Since Dongxiang wild rice has better cold tolerance than cultivated rice, abundant cold resistance gene resources should be explored. In this study, members of the OrCaM/OrCML gene family from Dongxiang wild rice were identified at the whole-genome level and their physicochemical properties were analyzed, and the expression patterns of the OrCaM/OrCML gene family were investigated after cold stress. The results showed that there were 40 members of the OrCaM/OrCML family in Dongxiang wild rice, distributed in subgroups Ⅰ to Ⅶ in the phylogenetic tree. The members of each group had no other known functional domain except EF-hand. The types and quantities of promoter cis-elements of OrCaM/OrCML genes differed, 14 OrCaM/OrCML genes with either CRT/DRE or CM2 cis-elements were selected to examine their responses to cold stress. The results showed that OrCML1, OrCML6 and OrCML18 were the three most rapidly activated genes after cold stress. The results of this study provide a reference for studying the molecular mechanisms of the OrCaM/OrCML gene family response to cold stresses.- DOI:10.3969/j.issn.1000-1565.2025.03.005东乡野生稻OrCaM/OrCML基因家族鉴定与冷胁迫下表达模式分析霍晨敏1,许天运1,王娇2,周硕2(1. 河北经贸大学, 生物科学与工程学院, 河北 石家庄 050061; 2. 河北省农林科学院, 生物技术与食品科学研究所,河北省植物基因工程重点实验室, 河北 石家庄 050051)摘 要:东乡野生稻的耐冷性优于栽培稻,具有丰富的抗冷基因资源.本研究对东乡野生稻OrCaM/OrCML基因家族成员进行全基因组水平鉴定和理化性质分析,并探究家族成员冷胁迫后表达模式.结果显示,东乡野生稻中有40个OrCaM/OrCML家族成员,在系统进化树中分布于亚组Ⅰ~Ⅶ.各组成员除EF手单元,无其他已知功能的结构域.OrCaM/OrCML基因的启动子顺式元件种类和数量不同,笔者研究了14个具有CRT/DRE或CM2顺式元件的OrCaM/OrCML基因对冷胁迫的反应.结果表明,OrCML1、OrCML6和OrCML18属于冷胁迫后激活最快的3个基因.本结果对于研究OrCaM/OrCML基因家族响应冷胁迫的分子机制提供了参考.关键词:东乡野生稻; 钙调蛋白/类钙调蛋白; 保守基序; EF手单元; 启动子分析中图分类号:Q943 文献标志码:A 文章编号:1000-1565(2025)03-0266-12Identification of OrCaM/OrCML gene family in Dongxiang wild rice and analysis of expression patterns under cold stressHUO Chenmin1, XU Tianyun1, WANG Jiao2, ZHOU Shuo2(1. College of Bioscience and Engineering, Hebei University of Economics and Business, Shijiazhuang 050061,China;2. Hebei Key Laboratory of Plant Genetic Engineering, Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051,China)Abstract: Since Dongxiang wild rice has better cold tolerance than cultivated rice, abundant cold resistance gene resources should be explored. In this study, members of the OrCaM/OrCML gene family from Dongxiang wild rice were identified at the whole-genome level and their physicochemical properties were analyzed, and the expression patterns of the OrCaM/OrCML gene family were investigated after cold stress. The results showed that there were 40 members of the OrCaM/OrCML family in Dongxiang wild rice, distributed in subgroups Ⅰ to Ⅶ in the phylogenetic tree. The members of each group had no other known functional domain except EF-hand. The types and quantities of promoter cis-elements of OrCaM/OrCML genes differed, 14 OrCaM/OrCML genes with either CRT/DRE or CM2 cis-elements were selected to examine their responses to cold stress. The results showed that OrCML1, OrCML6 and OrCML18 were the three most rapidly activated genes after cold stress. The results of this study provide a reference for studying the molecular mechanisms of the OrCaM/OrCML gene family response to cold stresses.- 收稿日期:2024-09-06;修回日期:2024-10-14 基金项目:河北省自然科学基金项目(C2024207001);河北省农林科学院现代农业科技创新专项(2022KJCXZX-SSS-5) 第一作者:霍晨敏(1978—), 女,河北经贸大学副教授,主要从事作物遗传育种方向研究. E-mail: huochenmin@hueb.edu.cn 第3期霍晨敏等:东乡野生稻OrCaM/OrCML基因家族鉴定与冷胁迫下表达模式分析河北大学学报(自然科学版) 第45卷
[1] ZHANG J Y, LUO W, ZHAO Y, et al. Comparative metabolomic analysis reveals a reactive oxygen species-dominated dynamic model underlying chilling environment adaptation and tolerance in rice[J]. New Phytol, 2016, 211(4):1295-1310. DOI: 10.1111/nph.14011.
[2] MA Y, DAI X Y, XU Y Y, et al. COLD1 confers chilling tolerance in rice[J]. Cell, 2015, 160(6): 1209-1221. DOI: 10.1016/j.cell.2015.01.046.
[3] THOR K. Calcium-nutrient and messenger[J]. Front Plant Sci, 2019, 10:440. DOI: 10.3389/fpls.2019.00440.
[4] ZHU X, DUNAND C, SNEDDEN W, et al. CaM and CML emergence in the green lineage[J]. Trends Plant Sci, 2015, 20(8):483-489. DOI: 10.1016/j.tplants.2015.05.010.
[5] GALON Y, FINKLER A, FROMM H. Calcium-regulated transcription in plants[J]. Mol Plant, 2010, 3(4):653-669. DOI: 10.1093/mp/ssq019.
[6] REDDY A S N, ALI G S, CELESNIK H, et al. Coping with stresses: roles of calcium- and calcium/calmodulin-regulated gene expression[J]. Plant Cell, 2011, 23(6):2010-2032. DOI: 10.1105/tpc.111.084988.
[7] CHEVAL C, ALDON D, GALAUD J P, et al. Calcium/calmodulin-mediated regulation of plant immunity[J]. Biochim Biophys Acta, 2013, 1833(7):1766-1771.DOI: 10.1016/j.bbamcr.2013.01.031.
[8] MCCORMACK E, TSAI Y C, BRAAM J. Handling calcium signaling: Arabidopsis CaMs and CMLs[J]. Trends Plant Sci, 2005, 10(8):383-389. DOI: 10.1016/j.tplants.2005.07.001.
[9] BOONBURAPONG B, BUABOOCHA T. Genome-wide identification and analyses of the rice calmodulin and related potential calcium sensor proteins[J]. BMC Plant Biol, 2007, 7:4. DOI: 10.1186/1471-2229-7-4.
[10] ALEYNOVA O A, KISELEV K V, OGNEVA Z V, et al. The grapevine calmodulin-like protein gene CML21 is regulated by alternative splicing and involved in abiotic stress response[J]. Int J Mol Sci, 2020, 21(21):7939. DOI: 10.3390/ijms21217939.
[11] VERDE V L, DOMINICI P, ASTEGNO A. Towards understanding plant calcium signaling through calmodulin-like proteins: biochemical and structural perspective[J]. Int J Mol Sci, 2018, 19(5):1331. DOI: 10.3390/ijms19051331.
[12] CHU M X, LI J J, ZHANG J Y, et al. AtCaM4 interacts with a Sec14-like protein, PATL1, to regulate freezing tolerance in Arabidopsis in a CBF-independent manner[J]. J Exp Bot, 2018, 69(21):5241-5253. DOI: 10.1093/jxb/ery278.
[13] TERESINSKI H J, HAU B, SYMONDS K, et al. Arabidopsis calmodulin-like proteins CML13 and CML14 interact with proteins that have IQ domains[J]. Plant Cell Environ, 2023, 46(8):2470-2491. DOI: 10.1111/pce.14616.
[14] HAU B, SYMONDS K, TERESINSKI H, et al. Arabidopsis calmodulin-like proteins CML13 and CML14 interact with calmodulin-binding transcriptional activators and function in salinity stress response[J]. Plant Cell Physiol, 2024, 65(2):282-300. DOI: 10.1093/pcp/pcad152.
[15] YANG J, LIU S, JI L X, et al. Identification of novel OsCML16 target proteins and differential expression analysis under abiotic stresses in rice[J]. J Plant Physiol, 2020,249:153165. DOI: 10.1016/j.jplph.2020.153165.
[16] CHEN C J, WU Y, LI J W, et al. TBtools-II: A “one for all, all for one” bioinformatics platform for biological big-data mining[J]. Mol Plant, 2023,16(11):1733-1742. DOI:10.1016/j.molp.2023.09.010
[17] DOHERTY C J, VAN BUSKIRK H A, MYERS S J, et al. Roles for Arabidopsis CAMTA transcription factors in cold-regulated gene expression and freezing tolerance[J]. Plant Cell, 2009,21(3):972-984. DOI: 10.1105/tpc.108.063958.
[18] STOCKINGER E J, GILMOUR S J, THOMASHOW M F. Arabidopsis thaliana CBF1 encodes an AP2 domain-containing transcriptional activator that binds to the C-repeat/DRE, a cis-acting DNA regulatory element that stimulates transcription in response to low temperature and water deficit[J]. Proc Natl Acad Sci U S A, 1997,94(3):1035-1040. DOI: 10.1073/pnas.94.3.1035.
[19] VALLONE R, VERDE V L, DONOFRIO M, et al. Metal binding affinity and structural properties of calmodulin-like protein 14 from Arabidopsis thaliana[J]. Protein Sci, 2016,25(8):1461-1471. DOI: 10.1002/pro.2942.
[20] OGUNRINDE A, MUNRO K, DAVIDSON A, et al. Arabidopsis calmodulin-like proteins, CML15 and CML16 possess biochemical properties distinct from calmodulin and show non-overlapping tissue expression patterns[J]. Front Plant Sci, 2017,8:2175. DOI: 10.3389/fpls.2017.02175.
[21] DOBNEY S, CHIASSON D, LAM P, et al. The calmodulin-related calcium sensor CML42 plays a role in trichome branching[J]. J Biol Chem, 2009,284(46):31647-31657. DOI: 10.1074/jbc.M109.056770.
[22] ASTEGNO A, BONZA M C, VALLONE R, et al. Arabidopsis calmodulin-like protein CML36 is a calcium Ca2+ sensor that interacts with the plasma membrane Ca2+-ATPase isoform ACA8 and stimulates its activity[J]. J Biol Chem, 2017,292(36):15049-15061. DOI: 10.1074/jbc.M117.787796.
[23] VAN DER LUIT A H, OLIVARI C, HALEY A, et al. Distinct calcium signaling pathways regulate calmodulin gene expression in tobacco[J]. Plant Physiol, 1999,121(3):705-714. DOI: 10.1104/pp.121.3.705.
[24] DELK N A, JOHNSON K A, CHOWDHURY N I, et al. CML24, regulated in expression by diverse stimuli, encodes a potential Ca2+ sensor that functions in responses to abscisic acid, daylength, and ion stress[J]. Plant Physiol, 2005,139(1):240-253. DOI: 10.1104/pp.105.062612.
[25] MAGNAN F, RANTY B, CHARPENTEAU M, et al. Mutations in AtCML9, a calmodulin-like protein from Arabidopsis thaliana, alter plant responses to abiotic stress and abscisic acid[J]. Plant J, 2008,56(4):575-589. DOI: 10.1111/j.1365-313X.2008.03622.x. (
