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Structure-based prediction of protein–protein interactions between GhWlim5 Domain1 and GhACTIN-1 proteins: a practical evidence with improved fibre strength

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Abstract

Cotton fibre quality is a multigenic trait. Genetic modification of different genes to achieve high quality fibre is difficult without knowing the mechanism lying behind genes interaction. Based on background knowledge an attempt to explore the potential structural interactions between Gossypium hirsutum Wlim5 domain1 and Gossypium hirsutum ACTIN-1 proteins was done in current study. Sequence features of the LIM domain1 of GhWlim5 protein were identified through multiple sequence alignment analysis, and a phylogenetic tree was built to identify evolutionary relationships between sequences. Conservation indicated the evolutionary importance of side chain residues and the presence of several aliphatic and/or bulky residues, which stabilize the protein core and facilitate packing of zinc fingers. The structures of GhWlim5 domain1 and GhACTIN-1 proteins were modelled and validated through computational methods. Validation of GhACTIN-1 and GhWlim5 domain1 structures indicated good structural quality with 99.7% and 100% of the favoured number of residues in allowed regions and Z-score, within the ranges of − 9.87 and − 4.17, respectively. Docking analysis indicated various possible modes of interaction between these two proteins with favourable binding affinities. Based on our strong binding interaction results between GhWlim5 domain1 and GhACTIN-1 proteins, we further investigated the role of over-expression of GhWlim5 by transformation in cotton plants under fibre specific promoter and transgenic plants displayed significant increases in fibre strength.

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Abbreviations

ABPs:

Actin binding proteins

LIM:

LIN-11, ISL-1 and MEC-3

HMM:

Hidden Markov model

PDB:

Protein data bank

IDT:

Integrated DNA technologies

GUS:

β-glucuronidase

EDTA:

Ethylenediaminetetraacetic acid

RT-qPCR:

Quantitative reverse transcription polymerase chain reaction

GAPDH:

Glyceraldehyde 3-phosphate dehydrogenase

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Acknowledgements

This work was supported by the National Centre of Excellence in Molecular Biology University of the Punjab and the School of Plant Sciences, University of Arizona, USA. We extend our gratitude to the Center for Electron Microscopy Zhejiang University in Hangzhou China, for SEM microscopy and to the Central Cotton Research Institute, Multan, Pakistan for fibre analysis.

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Authors and Affiliations

  1. School of Plant Sciences and Bio5 Institute, University of Arizona, 341 Keating Building, Tucson, AZ, 85721, USA

    Adnan Iqbal & David W. Galbraith

  2. Centre of Excellence in Molecular Biology, University of Punjab, 87 West Canal Road, Lahore, 53700, Pakistan

    Adnan Iqbal, Ayesha Latif, Basit Jabbar, Muhmmad Azam Ali, Mukhtar Ahmed, Ambreen Gul, Abdul Qayyum Rao, Ahmad Ali Shahid & Tayyab Husnain

  3. Institute of Plant Stress Biology, School of Life Sciences, Henan University, Jin Ming Avenue, Kaifeng, 475004, China

    David W. Galbraith

Authors
  1. Adnan Iqbal
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  2. Ayesha Latif
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  3. David W. Galbraith
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  4. Basit Jabbar
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  5. Muhmmad Azam Ali
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  8. Abdul Qayyum Rao
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  9. Ahmad Ali Shahid
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  10. Tayyab Husnain
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Contributions

The concept and the experimental design were initiated by Adnan Iqbal and David W. Galbraith. Bio-informatics analyses was performed by Adnan Iqbal, Basit Jabbar and Muhammad Azam Ali. Cotton plant transformation was done by Adnan Iqbal and Ayesha Latif. Molecular characterization of transgenic cotton plants was done by Adnan Iqbal and Mukhtar Ahmad. Review of literature; Adnan Iqbal and Abdul Qayyum Rao. Data collection and analysis; Adnan Iqbal and Basit Jabbar. Preparation of main manuscript; Adnan Iqbal and Ahmad Ali Shahid. Critical review of manuscript; David W. Galbraith, Abdul Qayyum Rao and Tayyab Husnain; Approval of the final version of manuscript; Adnan Iqbal, Ambreen Gul, David W. Galbraith, Abdul Qayyum Rao and Tayyab Husnain. The manuscript was read by all authors and approved for publication.

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Correspondence to Adnan Iqbal.

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Iqbal, A., Latif, A., Galbraith, D.W. et al. Structure-based prediction of protein–protein interactions between GhWlim5 Domain1 and GhACTIN-1 proteins: a practical evidence with improved fibre strength. J. Plant Biochem. Biotechnol. 30, 373–386 (2021). https://doi.org/10.1007/s13562-020-00603-7

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