Ribonuclease III

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Ribonuclease III domain
PDB 1yyw EBI.jpg
Ribonuclease III structure interacting with double stranded RNA.
Identifiers
Symbol RNase_III
Pfam PF00636
InterPro IPR000999
PROSITE PDOC00448
SCOP 1jfz
SUPERFAMILY 1jfz

Ribonuclease III (RNase III or RNase C)[1](BRENDA 3.1.26.3) is a type of ribonuclease that recognizes dsRNA and cleaves it at specific targeted locations to transform them into mature RNAs.[2] These enzymes are a group of endoribonucleases that are characterized by their ribonuclease domain, which is labelled the RNase III domain.[3] They are ubiquitous compounds in the cell and play a major role in pathways such as RNA precursor synthesis, RNA Silencing, and the pnp autoregulatory mechanism.[4][5]

Types of RNase III[edit]

Within the RNase III superfamily, there are four known classes: 1, 2, 3, and 4. Each class is defined by both its functional and structural differences.

Class 1 RNase III

Class I ribonuclease III (Rnt1p) from Saccharomyces cerevisiae in complex with double-stranded RNA
  • Class 1 RNase III have a dimer structure whose function is to cleave dsRNA into multiple subunits. It is a Mg2+ dependent endonuclease and is largely found in bacteria, bacteriophage, and some fungi. Among the RNases III in the class are the rnc from E. coli, Pac1p from S. pombe, and Rnt1p from S. cerevisiae. They process precursors to ribosomal RNA, and in the case of fungi, process precursors to small nuclear RNA (snRNA) and small nucleolar RNA (snoRNA). The basic dsRNA cleavage function of Class 1 RNase III is similar in most of the organisms in which it is present. However, as the enzyme was conserved in various species over time, the restraints of its function has changed and expanded to meet the biological needs of each organism.[6]
Yeast nucleases with with the Class 1 RNase III domain:[7]
RNT1 (UniProtKB Q02555) - S. cerevisiae - this RNase III is involved in the transcription and processing of rDNA, the 3' end formation of U2 snRNA via cleavage of the terminal loop, cell wall stress response and degradation, and regulation of morphogenesis checkpoint genes.[8]
Pac1 (UniProtKB P22192) - S. pombe - this RNase III is located on chromosome II of the yeast nuclease and when over expressed, is directly involved in the sterility, lack of mating efficiency, abnormal mitotic cell cycle, and mutation suppression of the organism.[9]
Rnc (UniProtKB P0A7Y0) - E.Coli - this RNase III is involved in the processing of viral transcripts and some mRNAs through the cleavage of multiple areas on the dsRNA. This cleavage can be influenced by ribosomal protein presence.[10]

Class 2 RNase III

The crystal structure of the human Drosha ribonuclease enzyme in complex with two C-terminal helices of the DGCR8 protein.
  • Class 2 RNases III include the Drosha family of enzymes known to function in maturation of precursors to miRNA.[11]

Class 3 RNase III

  • Class 3 RNases III include the Dicer family of enzymes known to function in RNA interference (RNAi).[12] Class III Rinases are S-Rnases components. It is a component of the self-incompatibility system in Rosaceae, Solanaceae, and Plantaginaceae. They are recruited to cope with various environmental stress scenarios.[13]
  • Dicer enzymes process dsRNA subtrates into small RNA fragments of individual size ranging from 21-27 nucleotides in length.[14] Dicer has an N-terminal helicase/ATPase domain which is followed by another domain of an unknown function. It is centrally positioned PAZ domain and a C-terminal configuration which includes one dsRBD and two RNase III catalytic domains.[15] Interactions of Dicer occurs with other proteins, which includes TRBP, PACT, and Ago2.[16] RNAs that are produced by Dicer act as guides for a sequence of particular silencing of cognate genes through RNAi and related pathways.[14]

Class 4 RNase III

  • Class 4 RNases III, called Mini-III, are homodimeric enzymes and consist solely of the RNase III domains.[17]

Human proteins containing RNase III domain[edit]

See also[edit]

References[edit]

  1. ^ Filippov, Valery; Solovyev, Victor; Filippova, Maria; Gill, Sarjeet S. (7 March 2000). "A novel type of RNase III family proteins in eukaryotes". Gene. 245 (1): 213–221. doi:10.1016/S0378-1119(99)00571-5. 
  2. ^ Zamore, Phollip D. (December 2001). "Thirty-Three Years Later, a Glimpse at the Ribonuclease III Active Site". Molecular Cell. 8 (6): 1158–1160. doi:10.1016/S1097-2765(01)00418-X. 
  3. ^ Conrad, Christian; Rauhut, Reinhard (February 2002). "Ribonuclease III: new sense from nuisance". The International Journal of Biochemistry & Cell Biology. 34 (2): 116–129. doi:10.1016/S1357-2725(01)00112-1. 
  4. ^ Inada, T.; Nakamura, Y. (1995). "Lethal double-stranded RNA processing activity of ribonuclease III in the absence of SuhB protein of Escherichia coli". Biochimie. 77 (4): 294–302. doi:10.1016/0300-9084(96)88139-9. 
  5. ^ Park, Hongmarn; Yakhnin, Helen; Connolly, Michael; Romeo, Tony; Babitzke, Paul; Gourse, R. L. (15 December 2015). "CsrA Participates in a PNPase Autoregulatory Mechanism by Selectively Repressing Translation of Transcripts That Have Been Previously Processed by RNase III and PNPase". Journal of Bacteriology. 197 (24): 3751–3759. doi:10.1128/JB.00721-15. 
  6. ^ Kreuze, Jan F.; Savenkov, Eugene I.; Cuellar, Wilmer; Li, Xiangdong; Valkonen, Jari P. T. (1 June 2005). "Viral Class 1 RNase III Involved in Suppression of RNA Silencing". Journal of Virology. 79 (11): 7227–7238. doi:10.1128/JVI.79.11.7227-7238.2005. ISSN 0022-538X. Retrieved 5 November 2016. 
  7. ^ Wu, Chang-Xian; Xu, Xian-Jin; Zheng, Ke; Liu, Fang; Yang, Xu-Dong; Chen, Chuang-Fu; Chen, Huan-Chun; Liu, Zheng-Fei (1 April 2016). "Characterization of ribonuclease III from Brucella". Gene. 579 (2): 183–192. doi:10.1016/j.gene.2015.12.068. 
  8. ^ "RNT1/YMR239C Overview". www.yeastgenome.org. Stanford University. Retrieved 5 November 2016. 
  9. ^ "pac1 (SPBC119.11c)". www.pombase.org. EMBL-EBI. Retrieved 5 November 2016. 
  10. ^ "rnc - Ribonuclease 3 - Escherichia coli (strain K12) - rnc gene & protein". www.uniprot.org. UniProt Consortium. Retrieved 5 November 2016. 
  11. ^ Filippov V, Solovyev V, Filippova M, Gill SS (Mar 2000). "A novel type of RNase III family proteins in eukaryotes". Gene. 245 (1): 213–221. doi:10.1016/S0378-1119(99)00571-5. PMID 10713462. 
  12. ^ Bernstein E, Caudy AA, Hammond SM, Hannon GJ (2001). "Role for a bidentate ribonuclease in the initiation step of RNA interference". Nature. 409 (6818): 363–6. doi:10.1038/35053110. PMID 11201747. 
  13. ^ Rojas, Hernán; Floyd, Brice; Morriss, Stephanie C.; Bassham, Diane; MacIntosh, Gustavo C.; Goldraij, Ariel (1 July 2015). "NnSR1, a class III non-S-RNase specifically induced in Nicotiana alata under phosphate deficiency, is localized in endoplasmic reticulum compartments". Plant Science. 236: 250–259. doi:10.1016/j.plantsci.2015.04.012. Retrieved 7 November 2016. 
  14. ^ a b MacRae, Ian J; Doudna, Jennifer A (February 2007). "Ribonuclease revisited: structural insights into ribonuclease III family enzymes". Current Opinion in Structural Biology. 17 (1): 138–145. doi:10.1016/j.sbi.2006.12.002. 
  15. ^ Redko, Yulia; Bechhofer, David H.; Condon, Ciarán (June 2008). "Mini-III, an unusual member of the RNase III family of enzymes, catalyses 23S ribosomal RNA maturation in B. subtilis". Molecular Microbiology. 68 (5): 1096–1106. doi:10.1111/j.1365-2958.2008.06207.x. 
  16. ^ Nicholson, Allen W. (January 2014). "Ribonuclease III mechanisms of double-stranded RNA cleavage". Wiley Interdisciplinary Reviews: RNA. 5 (1): 31–48. doi:10.1002/wrna.1195. 
  17. ^ Glow, D.; Pianka, D.; Sulej, A. A.; Kozlowski, Lukasz P.; Czarnecka, J.; Chojnowski, G.; Skowronek, K. J.; Bujnicki, J. M. (2015). "Sequence-specific cleavage of dsRNA by Mini-III RNase". Nucleic Acids Research. 43 (5): 2864–2873. doi:10.1093/nar/gkv009. ISSN 0305-1048. PMID 25634891. 
  18. ^ "Tissue expression of DICER1 - Summary". www.proteinatlas.org. The Human Protein Atlas. Retrieved 5 November 2016. 
  19. ^ "Tissue expression of DROSHA - Summary". www.proteinatlas.org. The Human Protein Atlas. Retrieved 5 November 2016. 

This article incorporates text from the public domain Pfam and InterPro IPR000999

External links[edit]

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