Proteome database of Pseudomonas protegens Pf-5

Harbouring a large genome relative to bacterial standards, the Gram-negative bacterium, Pseudomonas protegens Pf-5 possess a versatile metabolism that enables it to colonize a variety of environments. More importantly, P. protegens Pf-5 has found applications in biotechnology such as its emerging role as a useful bacterium for leaching precious metals from electronic scrap materials. Biotechnology potential aside, P. protegens Pf-5 is fundamentally interesting given its large genome harbouring hitherto unknown metabolic and signalling pathways that may find use in biotechnology. This work sought to provide some fundamental information about P. protegens Pf-5 through constructing a proteome database of the organism at the global level. Parsed by an in-house MATLAB software, the database comprises protein name, amino acid sequence, number of residues, molecular weight and corresponding nucleotide sequence of the protein. The latter three features were calculated using MATLAB built-in functions. Overall, the proteome database of P. protegens Pf-5 should inform researchers of the ensemble of proteins detected in the species, which forms the foundation on which a variety of fundamental and applied microbiology studies could be tackled.

相较于细菌的标准基因组（genome）规模，革兰氏阴性菌（Gram-negative bacterium）假单胞菌Pf-5（Pseudomonas protegens Pf-5）拥有多样化的代谢能力，使其能够定殖于多种环境中。更为关键的是，该菌株已在生物技术领域得到应用，例如其作为可从电子废料中浸出贵金属的实用菌株的新兴应用价值。抛开其生物技术应用潜力不谈，假单胞菌Pf-5因其庞大的基因组中蕴含迄今未知的代谢与信号通路（metabolic and signalling pathways）而具备基础研究价值，这些通路或可在生物技术领域得到进一步应用。本研究旨在通过构建该菌株的全局蛋白质组数据库（proteome database），为假单胞菌Pf-5提供基础研究相关信息。该数据库由自研MATLAB软件解析处理，包含蛋白质名称、氨基酸序列（amino acid sequence）、残基数量（number of residues）、分子量（molecular weight）以及对应的蛋白质核苷酸序列（nucleotide sequence）。上述后三项特征均通过MATLAB内置函数计算得到。总体而言，假单胞菌Pf-5的蛋白质组数据库可向研究人员展示该物种中检测到的全套蛋白质，为各类基础与应用微生物学研究奠定坚实基础。