Bioinformatic and Expression Analysis of HD-Zip Family Gene in Betula platyphylla

doi:10.7525/j.issn.1673-5102.2018.06.017

Abstract

Abstract: Homeodomain-leucine zipper (HD-Zip) proteins are ubiquitous in plants and participate in various aspects of plant growth and developmental processes as well as environmental responses. Using birch genome database, we acquired 35 putative HD-Zip genes. These genes were classified into four subfamilies, Ⅰ to Ⅳ, based on phylogenetic analysis. The additional conserved domains, protein structures, chromosome distribution and physiological functions of these members were further predicted and analyzed. To gain more insights into the roles of birch HD-Zip genes in salinity tolerance, we identified seven genes which were highly induced by salt stress using transcriptomic data. This study provides a solid foundation for uncovering the biological roles of HD-Zip genes in salt response from Betula platyphylla.

Key words: Betula platyphylla Suk., HD-Zip, gene family, bioinformatic analysis

CLC Number:

S722.3+6

WANG Jia-Qi, ZHANG Xi, LI Li. Bioinformatic and Expression Analysis of HD-Zip Family Gene in Betula platyphylla[J]. Bulletin of Botanical Research, 2018, 38(6): 931-938.

References

1. Liu Q,Zhang G Y,Chen S Y. Structure and regulatory function of plant transcription factors[J]. Chinese Science Bulletin,2001,46(4):271-278.
2. Nakashima K,Ito Y,Yamaguchi-Shinozaki K. Transcriptional regulatory networks in response to abiotic stresses in Arabidopsis and grasses[J]. Plant Physiology,2009,149(1):88-95.
3. Golldack D,Lüking I,Yang O. Plant tolerance to drought and salinity:stress regulating transcription factors and their functional significance in the cellular transcriptional network[J]. Plant Cell Reports,2011,30(8):1383-1391.
4. Wang H Y,Wang H L,Shao H B,et al. Recent advances in utilizing transcription factors to improve plant abiotic stress tolerance by transgenic technology[J]. Frontiers in Plant Science,2016,7:67.
5. Todaka D,Shinozaki K,Yamaguchi-Shinozaki K. Recent advances in the dissection of drought-stress regulatory networks and strategies for development of drought-tolerant transgenic rice plants[J]. Frontiers in Plant Science,2015,6:84.
6. Viola I L,Gonzalez D H. Chapter 6-structure and evolution of plant homeobox genes[J]. Plant Transcription Factors:Evolutionary,Structural and Functional Aspects,2016:101-112.
7. Ariel F D,Manavella P A,Dezar C A,et al. The true story of the HD-Zip family[J]. Trends in Plant Science,2007,12(9):419-426.
8. Elhiti M,Stasolla C. Structure and function of homodomain-leucine zipper(HD-Zip) proteins[J]. Plant Signaling & Behavior,2009,4(2):86-88.
9. Arce A L,Raineri J,Capella M,et al. Uncharacterized conserved motifs outside the HD-Zip domain in HD-Zip subfamily I transcription factors; a potential source of functional diversity[J]. BMC Plant Biology,2011,11:42.
10. Henriksson E,Olsson A S B,Johannesson H,et al. Homeodomain leucine zipper class I genes in Arabidopsis expression patterns and phylogenetic relationships[J]. Plant Physiology,2005,139(1):509-518.
11. Aoyama T,Dong C H,WU Wu Y,et al. Ectopic expression of the Arabidopsis transcriptional activator Athb-1 alters leaf cell fate in tobacco[J]. The Plant Cell,1995,7(11):1773-1785.
12. Kim Y K,Son O,Kim M R,et al. ATHB23,an Arabidopsis class Ⅰ homeodomain-leucine zipper gene,is expressed in the adaxial region of young leaves[J]. Plant Cell Reports,2007,26(8):1179-1185.
13. Harris J C,Sornaraj P,Taylor M,et al. Molecular interactions of the γ-clade homeodomain-leucine zipper class Ⅰ transcription factors during the wheat response to water deficit[J]. Plant Molecular Biology,2016,90(4-5):435-452.
14. Zhao Y,Ma Q,Jin X L,et al. A novel maize homeodomain-leucine zipper(HD-Zip) Ⅰ gene, Zmhdz10,positively regulates drought and salt tolerance in both rice and Arabidopsis[J]. Plant and Cell Physiology,2014,55(6):1142-1156.
15. Ciarbelli A R,Ciolfi A,Salvucci S,et al. The Arabidopsis homeodomain-leucine Zipper Ⅱ gene family:diversity and redundancy[J]. Plant Molecular Biology,2008,68:465.
16. Franklin K A,Praekelt U,Stoddart W M,et al. Phytochromes B,D and E act redundantly to control multiple physiological responses in Arabidopsis[J]. Plant Physiology,2003,131(3):1340-1346.
17. Carabelli M,Turchi L,Ruzza V,et al. Homeodomain-Leucine zipper Ⅱ family of transcription factors to the limelight:central regulators of plant development[J]. Plant Signaling & Behavior,2013,8(9):e25447.
18. Park M Y,Kim S A,Lee S J,et al. ATHB17 is a positive regulator of abscisic acid response during early seedling growth[J]. Molecules and Cells,2013,35(2):125-133.
19. Mukherjee K,Bürglin T R. MEKHLA,a novel domain with similarity to PAS domains,is fused to plant homeodomain-leucine zipper Ⅲ proteins[J]. Plant Physiology,2006,140(4):1142-1150.
20. Prigge M J,Otsuga D,Alonso J M,et al. Class Ⅲ homeodomain-leucine zipper gene family members have overlapping,antagonistic,and distinct roles in Arabidopsis development[J]. The Plant Cell,2005,17(1):61-76.
21. Zhu Y Y,Song D L,Sun J Y,et al. PtrHB7,a class Ⅲ HD-Zip gene,plays a critical role in regulation of vascular cambium differentiation in Populus[J]. Molecular Plant,2013,6(4):1331-1343.
22. Robischon M,Du J,Miura E,et al. The Populus class Ⅲ HD ZIP, popREVOLUTA,influences cambium initiation and patterning of woody stems[J]. Plant Physiology,2011,155(3):1214-1225.
23. Chew W,Hrmova M,Lopato S. Role of homeodomain leucine zipper(HD-Zip) Ⅳ transcription factors in plant development and plant protection from deleterious environmental factors[J]. International Journal of Molecular Sciences,2013,14(4):8122-8147.
24. Ingram G C,Boisnard-Lorig C,Dumas C,et al. Expression patterns of genes encoding HD-Zip Ⅳ homeo domain proteins define specific domains in maize embryos and meristems[J]. The Plant Journal,2000,22(5):401-414.
25. Ito M,Sentoku N,Nishimura A,et al. Position dependent expression of GL2 -type homeobox gene,Roc1:significance for protoderm differentiation and radial pattern formation in early rice embryogenesis[J]. The Plant Journal,2002,29(4):497-507.
26. Nakamura M,Katsumata H,Abe M,et al. Characterization of the class Ⅳ homeodomain-leucine zipper gene family in Arabidopsis[J]. Plant Physiology,2006,141(4):1363-1375.
27. Ciarbelli A R,Ciolfi A,Salvucci S,et al. The Arabidopsis Homeodomain-leucine Zipper Ⅱ gene family:diversity and redundancy[J]. Plant Molecular Biology,2008,68(4-5):465-478.
28. Agalou A,Purwantomo S,Övernäs E,et al. A genome-wide survey of HD-Zip genes in rice and analysis of drought-responsive family members[J]. Plant Molecular Biology,2008,66(1-2):87-103.
29. Chen J H,Song Y P,Zhang H,et al. Genome-wide analysis of gene expression in response to drought stress in Populus simonii[J]. Plant Molecular Biology Reporter,2013,31(4):946-962.
30. Hu R B,Chi X Y,Chai G H,et al. Genome-wide identification,evolutionary expansion,and expression profile of homeodomain-leucine zipper gene family in poplar(Populus trichocarpa)[J]. PLoS One,2012,7(2):e31149.
31. Yue H,Shu D T,Wang M,et al. Genome-wide identification and expression analysis of the HD-Zip gene family in wheat(Triticum aestivum L.)[J]. Genes,2018,9(2):70.
32. Zhang J,Zhu Q H,Moncuquet P,et al. Genome-wide identification and characterization of the homeodomain-leucine zipper Ⅰ family of genes in cotton(Gossypium spp.)[J]. Plant Gene,2016,7:50-61.
33. Belamkar V,Weeks N T,Bharti A K,et al. Comprehensive characterization and RNA-Seq profiling of the HD-Zip transcription factor family in soybean(Glycine max) during dehydration and salt stress[J]. BMC Genomics,2014,15:950.
34. Zhao Y,Zhou Y Q,Jiang H Y,et al. Systematic analysis of sequences and expression patterns of drought-responsive members of the HD-Zip gene family in maize[J]. PLoS One,2011,6(12):e28488.
35. Ding Z H,Fu L L,Yan Y,et al. Genome-wide characterization and expression profiling of HD-Zip gene family related to abiotic stress in cassava[J]. PLoS One,2017,12(3):e0173043.
36. Perotti M F,Ribone P A,Chan R L. Plant transcription factors from the homeodomain-leucine zipper family Ⅰ. Role in development and stress responses[J]. IUBMB Life,2017,69(5):280-289.
37. Nakashima K,Jan A,Todaka D,et al. Comparative functional analysis of six drought-responsive promoters in transgenic rice[J]. Planta,2014,239(1):47-60.
38. Ariel F,Diet A,Verdenaud M,et al. Environmental regulation of lateral root emergence in Medicago truncatula requires the HD-Zip Ⅰ transcription factor HB1[J]. The Plant Cell,2010,22(7):2171-2183.
39. Dezar C A,Gago G M,González D H,et al. Hahb-4,a sunflower homeobox-leucine zipper gene,is a developmental regulator and confers drought tolerance to Arabidopsis thaliana plants[J]. Transgenic Research,2005,14(4):429-440.

[1]	Xueying WANG, Ruiqi WANG, Yang ZHANG, Cong LIU, Dean XIA, Zhigang WEI. Genome‑wide Identification and Stress Response Analysis of Cyclic Nucleotide-gated Channels(CNGC) Gene Family in Populus trichocarpa [J]. Bulletin of Botanical Research, 2022, 42(4): 613-625.
[2]	Shuang-Hui TIAN, He CHENG, Yang ZHANG, Cong LIU, De-An XIA, Zhi-Gang WEI. Genome-wide Identification and Expressional Analysis of Carotenoid Cleavage Dioxygenases(CCD) Gene Family in Populus trichocarpa under Drought and Salt Stress [J]. Bulletin of Botanical Research, 2021, 41(6): 993-1005.
[3]	LI Chan, ZHANG Xiang, ZHENG Lan, CHANG Cheng-Long, LIU Cai-Xia, ZHENG Mi, YOU Xiang-Ling. Genetic Transformation of PsnHB22 Gene from Populus simonii×P.nigra in Tobacco [J]. Bulletin of Botanical Research, 2020, 40(5): 760-767.
[4]	QIN Lin-Lin, ZHANG Xi, JIANG Cheng, LI Li. Cloning and Functional Analysis of BpZFP4 Promoter from Birch(Betula platyphylla) [J]. Bulletin of Botanical Research, 2019, 39(6): 917-926.
[5]	ZHU Li-Li, QING Jun, DU Qing-Xin, HE Feng, DU Hong-Yan. Genome-wide Identification and Expression Characteristics of LOX Gene Family in Eucommia ulmoides [J]. Bulletin of Botanical Research, 2019, 39(6): 927-934.
[6]	ZHANG Xue-Mei, YAO Wen-Jing, ZHAO Kai, JIANG Ting-Bo, ZHOU Bo-Ru. Bioinformatics and Response to Salt Stress Analysis of the HD-Zip Transcription Factor Family in Populus simonii×P.nigra [J]. Bulletin of Botanical Research, 2017, 37(5): 715-721.
[7]	GUAN Qing-Jie1,2；WANG Zhen-Juan1；ZHENG Heng1；LIU Guang-Tao3；LIU Shen-Kui3. OsLOL2 Gene Clone of Rice and the Salt Resistance Analysis of Overexpression Arabidopsis thaliana [J]. Bulletin of Botanical Research, 2015, 35(2): 259-269.
[8]	WU Xiang-Yu;XU Zhi-Ru;QU Chun-Pu;LI Wei;SUN Qi;LIU Guan-Jun. Genome-wide Identification and Characterization of NLP* Gene Family in Populus trichocarpa [J]. Bulletin of Botanical Research, 2014, 34(1): 37-43.
[9]	FAN A-Qi;;MAO Juan;;LIU Si-Yan;;ZHANG Jun-Lian;;WANG Di;;BAI Jiang-Ping;. Cloning and Bioinformatic Analysis of StSnRK2.2 Gene in Solanum tuberosum* [J]. Bulletin of Botanical Research, 2013, 33(3): 294-301.
[10]	LU Yu-Jian;LIU Heng;LI Yu-Xi;LIANG Da-Wei;ZHAO Peng;JIA Peng-Fei;NIU Song-Zhao. Preliminary Study on the Subcellular Localization of Arabidopsis thaliana* AtZW10 [J]. Bulletin of Botanical Research, 2013, 33(2): 174-180.