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Identification of aquaporins and deciphering their role under salinity stress in pomegranate (Punica granatum)

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Abstract

Aquaporins (AQPs), pore-forming proteins, are known to involve in the transport of water and many other small solutes, and play a diverse role in physiological processes. In this study, 38 AQPs were identified from pomegranate (Punica granatum) genome based on the phylogenetic distribution and homology with known AQPs from Arabidopsis thaliana and Oryza sativa. The pomegranate AQPs were further classified into five subgroup representing 12 plasma membrane intrinsic proteins (PIPs), 8 Nod26-like intrinsic proteins (NIPs), 14 tonoplast intrinsic proteins (TIPs), three small and basic intrinsic proteins (SIPs) and one uncategorized intrinsic protein (XIPs). Extensive computational analysis was performed to understand the pore morphology, exon–intron structure, and subcellular localization of the AQPs. The identified AQPs were further confirmed for the conserved NPA motifs, ar/R selectivity filters, and Froger’s residues. Analysis of the available transcriptomic data revealed tissue specific expression of different aquaporins, for instance, under salinity stress PgNIP6-1 showed increased expression in root. The co-expression has been observed among PgTIP3-1, PgTIP1-4, PgTIP1-8, PgTIP1-1, PgSIP1-1, PgPIP2-4, PgPIP1-3, and PgPIP1-2. Moreover, PgTIP3-1 showed a negative correlation with remaining seven AQPs. Further, the expression analysis of PgNIP6-1, PgTIP3-1 and PgNIP3-1 using quantitative real-time PCR showed increased transcript level of these genes under salinity stress suggesting their key role in stress related mechanism. The information presented here will provide insights into AQPs role in development and stress tolerance in plants.

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Data availability

Data sharing is not applicable to this article as all new created data is already contained within this article and the supplementary material of this article.

Code availability

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Abbreviations

AQPs:

Aquaporins

PIPs:

Plasma membrane intrinsic proteins

SIPs:

Small and basic intrinsic proteins

NIPs:

Nod26-like intrinsic proteins\

TIPs:

Tonoplast intrinsic proteins

XIPs:

Uncategorized intrinsic proteins

RPKM:

Reads Per Kilobase of the transcript per Million mapped reads

qRT-PCR:

Quantitative reverse-transcription PCR

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Acknowledgements

Authors are also thankful to the Department of Biotechnology (DBT), India for Ramalingaswami fellowship to RD and HS.

Funding

We thank the Department of Biotechnology, Government of India for Ramalingaswami Fellowship, and Science and Engineering Research Board (SERB), Department of Science and Technology, Government of India for funding support (CRG/2019/006599) to RD and HS.

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Author notes

  1. Surbhi Kumawat and Bharti Aggarwal have contributed equally.

Authors and Affiliations

  1. National Agri-Food Biotechnology Institute (NABI), Sector 80, SAS Nagar, Mohali, Punjab, 140306, India

    Surbhi Kumawat, Bharti Aggarwal, Nitika Rana, Rushil Mandlik, Akrity Mehra, S. M. Shivaraj, Humira Sonah & Rupesh Deshmukh

  2. Department of Biotechnology, Panjab University, Chandigarh, India

    Surbhi Kumawat, Nitika Rana & Rushil Mandlik

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  1. Surbhi Kumawat
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Contributions

SK and BA compiled the data, performed analysis. SK performed transcriptome data analysis and qPCR experiment. SK, BA, NR, RM and AM contributed in data analysis and first draft of the MS. SMS, RD and HS edited and finalized the draft. RD and HS conceptualized the study, drew the conclusions.

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Correspondence to Rupesh Deshmukh.

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Supplementary Information

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Supplementary file1 (DOCX 162 KB)

Supplementary Table 1 Details of Primers used for Quantitative Real Time PCR (XLSX 9 KB)

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Supplementary Table 2 Details of Blastp results performed using BioEdit showing highest bit score against respective queries from Arabidopsis thaliana and Oryza sativa (XLSX 10 KB)

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Supplementary Table 3 Conserved domain analysis of identified Pomegranate aquaporins using NCBI conserved Domain Search (XLSX 10 KB)

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Supplementary Table 4 Biosequence analysis of Pomegranate aquaporins using profile hidden Markov Models (HMMER) (https://www.ebi.ac.uk/Tools/hmmer/) (XLSX 10 KB)

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Supplementary Table 5 Transmembrane domain identified by using TMHMM and SOSUI servers in Pomegranate aquaporins (XLSX 10 KB)

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Supplementary Table 6 Details of the sub-cellular location, molecular weight (Mw) and isoelectric point (pI) predicted for aquaporins identified in Punica granatum genome (XLSX 10 KB)

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Supplementary Table 7 Details of Asn-Pro-Ala (NPA) domains, aromatic/arginine (Ar/R) filters, Froger’s residues and Mitani’s residues located in 38 aquaporins identified in Punica granatum genome (XLSX 12 KB)

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Kumawat, S., Aggarwal, B., Rana, N. et al. Identification of aquaporins and deciphering their role under salinity stress in pomegranate (Punica granatum). J. Plant Biochem. Biotechnol. 30, 930–942 (2021). https://doi.org/10.1007/s13562-021-00738-1

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