Divalent metal-dependent catalysis and cleavage specificity of CSP41, a chloroplast endoribonuclease belonging to the short chain dehydrogenase/reductase superfamily

Nucleic Acids Research

Volumn 31, Issue 15, 2003, Pages 4317-4325

  Bollenbach, Thomas J ^a   Stern, David B ^a  

^a United States Department of Agriculture Agricultural Research Service and Boyce Thompson Institute for Plant Research   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANGIOTENSIN; ASPARAGINE; CALCIUM CHLORIDE; CALCIUM ION; CHLOROPLAST RNA; COPPER ION; DOUBLE STRANDED RNA; ENDONUCLEASE; MAGNESIUM CHLORIDE; MAGNESIUM ION; MANGANESE; METAL; OXIDOREDUCTASE; RNA BINDING PROTEIN; ZINC ION; CALCIUM; CYTOCHROME B; CYTOCHROME B6F; DIVALENT CATION; ENDORIBONUCLEASE CSP41; MAGNESIUM; PETD PROTEIN, CYTOCHROME B(6)F COMPLEX; PLANT RNA; RIBONUCLEASE;

AMINO ACID ANALYSIS; ARTICLE; BINDING SITE; CATALYSIS; CHLOROPLAST; CONTROLLED STUDY; ENZYME ACTIVITY; ENZYME MECHANISM; GENE CONTROL; LEAF DEVELOPMENT; METAL BINDING; MOLECULAR RECOGNITION; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT DEVELOPMENT; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN FUNCTION; RNA CLEAVAGE; SITE DIRECTED MUTAGENESIS; CHEMISTRY; CLASSIFICATION; ENZYME SPECIFICITY; ENZYMOLOGY; GENETICS; METABOLISM; MOLECULAR GENETICS; SEQUENCE ALIGNMENT;

BASE SEQUENCE; BINDING SITES; CALCIUM; CATALYSIS; CATIONS, DIVALENT; CHLOROPLASTS; CYTOCHROME B GROUP; CYTOCHROME B6F COMPLEX; ENDORIBONUCLEASES; MAGNESIUM; MOLECULAR SEQUENCE DATA; MUTAGENESIS, SITE-DIRECTED; OXIDOREDUCTASES; RNA, PLANT; SEQUENCE ALIGNMENT; SUBSTRATE SPECIFICITY;

EID: 0043163808     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkg640     Document Type: Article

References (38)

1. Stern,D.B., Jones,H. and Gruissem,W. (1989) Function of plastid mRNA 3′ inverted repeats: RNA stabilization and gene-specific protein binding. J. Biol. Chem., 264, 18742-18750.
2. Chen,H.C. and Stern,D.B. (1991) Specific binding of chloroplast proteins in vitro to the 3′ untranslated region of spinach chloroplast petD messenger RNA. Mol. Cell. Biol., 11, 4380-4388.
3. Memon,A.R., Meng,B. and Mullet,J.E. (1996) RNA-binding proteins of 37/38 kDa bind specifically to the barley chloroplast psbA 3′-end untranslated RNA. Plant Mol. Biol., 30, 1195-1205.
4. Monde,R.A., Schuster,G. and Stern,D.B. (2000) Processing and degradation of chloroplast mRNA. Biochimie, 82, 573-582.
5. Klaff,P. (1995) mRNA decay in spinach chloroplasts: psbA mRNA degradation is initiated by endonucleolytic cleavages within the coding region. Nucleic Acids Res., 23, 4885-4892.
6. Kudla,J., Hayes,R. and Gruissem,W. (1996) Polyadenylation accelerates degradation of chloroplast mRNA. EMBO J., 15, 7137-7146.
7. Chen,H. and Stern,D.B. (1991) Specific ribonuclease activities in spinach chloroplasts promote mRNA maturation and degradation. J. Biol. Chem., 266, 24205-24211.
8. Nickelsen,J. and Link,G. (1993) The 54 kDa RNA-binding protein from mustard chloroplasts mediates endonucleolytic transcript 3′ end formation in vitro. Plant J., 3, 537-544.
9. Yang,J., Schuster,G. and Stern,D.B. (1996) CSP41, a sequence-specific chloroplast mRNA binding protein, is an endoribonuclease. Plant Cell, 8, 1409-1420.
10. Yang,J. and Stern,D.B. (1997) The spinach chloroplast endoribonuclease CSP41 cleaves the 3′ untranslated region of petD mRNA primarily within its terminal stem-loop structure. J. Biol. Chem., 272, 12784-12880.
11. Baker,M.E., Grundy,W.N. and Elkan,C.P. (1998) Spinach CSP41, an mRNA-binding protein and ribonuclease, is homologous to nucleotide-sugar epimerases and hydroxysteriod dehydrogenases. Biochem. Biophys. Res. Commun., 248, 250-254.
12. Bollenbach,T.J. and Stern,D.B. (2003) Secondary structures common to chloroplast mRNA 3′ UTRs direct cleavage by CSP41, an endoribonuclease belonging to the short chain dehydrogenase/reductase superfamily. J. Biol. Chem., 278, in press.
13. Evguenieva-Hackenberg,E., Schiltz,E. and Klug,G. (2002) Dehydrogenases from all three domains of life cleave RNA. J. Biol. Chem., 277, 46145-46150.
14. Shi,J., Krishnamoorthy,G., Yang,Y., Hu,L., Chaturvedi,N., Harilal,D., Qin,J. and Cui,J. (2002) Mechanism of magnesium activation of calcium-activated potassium channels. Nature, 418, 876-880.
15. Needham,J.V., Chen,T.Y. and Falke,J.J. (1993) Novel ion specificity of a carboxylate cluster Mg(II) binding site: strong charge selectivity and weak size selectivity. Biochemistry, 32, 3363-3367.
16. Horlitz,M. and Klaff,P. (2000) Gene-specific trans-regulatory functions of magnesium for chloroplast mRNA stability in higher plants. J. Biol. Chem., 275, 35638-35645.
17. 2+ by using a fluorescent probe and necessity of stromal alkalinization. Arch. Biochem. Biophys., 412, 126-132.
18. Stern,D.B. and Gruissem,W. (1987) Control of plastid gene expression: 3′ inverted repeats act as mRNA processing and stabilizing elements, but do not terminate transcription. Cell, 51, 1145-1157.
19. Mathews,D.H., Sabina,J., Zuker,M. and Turner,D.H. (1999) Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol., 288, 911-940.
20. Zamore,P.D., Patton,J.G. and Green,M.R. (1992) Cloning and domain structure of the mammalian splicing factor U2AF. Nature, 355, 609-614.
21. protein and through interactions with U2 snRNP-A′ protein. Mol. Cell. Biol., 11, 1829-1839.
22. Nagy,E., Henics,T., Eckert,M., Miseta,A., Lightowlers,R.N. and Kellermayer,M. (2000) Identification of the NAD(+)-binding fold of glyceraldehyde-3-phosphate dehydrogenase as a novel RNA-binding domain. Biochem. Biophys. Res. Commun., 275, 253-260.
23. Deutscher,M.P. (1985) E.coli RNases: making sense of alphabet soup. Cell, 40, 731-732.
24. Li,H.L., Chelladurai,B.S., Zhang,K. and Nicholson,A.W. (1993) Ribonuclease III cleavage of a bacteriophage T7 processing signal. Divalent cation specificity and specific anion effects. Nucleic Acids Res., 21, 1919-1925.
25. Keck,J.L., Goedken,E.R. and Marqusee,S. (1998) Activation/attenuation model for RNase H. A one-metal, mechanism with second-metal inhibition. J. Biol. Chem., 273, 34128-34133.
26. Chai,Q., Qiu,J., Chapados,B.R. and Shen,B. (2001) Archaeoglobus fulgidus RNase HII in DNA replication: enzymological functions and activity regulation via metal cofactors. Biochem. Biophys. Res. Commun., 286, 1073-1081.
27. Claverie-Martin,F., Wang,M. and Cohen,S.N. (1997) ARD-1 cDNA from human cells encodes a site-specific single-strand endoribonuclease that functionally resembles Escherichia coli RNase E. J. Biol. Chem., 272, 13823-13828.
28. Szeberenyi,J., Roy,M.K. and Apirion,D. (1983) 7 S RNA: a single site substrate for the RNA processing enzyme ribonuclease E of Escherichia coli. Biochim. Biophys. Acta, 740, 282-290.
29. Campbell,F.E.,Jr, Cassano,A.G., Anderson,V.E. and Harris,M.E. (2002) Pre-steady-state and stopped-flow fluorescence analysis of Escherichia coli ribonuclease III: insights into mechanism and conformational changes associated with binding and catalysis. J. Mol. Biol., 317, 21-40.
30. 2+ ions reveals two divalent metals bound in the active site. J. Biol. Chem., 276, 7266-7271.
31. Katayanagi,K., Miyagawa,M., Matsushima,M., Ishikawa,M., Kanaya,S., Ikehara,M., Matsuzaki,T. and Morikawa,K. (1990) Three-dimensional structure of ribonuclease H from E.coli. Nature, 347, 306-309.
32. 2+. Biochemistry, 17, 131-138.
33. Chelladurai,B., Li,H., Zhang,K. and Nicholson,A.W. (1993) Mutational analysis of a ribonuclease III processing signal. Biochemistry, 32, 7549-7558.
34. Sola,M., Lopez-Hernandez,E., Cronet,P., Lacroix,E., Serrano,L., Coll,M. and Parraga,A. (2000) Towards understanding a molecular switch mechanism: thermodynamic and crystallographic studies of the signal transduction protein CheY. J. Mol. Biol., 303, 213-225.
35. Monde,R.A., Greene,J.C. and Stern,D.B. (2000) The sequence and secondary structure of the 3′-UTR affect 3′-end maturation, RNA accumulation and translation in tobacco chloroplasts. Plant Mol. Biol., 44, 529-542.
36. Johnson,C.H., Knight,M.R., Kondo,T., Masson,P., Sedbrook,J., Haley,A. and Trewavas,A. (1995) Circadian oscillations of cytosolic and chloroplastic free calcium in plants. Science, 269, 1863-1865.
37. 2+ concentration. Biochim. Biophys Acta, 461, 313-325.
38. 2+-dependent chloroplast inorganic pyrophosphatase from Sorghum vulgare leaves. Arch. Biochem. Biophys., 260, 277-284.