<i>ZmCOL</i>3<italic/>基因编码蛋白结构及功能的生物信息学分析

董柯清; 王雷立; 刘青青; 张严玲; 李安然; 仝帧翰; 董哲; 王翠玲

doi:10.19303/j.issn.1008-0384.2021.09.002

ZmCOL3基因编码蛋白结构及功能的生物信息学分析

doi: 10.19303/j.issn.1008-0384.2021.09.002

河南科技大学农学院，河南　洛阳　471023

基金项目: 河南省重点研发与推广专项（202102110010）；国家自然科学基金河南省联合基金项目（U2004153）；国家自然科学基金青年科学基金项目（31901561）

详细信息

作者简介:
董柯清（1997−），女，硕士研究生，研究方向：玉米分子遗传育种（E-mail：dongkq333@163.com）

通讯作者:
王翠玲（1974−），女，副教授，研究方向：玉米分子遗传育种（E-mail：lywgg@126.com）

中图分类号: S 513
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出版历程
- 收稿日期: 2021-05-06
- 修回日期: 2021-06-06
- 网络出版日期: 2021-08-10
- 刊出日期: 2021-09-28

Bioinformatics on Structure and Functions of ZmCOL3-encoded Protein

College of Agricultural, Henan University of Science and Technology, Luoyang, Henan　471023, China

摘要

摘要: 目的分析ZmCOL3基因编码蛋白的结构及功能，预测ZmCOL3基因可能具备的功能，为该基因在玉米开花调控及其他功能的研究提供思路。方法通过生物信息学的方法对ZmCOL3基因编码蛋白质的理化性质、保守结构域、二级结构、三级结构、信号肽、跨膜结构域、亚细胞定位及启动子顺式作用元件进行了预测，并对该基因在玉米不同组织的表达量进行了分析。结果 ZmCOL3基因所编码的蛋白包含335个氨基酸，相对分子质量为35.39 kD，理论等电点为5.04，属于酸性蛋白，具有亲水性和不稳定性，含有1个CCT结构域和1个B-box结构域，没有信号肽和跨膜结构域，主要定位在细胞核中，其二级结构主要是由无规则卷曲组成，其次是α螺旋，还含有少量的延伸链和β转角，同源建模相似度为64.15%，该基因的启动子不仅含有TATA-box、CAAT-box启动子基本的顺式作用元件，还含有Sp1等光响应作用元件，以及脱落酸、茉莉酸甲酯等激素响应元件。在玉米的种子、初生根、节间、叶、雌穗和雄穗等6个部位中，叶片中ZmCOL3基因的表达量最高，其次是雄穗，在种子中该基因表达量最低，总体上看ZmCOL3基因在叶片中的表达量显著高于其他部位。结论 ZmCOL3蛋白是一个亲水、不稳定的酸性蛋白，其含有CCT结构域和B-box结构域，符合CCT基因家族中COL亚家族的结构特征，属于该家族成员，可能参与生物钟的调控来影响玉米开花。启动子顺式作用元件分析发现ZmCOL3基因的启动子包含光响应及各种激素响应元件，推断该基因可能受到光周期调控和激素等非生物胁迫调控，暗示其可在多重反应调控网络中发挥作用。
- 玉米 /
- ZmCOL3 /
- 开花 /
- CCT基因家族 /
- 生物信息学分析
Abstract: Objective Functions of ZmCOL3 involving the flowering regulation and other mechanisms in maize were investigated by analyzing the structure and functions of the protein encoded by the gene. Method Based on bioinformatics, the physicochemical properties, conserved domain, secondary and tertiary structures, signal peptide, transmembrane domain, subcellular localization, and cis acting elements of ZmCOL3 protein were predicted. Expression of the gene in various organs of a maize plant were analyzed. Result The ZmCOL3-encoded protein contained 335 amino acids with a molecular weight of 35.39 KD and a theoretical isoelectric point of 5.04. It was an unstable acidic, hydrophilic protein located primarily in the nucleus and consisted of a CCT domain and a B-box domain but no signal peptide or transmembrane domain. Its secondary structure was mostly irregular coils with some α helixes and a small number of extended chains and β turns. The homology modeling similarity was 64.15%. The promoter of ZmCOL3 gene not only contained the basic cis acting elements, such as TATA and CAAT boxes, but also light response elements, such as SP1, as well as hormone response elements, such as abscisic acid and methyl jasmonate. In various tissues, the leaves, followed by the male ears, had the highest and significantly higher expression of ZmCOL3 than the primary roots, internodes, or tassels, while and the seeds the lowest. Conclusion The unstable acidic, hydrophilic ZmCOL3 protein contained CCT and B-box domains consistent with the structural characteristics of COL subfamily in the CCT gene family of which it belonged. It was postulated to participate in the regulation of biological clock that affects maize florescence. The promoter of ZmCOL3 gene contained the elements responding to light and various hormones that suggested a possible involvement on the multiple response network regulating the photoperiod and abiotic stress of a maize plant.
- Maize /
- ZmCOL3 /
- flowering /
- CCT gene family /
- bioinformatics analysis

HTML全文

图 1 玉米ZmCOL3基因的蛋白组分

注：A：丙氨酸；E：谷氨酸；R：精氨酸；P：脯氨酸；G：甘氨酸；S：丝氨酸；D：天冬氨酸；L：亮氨酸；V：缬氨酸；C：半胱氨酸；F：苯丙氨酸；H：组氨酸；K：赖氨酸；Y：酪氨酸；I：异亮氨酸；T：苏氨酸；M：蛋氨酸；N：天冬酰胺；Q：谷氨酰胺；W：色氨酸；O：吡咯赖氨酸；U：硒半胱氨酸；B、X、Z：酸水解后不确定的氨基酸

Figure 1. Composition of maize ZmCOL3

Note: A: Alanine; E: Glutamic acid; R: Arginine; P: Proline; G: Glycine; S: Serine; D: Aspartic acid; L: Leucine; V: Valine; C: Cysteine; F: Phenylalanine; H: Histidine; K: Lysine; Y: Tyrosine; I: Isoleucine; T: Threonine; M: Methionine; N: Asparagine; Q: Glutamine; W: Tryptophan; O: Pyrrolysine; U: Selenocysteine; B, X, and Z: Uncertain amino acids after acid hydrolysis.

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图 2 ZmCOL3蛋白保守结构域的预测

Figure 2. Predicted conserved domain of ZmCOL3 protein

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图 3 ZmCOL3蛋白二级结构的预测

Figure 3. Predicted secondary structure of ZmCOL3 protein

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图 4 ZmCOL3蛋白的三级结构的预测

Figure 4. Predicted tertiary structure ofZmCOL3 protein

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图 5 ZmCOL3蛋白的跨膜结构域的预测

Figure 5. Predicted transmembrane domain of ZmCOL3 protein

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图 6 ZmCOL3蛋白信号肽的预测

Figure 6. Predicted signal peptide of ZmCOL3 protein

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图 7 ZmCOL3蛋白的亚细胞定位

Figure 7. Subcellular localization of ZmCOL3 protein

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图 8 ZmCOL3基因在玉米不同组织部位的表达情况

注：不同小写字母表示差异显著性（P＜0.05）。

Figure 8. Expressions of ZmCOL3 in maize tissues

Note: Different lowercase letters indicate significant difference at P＜0.05.

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表 1 ZmCOL3启动子顺式作用元件分析

Table 1. Analysis on cis acting elements of ZmCOL3 promoter

元件名称 Element name	位置　　　　　　　　　 Site	功能 Function
AAGAA-motif	−222	胁迫响应 stress response element
A-box	−718，−768，−789，+1230，+1251，−1773	顺式作用调控元件 cis-acting regulatory element
ABRE	+1223，+1702，−2059，+2060，+2158	脱落酸响应顺式作用元件 cis-acting element involved in the abscisic acid responsiveness
ACE	+54	光响应顺式作用元件 cis-acting element involved in light responsiveness
ARE	+686，+959	厌氧诱导必需的顺式作用元件 cis-acting regulatory element essential for the anaerobic induction
CAAT-box	−6，−142，+283，+600，−946，+1018，−1031等	启动子和增强子区的共同顺式作用元件 common cis-acting element in promoter and enhancer regions
CAT-box	−350	与分生组织表达相关的顺式作用元件 cis-acting regulatory element related to meristem expression
CGTCA-motif	+860，+1215	茉莉酸甲酯响应的顺式作用元件 cis-acting regulatory element involved in the MeJA-responsiveness
DRE core	−894	ABRE的耦合功能元件 funtions as a coupling element of ABRE
ERE	−1299	乙烯响应元件 ethylene-responsive element
GATA-motif	+1023	光响应元件的一部分 part of a light responsive element
G-box	−22，−316，−1701，−1222，−2059	光响应顺式作用元件 cis-acting regulatory element involved in light responsiveness
GC-motif	−592	与缺氧特异性诱导相关的增强子类元件 enhancer-like element involved in anoxic specific inducibility
I-box	+971	光响应元件的一部分 part of a light responsive element
JERE	+900	JA和诱导子响应 JA and elicitor responsive
LTR	−764	低温响应的顺式作用元件 cis-acting element involved in low-temperature responsiveness
MYC	−1279	茉莉酸甲酯响应的顺式作用元件 cis-acting regulatory element involved in the MeJA-responsive
O2-site	+546，−1824	玉米醇溶蛋白调控的顺式作用元件 cis-acting regulatory element involved in zein metabolism
P-box	−293	赤霉素响应元件 gibberellin-responsive element
Sp1	+167，−583，−903，−2157	光响应元件 light responsive element
STRE	−235，−329，+865，−1080，+1242，−2053，−2076	热休克、渗透胁迫、低pH值、营养缺乏引起的活化 activation by heat shock, osmotic stress, low pH, nutrient starvation
TATA-box	−107，+110，−178，−181，+182，+802，+917等	转录起始点−30左右的核心启动子元件 core promoter element around −30 of transcription start
TCA-element	+195，−259	水杨酸响应的顺式作用元件 cis-acting element involved in salicylic acid responsiveness
TC-rich repeats	−1912	防御和应激响应的顺式作用元件 cis-acting element involved in defense and stress responsiveness
TCT-motif	+475	光响应元件的一部分 part of a light responsive element
TGACG-motif	−860，−1215	茉莉酸甲酯响应的顺式作用元件 cis-acting regulatory element involved in the MeJA-responsiveness
TGA-element	−446	生长素响应元件 auxin-responsive element
W box	−772	植物特异性转录调节因子WRKY的结合位点 binding sites for the WRKY plant-specific transcriptional regulators
WUN-motif	+982	创伤响应元件 wound-responsive element

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