龙眼CCCH锌指蛋白基因家族的全基因组特征鉴定及表达分析

doi:10.1016/S2095-3119(20)63460-8

摘要/Abstract

摘要：

CCCH（C3H）锌指转录因子(Zinc finger, Znf)是一种新型的Znf基因，其通过绑定于基因的mRNA上调控基因的表达，并在植物生长发育和抗非生物胁迫中发挥重要作用。龙眼是一种具有重要的经济价值热带、亚热带果树。然而，龙眼C3H的基因组信息及功能仍不清楚。本研究对龙眼C3H (DlC3H)基因家族进行了全基因组鉴定及表达分析。从龙眼基因组数据库中共鉴定出分布于3个进化枝中的49个DlC3H基因，并对其基因结构、motif组成、系统发育树和潜在功能等方面进行了基因特征分析。可变剪接事件(alternative splicing, AS)分析表明，DlC3H基因AS事件可能参与龙眼非胚性培养物向胚性培养物的转换。启动子分析显示，大多数DlC3H基因包含与激素和胁迫响应相关的顺式作用元件。实时荧光定量PCR（qRT-PCR）分析显示，26个具有MeJA和ABA响应顺式作用元件的DlC3Hs，在ABA、MeJA及其内源性抑制剂的作用下表现出不同的表达模式，提示DlC3Hs可能参与了ABA和MeJA信号通路。同时，在龙眼非胚性愈伤组织和3个胚胎培养阶段的表达谱显示，17个DlC3Hs成员中只有5个DlC3Hs的表达模式与转录组数据FPKM相同；DlC3H07/14/16/36/49在胚性愈伤组织中表达较高，而DlC3H04/38在球形胚中表达较高，说明它们在胚胎发育中具有不同的作用。通过改良RLM-RACE验证了DlC3H01/03/05/11/19/39被sRNAs调控。本研究首次对龙眼的C3H基因进行了系统分析，特别是C3H基因可能参与激素、胁迫反应以及体细胞胚胎形态建成有关。本试验的初步结果以期为进一步研究龙眼C3H基因家族的特征和功能提供线索。

Abstract: CCCH (C3H) Zinc finger (Znf) transcription factors (TFs), as a novel type of Znf gene, regulate the expression of genes by binding to their mRNAs and play important roles in plant growth and development and abiotic stress resistance. Longan (Dimocarpous longan) is a tropical/subtropical fruit tree of great economic importance in Southeast Asia. However, genomic information on C3H and their functions in longan are still unknown. In this study, a comprehensive analysis of the longan C3H (DlC3H) gene family was carried out. A total of 49 DlC3H genes in three clades were identified from the longan genome database. Characteristics of the genes were analyzed with respect to gene structure, motif composition, phylogenetic tree and potential functions. The analysis of alternative splicing (AS) events suggested that AS events in DlC3H genes were related to the transformation from longan non-embryonic to embryonic cultures. Promoter analysis indicated that most of the DlC3H genes included cis-acting elements associated with hormones and stresses responses. Quantitative real-time PCR (qRT-PCR) analysis indicated that 26 of the 49 DlC3Hs, which possess methyl jasmonate (MeJA) and abscisic acid (ABA) responsive cis-acting elements, showed differential expression patterns under treatment with ABA, MeJA and their endogenous inhibitors, suggesting that DlC3Hs might be involved in the ABA and MeJA signaling pathways. The expression profiles of 17 of the 49 DlC3Hs in non-embryonic callus and three tissues of embryonic cultures showed that only five of the 17 DlC3Hs had the same expression trends as the FPKM trends in transcriptome data; the expression levels of DlC3H07/14/16/36/49 in embryogenic callus and DlC3H04/38 in globular embryos were high, suggesting that they have different functions in embryonic development. Further, we verified that DlC3H01/03/05/11/19/39 were regulated by sRNAs by a modified 5´ RLM-RACE method. This study provides the first systematic analysis of C3H genes in longan, and found that C3H genes may be involved in hormone and stress responses, and somatic embryogenesis. Our preliminary investigation may provide clues to further studies on the characteristics and functions of this family in longan.

Key words: Dimocarpus longan Lour , CCCH Zinc finger , characteristic identification , expression profile

. 龙眼CCCH锌指蛋白基因家族的全基因组特征鉴定及表达分析[J]. Journal of Integrative Agriculture, 2022, 21(1): 113-130 .

SU Li-yao, XIAO Xue-chen, JIANG Meng-qi, HUANG Shu-qi, XUE Xiao-dong, LI Xue, LAI Zhong-xiong, LIN Yu-ling . Genome-wide analysis of the CCCH zinc finger family in longan: Characteristic identification and expression profiles in Dimocarpus longan Lour[J]. Journal of Integrative Agriculture, 2022, 21(1): 113-130 .

参考文献

Agnieszka G, Anita W, Norikazu T, Stefan M, Marcin F. 2009. Characterization of CsSEF1 gene encoding putative CCCH-type zinc finger protein expressed during cucumber somatic embryogenesis. Journal of Plant Physiology, 166, 310–323.
Antoine B, Paape T D, Peng Z, Roman B, Farmer A D, Joann M, Bharti A K, Woodward J E, May G D, Arnaud D, Déjardin A, Leplé J C, Lesagedescauses M C, Pilate G. 2007. Genome-wide analysis of LIM gene family in Populus trichocarpa, Arabidopsis thaliana and Oryza sativa. DNA Research, 14, 103–116.
Antoine B, Paape T D, Peng Z, Roman B, Farmer A D, Joann M, Bharti A K, Woodward J E, May G D, Laurent G. 2011. Whole-genome nucleotide diversity, recombination, and linkage disequilibrium in the model legume Medicago truncatula. Proceedings of the National Academy of Sciences of the United States of America, 108, 864–870.
Bakheet T, Williams B R G, Khabar K S A. 2006. ARED 3.0: The large and diverse AU-rich transcriptome. Nucleic Acids Research, 34, D111–D114.
Barreau C, Paillard L, Osborne H B. 2006. AU-rich elements and associated factors: Are there unifying principles? Nucleic Acids Research, 33, 7138–7150.
Bartel D P. 2004. MicroRNAs: Genomics, biogenesis, mechanism, and function. Cell, 116, 281–297.
Bogamuwa S, Jang J C. 2013. The Arabidopsis tandem CCCH zinc finger proteins AtTZF4, 5 and 6 are involved in light-, abscisic acid- and gibberellic acid-mediated regulation of seed germination. Plant Cell & Environment, 36, 1507–1519.
Chai G, Hu R, Zhang D, Guang Q, Ran Z, Cao Y, Chen P, Kong Y, Zhou G. 2012. Comprehensive analysis of CCCH zinc finger family in poplar (Populus trichocarpa). BMC Genomics, 13, 253–275.
Couture J F, Collazo E, Trievel R C. 2006. Molecular recognition of histone H3 by the WD40 protein WDR5. Nature Structural & Molecular Biology, 13, 698–703.
Cristian B, Torben J, Pere P, Vicient C M. 2004. Ankyrin repeat-containing proteins in Arabidopsis: Characterization of a novel and abundant group of genes coding ankyrin-transmembrane proteins. Gene, 340, 111–121.
Guo Y, Yu Y, Wang D, Wu C, Yang G, Huang J, Zheng C. 2009. GhZFP1, a novel CCCH-type zinc finger protein from cotton, enhances salt stress tolerance and fungal disease resistance in transgenic tobacco by interacting with GZIRD21A and GZIPR5. New Phytologist, 183, 62–75.
Initiative T A G. 2000. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature, 408, 796–815.
Jaillon O, Aury J, Noel B, Policriti A, Clepet C, Casagrande A, Choisne N, Aubourg S, Vitulo N, Jubin C, Vezzi A, Legeai F, Hugueney P, Dasilva C, Horner D, Mica E, Jublot D, Poulain J, Bruyère C, Billault A, et al. 2007. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature, 449, 463–468.
Jue D, Sang X, Liu L, Shu B, Wang Y, Xie J, Liu C, Shi S. 2018. The ubiquitin-conjugating enzyme gene family in Longan (Dimocarpus longan Lour.): Genome-wide identification and gene expression during flower Induction and abiotic stress responses. Molecules, 23, 662–680.
Kim D H, Yamaguchi S, Lim S, Oh E, Park J, Hanada A, Kamiya Y, Choi G. 2008. SOMNUS, a CCCH-type zinc finger protein in Arabidopsis, negatively regulates light-dependent seed germination downstream of PIL5. The Plant Cell, 20, 1260–1277.
Kong Z, Li M, Yang W, Xu W, Xue Y. 2006. A novel nuclear-localized CCCH-type zinc finger protein, OsDOS, is involved in delaying leaf senescence in rice. Plant Physiology, 141, 1376–1388.
Kosarev P, Mayer K F, Hardtke C S. 2002. Evaluation and classification of RING-finger domains encoded by the Arabidopsis genome. Genome Biology, 3, 1–12.
Lee S, Jung H J, Kang H, Kim S Y. 2012. Arabidopsis zinc finger proteins AtC3H49/AtTZF3 and AtC3H20/AtTZF2 are involved in ABA and JA responses. Plant & Cell Physiology, 53, 673–686.
Li J, Jia D, Chen X. 2001. HUA1, a regulator of stamen and carpel identities in Arabidopsis, codes for a nuclear RNA binding protein. Plant Cell, 13, 2269–2281.
Li X, Chen Y, Zhang S, Su L, Xu X, Chen X, Lai Z, Lin Y. 2020. Genome-wide identification and expression analyses of Sm genes reveal their involvement in early somatic embryogenesis in Dimocarpus longan Lour. PLoS ONE, 15, e0230795.
Li Y Q. 2014. Analysis of the biological function of the phytolasma-responsive novel miRNA in mulberry. MSc thesis, Shandong Agricultural University, China. (in Chinese)
Li Z, Tomas T L. 1998. PEI1, an embryo-specific zinc finger protein gene required for heart-stage embryo formation in Arabidopsis. Plant Cell, 10, 383–398.
Lin P C, Pomeranz M, Jikumaru Y, Kang S J, Hah C, Fujioka S, Kamiya Y, Jang J C. 2011. The Arabidopsis tandem zinc finger protein AtTZF1 affects ABA- and GA-mediated growth, stress and gene expression responses. The Plant Journal, 65, 253–268.
Lin Y, Lai Z. 2010. Reference gene selection for qPCR analysis during somatic embryogenesis in longan tree. Plant Science, 178, 359–365.
Lin Y, Lai Z. 2013a. Comparative analysis reveals dynamic changes in miRNAs and their targets and expression during somatic embryogenesis in longan (Dimocarpus longan Lour.). PLoS ONE, 8, e60337.
Lin Y, Lai Z. 2013b. Evaluation of suitable reference genes for normalization of microRNA expression by real-time reverse transcription PCR analysis during longan somatic embryogenesis. Plant Physiology & Biochemistry, 66, 20–25.
Lin Y, Lai Z, Lin L, Lai R, Tian Q, Wei Y, Zhang D, Yang M, Chen Y, Zhang Z. 2015a. Endogenous target mimics, microRNA167, and its targets ARF6 and ARF8 during somatic embryo development in Dimocarpus longan Lour. Molecular Breeding, 35, 227–242.
Lin Y, Lai Z, Tian Q, Lin L, Lai R, Yang M, Zhang D, Chen Y, Zhang Z. 2015b. Endogenous target mimics down-regulate miR160 mediation of ARF10, -16, and -17 cleavage during somatic embryogenesis in Dimocarpus longan Lour. Frontiers Plant Science, 6, 956–972.
Lin Y, Lin L, Lai R, Liu W, Chen Y, Zhang Z, Xu X H, Lai Z. 2015c. MicroRNA390-directed TAS3 cleavage leads to the production of tasiRNA-ARF3/4 during somatic embryogenesis in Dimocarpus longan Lour. Frontiers Plant Science, 6, 1119–1135.
Lin Y, Min J, Lai R, Wu Z, Chen Y, Yu L, Cheng C, Jin Y, Tian Q, Liu Q, Liu Y, Zhang C, Lin L, Hu Y, Zhang D, Thu M, Zhang Z, Liu S, Zhong C, Fang Z, et al. 2017. Genome-wide sequencing of longan (Dimocarpus longan Lour.) provides insights into molecular basis of its polyphenol-rich characteristics. Gigascience, 6, 1–14.
Liu S, Khan M R G, Li Y, Zhang J, Hu C. 2014. Comprehensive analysis of CCCH-type zinc finger gene family in citrus (Clementine mandarin) by genome-wide characterization. Molecular Genetics & Genomics, 289, 855–872.
Lorković Z J, Barata A. 2002. Genome analysis: RNA recognition motif (RRM) and K homology (KH) domain RNA-binding proteins from the flowering plant Arabidopsis thaliana. Nucleic Acids Research, 30, 623–635.
Mazumdar P, Lau S E, Wei Y W, Singh P, Harikrishna J A. 2017. Genome-wide analysis of the CCCH Zinc-Finger gene family in banana (Musa acuminata): An insight into motif and gene structure arrangement,evolution and salt stress responses. Tropical Plant Biology, 10, 177–193.
Mosavi L K, Minor D L, Peng Z. 2002. Consensus-derived structural determinants of the ankyrin repeat motif. Proceedings of the National Academy of Sciences of the United States of America, 99, 16029–16034.
Nocker S V, Ludwig P. 2003. The WD-repeat protein superfamily in Arabidopsis: conservation and divergence in structure and function. BMC Genomics, 4, 50–61.
Peng X, Zhao Y, Cao J, Zhang W, Jiang H, Li X, Ma Q, Zhu S, Cheng B. 2012. CCCH-type zinc finger family in maize: Genome-wide identification, classification and expression profiling under abscisic acid and drought treatments. PLoS ONE, 7, e40120.
Pradhan S, Kant C, Verma S, Bhatia S. 2017. Genome-wide analysis of the CCCH zinc finger family identifies tissue specific and stress responsive candidates in chickpea (Cicer arietinum L.). PLoS ONE, 12, e180469.
Riechmann J L, Heard J, Martin G, Reuber L, Jiang C, Keddie J, Adam L, Pineda O, Ratcliffe O J, Samaha R R. 2000. Arabidopsis transcription factors: Genome-wide comparative analysis among eukaryotes. Sciense, 290, 2105–2110.
Schnable P S, Doreen W, Fulton R S, Stein J C, Fusheng W, Shiran P, Chengzhi L, Jianwei Z, Lucinda F, Graves T A, Minx P, Reily A D, Courtney L, Kruchowski S S, Tomlinson C, Strong C, Delehaunty K, Fronick C, Courtney B, Rock S M, et al. 2015. The B73 maize genome: Complexity, diversity, and dynamics. Science, 326, 1112–1115.
Sun J, Jiang H, Xu Y, Li H, Wu X, Xie Q, Li C. 2007. The CCCH-type zinc finger proteins AtSZF1 and AtSZF2 regulate salt stress responses in Arabidopsis. Plant & Cell Physiology, 48, 1148.
Ülker B, Somssich I E. 2004. WRKY transcription factors: from DNA binding towards biological function. Current Opinion in Plant Biology, 7, 491–498.
Wang D, Guo Y, Wu C, Yang G, Li Y, Zheng C. 2008. Genome-wide analysis of CCCH zinc finger family in Arabidopsis and rice. BMC Genomics, 9, 44–64.
Wang W, Mauleon R, Hu Z, Chebotarov D, Tai S, Wu Z, Li M, Zheng T, Fuentes R R, Zhang F. 2018. Genomic variation in 3,010 diverse accessions of Asian cultivated rice. Nature, 557, 43–49.
Wang X, Zhong Y, Cheng Z. 2014. Evolution and expression analysis of the CCCH zinc finger gene family in Vitis vinifera. Plant Genome, 7, 16–25.
Wray G A, Hahn M W, Ehab A, Balhoff J P, Margaret P, Rockman M V, Romano L A. 2003. The evolution of transcriptional regulation in eukaryotes. Molecular Biology & Evolution, 20, 1377–1419.
Xu Q, Chen L, Ruan X, Chen D, Zhu A, Chen C, Bertrand D, Jiao W, Hao B, Lyon M P, Chen J, Gao S, Xing F, Lan H, Chang J, Ge X, Lei Y, Hu Q, Miao Y, Wang L, et al. 2013. The draft genome of sweet orange (Citrus sinensis). Nature Genetics, 45, 59–92.
Xu X, Chen X, Chen Y, Zhang Q, Su L, Chen X, Chen Y, Zhang Z, Lin Y, Lai Z. 2020. Genome-wide identification of miRNAs and their targets during early somatic embryogenesis in Dimocarpus longan Lour. Scientific Report, 10, 4626–4641.
Xu X P, Chen X, Lv K L, Chen X, Chen Y K, Lin Y L, Lai Z X. 2018. Genome-wide identification and function analysis of the Laccase gene family in Dimocarpus longan Lour. Chinese Journal of Applied and Envrionmental, 24, 833–844. (in Chinese)
Yanagisawa S. 2004. Dof domain proteins: Plant-specific transcription factors associated with diverse phenomena unique to plants. Plant & Cell Physiology, 45, 386–391.
Zhang C, Zhang H, Zhao Y, Jiang H, Zhu S, Cheng B, Xiang Y. 2013. Genome-wide analysis of the CCCH zinc finger gene family in Medicago truncatula. Plant Cell Report, 32, 1543–1555.
Zhang S, Zhu C, Lv Y, Chen Y, Zhang Z, Lai Z, Lin Y. 2020. Genome-wide identification, molecular evolution, and expression analysis provide new insights into the APETALA2/ethylene responsive factor (AP2/ERF) superfamily in Dimocarpus longan Lour. BMC Genomics, 21, 62–82.