Transcriptome and protein networks to elucidate the mechanism underlying nitrite degradation by Lactiplantibacillus plantarum. (June 2022)

• Record Type: Journal Article
• Authors: Li, Yuanyuan; Xiong, Die; Yuan, Lanyu; Fan, Pengfei; Xiao, Yao; Chen, Jiaping; Feng, Wu
• Is Part Of: Food research international. Volume 156(2022)
• Publication Date: 2022-06
• Subjects: Traditional Chinese pickle -- Lactiplantibacillus plantarum -- RNA-seq -- Nitrite degradation -- Pathways -- Protein-protein interactions -- Metabolism; NIT nitrite -- LAB Lactic acid bacteria -- RNA-seq RNA sequencing -- qRT-PCR quantitative real-time polymerase chain reaction -- DEG differential expression genes -- EggNOG Non-supervised Orthologous Groups -- GO gene ontology -- KEGG Kyoto Encyclopedia of Genes and Genomes -- PCA principal component analysis -- one-way ANOVA one-way analysis of variance -- PPI protein-protein interaction -- TA titratable acidity; Food -- Analysis -- Periodicals; Food industry and trade -- Periodicals; Food industry and trade -- Canada -- Periodicals; Food Technology -- Periodicals; Food -- Periodicals; Food-Processing Industry -- Periodicals; Aliments -- Industrie et commerce -- Périodiques; Aliments -- Industrie et commerce -- Canada -- Périodiques; Aliments -- Recherche -- Périodiques; Food industry and trade; Canada; Periodicals; Electronic journals; 664.005
• DOI: 10.1016/j.foodres.2022.111319
• Languages: English
• ISSNs: 0963-9969

Abstract

Graphical abstract: Highlights: The hub genes involved in nitrite degradation were identified. Combining microscopic and macroscopic analysis to study degradation mechanisms. Comparison of gene expression at key nodes in degradation. Pyruvate metabolism is important to maintain acid production. We explored the metabolic expression of bacteria in different environments. Abstract: Excessive nitrite residue is one of the bottlenecks in the production of many fermented foods. Lactiplantibacillus plantarum PK25 obtained from traditional Chinese pickles exhibited excellent nitrite degradation ability. Here, transcriptome, protein-protein interaction networks, and phenotype were performed to evaluate systematically the mechanism of nitrite degradation of L. plantarum PK25. The results demonstrated that genes expression varied considerably at key time points for nitrite degradation. 553 (upregulated: 366, downregulated: 187) and 767 (upregulated: 425, downregulated: 342) differentially expressed genes were identified at 6 h and 24 h, respectively. The hub genes were mainly enriched in carbohydrate metabolism, energy metabolism, and nucleotide synthesis. PK25 expanded its carbon source utilizing profile and improved glycolysis to produce more ATP to counteract environmental stress. The related enzymes including glycoside hydrolase, sugar ABC transporter protein, and PTS sugar transporter were 5.714, 5.885, and 3.578-fold upregulated at the transcriptional level. For strain to sustain energy levels and acid generation, pyruvate metabolism was critical, with the result that phosphoenolpyruvate synthase and pyruvate oxidase were up-regulated to accelerate the pyruvate transition. To repair DNA lesions induced by nitrite, both base excision repair mechanism and recombinational DNA repair pathway were exploited, such as endodeoxyribonuclease upregulated 5.314 and 19.687-fold at the two moments. The results provided a theoretical reference and practical possibility to reduce nitrite residue and improve safety during food fermented products.