Molecular Genetics and Genomics

, Volume 290, Issue 2, pp 443–460 | Cite as

Molecular evolution and functional divergence of X-intrinsic protein genes in plants

  • Jelli Venkatesh
  • Jae-Woong Yu
  • Daniel Gaston
  • Se Won Park
Original Paper

Abstract

X-intrinsic proteins (XIPs) are a novel class of major intrinsic proteins found in diverse organisms. Recently, XIP genes have been reported to be involved in the transport of a wide range of hydrophobic solutes; however, the evolutionary forces driving their structural and functional divergence in plants are poorly understood. In the present study, comprehensive bioinformatics analyses were performed to gain insight into the molecular and evolutionary mechanisms driving this structural and functional diversification. Phylogenetic analyses have revealed the major lineage-specific expansions of XIP genes in plants. Within the eudicots, XIP genes have diverged into Asterid and Rosid-specific phylogenetic lineages and have also undergone several independent duplications during the course of evolution. Investigation of functional divergence at the protein level showed evidence for shifting evolutionary rate and/or altered constraints on the physiochemical properties of specific amino acid sites following gene duplication. Selection pressure analyses suggest that purifying selection is the predominant evolutionary force acting on the XIP gene subfamily, along with episodic positive selection. However, only a few amino acid sites were found to be subjected to such episodic positive selection. Furthermore, protein functional divergence analysis has identified critical amino acid residues, which must be validated by future experimental studies, that could provide new insights into the role of XIPs in transport of a wide range solutes of physiological importance.

Keywords

Aquaporin Homologues Divergence Major intrinsic proteins Phylogenetics Selection pressure X-intrinsic protein 

Notes

Acknowledgments

This paper is resulted from the Konkuk University research support program.

Supplementary material

438_2014_927_MOESM1_ESM.jpg (136 kb)
Fig. S1 Phylogenetic analysis of the amino acid sequences of plant XIPs including other subfamily MIP sequences from Arabidopsis, potato, cotton and rice plant species. Predicted amino acid sequences were aligned using ClustalW2 sequence alignment program and the phylogenetic tree was constructed using Bootstrap NJ tree (1,000 replicates) method as implemented in MEGA6 software. MIP subfamilies such as PIP, TIP, NIP and SIPs subgroup branches are compressed and represented as black triangles. Supplementary material 1 (JPEG 136 kb)
438_2014_927_MOESM2_ESM.jpg (2.1 mb)
Fig. S2 Nucleotide sequence–based phylogenetic tree of plant XIP genes was constructed with the Maximum Likelihood method (100 reiterations) as implemented in the raxmlGUI1.3 program. Supplementary material 2 (JPEG 2199 kb)
438_2014_927_MOESM3_ESM.jpg (574 kb)
Fig. S3 Species tree used for reconciliation analyses of plant XIP genes. Supplementary material 3 (JPEG 573 kb)
438_2014_927_MOESM4_ESM.pdf (228 kb)
Fig. S4 Multiple alignment of protein sequences of representative XIP subgroups and other members of plant MIPs with experimentally proved post-translational modification sites highlighted. Supplementary material 4 (PDF 228 kb)
438_2014_927_MOESM5_ESM.pdf (3.4 mb)
Fig. S5 Results of selection pressure analysis of plant XIP genes determined by six different Maximum Likelihood methods (SLAC, FEL, IFEL, REL, FUBAR and MEME) are mapped on the XIP protein alignment.–, + and 0 indicates sites under negative, positive and neutral pressure, respectively. In case of MEME analysis, “–” indicates the absence of episodic selection pressure and “Ep” indicates presence of episodic selection pressure. Supplementary material 5 (PDF 3523 kb)
438_2014_927_MOESM6_ESM.docx (22 kb)
Supplementary material 6 (DOCX 21 kb)
438_2014_927_MOESM7_ESM.docx (35 kb)
Supplementary material 7 (DOCX 35 kb)

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Copyright information

© Springer-Verlag Berlin Heidelberg 2014

Authors and Affiliations

  • Jelli Venkatesh
    • 1
  • Jae-Woong Yu
    • 1
  • Daniel Gaston
    • 2
  • Se Won Park
    • 1
  1. 1.Department of Molecular BiotechnologyKonkuk UniversitySeoulRepublic of Korea
  2. 2.Department of PathologyDalhousie UniversityHalifaxCanada

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