Genome-wide Analysis of Proline-rich Extension-like Receptor Protein Kinase (PERK) in Brassica Rapa and Its Association with the Pollen Development

Overview

Journal BMC Genomics

Publisher Biomed Central

Specialty Genetics

Date 2020 Jun 17

PMID 32539701

Citations 7

Authors

Guohu Chen

Jian Wang

Hao Wang

Chenggang Wang

Xiaoyan Tang

Jie Li

Lei Zhang

Jianghua Song

Jinfeng Hou

Lingyun Yuan

Affiliations

Soon will be listed here.

Abstract

Background: Proline-rich extension-like receptor protein kinases (PERKs) are an important class of receptor kinases located in the plasma membrane, most of which play a vital role in pollen development.

Results: Our study identified 25 putative PERK genes from the whole Brassica rapa genome (AA). Phylogenetic analysis of PERK protein sequences from 16 Brassicaceae species divided them into four subfamilies. The biophysical properties of the BrPERKs were investigated. Gene duplication and synteny analyses and the calculation of Ka/Ks values suggested that all 80 orthologous/paralogous gene pairs between B. rapa and A. thaliana, B. nigra and B. oleracea have experienced strong purifying selection. RNA-Seq data and qRT-PCR analyses showed that several BrPERK genes were expressed in different tissues, while some BrPERKs exhibited high expression levels only in buds. Furthermore, comparative transcriptome analyses from six male-sterile lines of B. rapa indicated that 7 BrPERK genes were downregulated in all six male-sterile lines. Meanwhile, the interaction networks of the BrPERK genes were constructed and 13 PERK coexpressed genes were identified, most of which were downregulated in the male sterile buds.

Conclusion: Combined with interaction networks, coexpression and qRT-PCR analyses, these results demonstrated that two BrPERK genes, Bra001723.1 and Bra037558.1 (the orthologs of AtPERK6 (AT3G18810)), were downregulated beginning in the meiosis II period of male sterile lines and involved in anther development. Overall, this comprehensive analysis of some BrPERK genes elucidated their roles in male sterility.

Citing Articles

Genome-wide identification, transcript profiling and functional analyses of PCP gene family in Wucai (Brassica campestris).

Liu X, Wang Y, Tang X, Wang W, Khan A, Pang X Sci Rep. 2024; 14(1):28236.

PMID: 39548243 PMC: 11568302. DOI: 10.1038/s41598-024-79544-3.

Coronatine-Induced Maize Defense against Stalk Rot by Activating Antioxidants and Phytohormone Signaling.

Liu M, Sui Y, Yu C, Wang X, Zhang W, Wang B J Fungi (Basel). 2023; 9(12).

PMID: 38132756 PMC: 10744721. DOI: 10.3390/jof9121155.

Genome-wide association analysis for grain moisture content and dehydration rate on maize hybrids.

Dong Y, Feng Z, Ye F, Li T, Li G, Li Z Mol Breed. 2023; 43(1):5.

PMID: 37312866 PMC: 10248682. DOI: 10.1007/s11032-022-01349-x.

Insight into the Roles of Proline-Rich Extensin-like Receptor Protein Kinases of Bread Wheat ( L.).

Shumayla , Mendu V, Singh K, Upadhyay S Life (Basel). 2022; 12(7).

PMID: 35888032 PMC: 9323123. DOI: 10.3390/life12070941.

Genome-Wide Analysis and Characterization of the Proline-Rich Extensin-like Receptor Kinases (PERKs) Gene Family Reveals Their Role in Different Developmental Stages and Stress Conditions in Wheat ( L.).

Kesawat M, Kherawat B, Singh A, Dey P, Routray S, Mohapatra C Plants (Basel). 2022; 11(4).

PMID: 35214830 PMC: 8880425. DOI: 10.3390/plants11040496.

References

Bai L, Zhang G, Zhou Y, Zhang Z, Wang W, Du Y . Plasma membrane-associated proline-rich extensin-like receptor kinase 4, a novel regulator of Ca signalling, is required for abscisic acid responses in Arabidopsis thaliana. Plant J. 2009; 60(2):314-27. DOI: 10.1111/j.1365-313X.2009.03956.x. View

Huang S, Peng S, Liu Z, Li C, Tan C, Yao R . Investigation of the genes associated with a male sterility mutant (msm) in Chinese cabbage (Brassica campestris ssp. pekinensis) using RNA-Seq. Mol Genet Genomics. 2019; 295(1):233-249. DOI: 10.1007/s00438-019-01618-z. View

Shannon P, Markiel A, Ozier O, Baliga N, Wang J, Ramage D . Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003; 13(11):2498-504. PMC: 403769. DOI: 10.1101/gr.1239303. View

Szklarczyk D, Gable A, Lyon D, Junge A, Wyder S, Huerta-Cepas J . STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res. 2018; 47(D1):D607-D613. PMC: 6323986. DOI: 10.1093/nar/gky1131. View

Humphrey T, Haasen K, Aldea-Brydges M, Sun H, Zayed Y, Indriolo E . PERK-KIPK-KCBP signalling negatively regulates root growth in Arabidopsis thaliana. J Exp Bot. 2014; 66(1):71-83. PMC: 4265151. DOI: 10.1093/jxb/eru390. View

Gish L, Clark S . The RLK/Pelle family of kinases. Plant J. 2011; 66(1):117-27. PMC: 4657737. DOI: 10.1111/j.1365-313X.2011.04518.x. View

Tan C, Liu Z, Huang S, Li C, Ren J, Tang X . Pectin methylesterase inhibitor (PMEI) family can be related to male sterility in Chinese cabbage (Brassica rapa ssp. pekinensis). Mol Genet Genomics. 2017; 293(2):343-357. DOI: 10.1007/s00438-017-1391-4. View

Muhlhausen S, Kollmar M . Whole genome duplication events in plant evolution reconstructed and predicted using myosin motor proteins. BMC Evol Biol. 2013; 13:202. PMC: 3850447. DOI: 10.1186/1471-2148-13-202. View

Lin S, Miao Y, Su S, Xu J, Jin L, Sun D . Comprehensive analysis of Ogura cytoplasmic male sterility-related genes in turnip (Brassica rapa ssp. rapifera) using RNA sequencing analysis and bioinformatics. PLoS One. 2019; 14(6):e0218029. PMC: 6568414. DOI: 10.1371/journal.pone.0218029. View

10.

Shiu S, Bleecker A . Expansion of the receptor-like kinase/Pelle gene family and receptor-like proteins in Arabidopsis. Plant Physiol. 2003; 132(2):530-43. PMC: 166995. DOI: 10.1104/pp.103.021964. View

11.

Beilstein M, Nagalingum N, Clements M, Manchester S, Mathews S . Dated molecular phylogenies indicate a Miocene origin for Arabidopsis thaliana. Proc Natl Acad Sci U S A. 2010; 107(43):18724-8. PMC: 2973009. DOI: 10.1073/pnas.0909766107. View

12.

Nakhamchik A, Zhao Z, Provart N, Shiu S, Keatley S, Cameron R . A comprehensive expression analysis of the Arabidopsis proline-rich extensin-like receptor kinase gene family using bioinformatic and experimental approaches. Plant Cell Physiol. 2005; 45(12):1875-81. DOI: 10.1093/pcp/pch206. View

13.

Wang D, Zhang Y, Zhang Z, Zhu J, Yu J . KaKs_Calculator 2.0: a toolkit incorporating gamma-series methods and sliding window strategies. Genomics Proteomics Bioinformatics. 2010; 8(1):77-80. PMC: 5054116. DOI: 10.1016/S1672-0229(10)60008-3. View

14.

Wang Y, Tang H, DeBarry J, Tan X, Li J, Wang X . MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Res. 2012; 40(7):e49. PMC: 3326336. DOI: 10.1093/nar/gkr1293. View

15.

Trapnell C, Williams B, Pertea G, Mortazavi A, Kwan G, van Baren M . Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol. 2010; 28(5):511-5. PMC: 3146043. DOI: 10.1038/nbt.1621. View

16.

Shiu S, Bleecker A . Plant receptor-like kinase gene family: diversity, function, and signaling. Sci STKE. 2001; 2001(113):re22. DOI: 10.1126/stke.2001.113.re22. View

17.

Qanmber G, Liu J, Yu D, Liu Z, Lu L, Mo H . Genome-Wide Identification and Characterization of the Gene Family in Reveals Gene Duplication and Functional Divergence. Int J Mol Sci. 2019; 20(7). PMC: 6479967. DOI: 10.3390/ijms20071750. View

18.

Hu B, Jin J, Guo A, Zhang H, Luo J, Gao G . GSDS 2.0: an upgraded gene feature visualization server. Bioinformatics. 2014; 31(8):1296-7. PMC: 4393523. DOI: 10.1093/bioinformatics/btu817. View

19.

Florentino L, Santos A, Fontenelle M, Pinheiro G, Zerbini F, Baracat-Pereira M . A PERK-like receptor kinase interacts with the geminivirus nuclear shuttle protein and potentiates viral infection. J Virol. 2006; 80(13):6648-56. PMC: 1488943. DOI: 10.1128/JVI.00173-06. View

20.

Silva N, Goring D . The proline-rich, extensin-like receptor kinase-1 (PERK1) gene is rapidly induced by wounding. Plant Mol Biol. 2002; 50(4-5):667-85. DOI: 10.1023/a:1019951120788. View