冰冷杆菌PG-2的基因组测序及生物信息学分析

doi:10.13560/j.cnki.biotech.bull.1985.2022-0919

摘要/Abstract

摘要：

冰冷杆菌PG-2（Gelidibacter sp.PG-2）是一株能产类胡萝卜素的菌株，为深入研究其产类胡萝卜素的机制，对该菌株进行了全基因组测序。从PG-2中提取类胡萝卜素后通过LC-MS/MS进行定性分析，通过液体紫外全波长扫描计算其含量，基于全基因组测序结果对该菌株产类胡萝卜素的代谢通路进行了预测分析。结果表明，PG-2所产类胡萝卜素为玉米黄质，含量为185.81 μg/g菌体干重，PG-2全基因组大小为3 850 413 bp，GC含量为37.91%，rRNA共计5个，tRNA共计37个，sRNA共计19个，在COG、GO、KEGG数据库分别注释到基因3 401、1 797、1 495个。菌株PG-2含有3个与产类胡萝卜素相关的核心基因crtI、crtZ、lcyB，并对其代谢通路进行了预测。基因组框架测序数据提交至 NCBI 获得 GenBank登录号为JAMJTV000000000。上述结果表明，菌株PG-2具有产类胡萝卜素的能力，推测它产类胡萝卜素与基因crtI、crtZ和lcyB有关。

关键词: 冰冷杆菌, 全基因组测序, 液体紫外全波长扫描, 类胡萝卜素

Abstract:

Gelidibacter sp. PG-2 is a carotenoid-producing strain, and genome-wide sequencing was conducted in order to further study its carotenoid-producing mechanisms. After the carotenoids were extracted from PG-2, qualitative analysis was performed by LC-MS/MS, the content was calculated by liquid UV full wavelength scanning, and the metabolic pathways of carotenoid-producing in this strain were predicted based on the results of whole genome sequencing. The results showed that the carotenoids produced by PG-2 were zeaxanthin with a content of 185.81 μg/g of dry weight, the whole genome size of PG-2 was 3 850 413 bp, the GC content was 37.91%, the total rRNA was 5, the total tRNA was 37, and the sRNA was 19, which were annotated in COG, GO and KEGG databases to genes 3 401, 1 797 and 1 495, respectively. The strain PG-2 contained three core genes associated with carotenoid production, crtI, crtZ, and lcyB, and their metabolic pathways were predicted. GenBank accession number JAMJTV000000000 was obtained after Genome Framework Sequencing Data submitted to NCBI. The above results demonstrate that the strain PG-2 has the ability to produce carotenoids, and it is speculated that its carotenoid production is related to the genes crtI, crtZ and lcyB.

Key words: Gelidibacter sp., whole genome sequencing, liquid UV full wavelength scans, carotenoids

张志霞, 李天培, 曾虹, 朱稀贤, 杨天雄, 马斯楠, 黄磊. 冰冷杆菌PG-2的基因组测序及生物信息学分析[J]. 生物技术通报, 2023, 39(3): 290-300.

ZHANG Zhi-xia, LI Tian-pei, ZENG Hong, ZHU Xi-xian, YANG Tian-xiong, MA Si-nan, HUANG Lei. Genome Sequencing and Bioinformatics Analysis of Gelidibacter sp. PG-2[J]. Biotechnology Bulletin, 2023, 39(3): 290-300.

图/表 13

图1 菌株PG-2的菌落形态

Fig. 1 Colony morphology of strain PG-2

图2 菌株PG-2的扫描电镜图

Fig. 2 Scanning electron microscope（SEM）image of strain PG-2

图3 菌株PG-2的16S rRNA系统发育树

Fig. 3 Phylogenetic tree based on 16S rRNA gene sequen-ces for strain PG-2

图4 PG-2色素浸提液

Fig. 4 Pigment extract of PG-2

图5 显色反应 a：空白对照；b：色素提取物

Fig. 5 Color reaction a: Blank control; b: pigment extract

图6 浸提液分离后的部分质谱图谱

Fig. 6 Partial mass spectrogram after extraction

图7 类胡萝卜素液体紫外

Fig. 7 UV spectrophotometer of carotenoid liquid

表1 PG-2基因组测序和组装

Table 1 Genome sequencing and assembly statistics of strain PG-2

名称Name	数据 Data
原始碱基对Raw bases/bp	1 218 127 570
过滤碱基对Clean bases/bp	1 174 477 731
最长支架 Longest scaffold/bp	519 035
总长度 Total length/bp	3 850 413
GC含量 GC/%	37.91
N50/bp	257 421
基因数目 Gene number	4 262
总长 Total length/bp	3 850 413
GC含量（基因区域）GC%（gene region）	38.65
rRNA	5
16sRNA	2
23sRNA	1
5sRNA	2
tRNA	37
sRNA	19
基因组岛数目 gene iland No.	9
CRISPR-Cas 数目CRISPR-Cas No.	30

图8 菌株PG-2的COG分析

Fig. 8 COG analysis of strain PG-2

图9 菌株PG-2的GO分析

Fig. 9 GO analysis of strain PG-2

图10 菌株PG-2的KEGG代谢通路分类

Fig. 10 Classification of KEGG metabolic pathway of strain PG-2

图11 菌株PG-2类胡萝卜素合成通路预测图中红色部分表示每一步作用的酶

Fig. 11 Pathway prediction of carotenoid synthesis by strain PG-2 The red part of the figure indicates the enzymes of each step

表2 PG-2产类胡萝卜素核心基因

Table 2 Carotenoid-producing core genes in PG-2

基因 Gene	酶 Enzyme	菌名 Bacterial name	最大分 Max score	总分 Total score	覆盖率 Query cover/%	百分比同一性 Percent identity/%	长度 Length/aa	登录号 Accession
crtI	八氢番茄红素脱氢酶家族 Phytoene desaturase family protein	Gelidibacter japonicus Bio 7-1	1 008	1 008	100	98.38	495	WP_163516639.1
lcyB	番茄红素环化酶 Lycopene cyclase family protein	Gelidibacter japonicus Bio 7-1	704	704	100	98.70	384	WP_163516633.1
crtZ	甾醇去饱和酶家族蛋白 Sterol desaturase family protein	Gelidibacter japonicus Bio 7-1	226	226	100	99.17	149	WP_163516635.1

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