Genome-wide Characterization Deciphers Distinct Properties of Aquaporins in Six Phytophthora Species

Author(s): Abul Kalam Azad*, Jahed Ahmed, Al Hakim, Md. Mahbub Hasan, Md. Asraful Alum, Mahmudul Hasan, Topu Raihan, Takahiro Ishikawa, Yoshihiro Sawa

Journal Name: Current Bioinformatics

Volume 16 , Issue 6 , 2021


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Abstract:

Background: Aquaporins, also known as major intrinsic proteins (MIPs), facilitate the membrane diffusion of water and some other small solutes. The roles of MIPs in plant physiological processes are established and now their roles in plant-pathogen interactions are getting more attention.

Objective: To investigate the evolution, diversity, and structural insights of Phytophthora MIPs (PhyMIPs) and to compare them to those in other domains of life.

Methods: Bioinformatics approaches were used to identify and characterize the PhyMIPs. The phylogenetic analysis was done with MEGA7.0 using maximum likelihood method. The prediction of transmembrane α-helices was done by using SOSUI and TMpred servers, and that of subcellular localization was performed with WoLF PSORT and Cello prediction system. The structure of PhyMIP genes was predicted by GeneMark.hmm ES-3.0 program. The 3D homology models were generated using the Molecular Operating Environment software and the stereochemical quality of the templates and models was assessed by PROCHECK. The PoreWalker server was used to detect and characterize PhyMIP channels from their 3D structural models.

Results: Herein, we identified 17, 24, 27, 19, 19, and 22 full-length MIPs, respectively, in the genomes of six Phytophthora species, P. infestans, P. parasitica, P. sojae, P. ramorum, P. capsici, and P. cinnamomi. Phylogenetic analysis showed that the PhyMIPs formed a completely distinct clade from their counterparts in other taxa and were clustered into nine subgroups. Sequence and structural properties indicated that the primary selectivity-related constrictions, including aromatic arginine (ar/R) selectivity filter and Froger's positions in PhyMIPs were distinct from those in other taxa. The substitutions in the conserved Asn-Pro-Ala motifs in loops B and E of many PhyMIPs were also divergent from those in other taxonomic domains. The group-specific consensus sequences/ motifs deciphered in different loops and transmembrane α-helices of PhyMIPs were distinct from those in plants, animals, and other microbes.

Conclusion: This study represents PhyMIPs with distinct evolutionary and structural properties, and the data collectively indicates that PhyMIPs might have novel functions.

Keywords: Aquaporins, phytophthora, major intrinsic proteins, oomycetes, homology model, phylogeny.

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Article Details

VOLUME: 16
ISSUE: 6
Year: 2021
Published on: 04 February, 2021
Page: [880 - 898]
Pages: 19
DOI: 10.2174/1574893616666210204150332
Price: $65

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