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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: 2.6] [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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Cannone JJ, Subramanian S, Schnare MN, Collett JR, D'Souza LM, Du Y, Feng B, Lin N, Madabusi LV, Müller KM, Pande N, Shang Z, Yu N, Gutell RR. The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. BMC Bioinformatics 2002; 3:2. [PMID: 11869452 PMCID: PMC65690 DOI: 10.1186/1471-2105-3-2] [Citation(s) in RCA: 1092] [Impact Index Per Article: 49.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2001] [Accepted: 01/17/2002] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Comparative analysis of RNA sequences is the basis for the detailed and accurate predictions of RNA structure and the determination of phylogenetic relationships for organisms that span the entire phylogenetic tree. Underlying these accomplishments are very large, well-organized, and processed collections of RNA sequences. This data, starting with the sequences organized into a database management system and aligned to reveal their higher-order structure, and patterns of conservation and variation for organisms that span the phylogenetic tree, has been collected and analyzed. This type of information can be fundamental for and have an influence on the study of phylogenetic relationships, RNA structure, and the melding of these two fields. RESULTS We have prepared a large web site that disseminates our comparative sequence and structure models and data. The four major types of comparative information and systems available for the three ribosomal RNAs (5S, 16S, and 23S rRNA), transfer RNA (tRNA), and two of the catalytic intron RNAs (group I and group II) are: (1) Current Comparative Structure Models; (2) Nucleotide Frequency and Conservation Information; (3) Sequence and Structure Data; and (4) Data Access Systems. CONCLUSIONS This online RNA sequence and structure information, the result of extensive analysis, interpretation, data collection, and computer program and web development, is accessible at our Comparative RNA Web (CRW) Site http://www.rna.icmb.utexas.edu. In the future, more data and information will be added to these existing categories, new categories will be developed, and additional RNAs will be studied and presented at the CRW Site.
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MESH Headings
- Base Sequence/genetics
- Databases, Nucleic Acid
- Internet
- Molecular Sequence Data
- Nucleic Acid Conformation
- RNA/chemistry
- RNA/genetics
- RNA, Archaeal/chemistry
- RNA, Archaeal/genetics
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 23S/chemistry
- RNA, Ribosomal, 23S/genetics
- RNA, Ribosomal, 5S/chemistry
- RNA, Ribosomal, 5S/genetics
- RNA, Transfer/chemistry
- RNA, Transfer/genetics
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Affiliation(s)
- Jamie J Cannone
- Institute for Cellular and Molecular Biology, Section of Integrative Biology, University of Texas at Austin, 2500 Speedway, Austin, TX 78712-1095, USA
| | - Sankar Subramanian
- Institute for Cellular and Molecular Biology, Section of Integrative Biology, University of Texas at Austin, 2500 Speedway, Austin, TX 78712-1095, USA
- Department of Biology, Arizona State University, Tempe, AZ 85287-1501, USA
| | - Murray N Schnare
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4H7, Canada
| | - James R Collett
- Institute for Cellular and Molecular Biology, Section of Integrative Biology, University of Texas at Austin, 2500 Speedway, Austin, TX 78712-1095, USA
| | - Lisa M D'Souza
- Institute for Cellular and Molecular Biology, Section of Integrative Biology, University of Texas at Austin, 2500 Speedway, Austin, TX 78712-1095, USA
| | - Yushi Du
- Institute for Cellular and Molecular Biology, Section of Integrative Biology, University of Texas at Austin, 2500 Speedway, Austin, TX 78712-1095, USA
| | - Brian Feng
- Institute for Cellular and Molecular Biology, Section of Integrative Biology, University of Texas at Austin, 2500 Speedway, Austin, TX 78712-1095, USA
| | - Nan Lin
- Institute for Cellular and Molecular Biology, Section of Integrative Biology, University of Texas at Austin, 2500 Speedway, Austin, TX 78712-1095, USA
| | - Lakshmi V Madabusi
- Institute for Cellular and Molecular Biology, Section of Integrative Biology, University of Texas at Austin, 2500 Speedway, Austin, TX 78712-1095, USA
- Ambion, Inc., Austin, TX 78744-1832, USA
| | - Kirsten M Müller
- Institute for Cellular and Molecular Biology, Section of Integrative Biology, University of Texas at Austin, 2500 Speedway, Austin, TX 78712-1095, USA
- Department of Biology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Nupur Pande
- Institute for Cellular and Molecular Biology, Section of Integrative Biology, University of Texas at Austin, 2500 Speedway, Austin, TX 78712-1095, USA
| | - Zhidi Shang
- Institute for Cellular and Molecular Biology, Section of Integrative Biology, University of Texas at Austin, 2500 Speedway, Austin, TX 78712-1095, USA
| | - Nan Yu
- Institute for Cellular and Molecular Biology, Section of Integrative Biology, University of Texas at Austin, 2500 Speedway, Austin, TX 78712-1095, USA
| | - Robin R Gutell
- Institute for Cellular and Molecular Biology, Section of Integrative Biology, University of Texas at Austin, 2500 Speedway, Austin, TX 78712-1095, USA
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Hamada K, Kumazaki T, Satoh S. Effect of transforming RNA on the synthesis of a protein with a secretory signal sequence in vitro. J Biol Chem 1999; 274:15786-96. [PMID: 10336481 DOI: 10.1074/jbc.274.22.15786] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
U5 small nuclear RNA itself can act as a clastogenic and transforming agent when transfected into cells. In the previous work, the 3' half of the U5 small nuclear RNA first stem structure (designated RNA3S) was capable of driving normal cells into tumorigenic cells when expressed with a poly(A) tail (RNA3S+). This transformation critically depended upon the polypurine sequence GGAGAGGAA in RNA3S+. In this work, we first examined the pre-beta-lactamase and luciferase (model secretory and nonsecretory proteins) translation with the in vitro synthesized RNA3S in rabbit reticulocyte lysate. The capped RNA3S with a poly(A) tail suppressed the translation. In addition, the polypurine sequence played a crucial role in affecting the secretory protein synthesis, indicating a primary action of RNA3S+. Further studies revealed that the oligodeoxynucleotides, corresponding to the polypurine and its antisense sequences, directly contacted 28 S rRNA in ribosome and 7SL RNA in signal recognition particle, respectively, and differentially affected the nascent chain elongation of secretory protein synthesis. These results suggest that RNA3S+ blocks a physiological regulatory function played by signal recognition particle and the ribosome in the secretory protein synthesis and support the idea that the transformation might result from a repressed cellular activity.
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Affiliation(s)
- K Hamada
- Division of Cell Biology, Research Institute for Radiation Biology and Medicine, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-0037, Japan
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Gowda K, Black SD, Moeller I, Sakakibara Y, Liu MC, Zwieb C. Protein SRP54 of human signal recognition particle: cloning, expression, and comparative analysis of functional sites. Gene 1998; 207:197-207. [PMID: 9511762 DOI: 10.1016/s0378-1119(97)00627-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Signal recognition particle (SRP) plays a critical role in the targeting of secretory proteins to cellular membranes. An essential component of SRP is the protein SRP54, which interacts not only with the nascent signal peptide, but also with the SRP RNA. To understand better how protein targeting occurs in the human system, the human SRP54 gene was cloned, sequenced, and the protein was expressed in bacteria and insect cells. Recombinant SRP54 was purified from both sources. The protein bound to SRP RNA in the presence of protein SRP19, and associated with the signal peptide of in vitro translated pre-prolactin. Comparative sequence analysis of human SRP54 with homologs from all three phylogenetic domains was combined with high-stringency protein secondary structure prediction. A conserved RNA-binding loop was predicted in the largely helical M-domain of SRP54. Contrary to general belief, the unusually high number of methionine residues clustered outside the predicted helices, thus indicating a mechanism of signal peptide recognition that may involve methionine-rich loops.
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Affiliation(s)
- K Gowda
- Department of Molecular Biology, University of Texas Health Science Center at Tyler 75710, USA
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Lai C, Langley CH. A homologue of the 19 kDa signal recognition particle protein locus in Drosophila melanogaster. Gene 1997; 203:59-63. [PMID: 9426007 DOI: 10.1016/s0378-1119(97)00492-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
A homologue of 19 kDa signal recognition particle locus (SRP19) was cloned and molecularly characterized in Drosophila melanogaster. It is located in the 65F region of the left arm on the third chromosome, approx. 500 bp 5' of the quemao locus. The SRP19 transcript was determined from cDNA clones, Northern blot analysis, and the 5' rapid amplification of cDNA end method. SRP19 was expressed in all the developmental stages of Drosophila. The predicted amino acid sequence (163 aa) shows that SRP19 of Drosophila shares 44%, 29%, 17% and 19% identity with the homologues from human, rice and two yeast species (Saccharomyces and Yarrowia), respectively. The most conserved amino acid residues across these species are located at those sites required for in vitro association with the 7S RNA component of the SRP.
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Affiliation(s)
- C Lai
- Center for Population Biology, University of California, Davis 95616, USA.
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Melchers WJ, Hoenderop JG, Bruins Slot HJ, Pleij CW, Pilipenko EV, Agol VI, Galama JM. Kissing of the two predominant hairpin loops in the coxsackie B virus 3' untranslated region is the essential structural feature of the origin of replication required for negative-strand RNA synthesis. J Virol 1997; 71:686-96. [PMID: 8985400 PMCID: PMC191101 DOI: 10.1128/jvi.71.1.686-696.1997] [Citation(s) in RCA: 121] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Higher-order RNA structures in the 3' untranslated region (3'UTR) of enteroviruses are thought to play a pivotal role in viral negative-strand RNA synthesis. The structure of the 3'UTR was predicted by thermodynamic calculations using the STAR (structural analysis of RNA) computer program and experimentally verified using chemical and enzymatic probing of in vitro-synthesized RNA. A possible pseudoknot interaction between the 3D polymerase coding sequence and domain Y and a "kissing" interaction between domains X and Y was further studied by mutational analysis, using an infectious coxsackie B3 virus cDNA clone (domain designation as proposed by E. V. Pilipenko, S. V. Maslova, A. N. Sinyakov, and V.I. Agol (Nucleic Acids Res. 20:1739-1745, 1992). The higher-order RNA structure of the 3'UTR appeared to be maintained by an intramolecular kissing interaction between the loops of the two predominant hairpin structures (X and Y) within the 3'UTR. Disturbing this interaction had no effect on viral translation and processing of the polyprotein but exerted a primary effect on viral replication, as was demonstrated in a subgenomic coxsackie B3 viral replicon, in which the capsid P1 region was replaced by the luciferase gene. Mutational analysis did not support the existence of the pseudoknot interaction between hairpin loop Y and the 3D polymerase coding sequence. Based on these experiments, we constructed a three-dimensional model of the 3'UTR of coxsackie B virus that shows the kissing interaction as the essential structural feature of the origin of replication required for its functional competence.
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Affiliation(s)
- W J Melchers
- Department of Medical Microbiology, University of Nijmegen, The Netherlands.
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Yang AJ, Mulligan RM. Identification of a 4.5S-like ribonucleoprotein in maize mitochondria. Nucleic Acids Res 1996; 24:3601-6. [PMID: 8836189 PMCID: PMC146122 DOI: 10.1093/nar/24.18.3601] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Escherichia coli has a ribonucleoprotein complex that is composed of a 114 nucleotide 4.5S RNA and a 48 kDa polypeptide (P48) that has been demonstrated to function in translation and in the secretion of periplasmic polypeptides. A small RNA of approximately 220 nucleotides has been identified in maize mitochondria that includes sequence identity with the highly conserved domain of the bacterial 4.5S RNA. The transcript is mitochondrially encoded and maps to a region upstream of the gene for ATP synthase subunit I. The mitochondrial 4.5S-like RNA has 15 nucleotides of sequence identity with the highly conserved region of the bacterial 4.5S RNA. Sucrose density gradient centrifugation of a maize mitochondrial lysate demonstrated that the 4.5S RNA is a component of a high molecular weight complex under native conditions, and could be disrupted by phenol. Anti-P48 immune serum immuno-precipitated a mitochondrial protein of approximately 48 kDa, and RNA gel blot analysis of the immunoprecipitation reaction indicated that the 4.5S-like RNA co-immuno-precipitated with the 48 kDa polypeptide. The mitochondrial 4.5S ribonucleoprotein complex could function in translation or protein targeting.
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Affiliation(s)
- A J Yang
- Department of Developmental and Cell Biology, University of California, Irvine 92697-2300, USA
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Zwieb C, Müller F, Larsen N. Comparative analysis of tertiary structure elements in signal recognition particle RNA. FOLDING & DESIGN 1996; 1:315-24. [PMID: 9079393 DOI: 10.1016/s1359-0278(96)00044-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
BACKGROUND The signal recognition particle (SRP) is a ribonucleoprotein complex that associates with ribosomes to promote co-translational translocation of proteins across biological membranes. We have used comparative analysis of a large number of bacterial, archaeal, and eukaryotic SRP RNA sequences to derive shared tertiary SRP RNA structure elements. RESULTS A representative three-dimensional model of the human SRP RNA is shown that includes single-stranded intrahelical and interhelical RNA loops and incorporates data from enzymatic and chemical modification, electron microscopy, and site-directed mutagenesis. Properties of the SRP RNA model are an overall extended dumbbell-shaped structure (260 A x 70 A) with a pseudoknot in the small SRP domain (a pairing of 12-UGGC-15 with 33-GCUA-36), and a tertiary interaction in the large SRP domain (198-GA-199 with 232-GU-233). CONCLUSIONS The RNA 'knuckle' formed in helix 8 of SRP RNA appears to constitute the binding site for protein SRP54 or its bacterial equivalent, protein P48. A dynamic property of this feature may explain the hierarchial assembly of proteins SRP19 and SRP54 in the large SRP domain. Furthermore, the human SRP RNA model serves as a framework to understand details of the structure and function of SRP in all organisms and is presented to stimulate further experimentation in this area.
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Affiliation(s)
- C Zwieb
- Department of Molecular Biology, University of Texas Health Science Center, Tyler 75710, USA.
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Affiliation(s)
- M J Serra
- Department of Chemistry, Allegheny College, Meadville, Pennsylvania 16335, USA
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Serra MJ, Axenson TJ, Turner DH. A model for the stabilities of RNA hairpins based on a study of the sequence dependence of stability for hairpins of six nucleotides. Biochemistry 1994; 33:14289-96. [PMID: 7524674 DOI: 10.1021/bi00251a042] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Thermodynamic parameters are reported for hairpin formation in 1 M NaCl by RNA sequences of the type GGCXUAAUYGCC, where XY is the set of 10 possible mismatch base pairs. A nearest neighbor analysis of the data indicates the free energy for loop formation at 37 C varies from 2.9 to 4.5 kcal/mol. Thermodynamic parameters are also reported for hairpin formation by RNA sequences of the type GGXGUAAUAYCC (where XY are CG, GC, AU, UA, GU, and UG), with the common naturally occurring GA first mismatch (45% of small and large subunit rRNA loops of six). These results allow the development of a model to predict the stability of RNA hairpin loops. The model includes the size of the loop, the identity of the closing base pair, the free energy increment (delta G zero 37MM) for interaction of the closing base pair with the first mismatch, and an additional stabilization term for GA and UU first mismatches. delta G zero 37L(n) = delta G zero 37i(n) + delta G zero 37MM + 0.4 (if closed by AU or UA) -0.7 (if first mismatch is GA or UU). Here delta G zero 37i(n) is the free energy for initiating a loop of n nucleotides. delta G zero 37i(n) for n = 4-9 is 4.9, 4.4, 5.0, 5.0, 5.1, and 5.2 kcal/mol, respectively. The delta G zero 37MM is derived from measurements of model duplexes with terminal mismatches. The model gives good agreement when tested against four naturally occurring hairpin sequences.
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Affiliation(s)
- M J Serra
- Department of Chemistry, Allegheny College, Meadville, Pennsylvania 16335
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Sakakibara Y, Brown M, Hughey R, Mian IS, Sjölander K, Underwood RC, Haussler D. Stochastic context-free grammars for tRNA modeling. Nucleic Acids Res 1994; 22:5112-20. [PMID: 7800507 PMCID: PMC523785 DOI: 10.1093/nar/22.23.5112] [Citation(s) in RCA: 131] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Stochastic context-free grammars (SCFGs) are applied to the problems of folding, aligning and modeling families of tRNA sequences. SCFGs capture the sequences' common primary and secondary structure and generalize the hidden Markov models (HMMs) used in related work on protein and DNA. Results show that after having been trained on as few as 20 tRNA sequences from only two tRNA subfamilies (mitochondrial and cytoplasmic), the model can discern general tRNA from similar-length RNA sequences of other kinds, can find secondary structure of new tRNA sequences, and can produce multiple alignments of large sets of tRNA sequences. Our results suggest potential improvements in the alignments of the D- and T-domains in some mitochondrial tRNAs that cannot be fit into the canonical secondary structure.
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Affiliation(s)
- Y Sakakibara
- Sinsheimer Laboratories, University of California, Santa Cruz 95064
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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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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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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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Gutell RR, Power A, Hertz GZ, Putz EJ, Stormo GD. Identifying constraints on the higher-order structure of RNA: continued development and application of comparative sequence analysis methods. Nucleic Acids Res 1992; 20:5785-95. [PMID: 1454539 PMCID: PMC334417 DOI: 10.1093/nar/20.21.5785] [Citation(s) in RCA: 187] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Comparative sequence analysis addresses the problem of RNA folding and RNA structural diversity, and is responsible for determining the folding of many RNA molecules, including 5S, 16S, and 23S rRNAs, tRNA, RNAse P RNA, and Group I and II introns. Initially this method was utilized to fold these sequences into their secondary structures. More recently, this method has revealed numerous tertiary correlations, elucidating novel RNA structural motifs, several of which have been experimentally tested and verified, substantiating the general application of this approach. As successful as the comparative methods have been in elucidating higher-order structure, it is clear that additional structure constraints remain to be found. Deciphering such constraints requires more sensitive and rigorous protocols, in addition to RNA sequence datasets that contain additional phylogenetic diversity and an overall increase in the number of sequences. Various RNA databases, including the tRNA and rRNA sequence datasets, continue to grow in number as well as diversity. Described herein is the development of more rigorous comparative analysis protocols. Our initial development and applications on different RNA datasets have been very encouraging. Such analyses on tRNA, 16S and 23S rRNA are substantiating previously proposed associations and are now beginning to reveal additional constraints on these molecules. A subset of these involve several positions that correlate simultaneously with one another, implying units larger than a basepair can be under a phylogenetic constraint.
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Affiliation(s)
- R R Gutell
- MCD Biology, University of Colorado, Boulder 80309
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Zwieb C. Conformity of RNAs that interact with tetranucleotide loop binding proteins. Nucleic Acids Res 1992; 20:4397-400. [PMID: 1329024 PMCID: PMC334163 DOI: 10.1093/nar/20.17.4397] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
A group of RNA binding proteins, termed tetraloop binding proteins, includes ribosomal protein S15 and protein SRP19 of signal recognition particle. They are primary RNA binding proteins, recognize RNA tetranucleotide loops with a GNAR consensus motif, and require a helical region located adjacent to the tetraloop. Closely related RNA structures that fit these criteria appear in helix 6 of SRP RNA, in helices 22 and 23A of 16 S ribosomal RNA, and, as a pseudoknot, in the regulatory region of the rpsO gene.
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Affiliation(s)
- C Zwieb
- Department of Molecular Biology, University of Texas Health Science Center, Tyler 75710
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19
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Zwieb C. Recognition of a tetranucleotide loop of signal recognition particle RNA by protein SRP19. J Biol Chem 1992. [DOI: 10.1016/s0021-9258(19)49585-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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20
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Yaver DS, Matoba S, Ogrydziak DM. A mutation in the signal recognition particle 7S RNA of the yeast Yarrowia lipolytica preferentially affects synthesis of the alkaline extracellular protease: in vivo evidence for translational arrest. J Cell Biol 1992; 116:605-16. [PMID: 1309815 PMCID: PMC2289313 DOI: 10.1083/jcb.116.3.605] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Replacement of the signal recognition particle (SRP) 7S gene (SCR1) on a replicating plasmid with scr1-1 (G to A at 129 and A to T at 131 in the consensus sequence -GNAR- in the loop of domain III) resulted in temperature sensitivity for growth of cells in which both chromosomal SRP 7S RNA genes were deleted. Pulse-chase immunoprecipitation experiments were done after a shift to non-permissive temperature using the major secreted protein the alkaline extracellular protease (AEP) as a reporter molecule. No untranslocated AEP precursor was detected in a strain with scr1-1 on a plasmid, but the amount of the largest AEP precursor (55 kD) immunoprecipitated as a percentage of total protein synthesized was reduced 68% compared to an isogenic strain with SCR1 on the plasmid. The possibility that an untranslocated precursor was synthesized but not detected because of instability was largely eliminated by detection of a 53-kD untranslocated precursor of a mutated AEP (P17M; methionine replaced proline in the second position of the pro-peptide) which chased to the 55-kD translocated AEP precursor. Thus, SRP has a role in the biosynthesis of AEP. Possibly, the scr1-1 mutation does not affect signal recognition or translational arrest but instead results in maintenance of translational arrest of AEP synthesis. The results also suggest that AEP can be translocated in vivo either co-translationally in which SRP is at least involved in biosynthesis or posttranslationally without SRP involvement.
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Affiliation(s)
- D S Yaver
- Department of Microbiology, University of California, Davis 95616
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21
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Mans RM, Pleij CW, Bosch L. tRNA-like structures. Structure, function and evolutionary significance. EUROPEAN JOURNAL OF BIOCHEMISTRY 1991; 201:303-24. [PMID: 1935928 DOI: 10.1111/j.1432-1033.1991.tb16288.x] [Citation(s) in RCA: 88] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- R M Mans
- Department of Biochemistry, State University of Leiden, The Netherlands
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22
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Zwieb C. Interaction of protein SRP19 with signal recognition particle RNA lacking individual RNA-helices. Nucleic Acids Res 1991; 19:2955-60. [PMID: 1711676 PMCID: PMC328257 DOI: 10.1093/nar/19.11.2955] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Derivatives of human SRP-RNA were constructed by site-directed mutagenesis and tested for their ability to interact with protein SRP19. An RNA missing helix 6 barely interacts with SRP19, while the helix 8-deletion mutant retains much binding capability. A mutant RNA consisting just of helix 6 also binds the protein, but not as well as the unaltered molecule. SRP19 interacts to a full extent with the fourth mutant RNA composed of helices 6, 7, 8 and a portion of helix 5. It is concluded that helix 6- and not helix 8- is the major SRP19 binding site. Helices 7, 8 and portions of helix 5 contribute to the formation of a functional site. These results agree with data suggesting a proximity of helix 6 and the conserved part of SRP-RNA.
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Affiliation(s)
- C Zwieb
- Department of Molecular Biology, University of Texas Health Center, Tyler 75710
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23
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Abstract
Eubacterial RNase P contains a catalytic RNA that cleaves 5' leader sequences from precursor tRNAs. We review the current understanding of RNase P RNA structure and evolution, from the perspective of phylogenetic comparative analysis.
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Affiliation(s)
- J W Brown
- Department of Biology, Indiana University, Bloomington 47405
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24
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Abstract
The secondary structures of the RNAs from the signal recognition particle, termed SRP-RNA, were derived buy comparative analyses of an alignment of 39 sequences. The models are minimal in that only base pairs are included for which there is comparative evidence. The structures represent refinements of earlier versions and include a new short helix.
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Affiliation(s)
- N Larsen
- Department of Biostructural Chemistry, Arhus University, Denmark
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25
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Haas ES, Brown JW, Daniels CJ, Reeve JN. Genes encoding the 7S RNA and tRNA(Ser) are linked to one of the two rRNA operons in the genome of the extremely thermophilic archaebacterium Methanothermus fervidus. Gene 1990; 90:51-9. [PMID: 2116370 DOI: 10.1016/0378-1119(90)90438-w] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Analysis of gene structure in the extremely thermophilic archaebacterium, Methanothermus fervidus, has revealed the presence of a cluster of stable RNA-encoding genes arranged 5'-7S RNA-tRNA(Ser)-16S rRNA-tRNA(Ala)-23S rRNA-5S rRNA. The genome of M. fervidus contains two rRNA operons but only one operon has the closely linked 7S RNA-encoding gene. The sequences upstream from the two rRNA operons are identical for 206 bp but diverge at the 3' base of the tRNA(Ser) gene. The secondary structures predicted for the M. fervidus 7S, 16S rRNA, tRNA(Ala) and tRNA(Ser) have been compared with those of functionally homologous molecules from moderately thermophilic and mesophilic archaebacteria. A consensus secondary structure for archaebacterial 7S RNAs has been developed which incorporates bases and structural features also conserved in eukaryotic signal-recognition-particle RNAs and eubacterial 4.5S RNAs.
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MESH Headings
- Archaea/genetics
- Bacteria/genetics
- Base Sequence
- Cloning, Molecular
- DNA, Bacterial/genetics
- Genes, Bacterial
- Genetic Linkage
- Molecular Sequence Data
- Nucleic Acid Conformation
- Operon
- RNA Processing, Post-Transcriptional
- RNA, Ribosomal/genetics
- RNA, Ribosomal/ultrastructure
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 16S/ultrastructure
- RNA, Small Nuclear/genetics
- RNA, Small Nuclear/ultrastructure
- RNA, Transfer, Amino Acid-Specific/genetics
- RNA, Transfer, Ser/genetics
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Affiliation(s)
- E S Haas
- Department of Microbiology, Ohio State University, Columbus 43210
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