一株高产γ-氨基丁酸短乳杆菌TCCC13007全基因组测序及比较基因组分析

doi:10.13560/j.cnki.biotech.bull.1985.2025-0843

摘要/Abstract

摘要：

目的从东北酸白菜中筛选出一株高产γ-氨基丁酸（GABA）的短乳杆菌TCCC13007，对其开展全基因组测序组装工作，解析该菌株的全基因组序列信息，并进行比较基因组分析，旨在探究菌株TCCC13007高产GABA的分子机理。方法运用二代Illumina HiSeq技术测序，在PacBio平台完成三代测序，并结合二、三代测序数据校正结果，对菌株TCCC13007实施全基因组测序，并进行基因预测、功能注释以及比较基因组学分析。结果 TCCC13007的基因组总长度为2.58 Mb，GC含量为45.72%，包含2 581个编码基因。比较基因组分析结果显示，TCCC13007与低产GABA菌株YSJ3的亲缘关系最为接近，二者的共线性关系良好，但也存在少量的插入、倒位和易位等基因重排现象。与YSJ3相比，TCCC13007的gadA基因在基因组中的位置发生了明显的迁移，同时GadR蛋白序列的第104位突变为甘氨酸，另外该菌株中存在308个特异基因。这些特异基因可能在增强谷氨酸前体供应、维持激活谷氨酸脱羧酶（GAD）所需的酸性胞内环境、优化跨膜转运系统、辅因子与能量供应以及调控网络等方面协同发挥作用，从而使TCCC13007具备较高的GABA合成能力。结论全基因组测序和比较基因组学分析表明，菌株TCCC13007高产GABA特性并非依赖于基因组的显著扩张，而可能归因于更为精细和高效的基因组合及其调控网络。

关键词: γ-氨基丁酸, 短乳杆菌, 全基因组测序, 基因功能注释, 比较基因组学

Abstract:

Objective Lactobacillus brevis TCCC13007 was isolated from northeastern Chinese pickled cabbage as a high γ-aminobutyric acid (GABA)-producing strain. Whole-genome sequencing and assembly were performed to analyze its complete genomic sequence information. Comparative genomic analysis was conducted to investigate the molecular mechanism underlying the high GABA production of strain TCCC13007. Method Sequencing was conducted by employing second-generation Illumina HiSeq technology and third-generation sequencing on the PacBio platform. Combined second- and third-generation sequencing data were used for correction, and whole genome sequencing of strain TCCC13007, as well as gene prediction, functional annotation, and comparative genomic analysis. Result The TCCC13007 genome had a total length of 2.58 Mb with a GC content of 45.72% and contained 2 581 protein-coding genes. Comparative genomic analysis revealed that TCCC13007 was most closely related to the low-GABA-producing strain YSJ3, and the two had strong synteny alongside minor genomic rearrangements such as insertions, inversions, and translocations. Compared to YSJ3, the gadA gene in TCCC13007 was noticeably relocated within the genome, and a mutation at position 104 of the GadR protein sequence resulted in a glycine substitution. Additionally, TCCC13007 harbored 308 unique genes. These unique genes appeared to synergistically enhance glutamate precursor supply, maintain the acidic intracellular environment required for glutamate decarboxylase (GAD) activation, optimize transmembrane transport systems, ensure cofactor and energy supply, and modulate regulatory networks, thereby conferring high GABA synthesis capacity on TCCC13007. Conclusion Whole-genome sequencing and comparative genomic analysis of strain TCCC13007 reveal that its high GABA-producing characteristic is not due to significant genome expansion, but may be attributed to a more refined and efficient gene combination and its regulatory network.

Key words: γ-aminobutyric acid (GABA), Lactobacillus brevis, whole-genome sequencing, gene functional annotation, comparative genomics

苗昊翔, 张颖, 郭世鹏, 张健. 一株高产γ-氨基丁酸短乳杆菌TCCC13007全基因组测序及比较基因组分析[J]. 生物技术通报, 2025, 41(11): 166-176.

MIAO Hao-xiang, ZHANG Ying, GUO Shi-peng, ZHANG Jian. Whole Genome Sequencing and Comparative Genomic Analysis of a High-yielding γ-aminobutyric Acid-producing Lactobacillus brevis TCCC13007[J]. Biotechnology Bulletin, 2025, 41(11): 166-176.

图/表 8

图1 GABA的合成与分解途径

Fig. 1 Synthesis and degradation pathways of GABA

图2 短乳杆菌TCCC13007的染色体基因组圈

Fig. 2 Chromosome genomic circle of L. brevis TCCC13007

图3 短乳杆菌TCCC13007基因功能注释GO功能分类

Fig. 3 GO function classification of L. brevis TCCC13007 gene functions

图4 短乳杆菌TCCC13007 eggNOG 功能分类

Fig. 4 eggNOG function classification of L. brevis TCCC13007

图5 短乳杆菌TCCC13007基因功能注释KEGG代谢通路

Fig. 5 KEGG metabolic pathways annotated with the gene functions of L. brevis TCCC13007

表1 菌株 TCCC13007与其他短乳杆菌的基因组特征比较

Table 1 Comparison of genomic characteristics of strain TCCC13007 with other L. brevis

短乳杆菌菌株 L. brevis strain	基因组大小 Genome size （Mb）	GC含量 GC content （%）	蛋白编码基因 Protein-coding genes	质粒数量 Number of plasmids	登陆号 Accession number	GABA产量 GABA yield （g/L）	参考文献 References
TCCC13007	2.58	45.72	2581	5	PRJNA1290704	发酵180，转化280	本研究
CD0817	3.10	50.35	2990	4	PRJNA495163	404	［8］
NPS-QW-145	2.55	45.80	2391	0	PRJNA318996	2.302	［11］
YSJ3	2.5	46	2449	7	PRJNA804971	0.035	［12］
ATCC 14869	2.5	46	2630	0	PRJNA38325	0.05	［13］
DPC 6108	2.9	45	2743	0	PRJNA339712	16	［14］
CRL 2013	2.6	45.5	2543	0	PRJNA378171	26.9	［15］
LSF9-1	2.5	45.5	2370	0	PRJNA916067	16.935	［16］
G101	2.7	45.5	2467	0	PRJNA369571	3.542	［17］
ATCC 367	2.34	46.04	2180	2	PRJNA404	6.44	［18］

图6 基于单拷贝基因序列构建的最大似然法系统进化树

Fig. 6 A phylogenetic tree constructed from single-copy gene sequences using the Maximum Likelihood method

图7 菌株TCCC13007与菌株YSJ3基因组共线性分析

Fig. 7 Genomic collinearity analysis of strain TCCC13007 and strain YSJ3

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