Limits...
The similar and different evolutionary trends of MATE family occurred between rice and Arabidopsis thaliana

View Article: PubMed Central - PubMed

ABSTRACT

Background: Multidrug and toxic compound extrusion (MATE) transporter proteins are present in all organisms. Although the functions of some MATE gene family members have been studied in plants, few studies have investigated the gene expansion patterns, functional divergence, or the effects of positive selection.

Results: Forty-five MATE genes from rice and 56 from Arabidopsis were identified and grouped into four subfamilies. MATE family genes have similar exon-intron structures in rice and Arabidopsis; MATE gene structures are conserved in each subfamily but differ among subfamilies. In both species, the MATE gene family has expanded mainly through tandem and segmental duplications. A transcriptome atlas showed considerable differences in expression among the genes, in terms of transcript abundance and expression patterns under normal growth conditions, indicating wide functional divergence in this family. In both rice and Arabidopsis, the MATE genes showed consistent functional divergence trends, with highly significant Type-I divergence in each subfamily, while Type-II divergence mainly occurred in subfamily III. The Type-II coefficients between rice subfamilies I/III, II/III, and IV/III were all significantly greater than zero, while only the Type-II coefficient between Arabidopsis IV/III subfamilies was significantly greater than zero.

Results: A site-specific model analysis indicated that MATE genes have relatively conserved evolutionary trends. A branch-site model suggested that the extent of positive selection on each subfamily of rice and Arabidopsis was different: subfamily II of Arabidopsis showed higher positive selection than other subfamilies, whereas in rice, positive selection was highest in subfamily III. In addition, the analyses identified 18 rice sites and 7 Arabidopsis sites that were responsible for positive selection and for Type-I and Type-II functional divergence; there were no common sites between rice and Arabidopsis. Five coevolving amino acid sites were identified in rice and three in Arabidopsis; these sites might have important roles in maintaining local structural stability and protein functional domains.

Conclusions: We demonstrate that the MATE gene family expanded through tandem and segmental duplication in both rice and Arabidopsis. Overall, the results of our analyses contribute to improved understanding of the molecular evolution and functions of the MATE gene family in plants.

Electronic supplementary material: The online version of this article (doi:10.1186/s12870-016-0895-0) contains supplementary material, which is available to authorized users.

No MeSH data available.


Expression profiles of Arabidopsis thaliana MATE genes. The level of expression is shown by the color and its intensity: deep red indicates the highest level of expression, deep blue the lowest. Other hues indicate intermediate levels of expression. The proteins highlighted by the red outlined boxes represent small phylogenetic clades that have similar transcript abundance profiles
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
getmorefigures.php?uid=PMC5037600&req=5

Fig4: Expression profiles of Arabidopsis thaliana MATE genes. The level of expression is shown by the color and its intensity: deep red indicates the highest level of expression, deep blue the lowest. Other hues indicate intermediate levels of expression. The proteins highlighted by the red outlined boxes represent small phylogenetic clades that have similar transcript abundance profiles

Mentions: We compared the possible roles of homologous MATE genes in plant growth and development in rice and Arabidopsis by constructing heat maps using the Gene Pattern program [69]. The expression profiles indicated that most MATE family members of both species showed different expression levels in the tested tissues and organs (Figs. 4 and 5). Additionally, the MATE genes showed preferential expression: 84.4 % (38 of 45) and 85.7 % (48 of 56) of the MATE genes of rice and Arabidopsis, respectively, exhibited transcript abundance profiles with marked peaks in a single tissue. These results suggested that the MATE proteins function as tissue-specific regulators and are limited to discrete cells or organs. Approximately 17.8 %, 17.8 %, 20 %, and 26.7 % of MATE genes in rice showed their highest levels of transcript accumulation in the root, flower, leaf, and seed tissue, respectively. In Arabidopsis, approximately 8.9 %, 25 %, 12.5 %, and 25 % of MATE genes showed their highest levels of transcript accumulation in the root, flower, leaf and seed tissue, respectively. Surprisingly, only one rice MATE gene showed its highest level of transcript accumulation in the shoot apical meristem. In Arabidopsis, 3, 3, and 2 genes showed their highest levels of transcript accumulation in stamens, mature pollen, and the hypocotyl, respectively. The widely varying patterns of expression suggest that MATE genes in the two species are involved in the development of all tissues or organs under normal conditions. In addition, MATE genes that clustered in the branches of the heat map exhibited similar transcript abundance profiles. However, most MATE genes did not cluster in the phylogenetic tree but showed relatively distinct phylogenies. A few small phylogenetic clades had similar transcript abundance profiles; these are marked on the heat map by the red outlined boxes (Figs. 4 and 5). The genes in the two species that have high sequence similarity and share expression profiles represent good candidates for the evaluation of gene functions. We suggest that the genes in the red outlined boxes may have similar functions in the same tissues.Fig. 4


The similar and different evolutionary trends of MATE family occurred between rice and Arabidopsis thaliana
Expression profiles of Arabidopsis thaliana MATE genes. The level of expression is shown by the color and its intensity: deep red indicates the highest level of expression, deep blue the lowest. Other hues indicate intermediate levels of expression. The proteins highlighted by the red outlined boxes represent small phylogenetic clades that have similar transcript abundance profiles
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC5037600&req=5

Fig4: Expression profiles of Arabidopsis thaliana MATE genes. The level of expression is shown by the color and its intensity: deep red indicates the highest level of expression, deep blue the lowest. Other hues indicate intermediate levels of expression. The proteins highlighted by the red outlined boxes represent small phylogenetic clades that have similar transcript abundance profiles
Mentions: We compared the possible roles of homologous MATE genes in plant growth and development in rice and Arabidopsis by constructing heat maps using the Gene Pattern program [69]. The expression profiles indicated that most MATE family members of both species showed different expression levels in the tested tissues and organs (Figs. 4 and 5). Additionally, the MATE genes showed preferential expression: 84.4 % (38 of 45) and 85.7 % (48 of 56) of the MATE genes of rice and Arabidopsis, respectively, exhibited transcript abundance profiles with marked peaks in a single tissue. These results suggested that the MATE proteins function as tissue-specific regulators and are limited to discrete cells or organs. Approximately 17.8 %, 17.8 %, 20 %, and 26.7 % of MATE genes in rice showed their highest levels of transcript accumulation in the root, flower, leaf, and seed tissue, respectively. In Arabidopsis, approximately 8.9 %, 25 %, 12.5 %, and 25 % of MATE genes showed their highest levels of transcript accumulation in the root, flower, leaf and seed tissue, respectively. Surprisingly, only one rice MATE gene showed its highest level of transcript accumulation in the shoot apical meristem. In Arabidopsis, 3, 3, and 2 genes showed their highest levels of transcript accumulation in stamens, mature pollen, and the hypocotyl, respectively. The widely varying patterns of expression suggest that MATE genes in the two species are involved in the development of all tissues or organs under normal conditions. In addition, MATE genes that clustered in the branches of the heat map exhibited similar transcript abundance profiles. However, most MATE genes did not cluster in the phylogenetic tree but showed relatively distinct phylogenies. A few small phylogenetic clades had similar transcript abundance profiles; these are marked on the heat map by the red outlined boxes (Figs. 4 and 5). The genes in the two species that have high sequence similarity and share expression profiles represent good candidates for the evaluation of gene functions. We suggest that the genes in the red outlined boxes may have similar functions in the same tissues.Fig. 4

View Article: PubMed Central - PubMed

ABSTRACT

Background: Multidrug and toxic compound extrusion (MATE) transporter proteins are present in all organisms. Although the functions of some MATE gene family members have been studied in plants, few studies have investigated the gene expansion patterns, functional divergence, or the effects of positive selection.

Results: Forty-five MATE genes from rice and 56 from Arabidopsis were identified and grouped into four subfamilies. MATE family genes have similar exon-intron structures in rice and Arabidopsis; MATE gene structures are conserved in each subfamily but differ among subfamilies. In both species, the MATE gene family has expanded mainly through tandem and segmental duplications. A transcriptome atlas showed considerable differences in expression among the genes, in terms of transcript abundance and expression patterns under normal growth conditions, indicating wide functional divergence in this family. In both rice and Arabidopsis, the MATE genes showed consistent functional divergence trends, with highly significant Type-I divergence in each subfamily, while Type-II divergence mainly occurred in subfamily III. The Type-II coefficients between rice subfamilies I/III, II/III, and IV/III were all significantly greater than zero, while only the Type-II coefficient between Arabidopsis IV/III subfamilies was significantly greater than zero.

Results: A site-specific model analysis indicated that MATE genes have relatively conserved evolutionary trends. A branch-site model suggested that the extent of positive selection on each subfamily of rice and Arabidopsis was different: subfamily II of Arabidopsis showed higher positive selection than other subfamilies, whereas in rice, positive selection was highest in subfamily III. In addition, the analyses identified 18 rice sites and 7 Arabidopsis sites that were responsible for positive selection and for Type-I and Type-II functional divergence; there were no common sites between rice and Arabidopsis. Five coevolving amino acid sites were identified in rice and three in Arabidopsis; these sites might have important roles in maintaining local structural stability and protein functional domains.

Conclusions: We demonstrate that the MATE gene family expanded through tandem and segmental duplication in both rice and Arabidopsis. Overall, the results of our analyses contribute to improved understanding of the molecular evolution and functions of the MATE gene family in plants.

Electronic supplementary material: The online version of this article (doi:10.1186/s12870-016-0895-0) contains supplementary material, which is available to authorized users.

No MeSH data available.