Chenyu Wang , Jintao Wang , Chungeng Hong , Gang Chen , Wanying Ge , Yongxin Li , Huqing Yang
{"title":"Comparison of quality and flavor between on-tree storage and cold storage of Satsuma ‘Youliang’","authors":"Chenyu Wang , Jintao Wang , Chungeng Hong , Gang Chen , Wanying Ge , Yongxin Li , Huqing Yang","doi":"10.1016/j.fochms.2025.100280","DOIUrl":"10.1016/j.fochms.2025.100280","url":null,"abstract":"<div><div>This study investigates the effects of on-tree storage (OTS) on the quality and flavor of Satsuma ‘Youliang’ compared with cold storage (COS). Fruit quality was assessed based on sugar-acid ratio and juice flavor profiles. Comparative analysis revealed a progressive decline in soluble sugar content under COS, while OTS effectively preserved sugars, resulting in a higher sugar-acid ratio than COS-treated fruits. During storage, OTS fruits maintained significantly higher levels of sucrose, fructose, and malic acid than COS fruits. Additionally, OTS fruits exhibited a greater variety and higher concentrations of volatile organic compounds (VOCs), contributing to enhanced flavor. Transcriptome analysis indicated that OTS reduced sugar loss by upregulating soluble sugar metabolism-related genes (SUS, SPS). Furthermore, OTS upregulated tricarboxylic acid cycle-related genes (SSADH, NAD-MDH), accelerating malic acid synthesis. Additionally, OTS activated the expression of ACAT, GPS, and GPPS, promoting the production of terpenoid precursors GPP and GGPP. These findings suggest that OTS improves fruit acceptability and is more effective than COS for maintaining fruit quality.</div></div>","PeriodicalId":34477,"journal":{"name":"Food Chemistry Molecular Sciences","volume":"11 ","pages":"Article 100280"},"PeriodicalIF":4.1,"publicationDate":"2025-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144685585","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Enhanced catalytic activity of a novel trypsin by semi-rational design with mechanistic insights from molecular simulations","authors":"Jia Chen , Guangyang Jiang , Yongqiang Tian","doi":"10.1016/j.fochms.2025.100275","DOIUrl":"10.1016/j.fochms.2025.100275","url":null,"abstract":"<div><div>Trypsin is widely used in the food industry for meat processing, dairy production and seafood treatment. However, the industrial application of trypsin is constrained by the pathogenic risks associated with animal-derived trypsin and the low enzymatic activity of microbial-derived trypsin. This study aimed to enhance the catalytic activity of a novel trypsin heterologously expressed in <em>Bacillus subtilis</em> SCK6. Given the catalytic specificity of trypsin, numerous lysine and arginine residues within the trypsin are susceptible to autolytic cleavage, which may compromise the integrity and stability of its tertiary structure, thereby affecting its catalytic efficiency. To address this, a semi-rational design strategy was employed to introduce mutations at lysine and arginine residues. As a result, a trypsin variant with a 2.2-fold increase in enzymatic activity was obtained, reaching 93.9 U/ml. Further optimization of the fermentation process elevated the enzymatic activity to 132.8 U/ml. Additionally, this study pioneered molecular docking and molecular dynamics simulations in trypsin engineering, revealing that the introduced mutations stabilize the catalytic pocket and enhance enzyme activity. These findings demonstrate that structure-guided mutagenesis of autolysis-prone lysine and arginine residues can significantly improve the catalytic performance of microbial trypsin. This strategy provides a rational framework for the targeted engineering of trypsin variants and offers a practical approach for developing safer, high-activity preparations suitable for industrial food processing applications.</div></div>","PeriodicalId":34477,"journal":{"name":"Food Chemistry Molecular Sciences","volume":"11 ","pages":"Article 100275"},"PeriodicalIF":4.1,"publicationDate":"2025-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144685586","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Laura Bonfini , Moreno Colaiacovo , Cristian Savini , Christoph von Holst , Matteo Maretti , Francesco Gatto , Federica Magni , Paloma Pérez-Bello , Davide Scaglione
{"title":"A duplex sequencing approach for high-sensitivity detection of genome-edited plants","authors":"Laura Bonfini , Moreno Colaiacovo , Cristian Savini , Christoph von Holst , Matteo Maretti , Francesco Gatto , Federica Magni , Paloma Pérez-Bello , Davide Scaglione","doi":"10.1016/j.fochms.2025.100278","DOIUrl":"10.1016/j.fochms.2025.100278","url":null,"abstract":"<div><div>In this paper, we have evaluated a targeted high-throughput massive parallel sequencing approach for detecting single nucleotide mutations or small genomic changes generated by new genomic techniques (NGT).</div><div>We used unique molecular identifiers (UMIs) for the quantification of the mutant alleles and duplex sequencing to confirm a mutation on both strands to avoid polymerase chain reaction (PCR) artefacts or sequencing miss-calls. We tested the approach in blinded analyses on a set of mixed NGT-modified tomato lines and identified each single nucleotide mutation or small insert/deletion (InDel) down to a 0.1 % level. To our knowledge, this is the first performance evaluation of a duplex sequencing approach for detecting and quantifying small NGT DNA changes without a priori knowledge of the mutation type and position in a target region.</div><div>Our study advances the scientific discussion on detecting NGT-induced DNA modifications in plants and food products, evaluating the potential and current limitations of a cutting-edge NGS-approach.</div></div>","PeriodicalId":34477,"journal":{"name":"Food Chemistry Molecular Sciences","volume":"11 ","pages":"Article 100278"},"PeriodicalIF":4.1,"publicationDate":"2025-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144696443","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Siti Nurmilah , Andri Frediansyah , Yana Cahyana , Roostita L. Balia , Bibin Bintang Andriana , Gemilang Lara Utama
{"title":"Exploring microbial dynamics and metabolomic profiling of isoflavone transformation in black and yellow soybean tempe for sustainable functional foods","authors":"Siti Nurmilah , Andri Frediansyah , Yana Cahyana , Roostita L. Balia , Bibin Bintang Andriana , Gemilang Lara Utama","doi":"10.1016/j.fochms.2025.100279","DOIUrl":"10.1016/j.fochms.2025.100279","url":null,"abstract":"<div><div>Tempe, a traditional Indonesian fermented food, is rich in bioactive isoflavones and peptides, offering significant health benefits. This study explores how fermentation methods and soybean varieties shape isoflavone profiles and microbial communities. Two fermentation approaches were compared: Raprima™ starter culture and a co-culture of <em>Rhizopus oligosporus</em> and <em>R. stolonifer</em>. Metabolomic analysis showed that co-culture fermentation significantly increased genistein levels and enhanced isoflavone bioavailability. Proteobacteria (78 %) and Firmicutes (18 %) dominated bacterial communities, with yellow soybeans containing more Enterobacteriaceae. Co-culture fermentation enriched <em>Stenotrophomonas</em>, while Raprima™ favored <em>Acinetobacter</em>. The fungal community, primarily Mucoromycota (92 %), exhibited significant correlations with isoflavone transformation. Co-culture fermentation improved microbial synergy and metabolic efficiency, boosting isoflavone aglycone production. While yellow soybeans had higher isoflavone content, black soybeans, with elevated genistein, present a promising alternative. These findings emphasize fermentation's role in enhancing tempe's functionality for sustainable, nutritionally rich food development.</div></div>","PeriodicalId":34477,"journal":{"name":"Food Chemistry Molecular Sciences","volume":"11 ","pages":"Article 100279"},"PeriodicalIF":4.1,"publicationDate":"2025-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144696445","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Qiao Li, Zilong Liu, Yi Wu, Chunhui Wang, Xueyi Ma, Youji Ma
{"title":"Effects of dietary prickly ash seeds supplementation on muscle development and volatile compounds of Hu sheep","authors":"Qiao Li, Zilong Liu, Yi Wu, Chunhui Wang, Xueyi Ma, Youji Ma","doi":"10.1016/j.fochms.2025.100274","DOIUrl":"10.1016/j.fochms.2025.100274","url":null,"abstract":"<div><div>Prickly ash seeds (PAS), a nutrient-rich by-product, show potential as a sustainable feed for Hu sheep. The current study aims to explore the effects of dietary supplementation with PAS on muscle development and volatile compounds of Hu sheep through multi-omics analysis. The increased muscle fiber diameter and cross-sectional area was associated with dietary supplementation with PAS compared with the CK group (<em>P</em> < 0.05). Transcriptome analysis showed that <em>ACTC1</em>, <em>SERPINA3</em>, <em>COX2</em>, <em>MYBPH</em>, <em>FMOD</em>, and <em>KLHL34</em> were key differentially expressed genes (DEGs) involved in muscle growth and development, and played a role through oxidative phosphorylation, TCA cycle, fatty acid metabolism, and tryptophan metabolism. The combined analysis of transcriptome and volatile metabolomics showed that <em>LEP</em>, <em>ADCY1</em>, <em>TMEM54</em>, <em>COX2</em>, <em>PCK1</em>, and <em>CPT1A</em> may play an important regulatory role in the production of volatile compounds such as cetene, dodecanal, 2,6-dodecadien-1-al, palmitoleic acid, dodecanoic acid, ethyl ester by participating in lipid metabolism. In summary, PAS demonstrates promise for Hu sheep production, enhancing muscle development and influencing muscle flavor by modulating fatty acid metabolism-related genes</div></div>","PeriodicalId":34477,"journal":{"name":"Food Chemistry Molecular Sciences","volume":"11 ","pages":"Article 100274"},"PeriodicalIF":4.1,"publicationDate":"2025-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144633132","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Hanhan Luo , Jing Tang , Zhaoxiang Zeng , Jinlin Xu , Bixuan Chen , Xin Huang , Haijun Yang , Rongzeng Huang , Cheng Chen , Chengwu Song , Shuna Jin
{"title":"Metabolic dynamics of litchi pericarp and pulp during browning: Unraveling differential profiles through temporal clustering and untargeted metabolomics","authors":"Hanhan Luo , Jing Tang , Zhaoxiang Zeng , Jinlin Xu , Bixuan Chen , Xin Huang , Haijun Yang , Rongzeng Huang , Cheng Chen , Chengwu Song , Shuna Jin","doi":"10.1016/j.fochms.2025.100277","DOIUrl":"10.1016/j.fochms.2025.100277","url":null,"abstract":"<div><div>Litchi, valued for its vibrant appearance and nutritional content, undergoes rapid browning of the pericarp (PE), reducing its market value. However, the browning mechanism and the impact of browning on the pulp (PU) are not fully understood. This study, litchi fruits were considered at five browning stages. Untargeted LC–MS metabolomics and cluster analysis revealed more pronounced browning-related metabolic changes in the PE than in the PU, as shown by greater separation in PE via principal component analysis. Overall, 53 differential metabolites in PE and 24 in PU were characterized, including flavonoids and lipids. The correlation analysis results revealed that the metabolites strongly associated with the browning process in the PE were primarily lipid compounds. Pathway analysis indicated that PE browning was associated with flavonoid pathway and lipid metabolism. These findings offered insights into litchi browning metabolism and a basis for improving PE browning delay and post-harvest preservation.</div></div>","PeriodicalId":34477,"journal":{"name":"Food Chemistry Molecular Sciences","volume":"11 ","pages":"Article 100277"},"PeriodicalIF":4.1,"publicationDate":"2025-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144596263","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Shen Meng , Yan Jing , Wang Ruisen , Quan Xinhua , Yuan Ye , Yao Xiangtan , Jin Qunli
{"title":"Molecular mechanisms and horticultural implications of temperature-induced color variation in Stropharia rugosoannulata mushrooms","authors":"Shen Meng , Yan Jing , Wang Ruisen , Quan Xinhua , Yuan Ye , Yao Xiangtan , Jin Qunli","doi":"10.1016/j.fochms.2025.100276","DOIUrl":"10.1016/j.fochms.2025.100276","url":null,"abstract":"<div><div>Cap color is a critical commercial trait in <em>Stropharia rugosoannulata</em> mushrooms, yet the molecular mechanisms underlying its temperature-induced variation remain poorly understood. This study integrated metabolomic and transcriptomic approaches to identify key metabolites and genes associated with the transition of cap color from white to wine-red under different temperature conditions. Metabolomic analysis identified 1913 metabolites, with flavonoid derivatives such as quercetin-3-O-glucoside and kaempferol-based compounds accumulating preferentially in wine-red mushrooms at high temperatures. Transcriptomic analysis revealed 13,428 differentially expressed genes (DEGs), including 36 structural genes in the flavonoid biosynthesis pathway. Notably, upregulation of <em>SrGene13140</em> (F3′H) and <em>SrGene10248</em> (F3′5′H) was observed in wine-red mushrooms, suggesting their involvement in red pigment production. In contrast, <em>SrGene10253</em> (F3′H) was more highly expressed in yellow mushrooms, indicating isoform-specific hydroxylation activity. Integrated gene-metabolite correlation and network analysis highlighted key enzymes, including phenylalanine ammonia lyase (PAL), flavonoid 3′-hydroxylase (F3′H), and 4-coumarate: coenzyme A ligase (4CL), as central regulators of color-related flavonoid biosynthesis. These findings provide valuable insights into the molecular basis of temperature-induced color variation in <em>S. rugosoannulata</em> and offer potential applications in mushroom breeding and horticulture.</div></div>","PeriodicalId":34477,"journal":{"name":"Food Chemistry Molecular Sciences","volume":"11 ","pages":"Article 100276"},"PeriodicalIF":4.1,"publicationDate":"2025-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144702591","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Rabia Durrani , Sun Yutian , Hou Bowen , Hammad Ullah , Erwann Durand , Yang Meiyun , Long Yiyang , André Delavault , Muhammad Yasir , Huan Weiwei , Gao Fei , Song Lili
{"title":"Torreya grandis nut peptides regulate lipid-II inhibitors in high-fat diet-fed mice","authors":"Rabia Durrani , Sun Yutian , Hou Bowen , Hammad Ullah , Erwann Durand , Yang Meiyun , Long Yiyang , André Delavault , Muhammad Yasir , Huan Weiwei , Gao Fei , Song Lili","doi":"10.1016/j.fochms.2025.100273","DOIUrl":"10.1016/j.fochms.2025.100273","url":null,"abstract":"<div><div>Plant-derived bioactive peptides have drawn increasing attention in the field of nutrition and food science due to their biological activities, low cost, safety, and ease of industrial production. Functional peptides from <em>Torreya grandis</em> are being investigated due to their potential as dietary supplements. This study focuses on <em>T. grandis</em> nut peptides that regulate LIPID-II inhibitor in mice fed a high-fat diet. Proteome analysis identified a <em>Vicilin</em>-like antimicrobial peptide involved in host defense. 16S rRNA Sequencing revealed alteration in gut microbiota with <em>T. grandis</em> administration as manifested by increased <em>Akkermansia</em> and <em>Parabacteroides</em> concurrently by decreased <em>Firmicutes</em>. Beneficial bacteria i.e., <em>Akkermansia</em> improved intestinal functions and increased levels of short chain fatty acids (SCFAs). <em>T. grandis</em> supplementation in HFD mice reduced body weight, TC, TG, LDL, and decreased inflammation, while reducing oxidative stress and increasing HDL in the model group fed a high-fat diet. Lipid droplets in liver, muscles, and blood vessels were highly reduced, evoked by the high peptide group. Transcriptome analysis highlighted lipid regulation via the PPAR-α pathway, with molecular docking revealing 4 potential lipid II inhibitory peptides. These findings suggested <em>T. grandis</em> as a promising supplement in food and a key nut for nutraceutical purposes.</div></div>","PeriodicalId":34477,"journal":{"name":"Food Chemistry Molecular Sciences","volume":"11 ","pages":"Article 100273"},"PeriodicalIF":4.1,"publicationDate":"2025-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144633131","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Xun Liu , Hongyi Gu , Han Li , Shuanglian Chen , Zhen Tang , Wenli Quan
{"title":"Improving enzymatic properties of BlTDH from Bacillus licheniformis through site-directed mutagenesis","authors":"Xun Liu , Hongyi Gu , Han Li , Shuanglian Chen , Zhen Tang , Wenli Quan","doi":"10.1016/j.fochms.2025.100272","DOIUrl":"10.1016/j.fochms.2025.100272","url":null,"abstract":"<div><div>L-threonine dehydrogenase (TDH) is a rate-limiting enzyme in the biosynthesis pathway of 2,5-dimethylpyrazine and 2,3,5-trimethylpyrazine, which are widely used food additives. However, natural TDH enzymes suffer from low catalytic activity and poor environmental adaptability, limiting their industrial applications. This study hypothesized that strategic site-directed mutagenesis of conserved amino acid residues within the substrate-binding pocket and catalytic domain could affect both enzymatic activity and environmental stability of TDH. To test this hypothesis, BlTDH from <em>Bacillus licheniformis</em> was selected as the target enzyme, and structure-oriented alanine substitution mutagenesis was systematically applied to five conserved residues (T94, H95, N157, T293, and G294). The results showed that among the five mutants (T94A, H95A, N157A, T293A and G294A), N157A mutant had a specific enzyme activity of 120.47 ± 1.88 mU/mg, which was 2.1 times higher than that of the wild-type. In addition, the N157A mutant showed better temperature stability and pH adaptability. Structural analysis revealed that the side chain volume of N157A mutant decreased, thereby expanding substrate binding space and reducing steric hindrance, which was conducive to the catalytic reaction. These findings validated the original hypothesis, demonstrating that rational amino acid substitutions can significantly affect the catalytic performance of TDH. The superior N157A mutant presented immediate commercial viability for industrial-scale production of food-grade pyrazine additives. Meanwhile, the established structure-activity relationship provides an engineering framework for optimizing the application of relevant NAD<sup>+</sup>-dependent dehydrogenases in biotechnology.</div></div>","PeriodicalId":34477,"journal":{"name":"Food Chemistry Molecular Sciences","volume":"11 ","pages":"Article 100272"},"PeriodicalIF":4.1,"publicationDate":"2025-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144596262","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Integrated transcriptomic and metabolomic analysis reveals drivers of protein and oil variation in cottonseed","authors":"Chaoze Zhou , Yiwen Huang , Dayu Zhou , Yuzhen Wu , Shouyang Fu , Longyu Huang , Jun Peng , Meng Kuang","doi":"10.1016/j.fochms.2025.100270","DOIUrl":"10.1016/j.fochms.2025.100270","url":null,"abstract":"<div><div>The protein and oil content in cottonseed, known for their high quality, exhibits substantial variation across different cotton varieties. This study explored the regulatory mechanisms behind these differences by analyzing protein and oil accumulation patterns, transcriptomics, and metabolomics in two cotton varieties during seed development. Results showed that protein and oil rapidly accumulated between 15 and 30 days post-anthesis (DPA), but significant differences between varieties emerged after 40 DPA. Differentially expressed genes (DEGs) at 40 DPA were enriched in carbon allocation, fatty acid degradation, and nitrogen absorption pathways. Metabolomics identified lipids, lipid-like molecules, and organic acids as key differentially accumulated metabolites (DAMs). Furthermore, the gene <em>GhNIR1</em>, associated with nitrogen source absorption, was identified. Virus-induced gene silencing (VIGS) of this gene in cotton resulted in a significant reduction in protein content in the roots, stems, and leaves. These findings provide insights into protein and oil accumulation and offer genetic resources for improving cottonseed nutritional quality.</div></div>","PeriodicalId":34477,"journal":{"name":"Food Chemistry Molecular Sciences","volume":"11 ","pages":"Article 100270"},"PeriodicalIF":4.1,"publicationDate":"2025-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144502369","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}