Conserved mRNA-binding proteomes in eukaryotic organisms

Nature Structural and Molecular Biology

Volumn 22, Issue 12, 2015, Pages 1027-1033

  Matia González, Ana M ^a   Laing, Emma E ^a   Gerber, André P ^a  

^a UNIVERSITY OF SURREY   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; MESSENGER RNA BINDING PROTEIN; POLYADENYLATED RNA; RNA BINDING PROTEIN; UNCLASSIFIED DRUG; PROTEOME;

AMINO ACID SEQUENCE; APOPTOSIS; ARTICLE; CAENORHABDITIS ELEGANS; CONTROLLED STUDY; GENE INTERACTION; GENETIC CONSERVATION; GLYCOLYSIS; INTRACELLULAR SPACE; LARVAL STAGE; METABOLIC REGULATION; NONHUMAN; POLYADENYLATION; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN EXPRESSION; PROTEIN MOTIF; PROTEIN PURIFICATION; PROTEIN RNA BINDING; RNA METABOLISM; SACCHAROMYCES CEREVISIAE; ANIMAL; CHEMISTRY; COMPARATIVE STUDY; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; NUCLEOTIDE SEQUENCE;

ANIMALS; CAENORHABDITIS ELEGANS; CONSERVED SEQUENCE; GENE EXPRESSION REGULATION; PROTEOME; RNA, MESSENGER; RNA-BINDING PROTEINS; SACCHAROMYCES CEREVISIAE;

EID: 84949532380     PISSN: 15459993     EISSN: 15459985     Source Type: Journal    
DOI: 10.1038/nsmb.3128     Document Type: Article

References (45)

1. Glisovic T., Bachorik J.L., Yong J., & Dreyfuss G. RNA-binding proteins and post-Transcriptional gene regulation. FEBS Lett. 582, 1977-1986 (2008
2. Lukong K.E., Chang K.W., Khandjian E.W., & Richard S. RNA-binding proteins in human genetic disease. Trends Genet. 24, 416-425 (2008
3. Gerstberger S., Hafner M., & Tuschl T. A census of human RNA-binding proteins. Nat. Rev. Genet. 15, 829-845 (2014
4. Scherrer T., Mittal N., Janga S.C., & Gerber A.P. A screen for RNA-binding proteins in yeast indicates dual functions for many enzymes. PLoS ONE. 5, e15499 (2010
5. Tsvetanova N.G., Klass D.M., Salzman J., & Brown P.O. Proteome-wide search reveals unexpected RNA-binding proteins in Saccharomyces cerevisiae. PLoS ONE. 5, e12671 (2010
6. Castello A., et al. Insights into RNA biology from an atlas of mammalian mRNA-binding proteins. Cell. 149, 1393-1406 (2012
7. Baltz A.G., et al. The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts. Mol. Cell. 46, 674-690 (2012
8. Mitchell S.F., Jain S., She M., & Parker R. Global analysis of yeast mRNPs. Nat. Struct. Mol. Biol. 20, 127-133 (2013
9. Kwon S.C., et al. The RNA-binding protein repertoire of embryonic stem cells. Nat. Struct. Mol. Biol. 20, 1122-1130 (2013
10. Zhang L., Zhang K., Prandl R., & Schoffl F. Detecting DNA-binding of proteins in vivo by UV-crosslinking and immunoprecipitation. Biochem. Biophys. Res. Commun. 322, 705-711 (2004
11. Frey S., Pool M., & Seedorf M. Scp160p, an RNA-binding, polysome-Associated protein, localizes to the endoplasmic reticulum of Saccharomyces cerevisiae in a microtubule-dependent manner. J. Biol. Chem. 276, 15905-15912 (2001
12. Mittal N., Roy N., Babu M.M., & Janga S.C. Dissecting the expression dynamics of RNA-binding proteins in posttranscriptional regulatory networks. Proc. Natl. Acad. Sci. USA. 106, 20300-20305 (2009
13. Hogan D.J., Riordan D.P., Gerber A.P., Herschlag D., & Brown P.O. Diverse RNA-binding proteins interact with functionally related sets of RNAs, suggesting an extensive regulatory system. PLoS Biol. 6, e255 (2008
14. Arava Y., et al. Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA. 100, 3889-3894 (2003
15. Costanzo M.C., et al. Saccharomyces genome database provides new regulation data. Nucleic Acids Res. 42, D717-D725 (2014
16. UniProt Consortium Activities at the Universal Protein Resource (UniProt). Nucleic Acids Res. 42, D191-D198 (2014
17. Thomas M.P., & Lieberman J. Live or let die: posttranscriptional gene regulation in cell stress and cell death. Immunol. Rev. 253, 237-252 (2013
18. Gartner A., Milstein S., Ahmed S., Hodgkin J., & Hengartner M.O. A conserved checkpoint pathway mediates DNA damage-induced apoptosis and cell cycle arrest in C. elegans. Mol. Cell. 5, 435-443 (2000
19. Conradt B., & Horvitz H.R. The C. Elegans Protein EGL-1 Is Required for Programmed Cell Death and Interacts with the Bcl-2-like Protein CED-9. Cell. 93, 519-529 (1998
20. Francis R., Maine E., & Schedl T. Analysis of the multiple roles of gld-1 in germline development: interactions with the sex determination cascade and the glp-1 signaling pathway. Genetics. 139, 607-630 (1995
21. Tamburino A.M., Ryder S.P., & Walhout A.J. A Compendium of Caenorhabditis Elegans RNA Binding Proteins Predicts Extensive Regulation at Multiple Levels. G3 (Bethesda) 3, 297-304 (2013
22. Harris T.W., et al. WormBase 2014: new views of curated biology. Nucleic Acids Res. 42, D789-D793 (2014
23. Lettre G., et al. Genome-wide RNAi identifies p53-dependent and -independent regulators of germ cell apoptosis in C. elegans. Cell Death Differ. 11, 1198-1203 (2004
24. Huang C.Y., et al. C. elegans EIF-3.K promotes programmed cell death through CED-3 caspase. PLoS ONE. 7, e36584 (2012
25. Voutev R., Killian D.J., Ahn J.H., & Hubbard E.J. Alterations in ribosome biogenesis cause specific defects in C. elegans hermaphrodite gonadogenesis. Dev. Biol. 298, 45-58 (2006
26. Cléry A., Blatter M., & Allain F.H. RNA recognition motifs: boring?. Not quite. Curr. Opin. Struct. Biol. 18, 290-298 (2008
27. Ostlund G., et al. InParanoid 7: new algorithms and tools for eukaryotic orthology analysis. Nucleic Acids Res. 38, D196-D203 (2010
28. Strein C., Alleaume A.M., Rothbauer U., Hentze M.W., & Castello A. A versatile assay for RNA-binding proteins in living cells. RNA. 20, 721-731 (2014
29. Halbach A., et al. Cotranslational assembly of the yeast SET1C histone methyltransferase complex. EMBO J. 28, 2959-2970 (2009
30. Lee A.S., Kranzusch P.J., & Cate J.H. eIF3 targets cell-proliferation messenger RNAs for translational activation or repression. Nature. 522, 111-114 (2015
31. Henics T., et al. Mammalian Hsp70 and Hsp110 proteins bind to RNA motifs involved in mRNA stability. J. Biol. Chem. 274, 17318-17324 (1999
32. Zimmer C., von Gabain A., & Henics T. Analysis of sequence-specific binding of RNA to Hsp70 and its various homologs indicates the involvement of N- And C-Terminal interactions. RNA. 7, 1628-1637 (2001
33. Liu Z.R., Wilkie A.M., Clemens M.J., & Smith C.W. Detection of double-stranded RNA-protein interactions by methylene blue-mediated photo-crosslinking. RNA. 2, 611-621 (1996
34. Suh N., Jedamzik B., Eckmann C.R., Wickens M., & Kimble J. The GLD-2 poly(A) polymerase activates gld-1 mRNA in the Caenorhabditis elegans germ line. Proc. Natl. Acad. Sci. USA. 103, 15108-15112 (2006
35. Baumeister W., Walz J., Zuhl F., & Seemuller E. The proteasome: paradigm of a self-compartmentalizing protease. Cell. 92, 367-380 (1998
36. Schmid H.P., et al. The prosome: an ubiquitous morphologically distinct RNP particle associated with repressed mRNPs and containing specific ScRNA and a characteristic set of proteins. EMBO J. 3, 29-34 (1984
37. Kulichkova V.A., et al. 26S proteasome exhibits endoribonuclease activity controlled by extra-cellular stimuli. Cell Cycle. 9, 840-849 (2010
38. Mittenberg A., et al. Mass-spectrometric analysis of proteasome subunits exhibiting endoribonuclease activity. Cell Tissue Biol. 8, 423-440 (2014
39. Makino D.L., Halbach F., & Conti E. The RNA exosome and proteasome: common principles of degradation control. Nat. Rev. Mol. Cell Biol. 14, 654-660 (2013
40. Ciesla J. Metabolic enzymes that bind RNA: yet another level of cellular regulatory network?. Acta Biochim. Pol. 53, 11-32 (2006
41. Hentze M.W., & Preiss T. The REM phase of gene regulation. Trends Biochem. Sci. 35, 423-426 (2010
42. Keene J.D. RNA regulons: coordination of post-Transcriptional events. Nat. Rev. Genet. 8, 533-543 (2007
43. Scheckel C., Gaidatzis D., Wright J.E., & Ciosk R. Genome-wide analysis of GLD-1-mediated mRNA regulation suggests a role in mRNA storage. PLoS Genet. 8, e1002742 (2012
44. Huh W.K., et al. Global analysis of protein localization in budding yeast. Nature. 425, 686-691 (2003
45. Ghaemmaghami S., et al. Global analysis of protein expression in yeast. Nature. 425, 737-741 (2003