Genome-wide Identification, Structural and Gene Expression Analysis of the BZIP Transcription Factor Family in Sweet Potato Wild Relative Ipomoea Trifida

Overview

Journal BMC Genet

Publisher Biomed Central

Specialties Biotechnology
Molecular Biology

Date 2019 Apr 27

PMID 31023242

Citations 29

Authors

Zhengmei Yang

Jian Sun

Yao Chen

Panpan Zhu

Lei Zhang

Shaoyuan Wu

Daifu Ma

Qinghe Cao

Zongyun Li

Tao Xu

Affiliations

Soon will be listed here.

Abstract

Background: The basic leucine zipper (bZIP) transcription factor is one of the most abundant and conserved transcription factor families. In addition to being involved in growth and development, bZIP transcription factors also play an important role in plant adaption to abiotic stresses.

Results: A total of 41 bZIP genes that encode 66 proteins were identified in Ipomoea trifida. They were distributed on 14 chromosomes of Ipomoea trifida. Segmental and tandem duplication analysis showed that segmental duplication played an important role in the ItfbZIP gene amplification. ItfbZIPs were divided into ten groups (A, B, C, D, E, F, G, H, I and S groups) according to their phylogenetic relationships with Solanum lycopersicum and Arabidopsis thaliana. The regularity of the exon/intron numbers and distributions is consistent with the group classification in evolutionary tree. Prediction of the cis-acting elements found that promoter regions of ItfbZIPs harbored several stress responsive cis-acting elements. Protein three-dimensional structural analysis indicated that ItfbZIP proteins mainly consisted of α-helices and random coils. The gene expression pattern from transcriptome data and qRT-PCR analysis showed that ItfbZIP genes expressed with a tissue-specific manner and differently expressed under various abiotic stresses, suggesting that the ItfbZIPs were involved in stress response and adaption in Ipomoea trifida.

Conclusions: Genome-wide identification, gene structure, phylogeny and expression analysis of bZIP gene in Ipomoea trifida supplied a solid theoretical foundation for the functional study of bZIP gene family and further facilitated the molecular breeding of sweet potato.

Citing Articles

In-Depth Characterization of Genes in the Context of Endoplasmic Reticulum (ER) Stress in ssp. .

Ayaz A, Jalal A, Zhang X, Khan K, Hu C, Li Y Plants (Basel). 2024; 13(8).

PMID: 38674568 PMC: 11053814. DOI: 10.3390/plants13081160.

Genome-Wide Identification and Expression Analysis of the Gene Family in Sweet Potato and Its Two Diploid Relatives.

Zhou Z, Huang J, Wang Y, He S, Yang J, Wang Y Int J Mol Sci. 2024; 25(5).

PMID: 38474246 PMC: 10931741. DOI: 10.3390/ijms25053000.

A comprehensive overview of omics-based approaches to enhance biotic and abiotic stress tolerance in sweet potato.

Ahmed S, Khan M, Xue S, Islam F, Ikram A, Abdullah M Hortic Res. 2024; 11(3):uhae014.

PMID: 38464477 PMC: 10923648. DOI: 10.1093/hr/uhae014.

Genome-wide identification and expression analysis of the glutamate receptor gene family in sweet potato and its two diploid relatives.

Hu Y, Dai Z, Huang J, Han M, Wang Z, Jiao W Front Plant Sci. 2024; 14:1255805.

PMID: 38179475 PMC: 10764598. DOI: 10.3389/fpls.2023.1255805.

Comprehensive Functional Analysis of the bZIP Family in Reveals That Could Respond to Multiple Abiotic Stresses.

Zhou R, Zhao G, Zheng S, Xie S, Lu C, Liu S Int J Mol Sci. 2023; 24(20).

PMID: 37894883 PMC: 10607107. DOI: 10.3390/ijms242015202.

References

Baena-Gonzalez E, Rolland F, Thevelein J, Sheen J . A central integrator of transcription networks in plant stress and energy signalling. Nature. 2007; 448(7156):938-42. DOI: 10.1038/nature06069. View

Liao Y, Zou H, Wei W, Hao Y, Tian A, Huang J . Soybean GmbZIP44, GmbZIP62 and GmbZIP78 genes function as negative regulator of ABA signaling and confer salt and freezing tolerance in transgenic Arabidopsis. Planta. 2008; 228(2):225-40. DOI: 10.1007/s00425-008-0731-3. View

Liu J, Srivastava R, Howell S . Stress-induced expression of an activated form of AtbZIP17 provides protection from salt stress in Arabidopsis. Plant Cell Environ. 2008; 31(12):1735-43. DOI: 10.1111/j.1365-3040.2008.01873.x. View

FUKAZAWA J, Sakai T, Ishida S, Yamaguchi I, Kamiya Y, Takahashi Y . Repression of shoot growth, a bZIP transcriptional activator, regulates cell elongation by controlling the level of gibberellins. Plant Cell. 2000; 12(6):901-15. PMC: 149092. DOI: 10.1105/tpc.12.6.901. View

Nijhawan A, Jain M, Tyagi A, Khurana J . Genomic survey and gene expression analysis of the basic leucine zipper transcription factor family in rice. Plant Physiol. 2007; 146(2):333-50. PMC: 2245831. DOI: 10.1104/pp.107.112821. View

Guan Y, Ren H, Xie H, Ma Z, Chen F . Identification and characterization of bZIP-type transcription factors involved in carrot (Daucus carota L.) somatic embryogenesis. Plant J. 2009; 60(2):207-17. DOI: 10.1111/j.1365-313X.2009.03948.x. View

Gibalova A, Renak D, Matczuk K, Duplakova N, Chab D, Twell D . AtbZIP34 is required for Arabidopsis pollen wall patterning and the control of several metabolic pathways in developing pollen. Plant Mol Biol. 2009; 70(5):581-601. DOI: 10.1007/s11103-009-9493-y. View

Yao Q, Bollinger C, Gao J, Xu D, Thelen J . P(3)DB: An Integrated Database for Plant Protein Phosphorylation. Front Plant Sci. 2012; 3:206. PMC: 3435559. DOI: 10.3389/fpls.2012.00206. View

Yang O, Popova O, Suthoff U, Luking I, Dietz K, Golldack D . The Arabidopsis basic leucine zipper transcription factor AtbZIP24 regulates complex transcriptional networks involved in abiotic stress resistance. Gene. 2009; 436(1-2):45-55. DOI: 10.1016/j.gene.2009.02.010. View

10.

Liu J, Chen N, Chen F, Cai B, Dal Santo S, Tornielli G . Genome-wide analysis and expression profile of the bZIP transcription factor gene family in grapevine (Vitis vinifera). BMC Genomics. 2014; 15:281. PMC: 4023599. DOI: 10.1186/1471-2164-15-281. View

11.

Zhou Y, Xu D, Jia L, Huang X, Ma G, Wang S . Genome-Wide Identification and Structural Analysis of bZIP Transcription Factor Genes in Brassica napus. Genes (Basel). 2017; 8(10). PMC: 5664138. DOI: 10.3390/genes8100288. View

12.

Finkelstein R, Lynch T . The Arabidopsis abscisic acid response gene ABI5 encodes a basic leucine zipper transcription factor. Plant Cell. 2000; 12(4):599-609. PMC: 139856. DOI: 10.1105/tpc.12.4.599. View

13.

Mitchell P, Tjian R . Transcriptional regulation in mammalian cells by sequence-specific DNA binding proteins. Science. 1989; 245(4916):371-8. DOI: 10.1126/science.2667136. 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.

Chen H, Chen W, Zhou J, He H, Chen L, Chen H . Basic leucine zipper transcription factor OsbZIP16 positively regulates drought resistance in rice. Plant Sci. 2012; 193-194:8-17. DOI: 10.1016/j.plantsci.2012.05.003. View

16.

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

17.

Baloglu M, Eldem V, Hajyzadeh M, Unver T . Genome-wide analysis of the bZIP transcription factors in cucumber. PLoS One. 2014; 9(4):e96014. PMC: 3997510. DOI: 10.1371/journal.pone.0096014. View

18.

Zander M, La Camera S, Lamotte O, Metraux J, Gatz C . Arabidopsis thaliana class-II TGA transcription factors are essential activators of jasmonic acid/ethylene-induced defense responses. Plant J. 2009; 61(2):200-10. DOI: 10.1111/j.1365-313X.2009.04044.x. View

19.

Xiang Y, Tang N, Du H, Ye H, Xiong L . Characterization of OsbZIP23 as a key player of the basic leucine zipper transcription factor family for conferring abscisic acid sensitivity and salinity and drought tolerance in rice. Plant Physiol. 2008; 148(4):1938-52. PMC: 2593664. DOI: 10.1104/pp.108.128199. View

20.

Zhao J, Guo R, Guo C, Hou H, Wang X, Gao H . Evolutionary and Expression Analyses of the Apple Basic Leucine Zipper Transcription Factor Family. Front Plant Sci. 2016; 7:376. PMC: 4811886. DOI: 10.3389/fpls.2016.00376. View