Bioinformatics and Expression Pattern Analysis of Rice RR Gene Family

doi:10.13304/j.nykjdb.2024.0190

Abstract

Abstract:

The rice response regulators （RR） family play important roles in plant growth and development， so it is important to explore the evolution and biological characteristics of the RR genes in rice. There were 22 RR genes in rice， including 15 A-type and 7 B-type genes. Analysis results showed that the rice RR proteins differed in their physicochemical properties， among which the B-type RRs were all hydrophilic proteins （GRAVY<0）； homologous sequence analysis revealed that there were 5 paralogous gene pairs in the rice RR genes， namely， OsRR8 and OsRR15， OsRR5 and OsRR11， OsRR9 and OsRR10， OsRR1 and OsRR2， and OsRR20 and OsRR18， which were predicted to have similar functions with known functional genes； the conserved Motif 1 and Motif 3 both belonged to the REC superfamily， which acted as response regulators to receive signals from the two-component phosphotransferase system， and they distributed among 22 OsRR proteins. The analysis of regulatory elements and expression pattern revealed that RR genes had potential ability in the regulating hormone signals transduction such as abscisic acid， salicylic acid， jasmonic acid， gibberellin， and growth hormone， and participated in plant defense against stress such as low temperature， drought， and light and anaerobic signals response， and also involved in the the regulation of different developmental processes of rice etc. functions. The bioinformatics analysis of rice RR gene family provided a theoretical basis for the in-depth study of their functions， and layed the foundation for further revealing the growth， development， and signal transduction mechanisms of plant.

Key words: Oryza sativa L., RR family, bioinformatics, expression pattern analysis

摘要：

水稻反应调节因子（response regulators，RR）家族在植物生长发育中扮演着重要角色，探究RR基因在水稻中的进化及生物学特征具有重要意义。水稻RR基因家族共有22个成员，包含15个A型和7个B型基因。分析发现，水稻RR蛋白的理化性质存在差异，其中B型均为亲水蛋白（GRAVY<0）；水稻RR基因有5个旁系基因对，分别为OsRR8和OsRR15、OsRR5和OsRR11、OsRR9和OsRR10、OsRR1和OsRR2、OsRR20与OsRR18，预测其与已知功能基因具有相似的功能；保守基序Motif 1与Motif 3均属于REC超级家族，作为响应调节器接收来自双组分磷酸转移系统中的信号传导，在22个OsRR蛋白中均有分布。调控元件与表达模式分析表明，RR基因具有调控脱落酸、水杨酸、茉莉酸、赤霉素与生长素等多种信号转导的潜能，参与植物防御低温、干旱等胁迫及光和厌氧等信号响应过程，同时也具有调控水稻不同组织生长发育的功能。通过对水稻RR基因进行生物信息学分析，为后续深入研究水稻RR家族成员的功能提供理论依据，也为进一步揭示植物生长发育及信号传导机制奠定了基础。

关键词: 水稻, RR家族, 生物信息学, 表达模式分析

CLC Number:

S511

Mingdi CHEN, Guihua HU, Haiwen ZHANG, Wangtian WANG. Bioinformatics and Expression Pattern Analysis of Rice RR Gene Family[J]. Journal of Agricultural Science and Technology, 2024, 26(5): 20-29.

陈明迪, 胡桂花, 张海文, 王旺田. 水稻RR基因家族生物信息学及表达模式分析[J]. 中国农业科技导报, 2024, 26(5): 20-29.

Figures/Tables 6

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元件 Component	序列 Sequence	数量 Number	功能 Function	类别 Category
G-box	CACGTG	116	参与光反应的顺式作用调控元件 Cis-acting regulatory element involved in light responsiveness	光响应型 Light-responsive
Box 4	ATTAAT	36	参与光响应的保守DNA模块 A conserved DNA module involved in light responsiveness
GT1-motif	GGTTAA	31	光感应元件 Light-responsive element
TCT-motif	TCTTAC	19	光响应元件的一部分 Part of a light-responsive element
Sp1	GGGCGG	16	光感应元件 Light-responsive element
GATA-motif	GATAGGA/AAGGATAAGG	14	光响应元件的一部分 Part of a light-responsive element
TCCC-motif	TCTCCCT	13	光响应元件的一部分 Part of a light-responsive element
Box Ⅱ	ACACGTAGA/CCACGTGGC	7	光感应元件 Light-responsive element
I-box	GTATAAGGCC	6	发光元件的一部分 Part of a photoresponsive element
AE-box	AGAAACTT	5	光响应模块的一部分 Part of a photoresponsive module
MRE	AACCTAA	4	参与光响应的 MYB 结合位点 MYB binding site involved in light responsiveness
ACE	CTAACGTATT	3	参与光响应的顺式作用元件 Cis-acting element involved in photoresponsiveness
3-AF1 binding site	TAAGAGAGGAA	3	光响应元件 Light-responsive element
ABRE	GCCGCGTGGC	109	参与光响应性的顺式作用调控元件 Cis-acting regulatory element involved in light responsiveness	激素响应型 Hormone-responsive
TGACG-motif	TGACG	44	涉及茉莉酸响应性的顺式作用调控元件 Cis-acting regulatory element involved in jasmonic acid responsiveness
CGTCA-motif	CGTCA	44
AuxRR-core	GGTCCAT	10	参与生长素反应的顺式调节元件 cis-Regulatory element involved in growth hormone responsiveness
TGA-element	AACGAC	6
TCA-element	CCATCTTTTT	9	参与水杨酸反应的顺式作用元件 Cis-acting element involved in salicylic acid responsiveness
P-box	CCTTTTG	7	参与赤霉素反应的顺式作用元件 Cis-acting element involved in gibberellin responsiveness
GARE-motif	TCTGTTG	6
TATC-box	TATCCCA	1

元件 Component	序列 Sequence	数量 Number	功能 Function	类别 Category
G-box	CACGTG	116	参与光反应的顺式作用调控元件 Cis-acting regulatory element involved in light responsiveness	光响应型 Light-responsive
Box 4	ATTAAT	36	参与光响应的保守DNA模块 A conserved DNA module involved in light responsiveness
GT1-motif	GGTTAA	31	光感应元件 Light-responsive element
TCT-motif	TCTTAC	19	光响应元件的一部分 Part of a light-responsive element
Sp1	GGGCGG	16	光感应元件 Light-responsive element
GATA-motif	GATAGGA/AAGGATAAGG	14	光响应元件的一部分 Part of a light-responsive element
TCCC-motif	TCTCCCT	13	光响应元件的一部分 Part of a light-responsive element
Box Ⅱ	ACACGTAGA/CCACGTGGC	7	光感应元件 Light-responsive element
I-box	GTATAAGGCC	6	发光元件的一部分 Part of a photoresponsive element
AE-box	AGAAACTT	5	光响应模块的一部分 Part of a photoresponsive module
MRE	AACCTAA	4	参与光响应的 MYB 结合位点 MYB binding site involved in light responsiveness
ACE	CTAACGTATT	3	参与光响应的顺式作用元件 Cis-acting element involved in photoresponsiveness
3-AF1 binding site	TAAGAGAGGAA	3	光响应元件 Light-responsive element
ABRE	GCCGCGTGGC	109	参与光响应性的顺式作用调控元件 Cis-acting regulatory element involved in light responsiveness	激素响应型 Hormone-responsive
TGACG-motif	TGACG	44	涉及茉莉酸响应性的顺式作用调控元件 Cis-acting regulatory element involved in jasmonic acid responsiveness
CGTCA-motif	CGTCA	44
AuxRR-core	GGTCCAT	10	参与生长素反应的顺式调节元件 cis-Regulatory element involved in growth hormone responsiveness
TGA-element	AACGAC	6
TCA-element	CCATCTTTTT	9	参与水杨酸反应的顺式作用元件 Cis-acting element involved in salicylic acid responsiveness
P-box	CCTTTTG	7	参与赤霉素反应的顺式作用元件 Cis-acting element involved in gibberellin responsiveness
GARE-motif	TCTGTTG	6
TATC-box	TATCCCA	1

元件 Component	序列 Sequence	数量 Number	功能 Function	类别 Category
ARE	AAACCA	47	厌氧诱导所必需的顺式调节元件 Cis-regulatory elements essential for anaerobic induction	胁迫响应型 Stress-responsive
MBS	CAACTG	19	参与干旱诱导的 MYB 结合位点 MYB binding site involved in drought induction
GC-motif	CCCCCG	17	参与缺氧特异性诱导的增强子样元件 Enhancer-like elements involved in hypoxia-specific induction
LTR	CCGAAA	10	参与低温反应的顺式作用元件 Cis-acting elements involved in low temperature responsiveness
TC-rich repeats	GTTTTCTTAC	4	参与防御和应激反应的顺式作用元件 Cis-acting elements involved in defense and stress responses
CAT-box	GCCACT	18	与分生组织表达有关的顺式调控元件 Cis-acting regulatory elements associated with meristematic tissue expression	生长发育响应 Growth and Development Response
O2-site	GATGA（C/T）（A/G）TG（A/G）	17	参与调节酵母蛋白质代谢的顺式调节元件 Cis-regulatory elements involved in the regulation of yeast protein metabolism
Circadian	CAAAGATATC	7	参与控制昼夜节律的顺式调节元件 Cis-regulatory elements involved in the control of circadian rhythms
RY-element	CATGCATG	3	参与种子特异性调控的顺式调控元件 Cis-acting regulatory elements involved in seed-specific regulation
GCN4-motif	TGAGTCA	3	参与胚乳表达的顺式调控元件 cis-acting regulatory elements involved in endosperm expression
MBSI	aaaAaaC（G/C）GTTA	2	参与类黄酮生物合成基因调控的 MYB 结合位点 MYB binding site involved in flavonoid biosynthesis gene regulation
NON-box	AGATCGACG	1	参与韧皮部特异性激活的顺式作用调控元件 Cis-acting regulatory element involved in phloem-specific activation
MSA-like	TCAAACGGT	1	参与细胞周期调控的顺式作用调控元件 Cis-acting regulatory element involved in cell cycle regulation
Motif I	gGTACGTGGCG	1	顺式作用调控元件根特异性 Cis-acting regulatory element root specificity

元件 Component	序列 Sequence	数量 Number	功能 Function	类别 Category
ARE	AAACCA	47	厌氧诱导所必需的顺式调节元件 Cis-regulatory elements essential for anaerobic induction	胁迫响应型 Stress-responsive
MBS	CAACTG	19	参与干旱诱导的 MYB 结合位点 MYB binding site involved in drought induction
GC-motif	CCCCCG	17	参与缺氧特异性诱导的增强子样元件 Enhancer-like elements involved in hypoxia-specific induction
LTR	CCGAAA	10	参与低温反应的顺式作用元件 Cis-acting elements involved in low temperature responsiveness
TC-rich repeats	GTTTTCTTAC	4	参与防御和应激反应的顺式作用元件 Cis-acting elements involved in defense and stress responses
CAT-box	GCCACT	18	与分生组织表达有关的顺式调控元件 Cis-acting regulatory elements associated with meristematic tissue expression	生长发育响应 Growth and Development Response
O2-site	GATGA（C/T）（A/G）TG（A/G）	17	参与调节酵母蛋白质代谢的顺式调节元件 Cis-regulatory elements involved in the regulation of yeast protein metabolism
Circadian	CAAAGATATC	7	参与控制昼夜节律的顺式调节元件 Cis-regulatory elements involved in the control of circadian rhythms
RY-element	CATGCATG	3	参与种子特异性调控的顺式调控元件 Cis-acting regulatory elements involved in seed-specific regulation
GCN4-motif	TGAGTCA	3	参与胚乳表达的顺式调控元件 cis-acting regulatory elements involved in endosperm expression
MBSI	aaaAaaC（G/C）GTTA	2	参与类黄酮生物合成基因调控的 MYB 结合位点 MYB binding site involved in flavonoid biosynthesis gene regulation
NON-box	AGATCGACG	1	参与韧皮部特异性激活的顺式作用调控元件 Cis-acting regulatory element involved in phloem-specific activation
MSA-like	TCAAACGGT	1	参与细胞周期调控的顺式作用调控元件 Cis-acting regulatory element involved in cell cycle regulation
Motif I	gGTACGTGGCG	1	顺式作用调控元件根特异性 Cis-acting regulatory element root specificity

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