Ribonuclease III explained

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

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 .^[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 II is defined by the presence of an N-terminal domain (NTD), a RIIID, and a . 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

• Class 3 RNases III include the Drosha family of enzymes known to function in maturation of precursors to microRNA (miRNA).^[14]

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 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.

Human proteins containing RNase III domain

• DICER1^[20]
• DROSHA^[21]

See also

• RncO

Notes and References

1. Filippov. Valery. Solovyev. Victor. Filippova. Maria. Gill. Sarjeet S.. A novel type of RNase III family proteins in eukaryotes. Gene. 7 March 2000. 245. 1. 213–221. 10.1016/S0378-1119(99)00571-5. 10713462.
2. Zamore. Phillip D.. Thirty-Three Years Later, a Glimpse at the Ribonuclease III Active Site. Molecular Cell. December 2001. 8. 6. 1158–1160. 10.1016/S1097-2765(01)00418-X. 11885596. free.
3. Conrad. Christian. Rauhut. Reinhard. Ribonuclease III: new sense from nuisance. The International Journal of Biochemistry & Cell Biology. February 2002. 34. 2. 116–129. 10.1016/S1357-2725(01)00112-1. 11809414.
4. Inada. T.. Nakamura. Y.. Lethal double-stranded RNA processing activity of ribonuclease III in the absence of SuhB protein of Escherichia coli. Biochimie. 1995. 77. 4. 294–302. 10.1016/0300-9084(96)88139-9. 8589060.
5. Park. Hongmarn. Yakhnin. Helen. Connolly. Michael. Romeo. Tony. Babitzke. Paul. Gourse. R. L.. 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. 15 December 2015. 197. 24. 3751–3759. 10.1128/JB.00721-15. 26438818. 4652041.
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.. Viral Class 1 RNase III Involved in Suppression of RNA Silencing. Journal of Virology. 1 June 2005. 79. 11. 7227–7238. 10.1128/JVI.79.11.7227-7238.2005. en. 0022-538X. 15890961. 1112141.
9. Web site: rnc - Ribonuclease 3 - Escherichia coli (strain K12) - rnc gene & protein. www.uniprot.org. UniProt Consortium. 5 November 2016.
10. Glow. D.. Pianka. D.. Sulej. A. A.. Kozlowski. Lukasz P.. Czarnecka. J.. Chojnowski. G.. Skowronek. K. J.. Bujnicki. J. M.. Sequence-specific cleavage of dsRNA by Mini-III RNase. Nucleic Acids Research. 43. 5. 2015. 2864–2873. 0305-1048. 10.1093/nar/gkv009. 25634891. 4357697.
11. Wu. Chang-Xian. Xu. Xian-Jin. Zheng. Ke. Liu. Fang. Yang. Xu-Dong. Chen. Chuang-Fu. Chen. Huan-Chun. Liu. Zheng-Fei. Characterization of ribonuclease III from Brucella. Gene. 1 April 2016. 579. 2. 183–192. 10.1016/j.gene.2015.12.068. 26778206.
12. Web site: RNT1/YMR239C Overview. www.yeastgenome.org. Stanford University. 5 November 2016.
13. Web site: pac1 (SPBC119.11c). www.pombase.org. EMBL-EBI. 5 November 2016.
14. Filippov V, Solovyev V, Filippova M, Gill SS . A novel type of RNase III family proteins in eukaryotes . Gene . 245 . 1 . 213–221 . Mar 2000 . 10713462 . 10.1016/S0378-1119(99)00571-5 .
15. . Role for a bidentate ribonuclease in the initiation step of RNA interference . Nature . 409 . 6818 . 363–6 . 2001 . 11201747 . 10.1038/35053110 . 4371481 .
16. Rojas. Hernán. Floyd. Brice. Morriss. Stephanie C.. Diane Bassham. Bassham. Diane. MacIntosh. Gustavo C.. Goldraij. Ariel. NnSR1, a class III non-S-RNase specifically induced in Nicotiana alata under phosphate deficiency, is localized in endoplasmic reticulum compartments. Plant Science. 1 July 2015. 236. 250–259. 10.1016/j.plantsci.2015.04.012. 26025538. 11336/42800. free.
17. MacRae. Ian J. Doudna. Jennifer A. Ribonuclease revisited: structural insights into ribonuclease III family enzymes. Current Opinion in Structural Biology. February 2007. 17. 1. 138–145. 10.1016/j.sbi.2006.12.002. 17194582.
18. Redko. Yulia. Bechhofer. David H.. Condon. Ciarán. Mini-III, an unusual member of the RNase III family of enzymes, catalyses 23S ribosomal RNA maturation in B. subtilis. Molecular Microbiology. June 2008. 68. 5. 1096–1106. 10.1111/j.1365-2958.2008.06207.x. 18363798. free.
19. Nicholson. Allen W.. Ribonuclease III mechanisms of double-stranded RNA cleavage. Wiley Interdisciplinary Reviews: RNA. January 2014. 5. 1. 31–48. 10.1002/wrna.1195. 24124076. 3867540.
20. Web site: Tissue expression of DICER1 - Summary. www.proteinatlas.org. The Human Protein Atlas. 5 November 2016.
21. Web site: Tissue expression of DROSHA - Summary. www.proteinatlas.org. The Human Protein Atlas. 5 November 2016.