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Genome-Wide Identification, Structure Characterization, and Expression Pattern Profiling of the Aquaporin Gene Family in Betula pendula.
Int J Mol Sci. 2021 Jul 06; 22(14)IJ

Abstract

Aquaporin water channels (AQPs) constitute a large family of transmembrane proteins present throughout all kingdoms of life. They play key roles in the flux of water and many solutes across the membranes. The AQP diversity, protein features, and biological functions of silver birch are still unknown. A genome analysis of Betula pendula identified 33 putative genes encoding full-length AQP sequences (BpeAQPs). They are grouped into five subfamilies, representing ten plasma membrane intrinsic proteins (PIPs), eight tonoplast intrinsic proteins (TIPs), eight NOD26-like intrinsic proteins (NIPs), four X intrinsic proteins (XIPs), and three small basic intrinsic proteins (SIPs). The BpeAQP gene structure is conserved within each subfamily, with exon numbers ranging from one to five. The predictions of the aromatic/arginine selectivity filter (ar/R), Froger's positions, specificity-determining positions, and 2D and 3D biochemical properties indicate noticeable transport specificities to various non-aqueous substrates between members and/or subfamilies. Nevertheless, overall, the BpePIPs display mostly hydrophilic ar/R selective filter and lining-pore residues, whereas the BpeTIP, BpeNIP, BpeSIP, and BpeXIP subfamilies mostly contain hydrophobic permeation signatures. Transcriptional expression analyses indicate that 23 BpeAQP genes are transcribed, including five organ-related expressions. Surprisingly, no significant transcriptional expression is monitored in leaves in response to cold stress (6 °C), although interesting trends can be distinguished and will be discussed, notably in relation to the plasticity of this pioneer species, B. pendula. The current study presents the first detailed genome-wide analysis of the AQP gene family in a Betulaceae species, and our results lay a foundation for a better understanding of the specific functions of the BpeAQP genes in the responses of the silver birch trees to cold stress.

Authors+Show Affiliations

Université Clermont Auvergne, INRAE, PIAF, 63000 Clermont-Ferrand, France.Institute of Ecology and Earth Sciences, University of Tartu, 51005 Tartu, Estonia.Université Clermont Auvergne, INRAE, PIAF, 63000 Clermont-Ferrand, France.Université Clermont Auvergne, INRAE, PIAF, 63000 Clermont-Ferrand, France.Université Clermont Auvergne, INRAE, PIAF, 63000 Clermont-Ferrand, France. National Institute of Agronomy of Tunisia (INAT), Crop Improvement Laboratory, INRAT, Tunis CP 1004, Tunisia.Laboratory of Plant Biotechnology, Ecology and Ecosystem Valorization, Faculty of Sciences, University Chouaib Doukkali, El Jadida 24000, Morocco.State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China.State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China.Université Clermont Auvergne, INRAE, PIAF, 63000 Clermont-Ferrand, France.Université Clermont Auvergne, INRAE, PIAF, 63000 Clermont-Ferrand, France.Université Clermont Auvergne, INRAE, PIAF, 63000 Clermont-Ferrand, France.Institute of Ecology and Earth Sciences, University of Tartu, 51005 Tartu, Estonia.Université Clermont Auvergne, INRAE, PIAF, 63000 Clermont-Ferrand, France.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

34298887

Citation

Venisse, Jean-Stéphane, et al. "Genome-Wide Identification, Structure Characterization, and Expression Pattern Profiling of the Aquaporin Gene Family in Betula Pendula." International Journal of Molecular Sciences, vol. 22, no. 14, 2021.
Venisse JS, Õunapuu-Pikas E, Dupont M, et al. Genome-Wide Identification, Structure Characterization, and Expression Pattern Profiling of the Aquaporin Gene Family in Betula pendula. Int J Mol Sci. 2021;22(14).
Venisse, J. S., Õunapuu-Pikas, E., Dupont, M., Gousset-Dupont, A., Saadaoui, M., Faize, M., Chen, S., Chen, S., Petel, G., Fumanal, B., Roeckel-Drevet, P., Sellin, A., & Label, P. (2021). Genome-Wide Identification, Structure Characterization, and Expression Pattern Profiling of the Aquaporin Gene Family in Betula pendula. International Journal of Molecular Sciences, 22(14). https://doi.org/10.3390/ijms22147269
Venisse JS, et al. Genome-Wide Identification, Structure Characterization, and Expression Pattern Profiling of the Aquaporin Gene Family in Betula Pendula. Int J Mol Sci. 2021 Jul 6;22(14) PubMed PMID: 34298887.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Genome-Wide Identification, Structure Characterization, and Expression Pattern Profiling of the Aquaporin Gene Family in Betula pendula. AU - Venisse,Jean-Stéphane, AU - Õunapuu-Pikas,Eele, AU - Dupont,Maxime, AU - Gousset-Dupont,Aurélie, AU - Saadaoui,Mouadh, AU - Faize,Mohamed, AU - Chen,Song, AU - Chen,Su, AU - Petel,Gilles, AU - Fumanal,Boris, AU - Roeckel-Drevet,Patricia, AU - Sellin,Arne, AU - Label,Philippe, Y1 - 2021/07/06/ PY - 2021/05/19/received PY - 2021/06/29/revised PY - 2021/06/30/accepted PY - 2021/7/24/entrez PY - 2021/7/25/pubmed PY - 2021/8/6/medline KW - Betula pendula KW - RNA-seq KW - aquaporin KW - cold stress KW - functional diversity KW - plasticity JF - International journal of molecular sciences JO - Int J Mol Sci VL - 22 IS - 14 N2 - Aquaporin water channels (AQPs) constitute a large family of transmembrane proteins present throughout all kingdoms of life. They play key roles in the flux of water and many solutes across the membranes. The AQP diversity, protein features, and biological functions of silver birch are still unknown. A genome analysis of Betula pendula identified 33 putative genes encoding full-length AQP sequences (BpeAQPs). They are grouped into five subfamilies, representing ten plasma membrane intrinsic proteins (PIPs), eight tonoplast intrinsic proteins (TIPs), eight NOD26-like intrinsic proteins (NIPs), four X intrinsic proteins (XIPs), and three small basic intrinsic proteins (SIPs). The BpeAQP gene structure is conserved within each subfamily, with exon numbers ranging from one to five. The predictions of the aromatic/arginine selectivity filter (ar/R), Froger's positions, specificity-determining positions, and 2D and 3D biochemical properties indicate noticeable transport specificities to various non-aqueous substrates between members and/or subfamilies. Nevertheless, overall, the BpePIPs display mostly hydrophilic ar/R selective filter and lining-pore residues, whereas the BpeTIP, BpeNIP, BpeSIP, and BpeXIP subfamilies mostly contain hydrophobic permeation signatures. Transcriptional expression analyses indicate that 23 BpeAQP genes are transcribed, including five organ-related expressions. Surprisingly, no significant transcriptional expression is monitored in leaves in response to cold stress (6 °C), although interesting trends can be distinguished and will be discussed, notably in relation to the plasticity of this pioneer species, B. pendula. The current study presents the first detailed genome-wide analysis of the AQP gene family in a Betulaceae species, and our results lay a foundation for a better understanding of the specific functions of the BpeAQP genes in the responses of the silver birch trees to cold stress. SN - 1422-0067 UR - https://www.unboundmedicine.com/medline/citation/34298887/Genome_Wide_Identification_Structure_Characterization_and_Expression_Pattern_Profiling_of_the_Aquaporin_Gene_Family_in_Betula_pendula_ L2 - https://www.mdpi.com/resolver?pii=ijms22147269 DB - PRIME DP - Unbound Medicine ER -