Kudva R, Koch HG. The Sec translocon mediated protein transport in prokaryotes and eukaryotes. Mol Membr Biol 2014; 31:58-84. [DOI: 10.3109/09687688.2014.907455] [Citation(s) in RCA: 123] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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Andersen ES. The art of editing RNA structural alignments. Methods Mol Biol 2014; 1097:379-394. [PMID: 24639168 DOI: 10.1007/978-1-62703-709-9_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Manual editing of RNA structural alignments may be considered more art than science, since it still requires an expert biologist to take multiple levels of information into account and be slightly creative when constructing high-quality alignments. Even though the task is rather tedious, it is rewarded by great insight into the evolution of structure and function of your favorite RNA molecule. In this chapter I will review the methods and considerations that go into constructing RNA structural alignments at the secondary and tertiary structure level; introduce software, databases, and algorithms that have proven useful in semiautomating the work process; and suggest future directions towards full automatization.
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Bradshaw N, Walter P. The signal recognition particle (SRP) RNA links conformational changes in the SRP to protein targeting. Mol Biol Cell 2007; 18:2728-34. [PMID: 17507650 PMCID: PMC1924838 DOI: 10.1091/mbc.e07-02-0117] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The RNA component of the signal recognition particle (SRP) is universally required for cotranslational protein targeting. Biochemical studies have shown that SRP RNA participates in the central step of protein targeting by catalyzing the interaction of the SRP with the SRP receptor (SR). SRP RNA also accelerates GTP hydrolysis in the SRP.SR complex once formed. Using a reverse-genetic and biochemical analysis, we identified mutations in the E. coli SRP protein, Ffh, that abrogate the activity of the SRP RNA and cause corresponding targeting defects in vivo. The mutations in Ffh that disrupt SRP RNA activity map to regions that undergo dramatic conformational changes during the targeting reaction, suggesting that the activity of the SRP RNA is linked to the major conformational changes in the signal sequence-binding subunit of the SRP. In this way, the SRP RNA may coordinate the interaction of the SRP and the SR with ribosome recruitment and transfer to the translocon, explaining why the SRP RNA is an indispensable component of the protein targeting machinery.
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Affiliation(s)
- Niels Bradshaw
- Howard Hughes Medical Institute and Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA 94158
| | - Peter Walter
- Howard Hughes Medical Institute and Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA 94158
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Kiryu H, Tabei Y, Kin T, Asai K. Murlet: a practical multiple alignment tool for structural RNA sequences. ACTA ACUST UNITED AC 2007; 23:1588-98. [PMID: 17459961 DOI: 10.1093/bioinformatics/btm146] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
MOTIVATION Structural RNA genes exhibit unique evolutionary patterns that are designed to conserve their secondary structures; these patterns should be taken into account while constructing accurate multiple alignments of RNA genes. The Sankoff algorithm is a natural alignment algorithm that includes the effect of base-pair covariation in the alignment model. However, the extremely high computational cost of the Sankoff algorithm precludes its application to most RNA sequences. RESULTS We propose an efficient algorithm for the multiple alignment of structural RNA sequences. Our algorithm is a variant of the Sankoff algorithm, and it uses an efficient scoring system that reduces the time and space requirements considerably without compromising on the alignment quality. First, our algorithm computes the match probability matrix that measures the alignability of each position pair between sequences as well as the base pairing probability matrix for each sequence. These probabilities are then combined to score the alignment using the Sankoff algorithm. By itself, our algorithm does not predict the consensus secondary structure of the alignment but uses external programs for the prediction. We demonstrate that both the alignment quality and the accuracy of the consensus secondary structure prediction from our alignment are the highest among the other programs examined. We also demonstrate that our algorithm can align relatively long RNA sequences such as the eukaryotic-type signal recognition particle RNA that is approximately 300 nt in length; multiple alignment of such sequences has not been possible by using other Sankoff-based algorithms. The algorithm is implemented in the software named 'Murlet'. AVAILABILITY The C++ source code of the Murlet software and the test dataset used in this study are available at http://www.ncrna.org/papers/Murlet/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Hisanori Kiryu
- Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi, Koto-ku, Tokyo 135-0064, Japan.
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Matousek J, Junker V, Vrba L, Schubert J, Patzak J, Steger G. Molecular characterization and genome organization of 7SL RNA genes from hop (Humulus lupulus L.). Gene 1999; 239:173-83. [PMID: 10571047 DOI: 10.1016/s0378-1119(99)00352-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
A wide spectrum of hop 7SL RNA-encoding sequences was detected by temperature gradient-gel electrophoresis. Four hop 7SL RNA genes were cloned and characterized. A new subvariant of the upstream sequence element (USE) 5'TCCCACATGG 3' and two distinct variants of TATA signal were found at positions characteristic for RNA polymerase III-driven transcription in plants. In addition, a more distant conserved sequence element 5' CATGTATAAACTTTCTGC 3' was present in all cloned genes, about 160 bp upstream of the 7SL RNA coding sequence. Consensus secondary structures calculated for hop 7SL RNAs revealed characteristic features, although some structure differences from formerly published models were predicted. Specific in-vitro transcription of plant 7SL RNA genes was observed in a heterologous system (HeLa extract). This in-vitro transcription assay showed significant differences among individual clones in transcription rates, suggesting the requirement of complexity of 7SL RNA sequence for its efficient transcription in HeLa extract. Southern blot analysis of hop DNA revealed 12 7SL-specific signals corresponding to HindIII fragments ranging from 0.45 to 7.8 kb. Several 7SL RNA-encoding sequences and various intergenic spacers were amplified from the individual HindIII fragments of about 1.3 and 2.8 kb. These facts suggest that at least some of the hop 7SL RNA genes are organized in genomic clusters.
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MESH Headings
- Base Sequence
- Blotting, Southern
- Cloning, Molecular
- DNA, Plant/chemistry
- DNA, Plant/genetics
- Genes, Plant/genetics
- Genome, Plant
- HeLa Cells
- Humans
- Molecular Sequence Data
- Molecular Structure
- Nucleic Acid Conformation
- Phylogeny
- RNA, Small Cytoplasmic/genetics
- Rosales/chemistry
- Rosales/genetics
- Sequence Alignment
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Signal Recognition Particle/genetics
- Transcription, Genetic
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Affiliation(s)
- J Matousek
- Institute of Plant Molecular Biology AS CR, Ceske Budejovice, Czech Republic.
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Juan V, Wilson C. RNA secondary structure prediction based on free energy and phylogenetic analysis. J Mol Biol 1999; 289:935-47. [PMID: 10369773 DOI: 10.1006/jmbi.1999.2801] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We describe a computational method for the prediction of RNA secondary structure that uses a combination of free energy and comparative sequence analysis strategies. Using a homology-based sequence alignment as a starting point, all favorable pairings with respect to the Turner energy function are identified. Each potentially paired region within a multiple sequence alignment is scored using a function that combines both predicted free energy and sequence covariation with optimized weightings. High scoring regions are ranked and sequentially incorporated to define a growing secondary structure. Using a single set of optimized parameters, it is possible to accurately predict the foldings of several test RNAs defined previously by extensive phylogenetic and experimental data (including tRNA, 5 S rRNA, SRP RNA, tmRNA, and 16 S rRNA). The algorithm correctly predicts approximately 80% of the secondary structure. A range of parameters have been tested to define the minimal sequence information content required to accurately predict secondary structure and to assess the importance of individual terms in the prediction scheme. This analysis indicates that prediction accuracy most strongly depends upon covariational information and only weakly on the energetic terms. However, relatively few sequences prove sufficient to provide the covariational information required for an accurate prediction. Secondary structures can be accurately defined by alignments with as few as five sequences and predictions improve only moderately with the inclusion of additional sequences.
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Affiliation(s)
- V Juan
- Department of Biology and Center for the Molecular Biology of RNA, Sinsheimer Laboratories, University of California at Santa Cruz, Santa Cruz, CA, 95064, USA
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Stoesser G, Sterk P, Tuli MA, Stoehr PJ, Cameron GN. The EMBL Nucleotide Sequence Database. Nucleic Acids Res 1997; 25:7-14. [PMID: 9016493 PMCID: PMC146376 DOI: 10.1093/nar/25.1.7] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The EMBL Nucleotide Sequence Database is a comprehensive database of DNA and RNA sequences directly submitted from researchers and genome sequencing groups and collected from the scientific literature and patent applications. In collaboration with DDBJ and GenBank the database is produced, maintained and distributed at the European Bioinformatics Institute (EBI) and constitutes Europe's primary nucleotide sequence resource. Database releases are produced quarterly and are distributed on CD-ROM. EBI's network services allow access to the most up-to-date data collection via Internet and World Wide Web interface, providing database searching and sequence similarity facilities plus access to a large number of additional databases.
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Affiliation(s)
- G Stoesser
- EMBL Outstation, the EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
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8
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Riedel L, Volger U, Luckinger R, Pütz A, Sänger HL, Wassenegger M. Molecular analysis of the gene family of the signal recognition particle (SRP) RNA of tomato. PLANT MOLECULAR BIOLOGY 1996; 31:113-125. [PMID: 8704144 DOI: 10.1007/bf00020611] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The sequence variants of the signal recognition particle (SRP) RNA gene family from four tomato cultivars have been isolated and characterized which indicated the existence of SRP RNA pseudogenes. Sequence analysis revealed two conserved sequence motifs in the upstream region, a TATA-like box and an upstream sequence element (USE), 'TCCCACATCG', both located at a conserved distance to the transcription start point. These elements are identical to the DNA-dependent RNA polymerase III (pol III)-specific promoters of U-rich small nuclear RNA (UsnRNA) genes of plants. Moreover, T-rich stretches are found at the 3' end of the coding regions of the SRP RNA genes which could act as typical pol III termination signals. These findings and recent results from site-directed mutation analysis of the SRP RNA genes from Arabidopsis thaliana indicate that, in contrast to mammalian systems, plant pol III SRP RNA genes are most probably regulated by external promoter elements. According to the identical promoter organization between plant U3-, U6snRNA, MRP-like RNA and SRP RNA genes, one can group these genes into the 'pol III(EXT)USE' subclass of externally regulated USE-dependent pol III genes.
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Affiliation(s)
- L Riedel
- Max-Planck-Institut für Biochemie, Abteilung Viroidforschung, Martinsried, Germany
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Rodriguez-Tomé P, Stoehr PJ, Cameron GN, Flores TP. The European Bioinformatics Institute (EBI) databases. Nucleic Acids Res 1996; 24:6-12. [PMID: 8594602 PMCID: PMC145572 DOI: 10.1093/nar/24.1.6] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The European Bioinformatics Institute (EBI) maintains and distributes the EMBL Nucleotide Sequence database, Europe's primary nucleotide sequence data resource. The EBI also maintains and distributes the SWISS-PROT Protein Sequence database, in collaboration with Amos Bairoch of the University of Geneva. Over fifty additional specialist molecular biology databases, as well as software and documentation of interest to molecular biologists are available. The EBI network services include database searching and sequence similarity searching facilities.
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Lütcke H. Signal recognition particle (SRP), a ubiquitous initiator of protein translocation. EUROPEAN JOURNAL OF BIOCHEMISTRY 1995; 228:531-50. [PMID: 7737147 DOI: 10.1111/j.1432-1033.1995.tb20293.x] [Citation(s) in RCA: 130] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
In higher eukaryotes, most secretory and membrane proteins are synthesised by ribosomes which are attached to the membrane of the rough endoplasmic reticulum (RER). This allows the proteins to be translocated across that membrane already during their synthesis. The ribosomes are directed to the RER membrane by a cytoplasmic ribonucleoprotein particle, the signal recognition particle (SRP). SRP fulfills its task by virtue of three distinguishable activities: the binding of a signal sequence which, being part of the nascent polypeptide to be translocated, is exposed on the surface of a translating ribosome; the retardation of any further elongation; and the SRP-receptor-mediated binding of the complex of ribosome, nascent polypeptide and SRP to the RER membrane which results in the detachment of SRP from the signal sequence and the ribosome and the insertion of the nascent polypeptide into the membrane. Evidence is accumulating that SRP is not restricted to eukaryotes: SRP-related particles and SRP-receptor-related molecules are found ubiquitously and may function in protein translocation in every living organism. This review focuses on the mammalian SRP. A brief discussion of its overall structure is followed by a detailed description of the structures of its RNA and protein constituents and the requirements for their assembly into the particle. Homologues of SRP components from organisms other than mammals are mentioned to emphasize the components' conserved or less conserved features. Subsequently, the functions of each of the SRP constituents are discussed. This sets the stage for a presentation of a model for the mechanism by which SRP cyclically assembles and disassembles with translating ribosomes and the RER membrane. It may be expected that similar mechanisms are used by SRP homologues in organisms other than mammals. However, the mammalian SRP-mediated translocation mechanism may not be conserved in its entirety in organisms like Escherichia coli whose SRP lack components required for the function of the mammalian SRP. Possible translocation pathways involving the rudimentary SRP are discussed in view of the existence of alternative, chaperone-mediated translocation pathways with which they may intersect. The concluding two sections deal with open questions in two areas of SRP research. One formulates basic questions regarding the little-investigated biogenesis of SRP. The other gives an outlook over the insights into the mechanisms of each of the known activities of the SRP that are to be expected in the short and medium-term future.
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Affiliation(s)
- H Lütcke
- Zentrum für Molekulare Biologie Heidelberg (ZMBH), Germany
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11
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Lutcke H. Signal Recognition Particle (SRP), a Ubiquitous Initiator of Protein Translocation. ACTA ACUST UNITED AC 1995. [DOI: 10.1111/j.1432-1033.1995.0531m.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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12
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Emmert DB, Stoehr PJ, Stoesser G, Cameron GN. The European Bioinformatics Institute (EBI) databases. Nucleic Acids Res 1994; 22:3445-9. [PMID: 7937043 PMCID: PMC308299 DOI: 10.1093/nar/22.17.3445] [Citation(s) in RCA: 78] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
This paper describes the databases and services of the European Bioinformatics Institute (EBI). In collaboration with DDBJ and GenBank/NCBI, the EBI maintains and distributes the EMBL Nucleotide Sequence Database, Europe's primary nucleotide sequence data resource. The EBI also maintains and distributes the SWISS-PROT Protein Sequence Database, in collaboration with Amos Bairoch of the University of Geneva. Over thirty additional specialist molecular biology databases, as well as software and documentation of interest to molecular biologists, are also available. The EBI network services include database searching, entry retrieval, and sequence similarity searching facilities.
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Affiliation(s)
- D B Emmert
- European Bioinformatics Institute, Cambridge, UK
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13
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Abstract
The SRPDB (signal recognition particle database) provides aligned SRP RNA and protein sequences, annotated and phylogenetically ordered. This release includes 82 SRP RNAs (including 22 bacterial and 9 archaeal homologs) and a total of 20 protein sequences representing SRP9, SRP14, SRP19, SRP54, SRP68, and SRP72. The offerings also include representative RNA secondary structure diagrams.
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Affiliation(s)
- C Zwieb
- Department of Molecular Biology, University of Texas Health Science Center, Tyler 75710
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14
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Systematic site-directed mutagenesis of protein SRP19. Identification of the residues essential for binding to signal recognition particle RNA. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(17)32020-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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15
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Zwieb C. Site-directed mutagenesis of signal-recognition particle RNA. Identification of the nucleotides in helix 8 required for interaction with protein SRP19. EUROPEAN JOURNAL OF BIOCHEMISTRY 1994; 222:885-90. [PMID: 7517868 DOI: 10.1111/j.1432-1033.1994.tb18936.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The RNA component of signal recognition particle (SRP) consists of eight helices which form a functional unit with the proteins of the SRP. The primary binding site of the 19-kDa protein of SRP (SRP19) is a tetranucleotide loop (tetraloop) in helix 6 of the SRP RNA, but additional determinants are located in helix 8, which might play important roles in the assembly and the function of the particle. To determine the structural features in helix 8 essential for interaction with SRP19, we altered helix 8 systematically by site-directed mutagenesis, and determined the ability of protein SRP19 to interact with the various mutant SRP RNAs. Binding of SRP19 was affected by base changes introduced into the 5' portion (192A, 193G, 194G in the human SRP RNA), but not into the 3' portion (205 A, 206G, 207C) of the distally located conserved internal loop of helix 8. Of the three bases at positions 192-194, only a pyrimidine at position 192 impaired the association with SPR19. An important feature of the SRP19-RNA interaction were the three base pairs U195-G204, C196-G203 and G197-C202 which shape the helix-8 tetraloop. Some base-specific features in the base pairs were also recognized. The tetraloop bases of helix 8 were dispensable for the interaction with SRP19.
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Affiliation(s)
- C Zwieb
- Department of Molecular Biology, University of Texas Health Science Center at Tyler 75710
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16
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Abstract
We describe a general approach to several RNA sequence analysis problems using probabilistic models that flexibly describe the secondary structure and primary sequence consensus of an RNA sequence family. We call these models 'covariance models'. A covariance model of tRNA sequences is an extremely sensitive and discriminative tool for searching for additional tRNAs and tRNA-related sequences in sequence databases. A model can be built automatically from an existing sequence alignment. We also describe an algorithm for learning a model and hence a consensus secondary structure from initially unaligned example sequences and no prior structural information. Models trained on unaligned tRNA examples correctly predict tRNA secondary structure and produce high-quality multiple alignments. The approach may be applied to any family of small RNA sequences.
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Affiliation(s)
- S R Eddy
- MRC Laboratory of Molecular Biology, Cambridge, UK
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