副干酪乳酪杆菌PC-01不同表型菌落的基因组分析
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(内蒙古农业大学乳品生物技术与工程教育部重点实验室 农业农村部奶制品加工重点实验室内蒙古自治区乳品生物技术与工程重点实验室 乳酸菌与发酵乳制品省部共建协同创新中心 呼和浩特 010018)

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国家自然科学基金面上项目(31972054)


Genomic Analysis of Different Phenotypic Colonies of Lacticaseibacillus paracasei PC-01
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(Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Collaborative Innovative Center of Ministry of Education for Lactic Acid Bacteria and Fermented Dairy Products, Inner Mongolia Agricultural University, Hohhot 010018)

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    目的:探究副干酪乳酪杆菌PC-01经高密度发酵后,不同表型菌落的基因组差异。方法:采用第2代测序技术,对高密度发酵的10株具有不同表型特征的副干酪乳酪杆菌 PC-01分离株进行全基因组测序,通过比较基因组学方法揭示这10株分离株之间的差异。结果:10株副干酪乳酪杆菌PC-01分离株的基因组大小为2.69~2.83 Mb,GC含量为46.50%~46.64%,CDs数目为2 793~3 406个,不同菌落的基因组大小、GC含量存在较小差异。功能注释结果显示不同菌株编码碳水化合物、蛋白质代谢以及参与氨基酸及其衍生物合成和降解的基因数量及种类均存在差异。基于核心基因构建系统发育树,发现具有相似菌落形态的菌株在同一分支。单核苷酸多态性(SNPs)结果表明:每两个相同菌落形态的不同分离株存在相同的突变位点,这也进一步证实菌落形态与基因型相关联。分析发现10株分离株中均存在糖基转移酶(epsJ、pbpF、ponA等)及ABC蛋白家族(yheS、bceB、bceA、pcrA和uvrA等)相关基因发生非同义突变,使菌株在高密度发酵过程中,能更好地适应环境而存活下来。菌落PC-01-3和PC-01-4与其它菌落形态具有明显差异,ltaS基因发生非同义突变。脂磷壁酸合酶(LtaS)的缺乏会导致细菌表现出细胞分裂受损和生长缺陷,这可能是导致菌落形态差异的主要原因。结论:从全基因组水平完成了副干酪乳酪杆菌PC-01的10个分离株的比较分析,解析了同一菌株高密度发酵后不同表型菌落之间的差异,为副干酪乳酪杆菌PC-01的后续研究提供数据支持。

    Abstract:

    Objective: To investigate the genomic differences of different phenotypic colonies of Lacticaseibacillus paracasei PC-01 after high-density fermentation. Methods: Ten L. paracasei PC-01 isolates with different phenotypic characteristics after high-density fermentation were subjected to whole-genome sequencing using second-generation sequencing technology, and the differences between these ten L. paracasei isolates were revealed by comparative genomics methods. Results: The genome size of the 10 L. paracasei PC-01 isolates ranged from 2.69 to 2.83 Mb, the GC content ranged from 46.50% to 46.64%, and the number of CDs ranged from 2 793 to 3 406, with small differences in genome size and GC content among the different colonies. The results of functional annotation showed that the number and types of genes encoding carbohydrate and protein metabolism, as well as genes involved in the synthesis and degradation of amino acids and their derivatives varied among different strains. Phylogenetic trees were constructed based on the core genes, and it was found that strains with similar colony morphology were located in the same branch. SNPs showed that every two isolates with the same colony morphology had the same mutation site, which further confirmed the association between colony morphology and genotype. Analysis revealed non-synonymous mutations in genes related to glycosyltransferases (epsJ, pbpF, ponA, etc.) and the ABC protein family (yheS, bceB, bceA, pcrA and uvrA, etc.) in all 10 isolates, allowing the strains to better adapt to their environment and thus survive the high density fermentation process. Colonies PC-01-3 and PC-01-4 differed markedly from other colony morphologies with non-synonymous mutations in the ltaS gene. The deficiency of lipophosphatidic acid synthase(LtaS) caused the bacteria to exhibit impaired cell division and growth defects, which may be the main cause of the differences in colony morphology. Conclusion: In this study, 10 isolates of L. paracasei PC-01 were analyzed at the genome-wide level, and the differences between colonies of the same strain were resolved to provide data for the follow-up study of L. paracasei PC-01.

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张静雯,田桂铭,孙志宏,于洁.副干酪乳酪杆菌PC-01不同表型菌落的基因组分析[J].中国食品学报,2024,24(3):221-230

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  • 收稿日期:2023-03-11
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  • 在线发布日期: 2024-04-16
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