Investigating proteome and transcriptome response of Cryptococcus podzolicus Y3 to citrinin and the mechanisms involved in its degradation

Wang, Kaili; Lin, Zhen; Zhang, Hongyin; Zhang, Xiaoyun; Zheng, Xizhong; Zhao, Lina; Yang, Qiya; Ahima, Joseph; Boateng, Nana Adwoa Serwah

doi:10.1016/j.foodchem.2019.01.052

Cited by 17 publications

(10 citation statements)

References 33 publications

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“…RT-qPCR experiment was repeated three times with each sample having three technique replicates. The relative expression level of genes was calculated using the 2 −ΔΔC T method, and standard deviation was calculated between three biological replicates [13].…”

Section: Methodsmentioning

confidence: 99%

Comparative Transcriptomic Analysis of the Interaction between Penicillium expansum and Apple Fruit (Malus pumila Mill.) during Early Stages of Infection

et al. 2019

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Blue mold, caused by Penicillium expansum, is an important postharvest disease of apple, and can result in significant economic losses. The present study investigated the interaction between P. expansum and wounded apple fruit tissues during the early stages of the infection. Spores of P. expansum became activated one hour post-inoculation (hpi), exhibited swelling at 3 hpi, and the germ tubes were found entering into apple tissues at 6 hpi. RNA-seq was performed on samples of P. expansum and apple fruit tissue collected at 1, 3, and 6 hpi. The main differentially expressed genes (DEGs) that were identified in P. expansum were related to interaction, cell wall degradation enzymes, anti-oxidative stress, pH regulation, and effectors. Apple tissues responded to the presence of P. expansum by activating pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) at 1 hpi, then activated effector-triggered immunity (ETI) at 3 hpi. This research provides new information on the interaction between P. expansum and apple fruit tissue at an early stage of the infection process.

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Section: Methodsmentioning

confidence: 99%

Comparative Transcriptomic Analysis of the Interaction between Penicillium expansum and Apple Fruit (Malus pumila Mill.) during Early Stages of Infection

et al. 2019

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“…During limonene biotransformation, the DEGs correlated to energy metabolism were significantly down-regulated ( Table 3). TCA cycle can generate metabolic intermediates and energy by a series of enzymes (Wang et al, 2019). In the present study, it is observed that most genes participated in TCA cycle were down-regulated after limonene induction, such as isocitrate dehydrogenase (IDH, PDIDSM_28150), succinate dehydrogenase (SDH, PDIDSM_53370), malate dehydrogenase (MDH, PDIDSM_47510), 2-oxoglutarate dehydrogenase (OGDH, PDIDSM_43060), phosphoenolpyruvate carboxykinase (pckA, PDIDSM_36580), pyruvate carboxylase (PDIDSM_16200), and so on.…”

Section: Identification Of the Differentially Expressed Genes Involvementioning

confidence: 99%

Genomic and Transcriptomic Study for Screening Genes Involved in the Limonene Biotransformation of Penicillium digitatum DSM 62840

et al. 2020

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α-Terpineol has been widely used in daily chemical, pharmaceutical, food, and flavor industries due to its pleasant odor with high economic value and pharmacological action. Our previous study showed that Penicillium digitatum DSM 62840 was an efficient biocatalyst for the transformation of limonene to α-terpineol. Thus, it was meaningful to explore the genome features and the gene expression differences of strain DSM 62840 during limonene biotransformation, and the detailed bioconversion pathways. In this study, the functional genes related to limonene bioconversion were investigated using genome and transcriptome sequences analysis. The results showed that the P. digitatum DSM 62840 genome was estimated to be 29.09 Mb and it encoded 9,086 protein-encoding genes. The most annotated genes were associated to some protein metabolism and energy metabolism functions. When the threshold for differentially expressed genes (DEGs) was set at twofold ratio, a total of 4,128, and 4,148 DEGs were identified in P_L_12h (limonene-treated condition) compared with P_0h (blank) and P_12h (limonene-untreated blank), respectively. Among them, the expression levels of genes involved in the biosynthesis of secondary metabolites, energy metabolism and ATP-binding cassette (ABC) transporters were significantly altered during the biotransformation. And the reliability of these results was further confirmed by quantitative real-time polymerase chain reaction (RT-qPCR). Moreover, we found that the enzyme participated in limonene biotransformation was inducible. This enzyme was located in the microsome, and it was inhibited by cytochrome P450 inhibitors. This indicated that the cytochrome P450 may be responsible for the limonene bioconversion. Several differentially expressed cytochrome P450 genes were further identified, such as PDIDSM_85260 and PDIDSM_67430, which were significantly upregulated with limonene treatment. These genes may be responsible for converting limonene to α-terpineol. Totally, the genomic and transcriptomic data could provide valuable information in the discovery of related-genes which was involved in limonene biotransformation, pathogenicity of fungi, and investigation of metabolites and biological pathways of strain DSM 62840.

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“…For example, the proteomic response of Cryptococcus podzolicus Y3 to citrinin suggested that the up-and down-regulated proteins were associated with structural maintenance of chromosomes (DNA double-strand break repair Rad50 ATPase, etc. ), cell apoptosis (cytochrome C), detoxification and energy metabolism (Glyco-syltransferase and malate dehydrogenase), and oxidative stress response (superoxide dismutase [Cu-Zn] and cysteine peroxiredoxin) (Wang et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

iTRAQ-Based Comparative Proteomic Analysis of Acinetobacter baylyi ADP1 Under DNA Damage in Relation to Different Carbon Sources

Jiang

Xing

et al. 2020

Front. Microbiol.

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DNA damage response allows microorganisms to repair or bypass DNA damage and maintain the genome integrity. It has attracted increasing attention but the underlying influential factors affecting DNA damage response are still unclear. In this work, isobaric tags for relative and absolute quantification (iTRAQ)-based proteomic analysis was used to investigate the influence of carbon sources on the translational response of Acinetobacter baylyi ADP1 to DNA damage. After cultivating in a nutrient-rich medium (LB) and defined media supplemented with four different carbon sources (acetate, citrate, pyruvate, and succinate), a total of 2807 proteins were identified. Among them, 84 proteins involved in stress response were significantly altered, indicating the strong influence of carbon source on the response of A. baylyi ADP1 to DNA damage and other stresses. As the first study on the comparative global proteomic changes in A. baylyi ADP1 under DNA damage across nutritional environments, our findings revealed that DNA damage response in A. baylyi ADP1 at the translational level is significantly altered by carbon source, providing an insight into the complex protein interactions across carbon sources and offering theoretical clues for further study to elucidate their general regulatory mechanism to adapt to different nutrient environments.

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Investigating proteome and transcriptome response of Cryptococcus podzolicus Y3 to citrinin and the mechanisms involved in its degradation

Cited by 17 publications

References 33 publications

Comparative Transcriptomic Analysis of the Interaction between Penicillium expansum and Apple Fruit (Malus pumila Mill.) during Early Stages of Infection

Comparative Transcriptomic Analysis of the Interaction between Penicillium expansum and Apple Fruit (Malus pumila Mill.) during Early Stages of Infection

Genomic and Transcriptomic Study for Screening Genes Involved in the Limonene Biotransformation of Penicillium digitatum DSM 62840

iTRAQ-Based Comparative Proteomic Analysis of Acinetobacter baylyi ADP1 Under DNA Damage in Relation to Different Carbon Sources

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