Dataset Information

Transcriptome Analysis of the Global Response of Pseudomonas fragi NMC25 to Modified Atmosphere Packaging Stress.

ABSTRACT: Pseudomonas fragi is usually isolated from chilled meats in relation to their spoilage, while many studies have shown that the application of modified atmosphere packaging (MAP) inhibits the spoilage potential of P. fragi. The effects of MAP on P. fragi NMC25 metabolism were determined in the present study by exposing this organism to different air conditions and comparing the resulting transcriptome profiles. We found 559 differentially expressed genes by RNA-seq, and the results revealed that MAP decreases the expression of genes involved in the electron transport chain (nuoAB), resulting in an inhibition of aerobic respiration. Meanwhile, MAP also induced the downregulation of genes responsible for ATP-binding cassette transporters, flagellar and type I fimbrial proteins, and DNA replication and repair, which may further influence nutrient uptake, motility, and growth. In addition, NMC25 cells modified their pathways for energy production, amino acid synthesis, membrane lipid composition, and other metabolic patterns to adapt to MAP. These data show that P. fragi NMC25 survives under MAP but reduces part of its metabolism related to its spoilage ability.

SUBMITTER: Wang G

PROVIDER: S-EPMC6004401 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature

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Transcriptome Analysis of the Global Response of Pseudomonas fragi NMC25 to Modified Atmosphere Packaging Stress.

Wang Guangyu G Ma Fang F Chen Xiaojing X Han Yanqing Y Wang Huhu H Xu Xinglian X Zhou Guanghong G

Frontiers in microbiology 20180611

Pseudomonas fragi is usually isolated from chilled meats in relation to their spoilage, while many studies have shown that the application of modified atmosphere packaging (MAP) inhibits the spoilage potential of P. fragi. The effects of MAP on P. fragi NMC25 metabolism were determined in the present study by exposing this organism to different air conditions and comparing the resulting transcriptome profiles. We found 559 differentially expressed genes by RNA-seq, and the r ...[more]

PMID: 29942299

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Project description:A long green period is essential for a turfgrass species with high ornamental value and a wide area of use. Zoysiagrasses (Zoysia spp. Willd.) are perennial turfgrass species popular in tropical, subtropical and temperate zones, possessing many properties necessary to be economically useful turfgrass. They do not have a long green period because of cold sensitivity. A main focus in zoysiagrass research is to develop cold tolerant cultivars. Understanding the cold response in zoysiagrass is a fundamental area of research. In the present study, 'Meyer' zoysiagrass (Zoysia japonica), a widely cultivated variety in the genus, is used. We employed RNA-Seq to investigate genome-wide gene expression profiles in leaves under cold stress (4°C). Using the Illumina sequencing platform, we obtained approximately 206 million high-quality paired-end reads from three libraries (0 h, 2 h, and 72 h cold treatment at 4°C). After de novo assembly and quantitative assessment, 46,412 unigenes were generated with an average length of 998 bp and an N50 of 1,522 bp. A total of 25,644 (55.2%) unigenes were annotated by alignment with public protein databases including NR, SwissProt, KEGG and KOG. Differentially expressed genes (DEGs) were investigated using the RPKM method. A total of 756 DEGs were identified between 0 h and 2 h-cold treatment, with 522 up-regulated and 234 down-regulated; and 5327 DEGs were identified between 0 h and 72 h-cold treatment, with 2453 up-regulated and 2874 down-regulated. The expression profile of 15 DEGs selected randomly was confirmed with qRT-PCR. The results suggest that cold stress can induce desiccation and oxidative stress, inhibit photosynthesis and substance transport. In response to the stress, genes involved in proline synthesis, in starch hydrolysis, in methionine and ascorbic acid metabolism, in SOD activity, and in DREBs response pathway were up-regulated. GA metabolism, ABA and JA stimulus response were affected under cold exposure. This is the first transcriptome sequencing of Z. japonica, providing a large set of sequence data as well as gene expression profiles under cold stress. It will improve our current understanding of the cold response of zoysiagrass and be beneficial in breeding research.

Dataset Information

Transcriptome Analysis of the Global Response of Pseudomonas fragi NMC25 to Modified Atmosphere Packaging Stress.

Publications

Transcriptome Analysis of the Global Response of <i>Pseudomonas fragi</i> NMC25 to Modified Atmosphere Packaging Stress.

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