The chemical mechanisms of the enzymes in the branched-chain amino acids biosynthetic pathway and their applications

Liang, Yao-Dong; Long, Zi-Xian; Zhang, Ya-Jian; Luo, Cai-Yun; Yan, Le-Tian; Li, Heng

doi:10.1016/j.biochi.2021.02.008

Cited by 25 publications

(15 citation statements)

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“…These genes are related to the replication process, which agrees with functions found in the enriched analysis ( Araki et al, 1992 ; Storfie and Saville, 2021 ). Moreover, another interesting hub is UMAG_05113 in the Grey60 module, it codes for Threonine dehydratase which is a key enzyme in BCAA synthesis, which catalyzes the conversion L-threonine into α-ketobutyrate, furthermore, this enzyme is inhibited by the end product of the metabolic pathway ( Liang et al, 2021 ). Finally, in Sienna3, Brown, Cyan, and Magenta the hubs are UMAG_04807, UMAG_03644, UMAG_05198, and UMAG_10929, respectively, which code for hypothetical proteins ( Table 2 ).…”

Section: Resultsmentioning

confidence: 99%

Construction and analysis of gene co-expression network in the pathogenic fungus Ustilago maydis

et al. 2022

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IntroductionBiological systems respond to environmental disturbances and a wide range of compounds through complex gene interaction networks. The enormous growth of experimental information obtained using large-scale genomic techniques such as microarrays and RNA sequencing led to the construction of a wide variety of gene co-expression networks in recent years. These networks allow the discovery of clusters of co-expressed genes that potentially work in the same process linking them to biological processes often of interest to industrial, medicinal, and academic research.MethodsIn this study, we built the gene co-expression network of Ustilago maydis from the gene expression data of 168 samples belonging to 19 series, which correspond to the GPL3681 platform deposited in the NCBI using WGCNA software. This network was analyzed to identify clusters of co-expressed genes, gene hubs and Gene Ontology terms. Additionally, we identified relevant modules through a hypergeometric approach based on a predicted set of transcription factors and virulence genes.Results and DiscussionWe identified 13 modules in the gene co-expression network of U. maydis. The TFs enriched in the modules of interest belong to the superfamilies of Nucleic acid-binding proteins, Winged helix DNA-binding, and Zn2/Cys6 DNA-binding. On the other hand, the modules enriched with virulence genes were classified into diseases related to corn smut, Invasive candidiasis, among others. Finally, a large number of hypothetical, a large number of hypothetical genes were identified as highly co-expressed with virulence genes, making them possible experimental targets.

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Section: Resultsmentioning

confidence: 99%

Construction and analysis of gene co-expression network in the pathogenic fungus Ustilago maydis

et al. 2022

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“…ilvB , ilvC , ilvD apply to encode dedicated enzymes for catalysing to obtain products 2‐keto‐3‐methyl butyrate and 2‐Ketoisovalerate. After that, part of the former product and all of the latter one is converted into L‐valine and L‐isoleucine, respectively, and the other part of the former compound will enter the L‐leucine biosynthesis using enzyme encoded by leuABCD genes (Figure 4) (Franco & Blanchard, 2017; Liang et al, 2021). Downregulation of ilvD impaired BCAA synthesis, pantothenate, and subsequently the synthesis of CoA for which pantothenate is a precursor (Franco & Blanchard, 2017).…”

Section: Discussionmentioning

confidence: 99%

The combination of thymol and cinnamaldehyde reduces the survival and virulence of Listeria monocytogenes on autoclaved chicken breast

Liang

Wang

et al. 2022

Journal of Applied Microbiology

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Aims:To reveal the antibacterial mechanism of the combination of thymol and cinnamaldehyde to Listeria monocytogenes ATCC 19115 on autoclaved chicken breast. Methods and Results:In this study, L. monocytogenes ATCC 19115 on autoclaved chicken breast was exposed to the stress of 125 μg/ml thymol and 125 μg/ml cinnamaldehyde, and transcriptome analysis was used to reveal the crucial antibacterial mechanism. According to the results, 1303 significantly differentially expressed genes (DEGs) were identified. Treated by thymol and cinnamaldehyde in combination, pyrimidine and branched-chain amino acid biosynthesis of L. monocytogenes were thwarted which impairs its nucleic acid biosynthesis and intracellular metabolism. The up-regulated DEGs involved in membrane composition and function contributed to membrane repair. Besides, pyruvate catabolism and TCA cycle were restrained which brought about the disturbance of amino acid metabolism. ABC transporters were also perturbed, for instance, the uptake of cysteine, D-methionine, and betaine was activated, while the uptake of vitamin, iron, and carnitine was repressed. Thus, L. monocytogenes tended to activate PTS, glycolysis, glycerol catabolism, and pentose phosphate pathways to obtain energy to adapt to the hostile condition. Noticeably, DEGs involved in virulence factors were totally down-regulated, including genes devoted to encoding flagella, chemotaxis, biofilm formation, internalin as well as virulence gene clusters. Conclusions:The combination of thymol and cinnamaldehyde is effective to reduce the survival and potential virulence of L. monocytogenes on autoclaved chicken breast.

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“…Effect sizes were reported for 6 studies related to cancer and 3 studies related to all-cause mortality. (5), smoking (6), aspirin use or regular aspirin use (7), energy intake (8), calcium intake or dairy calcium intake (9) menopausal status (10), postmenopausal hormone use or hormone therapy (11), family history of colorectal cancer (12), marital status (13), occupational physical activity (14), physical activity (15), study center (16), year of interview (17), family history of special cancer (18), diabetes or type 2 diabetes (19), SBP (20), DBP (21), TC (22), TAG (23), UA (24), URP (25), LDL (26), HDL (27), supplement use (28), breast-feeding or total breast-feeding (29), SES (30), residency (31), history of endoscopy (32), height (33) (5), smoking (6), aspirin use or regular aspirin use (7), energy intake (8), calcium intake or dairy calcium intake (9) menopausal status (10), postmenopausal hormone use or hormone therapy (11), family history of colorectal cancer (12), marital status (13), occupational physical activity (14), physical activity (15), study center (16), year of interview (17), family history of special cancer (18), diabetes or type 2 diabetes (19), SBP (20), DBP (21), TC (22), TAG (23), UA (24), URP (25), LDL (26), HDL (27), supplement use (28), breast-feeding or total breast-feeding (29), SES…”

Section: Literature Searchmentioning

confidence: 99%

Dietary branched chain amino acids relationship with cancer and mortality: A systematic review and meta-analysis

Tabesh

Teymoori

Ahmadirad

et al. 2022

Preprint

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Background Dietary branched chain amino acids (BCAAs) are proposed as a potential related factor in various diseases, including cancer. We aimed to investigate the relationship between dietary intake of BCAAs and their components with cancer and all-cause mortality in a meta-analysis study of observational studies. Methods To identify relevant studies, a comprehensive search was conducted between electronic databases (PubMed, Scopus, and Web of Science) until September 2022. Odds ratios (OR), hazard ratios (HR), and relative risks (RR) with 95% confidence interval (CI) were extracted from eligible studies, and a meta-analysis was performed to calculate the combined effect size. Results Eight articles (3 case-control and 5 cohorts) were included in this meta-analysis. 6 studies reported effect sizes for cancer risk and 3 for cancer or all-cause mortality. Overall, we did not observe any statistically significant association between dietary intake of BCAAs and their components with cancer (RRBCAA: 0.87, 95%CI: 0.68–1.10, RRLeucine: 0.74, 95%CI: 0.52–1.04, RRIsoleucine: 0.98, 95%CI: 0.93–1.04, RRValine: 0.76, 95%CI: 0.55–1.05). Also, we observed any significant relationship between dietary BCAAs and their components with both cancer mortality (RRBCAA: 0.95, 95%CI: 0.68–1.33, RRLeucine: 0.95, 95%CI: 0.79–1.15, RRIsoleucine: 0.95, 95%CI: 0.79–1.14, RRValine: 1.01, 95%CI: 0.84–1.21) and all-cause mortality (RRBCAA: 0.98, 95%CI: 0.73–1.32, RRLeucine: 1.02, 95%CI: 0.81–1.29, RRIsoleucine: 0.96, 95%CI: 0.73–1.27, RRValine: 1.02, 95% CI: 0.79–1.32). Conclusions The findings of the present study showed no significant association between dietary intake of BCAA and its components with cancer, cancer mortality, and all-cause mortality.

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The chemical mechanisms of the enzymes in the branched-chain amino acids biosynthetic pathway and their applications

Cited by 25 publications

References 174 publications

Construction and analysis of gene co-expression network in the pathogenic fungus Ustilago maydis

Construction and analysis of gene co-expression network in the pathogenic fungus Ustilago maydis

The combination of thymol and cinnamaldehyde reduces the survival and virulence of Listeria monocytogenes on autoclaved chicken breast

Dietary branched chain amino acids relationship with cancer and mortality: A systematic review and meta-analysis

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