Distinct roles of non-canonical poly(A) polymerases in RNA metabolism

SAN PAOLO, Salvatore, Štěpánka VAŇÁČOVÁ, L. SCHENK, T. SCHERRER, Diana BLANK, Walter KELLER and Andre P. GERBER. Distinct roles of non-canonical poly(A) polymerases in RNA metabolism. PLoS Genetics. Public Library of Science, 2009, vol. 5, No 7, p. e1000555, 17 pp. ISSN 1553-7390.

Basic information

• Original name: Distinct roles of non-canonical poly(A) polymerases in RNA metabolism
• Name in Czech: Distinct roles of non-canonical poly(A) polymerases in RNA metabolism
• Authors: SAN PAOLO, Salvatore (380 Italy), Štěpánka VAŇÁČOVÁ (203 Czech Republic, guarantor), L. SCHENK (756 Switzerland), T. SCHERRER (756 Switzerland), Diana BLANK (756 Switzerland), Walter KELLER (276 Germany) and Andre P. GERBER (756 Switzerland).
• Edition: PLoS Genetics, Public Library of Science, 2009, 1553-7390.

Other information

• Original language: English
• Type of outcome: Article in a journal
• Field of Study: Genetics and molecular biology
• Country of publisher: United States of America
• Confidentiality degree: is not subject to a state or trade secret
• WWW: URL
• Impact factor: Impact factor: 9.532
• RIV identification code: RIV/00216224:14310/09:00036231
• Organization unit: Faculty of Science
• UT WoS: 000269219500032
• Keywords (in Czech): TRAMP; polyadenylation; RNA degradation; RNA quality control; Trf4; Trf5
• Keywords in English: TRAMP; polyadenylation; RNA degradation; RNA quality control; Trf4; Trf5
• Tags: polyadenylation, RNA degradation, RNA quality control, TRAMP, Trf4, Trf5
• Tags: International impact, Reviewed

Abstract

Trf4p and Trf5p are non canonical poly(A) polymerases and are part of the heteromeric protein complexes TRAMP4 and TRAMP5 that promote the degradation of aberrant and short lived RNA substrates by interacting with the nuclear exosome. To assess the level of functional redundancy between the paralogous Trf4 and Trf5 proteins and to investigate the role of the Trf4 dependent polyadenylation in vivo, we used DNA microarrays to compare gene expression of the wild-type yeast strain of S. cerevisiae with either that of trf4delta or trf5delta mutant strains or the trf4delta mutant expressing the polyadenylation-defective Trf4(DADA) protein. We found little overlap between the sets of transcripts with altered expression in the trf4delta or the trf5delta mutants, suggesting that Trf4p and Trf5p target distinct groups of RNAs for degradation. Surprisingly, most RNAs the expression of which was altered by the trf4 deletion were restored to wild type levels by overexpression of TRF4(DADA), showing that the polyadenylation activity of Trf4p is dispensable in vivo. Apart from previously reported Trf4p and Trf5p target RNAs, this analysis along with in vivo cross-linking and RNA immunopurification chip experiments revealed that both the TRAMP4 and the TRAMP5 complexes stimulate the degradation of spliced out introns via a mechanism that is independent of the polyadenylation activity of Trf4p. In addition, we show that disruption of trf4 causes severe shortening of telomeres suggesting that TRF4 functions in the maintenance of telomere length. Finally, our study demonstrates that TRF4, the exosome, and TRF5 participate in antisense RNA mediated regulation of genes involved in phosphate metabolism. In conclusion, our results suggest that paralogous TRAMP complexes have distinct RNA selectivities with functional implications in RNA surveillance as well as other RNA related processes. This indicates widespread and integrative functions of TRAMP complexes for the coordination of different gene expression regulatory processes.

Abstract (in Czech)

Trf4p and Trf5p are non canonical poly(A) polymerases and are part of the heteromeric protein complexes TRAMP4 and TRAMP5 that promote the degradation of aberrant and short lived RNA substrates by interacting with the nuclear exosome. To assess the level of functional redundancy between the paralogous Trf4 and Trf5 proteins and to investigate the role of the Trf4 dependent polyadenylation in vivo, we used DNA microarrays to compare gene expression of the wild-type yeast strain of S. cerevisiae with either that of trf4delta or trf5delta mutant strains or the trf4delta mutant expressing the polyadenylation-defective Trf4(DADA) protein. We found little overlap between the sets of transcripts with altered expression in the trf4delta or the trf5delta mutants, suggesting that Trf4p and Trf5p target distinct groups of RNAs for degradation. Surprisingly, most RNAs the expression of which was altered by the trf4 deletion were restored to wild type levels by overexpression of TRF4(DADA), showing that the polyadenylation activity of Trf4p is dispensable in vivo. Apart from previously reported Trf4p and Trf5p target RNAs, this analysis along with in vivo cross-linking and RNA immunopurification chip experiments revealed that both the TRAMP4 and the TRAMP5 complexes stimulate the degradation of spliced out introns via a mechanism that is independent of the polyadenylation activity of Trf4p. In addition, we show that disruption of trf4 causes severe shortening of telomeres suggesting that TRF4 functions in the maintenance of telomere length. Finally, our study demonstrates that TRF4, the exosome, and TRF5 participate in antisense RNA mediated regulation of genes involved in phosphate metabolism. In conclusion, our results suggest that paralogous TRAMP complexes have distinct RNA selectivities with functional implications in RNA surveillance as well as other RNA related processes. This indicates widespread and integrative functions of TRAMP complexes for the coordination of different gene expression regulatory processes.

Links

• MSM0021622413, plan (intention): Name: Proteiny v metabolismu a při interakci organismů s prostředím

Investor: Ministry of Education, Youth and Sports of the CR, Proteins in metabolism and interaction of organisms with the environment