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Integrative analyses reveal transcriptome-proteome correlation in biological pathways and secondary metabolism clusters in A. flavus in response to temperature.

ABSTRACT: To investigate the changes in transcript and relative protein levels in response to temperature, complementary transcriptomic and proteomic analyses were used to identify changes in Aspergillus flavus grown at 28?°C and 37?°C. A total of 3,886 proteins were identified, and 2,832 proteins were reliably quantified. A subset of 664 proteins was differentially expressed upon temperature changes and enriched in several Kyoto Encyclopedia of Genes and Genomes pathways: translation-related pathways, metabolic pathways, and biosynthesis of secondary metabolites. The changes in protein profiles showed low congruency with alterations in corresponding transcript levels, indicating that post-transcriptional processes play a critical role in regulating the protein level in A. flavus. The expression pattern of proteins and transcripts related to aflatoxin biosynthesis showed that most genes were up-regulated at both the protein and transcript level at 28?°C. Our data provide comprehensive quantitative proteome data of A. flavus at conducive and nonconducive temperatures.

SUBMITTER: Bai Y

PROVIDER: S-EPMC4586720 | biostudies-literature | 2015 Sep

REPOSITORIES: biostudies-literature

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Integrative analyses reveal transcriptome-proteome correlation in biological pathways and secondary metabolism clusters in A. flavus in response to temperature.

Bai Youhuang Y Wang Sen S Zhong Hong H Yang Qi Q Zhang Feng F Zhuang Zhenhong Z Yuan Jun J Nie Xinyi X Wang Shihua S

Scientific reports 20150929

To investigate the changes in transcript and relative protein levels in response to temperature, complementary transcriptomic and proteomic analyses were used to identify changes in Aspergillus flavus grown at 28 °C and 37 °C. A total of 3,886 proteins were identified, and 2,832 proteins were reliably quantified. A subset of 664 proteins was differentially expressed upon temperature changes and enriched in several Kyoto Encyclopedia of Genes and Genomes pathways: translation-related pathways, me ...[more]

PMID: 26416011

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Project description:As a natural severe contaminant of stored grains and other crops worldwide, Aspergillus flavus can produce aflatoxins (AFs), the most powerful naturally producing toxic and hepatocarcinogenic compounds. AFs production is regulated by diverse factors including AFs cluster genes, transcription factors, regulators, and environmental factors. Among them, crop substrate is one of the most important factors. Here, we found that AFB1 production was significantly higher in maize and rice broth than in peanut broth. To clarify the mechanisms involved, complementary transcriptomic and proteomic analyses were performed to identify changes in A. flavus incubated in the three crop substrates. The results indicated that fewer genes and proteins were differentially expressed between maize and rice substrates, whereas more differentially expressed genes were observed between maize/rice broth and peanut broth. In particular, the genes involved in the initial step of AFs biosynthesis (aflA, aflB, and aflC) and the ACCase-encoding gene accA were significantly upregulated on the maize and rice substrates. Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) enrichment analyses indicated that carbon-metabolism-related genes were obviously enriched in the maize broth, and the genes involved in acetyl-CoA accumulation and consumption were up- and downregulated, respectively. Several genes involved in the regulation of AFs biosynthesis, including veA, ppoB, snf1, and the G-protein-coupled receptor (GPCR) genes, were differentially expressed on the three substrates, suggesting that these genes may be also involved in sugar signal sensing, transfer, and regulation. Interestingly, by the correlation analyses of transcriptome and proteome, trehalose metabolism genes, aldehyde dehydrogenase gene, and tryptophan synthase gene were found to be relevant with the regulation of AFs production on different crop substrates. Taken together, the differential expressions of the AFs cluster genes, several regulatory genes, and carbon metabolism genes were involved in the comprehensive modulation of AFs production on different crop substrates.

Project description:Streptomycetes are multicellular bacteria with complex developmental cycles. They are of biotechnological importance as they produce most bioactive compounds used in biomedicine, e.g. antibiotic, antitumoral and immunosupressor compounds. Streptomyces genomes encode many Ser/Thr/Tyr kinases, making this genus an outstanding model for the study of bacterial protein phosphorylation events. We used mass spectrometry based quantitative proteomics and phosphoproteomics to characterize bacterial differentiation and activation of secondary metabolism of Streptomyces coelicolor We identified and quantified 3461 proteins corresponding to 44.3% of the S. coelicolor proteome across three developmental stages: vegetative hypha (first mycelium); secondary metabolite producing hyphae (second mycelium); and sporulating hyphae. A total of 1350 proteins exhibited more than 2-fold expression changes during the bacterial differentiation process. These proteins include 136 regulators (transcriptional regulators, transducers, Ser/Thr/Tyr kinases, signaling proteins), as well as 542 putative proteins with no clear homology to known proteins which are likely to play a role in differentiation and secondary metabolism. Phosphoproteomics revealed 85 unique protein phosphorylation sites, 58 of them differentially phosphorylated during differentiation. Computational analysis suggested that these regulated protein phosphorylation events are implicated in important cellular processes, including cell division, differentiation, regulation of secondary metabolism, transcription, protein synthesis, protein folding and stress responses. We discovered a novel regulated phosphorylation site in the key bacterial cell division protein FtsZ (pSer319) that modulates sporulation and regulates actinorhodin antibiotic production. We conclude that manipulation of distinct protein phosphorylation events may improve secondary metabolite production in industrial streptomycetes, including the activation of cryptic pathways during the screening for new secondary metabolites from streptomycetes.

Dataset Information

Integrative analyses reveal transcriptome-proteome correlation in biological pathways and secondary metabolism clusters in A. flavus in response to temperature.

Publications

Integrative analyses reveal transcriptome-proteome correlation in biological pathways and secondary metabolism clusters in A. flavus in response to temperature.

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