Genomes and Genes
Summary: Enzymes that catalyze the template-directed incorporation of ribonucleotides into an RNA chain. EC 2.7.7.-.
- Grandori C, Mac J, Siebelt F, Ayer D, Eisenman R. Myc-Max heterodimers activate a DEAD box gene and interact with multiple E box-related sites in vivo. EMBO J. 1996;15:4344-57 pubmed..Therefore, Myc may exert its effects on cell behavior through proteins that affect RNA structure and metabolism. ..
- Hayashi N, Seino H, Irie K, Watanabe M, Clark K, Matsumoto K, et al. Genetic interaction of DED1 encoding a putative ATP-dependent RNA helicase with SRM1 encoding a mammalian RCC1 homolog in Saccharomyces cerevisiae. Mol Gen Genet. 1996;253:149-56 pubmed..cerevisiae Ran homolog GSP1 suppresses prp20-1, but not srm1-1 or mtr1-2. ..
- Tseng S, Weaver P, Liu Y, Hitomi M, Tartakoff A, Chang T. Dbp5p, a cytosolic RNA helicase, is required for poly(A)+ RNA export. EMBO J. 1998;17:2651-62 pubmed..The functions of Dbp5p are likely to be conserved, since its potential homologues can be found in a variety of eukaryotic cells. ..
- Wang H, Hill K, Perry S. An Arabidopsis RNA lariat debranching enzyme is essential for embryogenesis. J Biol Chem. 2004;279:1468-73 pubmed
- Toh Y, Takeshita D, Numata T, Fukai S, Nureki O, Tomita K. Mechanism for the definition of elongation and termination by the class II CCA-adding enzyme. EMBO J. 2009;28:3353-65 pubmed publisher..The results collectively suggest that, in the class II CCA-adding enzyme, the head and neck domains collaboratively and dynamically define the number of nucleotide additions and the specificity of nucleotide selection. ..
- Zhao Y, Yu Y, Zhai J, Ramachandran V, Dinh T, Meyers B, et al. The Arabidopsis nucleotidyl transferase HESO1 uridylates unmethylated small RNAs to trigger their degradation. Curr Biol. 2012;22:689-94 pubmed publisher..We show that uridylation leads to miRNA degradation, and the degradation is most likely through an enzyme that is distinct from that causing the 3' truncation in hen1 mutants. ..
- Cho H, Verlinde C, Weiner A. Reengineering CCA-adding enzymes to function as (U,G)- or dCdCdA-adding enzymes or poly(C,A) and poly(U,G) polymerases. Proc Natl Acad Sci U S A. 2007;104:54-9 pubmed..Collaboration between RNA and protein in the form of a ribonucleoprotein template may help to explain the evolutionary diversity of the nucleotidyltransferase family. ..
- Zhu L, Cudny H, Deutscher M. A mutation in Escherichia coli tRNA nucleotidyltransferase that affects only AMP incorporation is in a sequence often associated with nucleotide-binding proteins. J Biol Chem. 1986;261:14875-7 pubmed..However, other sequences often associated with ATP-binding domains are not found in tRNA nucleotidyltransferase. The implications of these findings for our understanding of nucleotide-binding domains are discussed. ..
- Ren G, Chen X, Yu B. Uridylation of miRNAs by hen1 suppressor1 in Arabidopsis. Curr Biol. 2012;22:695-700 pubmed publisher..This study shall have implications on piRNA uridylation in hen1 in animals. ..
- Gruidl M, Smith P, Kuznicki K, McCrone J, Kirchner J, Roussell D, et al. Multiple potential germ-line helicases are components of the germ-line-specific P granules of Caenorhabditis elegans. Proc Natl Acad Sci U S A. 1996;93:13837-42 pubmed..As these very similar glh genes physically map within several hundred kilobases of one another, it seems likely that they represent a fairly recent gene duplication event. ..
- Lemaire L, Heinlein U. High-level expression in male germ cells of murine P68 RNA helicase mRNA. Life Sci. 1993;52:917-26 pubmed..The signal was restricted to late pachytene spermatocytes and haploid spermatids. Northern blot analyses corroborated these results but suggested that expression of related mRNA species occurs in a variety of other tissues. ..
- Ladomery M, Wade E, Sommerville J. Xp54, the Xenopus homologue of human RNA helicase p54, is an integral component of stored mRNP particles in oocytes. Nucleic Acids Res. 1997;25:965-73 pubmed..On isolating Xp54 from mRNP particles, it is shown to possess an ATP-dependent RNA helicase activity. Possible functions of Xp54 are discussed in relation to the assembly and utilization of mRNP particles. ..
- Augustin M, Reichert A, Betat H, Huber R, Mörl M, Steegborn C. Crystal structure of the human CCA-adding enzyme: insights into template-independent polymerization. J Mol Biol. 2003;328:985-94 pubmed..Based on our results, we introduce a corkscrew model for CCA addition that includes a fixed active site and a traveling tRNA-binding region formed by flexible parts of the protein. ..
- Kos M, Tollervey D. The Putative RNA Helicase Dbp4p Is Required for Release of the U14 snoRNA from Preribosomes in Saccharomyces cerevisiae. Mol Cell. 2005;20:53-64 pubmed..Point mutations in helicase motifs I and III of Dbp4p blocked release of U14 from preribosomes. We conclude that the helicase activity of Dbp4p is required to unwind U14 and snR41 from the pre-rRNA. ..
- Pratico E, Silverman S. Ty1 reverse transcriptase does not read through the proposed 2',5'-branched retrotransposition intermediate in vitro. RNA. 2007;13:1528-36 pubmed..This suggests that Dbr1p acts as other than a 2',5'-phosphodiesterase during Ty1 retrotransposition. ..
- Coller J, Tucker M, Sheth U, Valencia Sanchez M, Parker R. The DEAD box helicase, Dhh1p, functions in mRNA decapping and interacts with both the decapping and deadenylase complexes. RNA. 2001;7:1717-27 pubmed..Interestingly, Dhh1p homologs in others species function in maternal mRNA storage. This provides a novel link between the mechanisms of decapping and maternal mRNA translational repression. ..
- Kim H, Kim G, Yang J, Ki J. Cloning, expression, and complementation test of the RNA lariat debranching enzyme cDNA from mouse. Mol Cells. 2001;11:198-203 pubmed..The integration of the mDBR1 cDNA in the chromosome of S. pombe also complemented both intron accumulation and slow growth phenotypes of the S. pombe dbr1 knock-out mutant strain. ..
- Smillie D, Sommerville J. RNA helicase p54 (DDX6) is a shuttling protein involved in nuclear assembly of stored mRNP particles. J Cell Sci. 2002;115:395-407 pubmed
- Tomita K, Fukai S, Ishitani R, Ueda T, Takeuchi N, Vassylyev D, et al. Structural basis for template-independent RNA polymerization. Nature. 2004;430:700-4 pubmed publisher..Our structure represents the 'pre-insertion' stage of selecting the incoming nucleotide and provides the structural basis for the mechanism underlying template-independent RNA polymerization...
- Neuenfeldt A, Just A, Betat H, Mörl M. Evolution of tRNA nucleotidyltransferases: a small deletion generated CC-adding enzymes. Proc Natl Acad Sci U S A. 2008;105:7953-8 pubmed publisher..Yet, experimental data indicate that it is possible that A-adding activities also evolved from CCA-adding enzymes by the occurrence of individual point mutations. ..
- Strauss E, Guthrie C. PRP28, a 'DEAD-box' protein, is required for the first step of mRNA splicing in vitro. Nucleic Acids Res. 1994;22:3187-93 pubmed..Interestingly, PRP28 is not a stably associated snRNP protein. Strand displacement assays indicate that PRP28 does not exhibit RNA helicase activity, suggesting that an additional factor or factors may be required for its activation. ..
- Shi P, Maizels N, Weiner A. CCA addition by tRNA nucleotidyltransferase: polymerization without translocation?. EMBO J. 1998;17:3197-206 pubmed..The template for CCA addition would be a dynamic ribonucleoprotein structure. ..
- Valdez B, Henning D, Perumal K, Busch H. RNA-unwinding and RNA-folding activities of RNA helicase II/Gu--two activities in separate domains of the same protein. Eur J Biochem. 1997;250:800-7 pubmed..Amino acids 646-801 fold single-stranded RNA but lack helicase activity. This report shows distinct RNA-unwinding and RNA-folding activities residing in separate domains within the same protein. ..
- Missel A, Souza A, N rskau G, G ringer H. Disruption of a gene encoding a novel mitochondrial DEAD-box protein in Trypanosoma brucei affects edited mRNAs. Mol Cell Biol. 1997;17:4895-903 pubmed..The results suggest an involvement of mHel61p in the control of the abundance of edited mRNAs and thus reveal a novel function for DEAD-box proteins...
- Teigelkamp S, Mundt C, Achsel T, Will C, Luhrmann R. The human U5 snRNP-specific 100-kD protein is an RS domain-containing, putative RNA helicase with significant homology to the yeast splicing factor Prp28p. RNA. 1997;3:1313-26 pubmed
- Nakagawa Y, Morikawa H, Hirata I, Shiozaki M, Matsumoto A, Maemura K, et al. Overexpression of rck/p54, a DEAD box protein, in human colorectal tumours. Br J Cancer. 1999;80:914-7 pubmed..In view of activities of rck/p54 determined in other tissue types, we suggest that rck/p54 may contribute to the cell proliferation and carcinogenesis at the translational level in the development of colorectal tumours. ..
- Zhu L, Johnson C, Bakovic M. Stimulation of the human CTP:phosphoethanolamine cytidylyltransferase gene by early growth response protein 1. J Lipid Res. 2008;49:2197-211 pubmed publisher..Together, these data demonstrate that EGR1 is an important transcriptional stimulator of the human PCYT2 and that conditions that modify EGR1 also affect the function of ECT and consequently PE synthesis. ..
- Franze de Fernandez M, Hayward W, August J. Bacterial proteins required for replication of phage Q ribonucleic acid. Pruification and properties of host factor I, a ribonucleic acid-binding protein. J Biol Chem. 1972;247:824-31 pubmed
- Cougot N, Babajko S, Seraphin B. Cytoplasmic foci are sites of mRNA decay in human cells. J Cell Biol. 2004;165:31-40 pubmed..The occurrence of 5'-3' mRNA decay in specific subcellular locations in human cells suggests that the cytoplasm of eukaryotic cells may be more organized than previously anticipated. ..
- Khalid M, Damha M, Shuman S, Schwer B. Structure-function analysis of yeast RNA debranching enzyme (Dbr1), a manganese-dependent phosphodiesterase. Nucleic Acids Res. 2005;33:6349-60 pubmed..Dbr1 sediments as a monomer and requires manganese as the metal cofactor for debranching. ..
- Audhya A, Hyndman F, McLeod I, Maddox A, Yates J, Desai A, et al. A complex containing the Sm protein CAR-1 and the RNA helicase CGH-1 is required for embryonic cytokinesis in Caenorhabditis elegans. J Cell Biol. 2005;171:267-79 pubmed..Cumulatively, our results suggest that CAR-1 functions with CGH-1 to regulate a specific set of maternally loaded RNAs that is required for anaphase spindle structure and cytokinesis. ..
- Okanami M, Meshi T, Iwabuchi M. Characterization of a DEAD box ATPase/RNA helicase protein of Arabidopsis thaliana. Nucleic Acids Res. 1998;26:2638-43 pubmed..These results show that AtDRH1 is a novel type of ATP/dATP-dependent RNA helicase and polynucleotide-dependent ATPase. ..
- Kim J, Kim H, Kim G, Yang J, Boeke J, Nam K. Human RNA lariat debranching enzyme cDNA complements the phenotypes of Saccharomyces cerevisiae dbr1 and Schizosaccharomyces pombe dbr1 mutants. Nucleic Acids Res. 2000;28:3666-73 pubmed..Comparison of the amino acid sequence of hDBR1 with the other DBR protein sequences showed several conserved regions, with 40, 44 and 43% identity to the S. cerevisiae, S. pombe and C. elegans debranching enzymes, respectively. ..
- Nam K, Lee G, Trambley J, Devine S, Boeke J. Severe growth defect in a Schizosaccharomyces pombe mutant defective in intron lariat degradation. Mol Cell Biol. 1997;17:809-18 pubmed..The growth defect of the S. pombe dbr1::leu1+ strain suggests that debranching activity is critical for efficient intron RNA degradation and that blocking this pathway interferes with cell growth. ..
- Yue D, Weiner A, Maizels N. The CCA-adding enzyme has a single active site. J Biol Chem. 1998;273:29693-700 pubmed
- Peelman L, Chardon P, Nunes M, Renard C, Geffrotin C, Vaiman M, et al. The BAT1 gene in the MHC encodes an evolutionarily conserved putative nuclear RNA helicase of the DEAD family. Genomics. 1995;26:210-8 pubmed..An MspI RFLP was detected in an SLA class I typed family, confirming the localization of the BAT1 gene in the porcine MHC. BAT1 thus encodes a putative nuclear ATP-dependent RNA helicase and is likely to have an indispensable function. ..
- Maekawa H, Nakagawa T, Uno Y, Kitamura K, Shimoda C. The ste13+ gene encoding a putative RNA helicase is essential for nitrogen starvation-induced G1 arrest and initiation of sexual development in the fission yeast Schizosaccharomyces pombe. Mol Gen Genet. 1994;244:456-64 pubmed..Expression of ME31B cDNA in S. pombe suppresses the ste13 mutation. These two evolutionarily conserved genes encoding putative RNA helicases may play a pivotal role in sexual development. ..
- Bladergroen B, Houweling M, Geelen M, van Golde L. Cloning and expression of CTP:phosphoethanolamine cytidylyltransferase cDNA from rat liver. Biochem J. 1999;343 Pt 1:107-14 pubmed..Between day 17 of gestation and birth, the amount of mRNA in fetal rat liver increased approx. 6-fold, suggesting the regulation of ET at both pretranslational and post-translational levels during rat liver development. ..
- Zhu L, Deutscher M. tRNA nucleotidyltransferase is not essential for Escherichia coli viability. EMBO J. 1987;6:2473-7 pubmed..These findings indicate that tRNA nucleotidyltransferase is not essential for E. coli viability, and therefore, that all essential tRNA genes in this organism encode the -C-C-A sequence. ..
- Xiong Y, Steitz T. Mechanism of transfer RNA maturation by CCA-adding enzyme without using an oligonucleotide template. Nature. 2004;430:640-5 pubmed publisherTransfer RNA nucleotidyltransferases (CCA-adding enzymes) are responsible for the maturation or repair of the functional 3' end of tRNAs by means of the addition of the essential nucleotides CCA...
- Yang W, Mason C, Pollock S, Lavezzi T, Moroney J, Moore T. Membrane lipid biosynthesis in Chlamydomonas reinhardtii: expression and characterization of CTP:phosphoethanolamine cytidylyltransferase. Biochem J. 2004;382:51-7 pubmed..reinhardtii cells was observed during the cell cycle, increasing during the dark and then decreasing during the light period, while the mRNA level did not alter, providing evidence for post-translational regulation. ..
- Stuart K, Schnaufer A, Ernst N, Panigrahi A. Complex management: RNA editing in trypanosomes. Trends Biochem Sci. 2005;30:97-105 pubmed..The dynamic processes, which might entail interactions among multiprotein complexes and changes in their composition and conformation, remain to be elucidated. ..
- Betat H, Rammelt C, Martin G, Mörl M. Exchange of regions between bacterial poly(A) polymerase and the CCA-adding enzyme generates altered specificities. Mol Cell. 2004;15:389-98 pubmed..This seems to be the prerequisite for the observed reprogramming of the catalytic center of PAP to incorporate a sequence of defined length and composition instead of long stretches of A residues. ..
- Savitsky K, Ziv Y, Bar Shira A, Gilad S, Tagle D, Smith S, et al. A human gene (DDX10) encoding a putative DEAD-box RNA helicase at 11q22-q23. Genomics. 1996;33:199-206 pubmed..2-kb transcript in a variety of human tissues. A processed pseudogene of DDX10 was detected at chromosome 9q21-q22. We observed a rare trinucleotide repeat length polymorphism within the coding sequence of DDX10. ..
- Yue D, Maizels N, Weiner A. CCA-adding enzymes and poly(A) polymerases are all members of the same nucleotidyltransferase superfamily: characterization of the CCA-adding enzyme from the archaeal hyperthermophile Sulfolobus shibatae. RNA. 1996;2:895-908 pubmed..One implication of these data is that there may have been intraconversion of CCA-adding and poly(A) polymerase activities early in evolution...
- Miyaji K, Nakagawa Y, Matsumoto K, Yoshida H, Morikawa H, Hongou Y, et al. Overexpression of a DEAD box/RNA helicase protein, rck/p54, in human hepatocytes from patients with hepatitis C virus-related chronic hepatitis and its implication in hepatocellular carcinogenesis. J Viral Hepat. 2003;10:241-8 pubmed..These findings suggest that rck/p54 protein is possibly involved in the replication of HCV genomes in hepatocytes and in tumourigenesis of hepatocellular carcinomas. ..
- Buelt M, Glidden B, Storm D. Regulation of p68 RNA helicase by calmodulin and protein kinase C. J Biol Chem. 1994;269:29367-70 pubmed..Both phosphorylation and calmodulin binding inhibited p68 ATPase activity, suggesting that the RNA unwinding activity of p68 may be regulated by dual Ca2+ signal transduction pathways through its IQ domain. ..
- Minshall N, Thom G, Standart N. A conserved role of a DEAD box helicase in mRNA masking. RNA. 2001;7:1728-42 pubmed..These data suggest that this helicase family represses translation of maternal mRNA in early development, and that its activity may be attenuated during meiotic maturation, prior to cytoplasmic polyadenylation. ..
- Navarro R, Shim E, Kohara Y, Singson A, Blackwell T. cgh-1, a conserved predicted RNA helicase required for gametogenesis and protection from physiological germline apoptosis in C. elegans. Development. 2001;128:3221-32 pubmed..elegans certain aspects of oocyte development are monitored by the physiological germline apoptosis pathway, and that similar surveillance mechanisms may contribute to germline apoptosis in other species. ..
- De la Cruz J, Kressler D, Rojo M, Tollervey D, Linder P. Spb4p, an essential putative RNA helicase, is required for a late step in the assembly of 60S ribosomal subunits in Saccharomyces cerevisiae. RNA. 1998;4:1268-81 pubmed..We propose that Spb4p is involved directly in a late and essential step during assembly of 60S ribosomal subunits, presumably by acting as an rRNA helicase. ..