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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.


Chromosomal distribution of rice MATE genes. Chromosome sizes are indicated by relative lengths. Tandemly duplicated genes are indicated by the boxes with blue outlines. Segmentally duplicated genes are indicated by the red dots to the left. The figure was produced using the Map Inspector program
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Fig1: Chromosomal distribution of rice MATE genes. Chromosome sizes are indicated by relative lengths. Tandemly duplicated genes are indicated by the boxes with blue outlines. Segmentally duplicated genes are indicated by the red dots to the left. The figure was produced using the Map Inspector program

Mentions: The two plant species selected here, the monocot Oryza sativa and the dicot Arabidopsis thaliana, represent model organisms for the two major plant lineages. A BLASTP search of the Phytozome database (https://phytozome.jgi.doe.gov/pz/portal.html) identified 45 MATE genes in Oryza sativa and 56 in Arabidopsis thaliana. Both PFAM and SMART databases confirmed the presence of the conserved domain in the MATE gene family. The protein sequences (Additional file 1), coding sequences (Additional file 2), and genomic sequences (Additional file 3) were all obtained from the Phytozome database. Basic information on the rice and Arabidopsis MATE genes (including gene name, locus, protein length, intron number, PI value, and molecular weight) is provided in Additional files 4 and 5. The 45 MATE rice genes encoded proteins of 392 to 644 amino acids, with molecular weights ranging from 41.3 to 65.8 kD, and pI values from 5.14 to 10.07. Likewise, the 56 Arabidopsis genes encoded proteins with amino acid sequence lengths of 469 to 575 amino acids, molecular weights from 50.8 to 63.5 kD, and pI values ranging from 4.66 to 8.67. These results implied that the amino acid sequence length and physicochemical properties of rice and Arabidopsis MATE proteins might have changed to meet different functions. The genes for the rice and Arabidopsis MATE proteins were mapped to their chromosomes (Figs. 1 and 2). In Arabidopsis, the predicted 56 AtMATE (Arabidopsis thaliana MATE protein) genes were located on five chromosomes. Chromosome 1 had 21 AtMATE genes, while 10, 7, 9, and 9 AtMATE genes were found on chromosomes 2, 3, 4, and 5, respectively. In rice, the predicted 45 OsMATE (Oryza sativa MATE protein) genes were located on 12 chromosomes. Chromosomes 3, 10, and 6 contained 9, 7, and 5 OsMATE genes, respectively, while chromosomes 2 and 5 had 1 OsMATE gene each. Chromosomes 4 and 11 contained 2 OsMATE genes each, chromosomes 7 and 9 contained 3 OsMATE genes each, and chromosomes 1, 8, and 12 contained 4 OsMATE genes each.Fig. 1


The similar and different evolutionary trends of MATE family occurred between rice and Arabidopsis thaliana
Chromosomal distribution of rice MATE genes. Chromosome sizes are indicated by relative lengths. Tandemly duplicated genes are indicated by the boxes with blue outlines. Segmentally duplicated genes are indicated by the red dots to the left. The figure was produced using the Map Inspector program
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig1: Chromosomal distribution of rice MATE genes. Chromosome sizes are indicated by relative lengths. Tandemly duplicated genes are indicated by the boxes with blue outlines. Segmentally duplicated genes are indicated by the red dots to the left. The figure was produced using the Map Inspector program
Mentions: The two plant species selected here, the monocot Oryza sativa and the dicot Arabidopsis thaliana, represent model organisms for the two major plant lineages. A BLASTP search of the Phytozome database (https://phytozome.jgi.doe.gov/pz/portal.html) identified 45 MATE genes in Oryza sativa and 56 in Arabidopsis thaliana. Both PFAM and SMART databases confirmed the presence of the conserved domain in the MATE gene family. The protein sequences (Additional file 1), coding sequences (Additional file 2), and genomic sequences (Additional file 3) were all obtained from the Phytozome database. Basic information on the rice and Arabidopsis MATE genes (including gene name, locus, protein length, intron number, PI value, and molecular weight) is provided in Additional files 4 and 5. The 45 MATE rice genes encoded proteins of 392 to 644 amino acids, with molecular weights ranging from 41.3 to 65.8 kD, and pI values from 5.14 to 10.07. Likewise, the 56 Arabidopsis genes encoded proteins with amino acid sequence lengths of 469 to 575 amino acids, molecular weights from 50.8 to 63.5 kD, and pI values ranging from 4.66 to 8.67. These results implied that the amino acid sequence length and physicochemical properties of rice and Arabidopsis MATE proteins might have changed to meet different functions. The genes for the rice and Arabidopsis MATE proteins were mapped to their chromosomes (Figs. 1 and 2). In Arabidopsis, the predicted 56 AtMATE (Arabidopsis thaliana MATE protein) genes were located on five chromosomes. Chromosome 1 had 21 AtMATE genes, while 10, 7, 9, and 9 AtMATE genes were found on chromosomes 2, 3, 4, and 5, respectively. In rice, the predicted 45 OsMATE (Oryza sativa MATE protein) genes were located on 12 chromosomes. Chromosomes 3, 10, and 6 contained 9, 7, and 5 OsMATE genes, respectively, while chromosomes 2 and 5 had 1 OsMATE gene each. Chromosomes 4 and 11 contained 2 OsMATE genes each, chromosomes 7 and 9 contained 3 OsMATE genes each, and chromosomes 1, 8, and 12 contained 4 OsMATE genes each.Fig. 1

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.