Functional Evolution in Orthologous Cell-encoded RNA-dependent RNA Polymerases

Many eukaryotic organisms encode more than one RNA-dependent RNA polymerase (RdRP) that likely emerged as a result of gene duplication. Such RdRP paralogs often participate in distinct RNA silencing pathways and show characteristic repertoires of enzymatic activities in vitro. However, to what exten...

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Main Authors: Qian, Xinlei, Hamid, Fursham M., El Sahili, Abbas, Darwis, Dina Amallia, Wong, Yee Hwa, Bhushan, Shashi, Makeyev, Eugene V., Lescar, Julien
Other Authors: School of Biological Sciences
Format: Article
Language:English
Published: 2016
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Online Access:https://hdl.handle.net/10356/81833
http://hdl.handle.net/10220/40997
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Institution: Nanyang Technological University
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spelling sg-ntu-dr.10356-818332023-02-28T16:58:20Z Functional Evolution in Orthologous Cell-encoded RNA-dependent RNA Polymerases Qian, Xinlei Hamid, Fursham M. El Sahili, Abbas Darwis, Dina Amallia Wong, Yee Hwa Bhushan, Shashi Makeyev, Eugene V. Lescar, Julien School of Biological Sciences RNA-dependent RNA polymerase small RNAs Many eukaryotic organisms encode more than one RNA-dependent RNA polymerase (RdRP) that likely emerged as a result of gene duplication. Such RdRP paralogs often participate in distinct RNA silencing pathways and show characteristic repertoires of enzymatic activities in vitro. However, to what extent members of individual paralogous groups can undergo functional changes during speciation remains an open question. We show that orthologs of QDE-1, an RdRP component of the quelling pathway in Neurospora crassa, have rapidly diverged in evolution at the amino acid sequence level. Analyses of purified QDE-1 polymerases from N. crassa (QDE-1Ncr) and related fungi, Thielavia terrestris (QDE-1Tte) and Myceliophthora thermophila (QDE-1Mth), show that all three enzymes can synthesize RNA but the precise modes of their action differ considerably. Unlike their QDE-1Ncr counterpart favoring processive RNA synthesis, QDE-1Tte and QDE-1Mth produce predominantly short RNA copies via primer-independent initiation. Surprisingly, a 3.19 Å-resolution crystal structure of QDE-1Tte reveals a quasi-symmetric dimer similar to QDE-1Ncr. Further electron microscopy analyses confirm that QDE-1Tte occurs as a dimer in solution and retains this status upon interaction with a template. We conclude that divergence of orthologous RdRPs can result in functional innovation while retaining overall protein fold and quaternary structure. MOE (Min. of Education, S’pore) NMRC (Natl Medical Research Council, S’pore) Accepted version 2016-07-27T02:30:13Z 2019-12-06T14:41:09Z 2016-07-27T02:30:13Z 2019-12-06T14:41:09Z 2016 Journal Article Qian, X., Hamid, F. M., El Sahili, A., Darwis, D. A., Wong, Y. H., Bhushan, S., et al. (2016). Functional Evolution in Orthologous Cell-encoded RNA-dependent RNA Polymerases. Journal of Biological Chemistry, 291(17), 9295-9309. 0021-9258 https://hdl.handle.net/10356/81833 http://hdl.handle.net/10220/40997 10.1074/jbc.M115.685933 26907693 en Journal of Biological Chemistry © 2016 The American Society for Biochemistry and Molecular Biology. This is the author created version of a work that has been peer reviewed and accepted for publication by Journal of Biological Chemistry, The American Society for Biochemistry and Molecular Biology. It incorporates referee’s comments but changes resulting from the publishing process, such as copyediting, structural formatting, may not be reflected in this document. The published version is available at: [http://dx.doi.org/10.1074/jbc.M115.685933]. 31 p. application/pdf
institution Nanyang Technological University
building NTU Library
continent Asia
country Singapore
Singapore
content_provider NTU Library
collection DR-NTU
language English
topic RNA-dependent RNA polymerase
small RNAs
spellingShingle RNA-dependent RNA polymerase
small RNAs
Qian, Xinlei
Hamid, Fursham M.
El Sahili, Abbas
Darwis, Dina Amallia
Wong, Yee Hwa
Bhushan, Shashi
Makeyev, Eugene V.
Lescar, Julien
Functional Evolution in Orthologous Cell-encoded RNA-dependent RNA Polymerases
description Many eukaryotic organisms encode more than one RNA-dependent RNA polymerase (RdRP) that likely emerged as a result of gene duplication. Such RdRP paralogs often participate in distinct RNA silencing pathways and show characteristic repertoires of enzymatic activities in vitro. However, to what extent members of individual paralogous groups can undergo functional changes during speciation remains an open question. We show that orthologs of QDE-1, an RdRP component of the quelling pathway in Neurospora crassa, have rapidly diverged in evolution at the amino acid sequence level. Analyses of purified QDE-1 polymerases from N. crassa (QDE-1Ncr) and related fungi, Thielavia terrestris (QDE-1Tte) and Myceliophthora thermophila (QDE-1Mth), show that all three enzymes can synthesize RNA but the precise modes of their action differ considerably. Unlike their QDE-1Ncr counterpart favoring processive RNA synthesis, QDE-1Tte and QDE-1Mth produce predominantly short RNA copies via primer-independent initiation. Surprisingly, a 3.19 Å-resolution crystal structure of QDE-1Tte reveals a quasi-symmetric dimer similar to QDE-1Ncr. Further electron microscopy analyses confirm that QDE-1Tte occurs as a dimer in solution and retains this status upon interaction with a template. We conclude that divergence of orthologous RdRPs can result in functional innovation while retaining overall protein fold and quaternary structure.
author2 School of Biological Sciences
author_facet School of Biological Sciences
Qian, Xinlei
Hamid, Fursham M.
El Sahili, Abbas
Darwis, Dina Amallia
Wong, Yee Hwa
Bhushan, Shashi
Makeyev, Eugene V.
Lescar, Julien
format Article
author Qian, Xinlei
Hamid, Fursham M.
El Sahili, Abbas
Darwis, Dina Amallia
Wong, Yee Hwa
Bhushan, Shashi
Makeyev, Eugene V.
Lescar, Julien
author_sort Qian, Xinlei
title Functional Evolution in Orthologous Cell-encoded RNA-dependent RNA Polymerases
title_short Functional Evolution in Orthologous Cell-encoded RNA-dependent RNA Polymerases
title_full Functional Evolution in Orthologous Cell-encoded RNA-dependent RNA Polymerases
title_fullStr Functional Evolution in Orthologous Cell-encoded RNA-dependent RNA Polymerases
title_full_unstemmed Functional Evolution in Orthologous Cell-encoded RNA-dependent RNA Polymerases
title_sort functional evolution in orthologous cell-encoded rna-dependent rna polymerases
publishDate 2016
url https://hdl.handle.net/10356/81833
http://hdl.handle.net/10220/40997
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