Structure prediction of the ACC protein from Pontibacter kalidii XAAS-72T with the plant growth-promoting character

doi:10.6048/j.issn.1001-4330.2024.07.026

Xinjiang Agricultural Sciences ›› 2024, Vol. 61 ›› Issue (7): 1778-1785.DOI: 10.6048/j.issn.1001-4330.2024.07.026

• Plant Protection·Soil Fertilizer • Previous Articles Next Articles

Structure prediction of the ACC protein from Pontibacter kalidii XAAS-72^T with the plant growth-promoting character

WANG Huinan¹^,²(), ZHU Jing², XIE Wenwen²^,³, HE Zixuan²^,³, BAI Xiaoyu¹, ZHU Yanlei¹(), ZHANG Zhidong¹^,²^,³()

1. College of Life Sciences, Xinjiang Normal University, Urumqi 830054, China
2. Xinjiang Key Laboratory of Special Environmental Microbiology/Institute of Applied Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
3. College of Life Sciences and Technology, Xinjiang University, Urumqi 830046, China

Received:2023-10-11 Online:2024-07-20 Published:2024-09-04
Correspondence author: ZHU Yanlei, ZHANG Zhidong
Supported by:
"Outstanding Youth Fund" of Natural Science Foundation of Xinjiang(2022D01E19);Key Science and Technology Innovation Incubation Project of Xinjiang Academy of Agricultural Sciences(xjkcpy-2022004);Xinjiang Academy of A gricultural Sciences Sci-entific and technological innovation support(xjnkywdzc-2023005)

一株海洋杆菌属新菌种XAAS-72^T的植物促生功能分析及ACC脱氨酶蛋白结构预测

王慧楠¹^,²(), 朱静², 谢文文²^,³, 何子璇²^,³, 柏晓玉¹, 朱艳蕾¹(), 张志东¹^,²^,³()

1.新疆师范大学生命科学学院,乌鲁木齐 8300541
2.新疆农业科学院微生物应用研究所/新疆特殊环境微生物实验室,乌鲁木齐 830091
3.新疆大学生命科学与技术学院,乌鲁木齐 830046

通讯作者: 朱艳蕾,张志东
作者简介:王慧楠(1999-),女,吉林长春人,硕士研究生,研究方向为微生物生态,(E-mail)18946303350@163.com
基金资助:
新疆维吾尔自治区自然科学基金项目“杰出青年基金”(2022D01E19);新疆农业科学院科技创新重点培育专项(xjkcpy-2022004);新疆农业科学院农业科技创新稳定支持专项(xjnkywdzc-2023005)

Abstract

Abstract:

【Objective】To explore the plant growth promotion function of a novel strain Pontibacter kalidii XAAS-72^T, and investigate the potential functional genes. 【Methods】The strain whole genome was sequenced, and the composition of function genes were analyzed. A candidate gene related to ACC deaminase synthesis was obtained, and the enzyme protein characteristics were predicted. 【Results】The results showed that the growth of wheat seed treated with Pontibacter kalidii XAAS-72^T was promoted significantly in pots.The genome length of strain XAAS-72 (accession no. CP111079) was 5,054,860 bp, containing one circular plasmid. A total GC content was 54.52%, and the number of annotated genes was 4,391, coding for 4,261 proteins. A variety of resistance and growth-promoting related genes was observed. It had the highest similarity of 72.48% to the ACC deaminase of Pontibacter sp. BAB1700. It an unstable hydrophilic protein, with none of transmembrane structure and signal peptide structure. 【Conclusion】Pontibacter kalidii XAAS-72^T harbors a lot of genes related to the stress resistance and the plant growth-promoting.

Key words: Pontibacter; plant growth-promoting character; ACC deaminase; structure prediction

摘要：

【目的】研究海洋杆菌属新菌种XAAS-72的植物促生功能,挖掘其潜在功能基因。【方法】通过对菌株全基因组测序,分析相关功能基因组成,挖掘ACC脱氨酶合成相关的候选基因,并进行功能预测。【结果】海洋杆菌属新种Pontibacter kalidii XAAS-72菌悬液处理可显著提高盆栽小麦麦苗生长,其基因组长度为5 054 860 bp,含1个环形质粒,总GC含量为54.52%,注释的基因数目为4 391个,编码蛋白数4 261个,具有多种抗逆和促生相关基因。其与Pontibacter sp. BAB1700的ACC脱氨酶(1-aminoeyclopropane-1-earboxylate-deaminase)相似度最高为72.48%。该蛋白属于不稳定亲水性蛋白,不具备跨膜结构,且无信号肽结构。【结论】海洋杆菌属新种XAAS-72蕴藏着丰富的抗逆和植物促生相关基因。

关键词: 海洋杆菌属, 植物促生特性, ACC脱氨酶, 结构预测

CLC Number:

S188

WANG Huinan, ZHU Jing, XIE Wenwen, HE Zixuan, BAI Xiaoyu, ZHU Yanlei, ZHANG Zhidong. Structure prediction of the ACC protein from Pontibacter kalidii XAAS-72^T with the plant growth-promoting character[J]. Xinjiang Agricultural Sciences, 2024, 61(7): 1778-1785.

王慧楠, 朱静, 谢文文, 何子璇, 柏晓玉, 朱艳蕾, 张志东. 一株海洋杆菌属新菌种XAAS-72^T的植物促生功能分析及ACC脱氨酶蛋白结构预测[J]. 新疆农业科学, 2024, 61(7): 1778-1785.

Figures/Tables 10

References 29

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基因ID Gene ID	酶编号 Enzyme number	基因 Gene	基因注释 Gene notes	KEGG注释编号 KEGG Note No	功能描述 Functional description
Chr1:3817900:3818805:-	EC:3.5.99.7		1-氨基环丙烷-1- 羧酸脱氨酶	K01505	ACC脱氨酶编码基因
Chr1:1392508:1394346:-	EC:3.2.1.141	treZ,glgZ	麦芽寡糖基海藻糖水解酶	K01236	参与耐盐渗透调节
Chr1:2091855:2093990:-	EC:3.2.1.68	ISA, treX	异淀粉酶	K01214
Chr1:4968277:4969896:-	3.2.1.28	TREH,treA,treF	海藻糖酶	K01194
Chrw1:405272:406936:-	-	betT,betS	胆碱/甘氨酸/脯氨酸甜菜碱转运蛋白	K02168
Chr1:1485258:1486622:-	-	nhaA	Na+/H+逆向转运蛋白	K03313	参与逆向转运系统
Chr1:2575687:2578005:-	EC: 2.4.1.15	TPS	海藻糖6-磷酸合酶/磷酸酶	K16055	促进植物生长
Chr1:340156:341550:-	EC: 4.1.1.19	speA	精氨酸脱羧酶	K01585
Chr1:813781:815514:+	E2.2.1.6L	ilvB, ilvG, ilvI	乙酰乳酸合成酶	K01652
Chr1:4768702:4769751:-	-	RecA	重组蛋白RecA	K03553	参与DNA修复
Chr1:2565780:2569433:-	-	sbcC, rad50	DNA修复蛋白	K03546
Chr1:202874:203482:+	-	recR	DNA修复蛋白	K06187
Chr1:4598147:4598860:+	-	recO	DNA修复蛋白	K03584
Chr1:1791331:1792521:-	EC:4.2.1.20	trpB	色氨酸合酶亚基	K01696	IAA产生
Chr1:928485:932990:-	EC:1.4.1.13	gltB	谷氨酸合酶	K00265	固氮及氮同化
Chr1:927028:928485:-	EC:1.4.1.13	gltD	谷氨酸合酶	K00266
Chr1:2561033:2561446:+	-	-iscU, nifU	固氮蛋白NifU及相关蛋白	K04488
Chr1:3771390:3772286:+	-	pstS	磷酸盐ABC转运体底物结合蛋白	K02040	磷酸盐代谢
Chr1:4580607:4581371:-	EC:7.3.2.1	pstB	磷酸盐ABC转运体atp结合蛋白	K02036
Chr1:4582284:4583159:-	-	pstC	磷酸盐转运体渗透酶亚基	K02037
Chr1:4579862:4580551:-	-	phoU	磷酸盐特异性转运系统辅助蛋白	K02039
Chr1:4765770:4766798:-	EC:2.7.13.3	phoR	双组分系统,ompr家族,磷酸盐调节传感器组氨酸激酶	K07636
Chr1:1334658:1335221:-	-	efp	延伸系数P	K02356	生物膜形成
Chr1:1553626:1554504:-	-	motB	鞭毛运动蛋白	K02557	生物膜形成
Chr1:595364:596620:-	EC:2.7.7.4	cysN	硫酸腺苷酰转移酶	K00956	硫同化及代谢
Chr1:597641:598360:-	EC:1.8.4.8 1.8.4.10	cysH	磷酸腺苷磷酸硫酸盐还原酶	K00390
Chr1:2069683:2070297:+	EC:2.7.1.25	cysC	腺苷酸硫酸激酶	K00860
Chr1:2189706:2190593:-	EC:2.5.1.144	cysM	半胱氨酸合酶B	K12339
Chr1:3367321:3368154:-	EC:2.3.1.30	cysE	丝氨酸O-乙酰转移酶	K00640
Chr1:2074:2508:-	-	osmC	渗透诱导蛋白	K04063	氧化还原酶
Chr1:639323:639814:+	EC:1.11.1.15	DOT5	过氧化物酶	K03564	氧化还原酶
Chr1:417073:417903:+	EC:2.1.1.80	cheR	趋化蛋白甲基转移酶	K00575	根定植趋化性
Chr1:417903:418475:+	EC:3.1.1.61 3.5.1.44	cheB	双组分系统,趋化性家族, 蛋白质-谷氨酸甲基酯酶/ 谷氨酰胺酶	K03412	根定植趋化性

基因ID Gene ID	酶编号 Enzyme number	基因 Gene	基因注释 Gene notes	KEGG注释编号 KEGG Note No	功能描述 Functional description
Chr1:3817900:3818805:-	EC:3.5.99.7		1-氨基环丙烷-1- 羧酸脱氨酶	K01505	ACC脱氨酶编码基因
Chr1:1392508:1394346:-	EC:3.2.1.141	treZ,glgZ	麦芽寡糖基海藻糖水解酶	K01236	参与耐盐渗透调节
Chr1:2091855:2093990:-	EC:3.2.1.68	ISA, treX	异淀粉酶	K01214
Chr1:4968277:4969896:-	3.2.1.28	TREH,treA,treF	海藻糖酶	K01194
Chrw1:405272:406936:-	-	betT,betS	胆碱/甘氨酸/脯氨酸甜菜碱转运蛋白	K02168
Chr1:1485258:1486622:-	-	nhaA	Na+/H+逆向转运蛋白	K03313	参与逆向转运系统
Chr1:2575687:2578005:-	EC: 2.4.1.15	TPS	海藻糖6-磷酸合酶/磷酸酶	K16055	促进植物生长
Chr1:340156:341550:-	EC: 4.1.1.19	speA	精氨酸脱羧酶	K01585
Chr1:813781:815514:+	E2.2.1.6L	ilvB, ilvG, ilvI	乙酰乳酸合成酶	K01652
Chr1:4768702:4769751:-	-	RecA	重组蛋白RecA	K03553	参与DNA修复
Chr1:2565780:2569433:-	-	sbcC, rad50	DNA修复蛋白	K03546
Chr1:202874:203482:+	-	recR	DNA修复蛋白	K06187
Chr1:4598147:4598860:+	-	recO	DNA修复蛋白	K03584
Chr1:1791331:1792521:-	EC:4.2.1.20	trpB	色氨酸合酶亚基	K01696	IAA产生
Chr1:928485:932990:-	EC:1.4.1.13	gltB	谷氨酸合酶	K00265	固氮及氮同化
Chr1:927028:928485:-	EC:1.4.1.13	gltD	谷氨酸合酶	K00266
Chr1:2561033:2561446:+	-	-iscU, nifU	固氮蛋白NifU及相关蛋白	K04488
Chr1:3771390:3772286:+	-	pstS	磷酸盐ABC转运体底物结合蛋白	K02040	磷酸盐代谢
Chr1:4580607:4581371:-	EC:7.3.2.1	pstB	磷酸盐ABC转运体atp结合蛋白	K02036
Chr1:4582284:4583159:-	-	pstC	磷酸盐转运体渗透酶亚基	K02037
Chr1:4579862:4580551:-	-	phoU	磷酸盐特异性转运系统辅助蛋白	K02039
Chr1:4765770:4766798:-	EC:2.7.13.3	phoR	双组分系统,ompr家族,磷酸盐调节传感器组氨酸激酶	K07636
Chr1:1334658:1335221:-	-	efp	延伸系数P	K02356	生物膜形成
Chr1:1553626:1554504:-	-	motB	鞭毛运动蛋白	K02557	生物膜形成
Chr1:595364:596620:-	EC:2.7.7.4	cysN	硫酸腺苷酰转移酶	K00956	硫同化及代谢
Chr1:597641:598360:-	EC:1.8.4.8 1.8.4.10	cysH	磷酸腺苷磷酸硫酸盐还原酶	K00390
Chr1:2069683:2070297:+	EC:2.7.1.25	cysC	腺苷酸硫酸激酶	K00860
Chr1:2189706:2190593:-	EC:2.5.1.144	cysM	半胱氨酸合酶B	K12339
Chr1:3367321:3368154:-	EC:2.3.1.30	cysE	丝氨酸O-乙酰转移酶	K00640
Chr1:2074:2508:-	-	osmC	渗透诱导蛋白	K04063	氧化还原酶
Chr1:639323:639814:+	EC:1.11.1.15	DOT5	过氧化物酶	K03564	氧化还原酶
Chr1:417073:417903:+	EC:2.1.1.80	cheR	趋化蛋白甲基转移酶	K00575	根定植趋化性
Chr1:417903:418475:+	EC:3.1.1.61 3.5.1.44	cheB	双组分系统,趋化性家族, 蛋白质-谷氨酸甲基酯酶/ 谷氨酰胺酶	K03412	根定植趋化性

Structure prediction of the ACC protein from Pontibacter kalidii XAAS-72^T with the plant growth-promoting character

一株海洋杆菌属新菌种XAAS-72^T的植物促生功能分析及ACC脱氨酶蛋白结构预测

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