Duplication of the class i cytosolic small heat shock protein gene and potential functional divergence revealed by sequence variations flanking the α-crystallin domain in the genus Rhododendron (Ericaceae)

Pei-Chun Liao, Tsan Piao Lin, Wei Chieh Lan, Jeng Der Chung, Shih-Ying Hwang

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6 Citations (Scopus)

Abstract

Background and Aims Positive selection in the α-crystallin domain (ACD) of the chloroplast small heat shock protein (CPsHSP) gene was found in a previous study and was suggested to be related to the ecological adaptation of Rhododendron species in the subgenus Hymenanthes. Consequently, it was of interest to examine whether gene duplication and subsequent divergence have occurred in other sHSP genes, for example class I cytosolic sHSP genes (CT1sHSPs) in Rhododendron in Taiwan, where many endemic species have evolved as a result of habitat differentiation.MethodsA phylogeny of CT1sHSP amino acid sequences was built from Rhododendron, Arabidopsis thaliana, Oryza sativa, Populus trichocarpa, Vitis vinifera and other species for elucidation of the phylogenetic relationships among CT1sHSPs. Phylogenies of Rhododendron CT1sHSP nucleotide and amino acid sequences were generated for positive selection and functional divergence analysis, respectively. Positively selected sites and amino acid differences between types of Rhododendron CT1sHSPs were mapped onto the wheat sHSP16·9 protein structure. Average genetic distance (Dxy) and dN/dS ratios between types of Rhododendron CT1sHSP genes were analysed using sliding window analysis. Gene conversion was also assessed between types of Rhododendron CT1sHSPs.Key ResultsTwo types of Rhododendron CT1sHSP were identified. A high level of genetic similarity and diversity within and flanking the ACD, respectively, between types of Rhododendron CT1sHSP were found. Main differences between the two types of Rhododendron CT1sHSPs were: (1) increased hydrophobicity by two positively selected amino acid sites and a seven-amino-acid insertion in the N-terminal arm; and (2) increased structural flexibility and solubility by a seven-amino-acid insertion in the N-terminal arm and one positively selected amino acid site in the C-terminal extension.ConclusionsFunctional conservation of the ACD of Rhododendron CT1sHSP genes was inferred because of strong purifying selection. However, sequence variations flanking the ACD in Rhododendron CT1sHSP gene duplicates may have resulted in functional divergence and played important roles in chaperon function enhancement.

Original languageEnglish
Pages (from-to)57-69
Number of pages13
JournalAnnals of Botany
Volume105
Issue number1
DOIs
Publication statusPublished - 2010 Jan 1

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crystallins
Ericaceae
Rhododendron
heat shock proteins
genes
amino acids
sequence diversity
phylogeny
amino acid sequences
duplicate genes
Populus balsamifera subsp. trichocarpa
gene conversion
wheat protein
gene duplication
protein structure
hydrophobicity
Vitis vinifera
genetic distance
solubility
Taiwan

Keywords

  • Cytosolic class I small heat shock protein (CT1sHSP)
  • Gene duplication
  • Hydrophobicity
  • Positive selection
  • Purifying selection
  • Rhododendron
  • Structural flexibility and solubility
  • α-crystallin domain (ACD)

ASJC Scopus subject areas

  • Plant Science

Cite this

@article{40267fef9f5b4f3b8b857ecdc9f81dab,
title = "Duplication of the class i cytosolic small heat shock protein gene and potential functional divergence revealed by sequence variations flanking the α-crystallin domain in the genus Rhododendron (Ericaceae)",
abstract = "Background and Aims Positive selection in the α-crystallin domain (ACD) of the chloroplast small heat shock protein (CPsHSP) gene was found in a previous study and was suggested to be related to the ecological adaptation of Rhododendron species in the subgenus Hymenanthes. Consequently, it was of interest to examine whether gene duplication and subsequent divergence have occurred in other sHSP genes, for example class I cytosolic sHSP genes (CT1sHSPs) in Rhododendron in Taiwan, where many endemic species have evolved as a result of habitat differentiation.MethodsA phylogeny of CT1sHSP amino acid sequences was built from Rhododendron, Arabidopsis thaliana, Oryza sativa, Populus trichocarpa, Vitis vinifera and other species for elucidation of the phylogenetic relationships among CT1sHSPs. Phylogenies of Rhododendron CT1sHSP nucleotide and amino acid sequences were generated for positive selection and functional divergence analysis, respectively. Positively selected sites and amino acid differences between types of Rhododendron CT1sHSPs were mapped onto the wheat sHSP16·9 protein structure. Average genetic distance (Dxy) and dN/dS ratios between types of Rhododendron CT1sHSP genes were analysed using sliding window analysis. Gene conversion was also assessed between types of Rhododendron CT1sHSPs.Key ResultsTwo types of Rhododendron CT1sHSP were identified. A high level of genetic similarity and diversity within and flanking the ACD, respectively, between types of Rhododendron CT1sHSP were found. Main differences between the two types of Rhododendron CT1sHSPs were: (1) increased hydrophobicity by two positively selected amino acid sites and a seven-amino-acid insertion in the N-terminal arm; and (2) increased structural flexibility and solubility by a seven-amino-acid insertion in the N-terminal arm and one positively selected amino acid site in the C-terminal extension.ConclusionsFunctional conservation of the ACD of Rhododendron CT1sHSP genes was inferred because of strong purifying selection. However, sequence variations flanking the ACD in Rhododendron CT1sHSP gene duplicates may have resulted in functional divergence and played important roles in chaperon function enhancement.",
keywords = "Cytosolic class I small heat shock protein (CT1sHSP), Gene duplication, Hydrophobicity, Positive selection, Purifying selection, Rhododendron, Structural flexibility and solubility, α-crystallin domain (ACD)",
author = "Pei-Chun Liao and Lin, {Tsan Piao} and Lan, {Wei Chieh} and Chung, {Jeng Der} and Shih-Ying Hwang",
year = "2010",
month = "1",
day = "1",
doi = "10.1093/aob/mcp272",
language = "English",
volume = "105",
pages = "57--69",
journal = "Annals of Botany",
issn = "0305-7364",
publisher = "Oxford University Press",
number = "1",

}

TY - JOUR

T1 - Duplication of the class i cytosolic small heat shock protein gene and potential functional divergence revealed by sequence variations flanking the α-crystallin domain in the genus Rhododendron (Ericaceae)

AU - Liao, Pei-Chun

AU - Lin, Tsan Piao

AU - Lan, Wei Chieh

AU - Chung, Jeng Der

AU - Hwang, Shih-Ying

PY - 2010/1/1

Y1 - 2010/1/1

N2 - Background and Aims Positive selection in the α-crystallin domain (ACD) of the chloroplast small heat shock protein (CPsHSP) gene was found in a previous study and was suggested to be related to the ecological adaptation of Rhododendron species in the subgenus Hymenanthes. Consequently, it was of interest to examine whether gene duplication and subsequent divergence have occurred in other sHSP genes, for example class I cytosolic sHSP genes (CT1sHSPs) in Rhododendron in Taiwan, where many endemic species have evolved as a result of habitat differentiation.MethodsA phylogeny of CT1sHSP amino acid sequences was built from Rhododendron, Arabidopsis thaliana, Oryza sativa, Populus trichocarpa, Vitis vinifera and other species for elucidation of the phylogenetic relationships among CT1sHSPs. Phylogenies of Rhododendron CT1sHSP nucleotide and amino acid sequences were generated for positive selection and functional divergence analysis, respectively. Positively selected sites and amino acid differences between types of Rhododendron CT1sHSPs were mapped onto the wheat sHSP16·9 protein structure. Average genetic distance (Dxy) and dN/dS ratios between types of Rhododendron CT1sHSP genes were analysed using sliding window analysis. Gene conversion was also assessed between types of Rhododendron CT1sHSPs.Key ResultsTwo types of Rhododendron CT1sHSP were identified. A high level of genetic similarity and diversity within and flanking the ACD, respectively, between types of Rhododendron CT1sHSP were found. Main differences between the two types of Rhododendron CT1sHSPs were: (1) increased hydrophobicity by two positively selected amino acid sites and a seven-amino-acid insertion in the N-terminal arm; and (2) increased structural flexibility and solubility by a seven-amino-acid insertion in the N-terminal arm and one positively selected amino acid site in the C-terminal extension.ConclusionsFunctional conservation of the ACD of Rhododendron CT1sHSP genes was inferred because of strong purifying selection. However, sequence variations flanking the ACD in Rhododendron CT1sHSP gene duplicates may have resulted in functional divergence and played important roles in chaperon function enhancement.

AB - Background and Aims Positive selection in the α-crystallin domain (ACD) of the chloroplast small heat shock protein (CPsHSP) gene was found in a previous study and was suggested to be related to the ecological adaptation of Rhododendron species in the subgenus Hymenanthes. Consequently, it was of interest to examine whether gene duplication and subsequent divergence have occurred in other sHSP genes, for example class I cytosolic sHSP genes (CT1sHSPs) in Rhododendron in Taiwan, where many endemic species have evolved as a result of habitat differentiation.MethodsA phylogeny of CT1sHSP amino acid sequences was built from Rhododendron, Arabidopsis thaliana, Oryza sativa, Populus trichocarpa, Vitis vinifera and other species for elucidation of the phylogenetic relationships among CT1sHSPs. Phylogenies of Rhododendron CT1sHSP nucleotide and amino acid sequences were generated for positive selection and functional divergence analysis, respectively. Positively selected sites and amino acid differences between types of Rhododendron CT1sHSPs were mapped onto the wheat sHSP16·9 protein structure. Average genetic distance (Dxy) and dN/dS ratios between types of Rhododendron CT1sHSP genes were analysed using sliding window analysis. Gene conversion was also assessed between types of Rhododendron CT1sHSPs.Key ResultsTwo types of Rhododendron CT1sHSP were identified. A high level of genetic similarity and diversity within and flanking the ACD, respectively, between types of Rhododendron CT1sHSP were found. Main differences between the two types of Rhododendron CT1sHSPs were: (1) increased hydrophobicity by two positively selected amino acid sites and a seven-amino-acid insertion in the N-terminal arm; and (2) increased structural flexibility and solubility by a seven-amino-acid insertion in the N-terminal arm and one positively selected amino acid site in the C-terminal extension.ConclusionsFunctional conservation of the ACD of Rhododendron CT1sHSP genes was inferred because of strong purifying selection. However, sequence variations flanking the ACD in Rhododendron CT1sHSP gene duplicates may have resulted in functional divergence and played important roles in chaperon function enhancement.

KW - Cytosolic class I small heat shock protein (CT1sHSP)

KW - Gene duplication

KW - Hydrophobicity

KW - Positive selection

KW - Purifying selection

KW - Rhododendron

KW - Structural flexibility and solubility

KW - α-crystallin domain (ACD)

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U2 - 10.1093/aob/mcp272

DO - 10.1093/aob/mcp272

M3 - Article

C2 - 19887471

AN - SCOPUS:73149091036

VL - 105

SP - 57

EP - 69

JO - Annals of Botany

JF - Annals of Botany

SN - 0305-7364

IS - 1

ER -