Ribonuclease III

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]

Ribonuclease III domain
Ribonuclease III structure interacting with double stranded RNA.
Identifiers
SymbolRNase_III
PfamPF00636
InterProIPR000999
PROSITEPDOC00448
SCOP21jfz / SCOPe / SUPFAM
Available protein structures:
Pfam  structures / ECOD  
PDBRCSB PDB; PDBe; PDBj
PDBsumstructure summary
PDB1o0wB:51-141 2a11A:41-134 1jfzA:37-121

1rc7A:37-121 1yywA:37-121 1i4sA:37-121 1rc5B:37-121 1yyoA:37-121 1yykB:37-121

1yz9A:37-121 2fflA:333-418 1u61A:10-111

Types of RNase III

The RNase III superfamily is divided into four known classes: 1, 2, 3, and 4. Each class is defined by its domain structure.[6]

Class 1 RNase III

  • Class 1 RNase III enzymes have a homodimeric structure whose function is to cleave dsRNA into multiple subunits. It is a Mg2+-dependent endonuclease and is largely found in bacteria and bacteriophage. Class 1 RNase III have been found in Glomeromycotan fungi, which was suspected to be the result of horizontal gene transfer from cyanobacteria.[7] Among the RNases III in the class are the rnc from E. coli. Typically, class I enzymes possess a single RNase III domain (RIIID) followed by a dsRNA-binding domain (dsRBD).[6] They process precursors to ribosomal RNA (rRNA), small nuclear RNA (snRNA) and small nucleolar RNA (snoRNA). The basic dsRNA cleavage function of Class 1 RNase III is retained in most of the organisms in which it is present. However, in a number of species the function has changed and taken on different or additional biological roles.[8]
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.[9]
The variances of Class 1 RNase III, called Mini-III, are homodimeric enzymes and consist solely of the RNase III domains.[10]

Class 2 RNase III

Class 2 ribonuclease III (Rnt1p) from Saccharomyces cerevisiae in complex with double-stranded RNA
  • Class II is defined by the presence of an N-terminal domain (NTD), a RIIID, and a dsRBD. Class II is found in some fungi species.[6] They process precursors to rRNA, snRNA, and snoRNA.
Yeast nucleases with the Class 2 RNase III domain:[11]
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.[12]
Pac1 (UniProtKB P22192) - S. pombe - this RNase III is located on chromosome II of the yeast genome and, when over expressed, is directly involved in the sterility, lack of mating efficiency, abnormal mitotic cell cycle, and mutation suppression of the organism.[13]

Class 3 RNase III

The crystal structure of the human Drosha ribonuclease enzyme in complex with two C-terminal helices of the DGCR8 protein.

Class 4 RNase III

  • Class 4 RNases III include the Dicer family of enzymes known to function in RNA interference (RNAi).[15] Class 4 III RNases are S-RNase 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.[16]
  • Dicer enzymes process dsRNA substrates into small RNA fragments of individual size ranging from 21-27 nucleotides in length.[17] Dicer has an N-terminal helicase/ATPase domain which is followed by another domain of an unknown function. It also comprises the centrally positioned PAZ domain and a C-terminal configuration which includes one dsRBD and two RNase III catalytic domains.[18] Interactions of Dicer occurs with other proteins, which includes TRBP, PACT, and Ago2.[19] RNAs that are produced by Dicer act as guides for a sequence of particular silencing of cognate genes through RNAi and related pathways.[17]

Human proteins containing RNase III domain

See also

References
  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. PMID 10713462.
  2. Zamore, Phillip 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. PMID 11885596.
  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. PMID 11809414.
  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. PMID 8589060.
  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. PMC 4652041. PMID 26438818.
  6. Liang Y-H, Lavoie M, Comeau M-A, Elela SA, Ji X. Structure of a Eukaryotic RNase III Post-Cleavage Complex Reveals a Double- Ruler Mechanism for Substrate Selection. Molecular cell. 2014;54(3):431-444. doi:10.1016/j.molcel.2014.03.006.
  7. Soon-Jae Lee, Mengxuan Kong, Paul Harrison, Mohamed Hijri; Conserved proteins of the RNA interference system in the arbuscular mycorrhizal fungus Rhizoglomus irregulare provide new insight into the evolutionary history of Glomeromycota, Genome Biology and Evolution, , evy002, https://doi.org/10.1093/gbe/evy002
  8. 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. PMC 1112141. PMID 15890961.
  9. "rnc - Ribonuclease 3 - Escherichia coli (strain K12) - rnc gene & protein". www.uniprot.org. UniProt Consortium. Retrieved 5 November 2016.
  10. 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. PMC 4357697. PMID 25634891.
  11. 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. PMID 26778206.
  12. "RNT1/YMR239C Overview". www.yeastgenome.org. Stanford University. Retrieved 5 November 2016.
  13. "pac1 (SPBC119.11c)". www.pombase.org. EMBL-EBI. Retrieved 5 November 2016.
  14. 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.
  15. 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. S2CID 4371481. closed access
  16. 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. hdl:11336/42800. PMID 26025538.
  17. 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. PMID 17194582.
  18. 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. PMID 18363798.
  19. 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. PMC 3867540. PMID 24124076.
  20. "Tissue expression of DICER1 - Summary". www.proteinatlas.org. The Human Protein Atlas. Retrieved 5 November 2016.
  21. "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
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