Step-wise and lineage-specific diversification of plant RNA polymerase genes and origin of the largest plant-specific subunits

Yaqiong Wang, Hong Ma

Research output: Contribution to journalArticle

9 Citations (Scopus)

Abstract

Proteins often function as complexes, yet little is known about the evolution of dissimilar subunits of complexes. DNA-directed RNA polymerases (RNAPs) are multisubunit complexes, with distinct eukaryotic types for different classes of transcripts. In addition to Pol I-III, common in eukaryotes, plants have Pol IV and V for epigenetic regulation. Some RNAP subunits are specific to one type, whereas other subunits are shared by multiple types. We have conducted extensive phylogenetic and sequence analyses, and have placed RNAP gene duplication events in land plant history, thereby reconstructing the subunit compositions of the novel RNAPs during land plant evolution. We found that Pol IV/V have experienced step-wise duplication and diversification of various subunits, with increasingly distinctive subunit compositions. Also, lineage-specific duplications have further increased RNAP complexity with distinct copies in different plant families and varying divergence for subunits of different RNAPs. Further, the largest subunits of Pol IV/V probably originated from a gene fusion in the ancestral land plants. We propose a framework of plant RNAP evolution, providing an excellent model for protein complex evolution.

Original languageEnglish (US)
Pages (from-to)1198-1212
Number of pages15
JournalNew Phytologist
Volume207
Issue number4
DOIs
StatePublished - Jan 1 2015

Fingerprint

Plant RNA
DNA-Directed RNA Polymerases
DNA-directed RNA polymerase
Embryophyta
embryophytes
Genes
genes
Gene Duplication
gene fusion
Gene Fusion
gene duplication
Eukaryota
Epigenomics
epigenetics
Sequence Analysis
eukaryotic cells
Proteins
proteins
History
history

All Science Journal Classification (ASJC) codes

  • Physiology
  • Plant Science

Cite this

@article{923bde5d7fe74f739940b94255abcfc6,
title = "Step-wise and lineage-specific diversification of plant RNA polymerase genes and origin of the largest plant-specific subunits",
abstract = "Proteins often function as complexes, yet little is known about the evolution of dissimilar subunits of complexes. DNA-directed RNA polymerases (RNAPs) are multisubunit complexes, with distinct eukaryotic types for different classes of transcripts. In addition to Pol I-III, common in eukaryotes, plants have Pol IV and V for epigenetic regulation. Some RNAP subunits are specific to one type, whereas other subunits are shared by multiple types. We have conducted extensive phylogenetic and sequence analyses, and have placed RNAP gene duplication events in land plant history, thereby reconstructing the subunit compositions of the novel RNAPs during land plant evolution. We found that Pol IV/V have experienced step-wise duplication and diversification of various subunits, with increasingly distinctive subunit compositions. Also, lineage-specific duplications have further increased RNAP complexity with distinct copies in different plant families and varying divergence for subunits of different RNAPs. Further, the largest subunits of Pol IV/V probably originated from a gene fusion in the ancestral land plants. We propose a framework of plant RNAP evolution, providing an excellent model for protein complex evolution.",
author = "Yaqiong Wang and Hong Ma",
year = "2015",
month = "1",
day = "1",
doi = "10.1111/nph.13432",
language = "English (US)",
volume = "207",
pages = "1198--1212",
journal = "New Phytologist",
issn = "0028-646X",
publisher = "Wiley-Blackwell",
number = "4",

}

Step-wise and lineage-specific diversification of plant RNA polymerase genes and origin of the largest plant-specific subunits. / Wang, Yaqiong; Ma, Hong.

In: New Phytologist, Vol. 207, No. 4, 01.01.2015, p. 1198-1212.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Step-wise and lineage-specific diversification of plant RNA polymerase genes and origin of the largest plant-specific subunits

AU - Wang, Yaqiong

AU - Ma, Hong

PY - 2015/1/1

Y1 - 2015/1/1

N2 - Proteins often function as complexes, yet little is known about the evolution of dissimilar subunits of complexes. DNA-directed RNA polymerases (RNAPs) are multisubunit complexes, with distinct eukaryotic types for different classes of transcripts. In addition to Pol I-III, common in eukaryotes, plants have Pol IV and V for epigenetic regulation. Some RNAP subunits are specific to one type, whereas other subunits are shared by multiple types. We have conducted extensive phylogenetic and sequence analyses, and have placed RNAP gene duplication events in land plant history, thereby reconstructing the subunit compositions of the novel RNAPs during land plant evolution. We found that Pol IV/V have experienced step-wise duplication and diversification of various subunits, with increasingly distinctive subunit compositions. Also, lineage-specific duplications have further increased RNAP complexity with distinct copies in different plant families and varying divergence for subunits of different RNAPs. Further, the largest subunits of Pol IV/V probably originated from a gene fusion in the ancestral land plants. We propose a framework of plant RNAP evolution, providing an excellent model for protein complex evolution.

AB - Proteins often function as complexes, yet little is known about the evolution of dissimilar subunits of complexes. DNA-directed RNA polymerases (RNAPs) are multisubunit complexes, with distinct eukaryotic types for different classes of transcripts. In addition to Pol I-III, common in eukaryotes, plants have Pol IV and V for epigenetic regulation. Some RNAP subunits are specific to one type, whereas other subunits are shared by multiple types. We have conducted extensive phylogenetic and sequence analyses, and have placed RNAP gene duplication events in land plant history, thereby reconstructing the subunit compositions of the novel RNAPs during land plant evolution. We found that Pol IV/V have experienced step-wise duplication and diversification of various subunits, with increasingly distinctive subunit compositions. Also, lineage-specific duplications have further increased RNAP complexity with distinct copies in different plant families and varying divergence for subunits of different RNAPs. Further, the largest subunits of Pol IV/V probably originated from a gene fusion in the ancestral land plants. We propose a framework of plant RNAP evolution, providing an excellent model for protein complex evolution.

UR - http://www.scopus.com/inward/record.url?scp=84938296683&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84938296683&partnerID=8YFLogxK

U2 - 10.1111/nph.13432

DO - 10.1111/nph.13432

M3 - Article

VL - 207

SP - 1198

EP - 1212

JO - New Phytologist

JF - New Phytologist

SN - 0028-646X

IS - 4

ER -