Cloning and expression pattern analysis of <i>FmPIF</i> gene family in <i>Fraxinus mandshurica</i>

Lü Yipin; Liang Nansong; Song Tingting; Cui Jinghong; Yu Lei; Zhan Yaguang

doi:10.12171/j.1000-1522.20200379

Journal of Beijing Forestry University > 2022 > 44(1): 58-68. > DOI: 10.12171/j.1000-1522.20200379

Lü Yipin, Liang Nansong, Song Tingting, Cui Jinghong, Yu Lei, Zhan Yaguang. Cloning and expression pattern analysis of FmPIF gene family in Fraxinus mandshurica[J]. Journal of Beijing Forestry University, 2022, 44(1): 58-68. DOI: 10.12171/j.1000-1522.20200379

Citation:

PDF (2578 KB)

Cloning and expression pattern analysis of FmPIF gene family in Fraxinus mandshurica

Key Laboratory of Saline-Alkali Vegetation Ecology Restoration of Ministry of Education, College of Life Science,Northeast Forestry University, Harbin 150040, Heilongjiang, China

More Information

Received Date: November 30, 2020
Revised Date: February 04, 2021
Accepted Date: November 29, 2021
Available Online: December 02, 2021
Published Date: January 24, 2022

Graphical Abstract

Abstract

Abstract

Objective This paper aims to explore the important role of Fraxinus mandshurica phytochrome interaction factors (PIFs) in the process of hormone regulation and abiotic stress response, and provide theoretical basis for revealing the molecular mechanism of Fraxinus mandshurica resistance and formulating forest genetic breeding strategies.
Method The FmPIFs gene was cloned from Fraxinus mandshurica, and its gene structure, protein physicochemical properties, conserved motifs, and phylogenetic relationships were analyzed by bioinformatics. The qRT-PCR method was used to analyze the expression patterns of FmPIFs genes in Fraxinus mandshurica in different tissues and under different hormones and stress conditions.
Result Five members of FmPIFs gene family of Fraxinus mandshurica were obtained and named as FmPIF1, FmPIF3, FmPIF4, FmPIF7 and FmPIF8. The corresponding proteins were all hydrophilic and unstable proteins, all of which were located in the nucleus. The results of multiple sequence alignment showed that FmPIFs all had APB conserved domains, and members FmPIF1 and FmPIF3 had unique APA domains. Tissue-specific analysis showed that FmPIFs were all expressed in leaves at the highest level, and member FmPIF8 expressed at the highest level, which was 3.96 times of control. However, it was expressed in a small amount in the stem, and the highest expression in stem was FmPIF3, which was only 0.21 time of control. The expression in root was extremely low. Stress response analysis showed that FmPIFs positively regulated the resistance of Fraxinus mandshurica plants to salt, alkali and drought stress, while negatively regulated plant cold resistance. The member FmPIF3 responded significantly to cold and salt stress, and the expression of FmPIF8 was significantly up-regulated under alkali stress, the expression of FmPIF1 was significantly up-regulated under drought stress. In the hormone response results, FmPIFs hadrelatively consistent responses to abscisic acid (ABA), salicylic acid (SA) and gibberellin (GA₃), while responses to auxin (IAA) and methyl jasmonate (MeJA) existed difference. FmPIF1 responded violently after MeJA application and its expression was significantly up-regulated, FmPIF7 was significantly up-regulated after SA treatment, and FmPIF3 and FmPIF4 were significantly up-regulated after GA₃ treatment.
Conclusion FmPIFs show high consistency in gene and protein structure. RT-qPCR results show that FmPIFs express the highest amount in the leaves of Fraxinus mandshurica. FmPIFs are induced to express by salt, alkali, drought and cold stress, and most of the expression patterns are similar. FmPIFs also play an important role in the regulation of Fraxinus mandshurica in response to IAA, ABA, MeJA, SA and GA₃ hormones.
- Fraxinus mandschurica,
- phytochrome interacting factor,
- gene clone,
- bioinformatics analysis,
- expression pattern

FullText(HTML)

References (49)

References

[1]	李秀坤, 许冬清. 植物光信号转导[J]. 自然杂志, 2019, 41(3):183−187. doi: 10.3969/j.issn.0253-9608.2019.03.004 Li X K, Xu D Q. Plant light signal transduction[J]. Journal of Nature, 2019, 41(3): 183−187. doi: 10.3969/j.issn.0253-9608.2019.03.004
[2]	Gabriela T O. The Arabidopsis basic/helix-loop-helix transcription factor family[J]. The Plant Cell, 2003, 8(15): 1749−1770.
[3]	Yu Z. A quartet of pif bhlh factors provides a transcriptionally centered signaling hub that regulates seedling morphogenesis through differential expression-patterning of shared target genes in Arabidopsis [J/OL]. PLoS Genetics, 2013, 1(9): e1003244[2020−10−31]. https://doi.org/10.1371/journal.pgen.1003244.
[4]	Liu X, Chen C Y, Wang K C, et al. Phytochrome interacting factor3 associates with the histone deacetylase hda15 in repression of chlorophyll biosynthesis and photosynthesis in etiolated Arabidopsis seedlings[J]. The Plant Cell, 2013, 25(4): 1258−1273. doi: 10.1105/tpc.113.109710
[5]	Leivar P, Monte E, Oka Y, et al. Multiple phytochrome-interacting bhlh transcription factors repress premature seedling photomorphogenesis in darkness[J]. Current Biology, 2008, 18(23): 1815−1823. doi: 10.1016/j.cub.2008.10.058
[6]	Leivar P, Quail P H. Pifs: pivotal components in a cellular signaling hub[J]. Trends in Plant Science, 2011, 16(1): 19−28. doi: 10.1016/j.tplants.2010.08.003
[7]	杨剑飞, 王宇, 杨琳, 等. 光敏色素互作因子PIFs是整合多种信号调控植物生长发育的核心元件[J]. 植物生理学报, 2014, 50(8):1109−1118. Yang J F, Wang Y, Yang L, et al. Phytochrome interaction factors pifs are the core elements that integrate multiple signals to regulate plant growth and development[J]. Acta Plant Physiology, 2014, 50(8): 1109−1118.
[8]	任小芸. ZmPIFs基因的克隆、表达及AtPIFs基因的抗旱功能研究[D]. 扬州: 扬州大学, 2017. Ren X Y. Cloning and expression of ZmPIFs gene and research on drought resistance function of AtPIFs gene[D]. Yangzhou: Yangzhou University, 2017.
[9]	Wang F, Chen X, Dong S, et al. Crosstalk of PIF4 and DELLA modulates CBF transcript and hormone homeostasis in cold response in tomato[J]. Plant Biotechnology Journal, 2020, 18(4): 1041−1055. doi: 10.1111/pbi.13272
[10]	Lau O S, Deng X W. Plant hormone signaling lightens up: integrators of light and hormones[J]. Current Opinion in Plant Biology, 2010, 13(5): 571−577. doi: 10.1016/j.pbi.2010.07.001
[11]	Nozue K, Harmer S L, Maloof J N. Genomic analysis of circadian clock-, light-, and growth-correlated genes reveals phytochrome-interacting factor 5 as a modulator of auxin signaling in Arabidopsis[J]. Plant Physiology, 2011, 156(1): 357−372. doi: 10.1104/pp.111.172684
[12]	Feng S H, Cristina M, Giuliana G, et al. Coordinated regulation of Arabidopsis thaliana development by light and gibberellins[J]. Nature, 2008, 451: 475−479.
[13]	Richter R, Behringer C, Muller I K, et al. The GATA-type transcription factors GNC and GNL/CGA1 repress gibberellin signaling downstream from DELLA proteins and PHYTOCHROME-INTERACTING FACTORS[J]. Genes & Development, 2010, 24(18): 2093−2104.
[14]	Keara A F, Sang H L, Dhaval P, et al. Phytochrome-interacting factor 4 (PIF4) regulates auxin biosynthesis at high temperature[J]. PNAS, 2011, 108(50): 20231−20235. doi: 10.1073/pnas.1110682108
[15]	Friml J Í, Wisniewska J, Benková E, et al. Lateral relocation of auxin efflux regulator PIN3 mediates tropism in Arabidopsis[J]. Nature, 2002, 415: 806−809. doi: 10.1038/415806a
[16]	Sun J Q, Qi L L, Li Y N, et al. Pif4-mediated activation of yucca8 expression integrates temperature into the auxin pathway in regulating Arabidopsis hypocotyl growth. [J/OL]. PLoS Genetics, 2012, 8(3): e1002594[2020−09−20]. https://doi.org/10.1371/journal.pgen.1002594.
[17]	Leivar P, Tepperman J M, Cohn M M, et al. Dynamic antagonism between phytochromes and PIF family basic helix-loop-helix factors induces selective reciprocal responses to light and shade in a rapidly responsive transcriptional network in Arabidopsis[J]. The Plant Cell, 2012, 24(4): 1398−1419. doi: 10.1105/tpc.112.095711
[18]	Leivar P, Monte E. PIFs: systems integrators in plant development[J]. The Plant Cell, 2014, 26(1): 56−78. doi: 10.1105/tpc.113.120857
[19]	Bernardo-García S, Delucas M, Martínez C, et al. BR-dependent phosphorylation modulates PIF4 transcriptional activity and shapes diurnal hypocotyl growth.[J]. Genes & Development, 2014, 28(15): 1681−1694.
[20]	Kim J, Kang H, Park J, et al. PIF1-interacting transcription factors and their binding sequence elements determine the in vivo targeting sites of PIF1[J]. The Plant Cell, 2016, 28(6): 1388−1405. doi: 10.1105/tpc.16.00125
[21]	周明琦. CBF信号途径在低温下对植物生长的调控及其育种应用[D]. 上海: 复旦大学, 2013. Zhou M Q. Regulation of CBF signaling pathway on plant growth under low temperature and its breeding application [D]. Shanghai: Fudan University, 2013.
[22]	Jiang B, Shi Y, Zhang X, et al. PIF3 is a negative regulator of the CBF pathway and freezing tolerance in Arabidopsis[J]. PNAS, 2017, 114(32): E6695−E6702. doi: 10.1073/pnas.1706226114
[23]	王峰. PhyA、HY5和PIF4在光质调控番茄低温抗性中的机制研究[D]. 杭州: 浙江大学, 2017. Wang F. Mechanism of Phya, HY5 and PIF4 in light quality regulation of low temperature resistance in tomato [D]. Hangzhou: Zhejiang University, 2017.
[24]	Gao Y, Jiang W, Dai Y, et al. A maize phytochrome-interacting factor 3 improves drought and salt stress tolerance in rice[J]. Plant Molecular Biology, 2015, 87(4/5): 413−428.
[25]	Kumar S V, Lucyshyn D, Jaeqer K E, et al. Transcription factor PIF4 controls the thermosensory activation of flowering [J]. Nature, 2012, 484: 242−245.
[26]	赵晓玲. 植物中与光敏色素相互作用的因子PIFs[J]. 植物生理学通讯, 2009, 45(6):531−536. Zhao X L. PIFs interacting with phytochrome in plants[J]. Journal of Plant Physiology, 2009, 45(6): 531−536.
[27]	Soy J, Leivar P, Nahuel G, et al. Phytochrome-imposed oscillations in PIF3 protein abundance regulate hypocotyl growth under diurnal light/dark conditions in Arabidopsis[J]. The Plant Journal, 2012, 71(3): 390−401.
[28]	Herbert K, Hans-Joachim G. The protein protocols handbook, 2nd edition [M]. Totowa: Humana Press, 2002.
[29]	孙平楠, 周小玲, 王正祥. 信号肽生物信息学分析在Neurospora crassa phyA基因鉴定中的应用[J]. 南方医科大学学报, 2009, 29(6):1098−1101. doi: 10.3321/j.issn:1673-4254.2009.06.003 Sun P N, Zhou X L, Wang Z X. Application of signal peptide bioinformatics analysis in identification of Neurospora crassa phyA gene[J]. Journal of Southern Medical University, 2009, 29(6): 1098−1101. doi: 10.3321/j.issn:1673-4254.2009.06.003
[30]	Thomas N P, Soren B, Gunnar V H, et al. Signalp 4.0: discriminating signal peptides from transmembrane regions[J]. Nature Methods, 2011, 8(10): 785−786. doi: 10.1038/nmeth.1701
[31]	Horton P, Park K J, Obayashi T, et al. Wolf psort: protein localization predictor [J]. Nucleic Acids Research, 2007, 35(Suppl.2): W585−W587.
[32]	Hu B, Jin L, Guo A Y, et al. GSDS 2.0: an upgraded gene feature visualization server[J]. Bioinformatics, 2015, 31(8): 1296−1297. doi: 10.1093/bioinformatics/btu817
[33]	Ma B, Yuan Y, Gao M, et al. Genome-wide identification, molecular evolution, and expression divergence of aluminum-activated malate transporters in apples[J]. International Journal of Molecular Sciences, 2018, 19(9): 2807−2809. doi: 10.3390/ijms19092807
[34]	Larkin M. Clustal W and Clustal X version 2.0[J]. Bioinformatics, 2007, 23(21): 2947−2948. doi: 10.1093/bioinformatics/btm404
[35]	Olsson H, Belfrage P. Phosphorylation and dephosphorylation of hormone-sensitive lipase interactions between the regulatory and basal phosphorylation sites[J]. FEBS Letters, 1988, 232(1): 78−82.
[36]	任小龙, 詹亚光, 梁雪, 等. 水曲柳花发育过程中AG、SOC1基因表达的qRT-PCR分析[J]. 植物研究, 2015, 35(4):612−617. doi: 10.7525/j.issn.1673-5102.2015.04.021 Ren X L, Zhan Y G, Liang X, et al. QRT-PCR analysis of AG and SOC1 gene expression during flower development of Fraxinus mandshurica[J]. Plant Research, 2015, 35(4): 612−617. doi: 10.7525/j.issn.1673-5102.2015.04.021
[37]	韦雪芳, 王冬梅, 刘思, 等. 信号肽及其在蛋白质表达中的应用[J]. 生物技术通报, 2006(6):38−42. doi: 10.3969/j.issn.1002-5464.2006.06.009 Wei X F, Wang D M, Liu S, et al. Signal peptide and its application in protein expression[J]. Biotechnology Bulletin, 2006(6): 38−42. doi: 10.3969/j.issn.1002-5464.2006.06.009
[38]	王镜岩, 朱圣庚, 徐长法. 生物化学[M]. 北京: 高等教育出版社, 2002. Wang J Y, Zhu S G, Xu C F. Biochemistry[M]. Beijing: Higher Education Press, 2002.
[39]	宋毓峰. 林烟草钾转运体基因NsHAK11的克隆与功能分析[D]. 北京: 中国农业科学院, 2014. Song Y F. Cloning and functional analysis of tobacco potassium transporter gene NsHAK11 [D]. Beijing: Chinese Academy of Agricultural Sciences, 2014.
[40]	高凯. NJ进化树构建方法的改进及其应用[D]. 北京: 北京工业大学, 2008. Gao K. Improvement and application of NJ evolutionary tree construction method [D]. Beijing: Beijing University of Technology, 2008.
[41]	Jeong J, Choi G. Phytochrome-interacting factors have both shared and distinct biological roles[J]. Molecules and Cells, 2013, 35(5): 371−380. doi: 10.1007/s10059-013-0135-5
[42]	Alabadí D, Gallego-Bartolomé J, Orlando L, et al. Gibberellins modulate light signaling pathways to prevent Arabidopsis seedling de-etiolation in darkness[J]. Plant Journal, 2010, 53(2): 324−335.
[43]	Shen H, Zhu L, Castillon A, et al. Light-induced phosphorylation and degradation of the negative regulator PIF1 depends upon its direct physical interactions with photoactivated phytochromes[J]. The Plant Cell, 2008, 20(6): 1586−1602. doi: 10.1105/tpc.108.060020
[44]	宋晓祎. 玉米中ZmPIFs基因的克隆与功能分析[D]. 泰安: 山东农业大学, 2016. Song X Y. Cloning and functional analysis of ZmPIFs gene in Zea mays [D]. Taian: Shandong Agricultural University, 2016.
[45]	刘浩浩. 过表达ZmPIF3转基因拟南芥植株抗盐分析[D]. 郑州: 河南农业大学, 2018. Liu H H. Salt tolerance analysis of transgenic Arabidopsis plants overexpressing ZmPIF3 [D]. Zhengzhou: Henan Agricultural University, 2018.
[46]	刘春浩, 梁楠松, 于磊, 等. 水曲柳TCP4转录因子克隆及胁迫和激素下的表达分析[J]. 北京林业大学学报, 2017, 39(6):22−31. Liu C H, Liang N S, Yu L, et al. Cloning and expression analysis of TCP4 transcription factor in Fraxinus mandshurica[J]. Journal of Beijing Forestry University, 2017, 39(6): 22−31.
[47]	Zheng P F, Wang X, Yang Y Y, et al. Identification of phytochrome-interacting factor family members and functional analysis of MdPIF4 in Malus domestica [J/OL]. International Journal of Molecular Sciences, 2020, 21(19): 7350[2020−11−11] . https://doi.org/10.3390/ijms21197350.
[48]	潘教文, 赵术珍, 张烨, 等. 光敏色素互作因子(PIFs)对植物生长发育的调控[J]. 山东农业科学, 2014, 46(6):150−156. Pan J W, Zhao S Z, Zhang Y, et al. Regulation of phytochrome interaction factors (PIFs) on plant growth and development[J]. Shandong Agricultural Sciences, 2014, 46(6): 150−156.
[49]	Oh E, Kang H, Yamaguchi S, et al. Genome-wide analysis of genes targeted by PHYTOCHROME INTERACTING FACTOR 3-LIKE 5 during seed germination in Arabidopsis[J]. The Plant Cell, 2009, 21(2): 403−419. doi: 10.1105/tpc.108.064691

Cited By

Get Citation

PDF

XML

Article views (1174) PDF downloads (69)

Turn off MathJax

Article Contents

Abstract

References

Cloning and expression pattern analysis of FmPIF gene family in Fraxinus mandshurica

Abstract

References

Catalog

Export File

Citation

Format

Content