Muhammad Usman Zahid , Nouman Rasheed Jatoi , Sumaiya Noor Gul , Sana Malik , Waqas Khan Kayani , Faiza Rasheed
{"title":"Molecular perspectives on Acacia Gum as a functional polysaccharide for biomedical and industrial applications: A review","authors":"Muhammad Usman Zahid , Nouman Rasheed Jatoi , Sumaiya Noor Gul , Sana Malik , Waqas Khan Kayani , Faiza Rasheed","doi":"10.1016/j.ijbiomac.2025.145412","DOIUrl":"10.1016/j.ijbiomac.2025.145412","url":null,"abstract":"<div><div>Acacia gum is a natural heteropolysaccharide derived from <em>Acacia senegal</em> and <em>Acacia seyal</em>. It has gained significant attention due to its unique macromolecular structure and functional biopolymer properties. This review critically evaluates its role in biomedical, pharmaceutical, and industrial applications, with emphasis on the molecular mechanisms that influence its interactions with biological and synthetic systems, especially the arabinogalactan polysaccharide complex of Acacia gum, which facilitates the electrostatic and hydrogen bonding interactions, influencing nanoparticle stability, drug delivery, and hydrogel formation. Similarly, comparative analysis with synthetic polymers such as polyethylene glycol, polyvinyl pyrrolidone, and polyacrylic acid displays its superior colloidal stability, biodegradability, and emulsifying properties, presenting it as a promising alternative for biomedical applications. However, its potential as a nanocarrier in nucleic acid delivery remains unexplored, which requires further research to fully understand the molecular-level interactions. By integrating recent molecular insights with practical considerations, this review establishes a critical foundation for advancing Acacia gum from a largely descriptive biopolymer to a strategically engineered material with significant translational applications in medicine and industry.</div></div>","PeriodicalId":333,"journal":{"name":"International Journal of Biological Macromolecules","volume":"319 ","pages":"Article 145412"},"PeriodicalIF":7.7,"publicationDate":"2025-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144330351","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Xueying Gao , Junwei Yuan , Bin Du , Mengshi Wang , Man Xu , Yunbin Jiang , Lijun Song , Weiwei Liu
{"title":"Thermal processing modulates starch and non-starch macromolecules digestibility in chestnut: Structural reconfiguration and molecular interactions","authors":"Xueying Gao , Junwei Yuan , Bin Du , Mengshi Wang , Man Xu , Yunbin Jiang , Lijun Song , Weiwei Liu","doi":"10.1016/j.ijbiomac.2025.145319","DOIUrl":"10.1016/j.ijbiomac.2025.145319","url":null,"abstract":"<div><div>The thermal process is the predominant method in chestnuts industry. However, it presents nutritional paradox due to high glycemic index (GI) conflicting with low-GI dietary guidelines. This study evaluated four conventional cooking methods systematically, revealing their striking differences in expected glycemic index (eGI). eGI values of moist-heat processed chestnuts (boiled: 81.40; steamed: 86.67) were higher than dry-heat chestnuts (baked: 69.47; fried: 69.85). Through structure analysis, texture profile analysis and <sup>1</sup>H low-field nuclear magnetic resonance (LF-NMR), the mechanisms of eGI differences were elucidated. Structural and texture in baked/fried samples demonstrated superior textural integrity, correlating with restricted starch accessibility. Furthermore, LF-NMR results shown that immobilized water (A21) in fresh chestnut (4.23) decreased after cooked, and A21 in moist-heat processed chestnuts (boiled: 2.25; steamed: 1.11) were higher than dry-heat counterparts (fried: 1.07; baked: 0.89), while free water (A22) increased inversely (boiled: 32.36; steamed: 27.34; fried: 22.02; baked: 20.18) when compared with fresh chestnut (14.15), indicating that the presence of immobilized water could block the binding of enzymes and starch, thereby slowing down the digestion. These results indicated that water phase transitions would be the predominant determination of chestnut GI. These findings provide valuable insights for designing low-GI chestnut products through targeted processing optimization.</div></div>","PeriodicalId":333,"journal":{"name":"International Journal of Biological Macromolecules","volume":"319 ","pages":"Article 145319"},"PeriodicalIF":7.7,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144330276","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Xinyao Su , Jia Liu , Jiarou Liu , Qiang Xue , Caixia Wang
{"title":"Three cytochrome P450 88A subfamily enzymes, CYP88A108, CYP88A164, and CYP88A222, act as β-amyrin 11-oxidases involved in triterpenoid biosynthesis in Melia azedarach L.","authors":"Xinyao Su , Jia Liu , Jiarou Liu , Qiang Xue , Caixia Wang","doi":"10.1016/j.ijbiomac.2025.145362","DOIUrl":"10.1016/j.ijbiomac.2025.145362","url":null,"abstract":"<div><div><em>Melia azedarach</em> L. serves as an important source of timber and bioactive triterpenoids, notably tetracyclic limonoids and pharmacologically active pentacyclic triterpenes such as β-amyrin derivatives. Although limonoid biosynthesis has been extensively characterized, the enzymatic machinery governing pentacyclic triterpene formation remains poorly defined. Through transcriptomic mining of <em>M. azedarach</em>, we identified three CYP88A subfamily cytochrome P450 genes (<em>MaCYP88A108</em>, <em>MaCYP88A164</em>, and <em>MaCYP88A222</em>). Functional characterization in both <em>Nicotiana benthamiana</em> transient expression systems and yeast microsomes demonstrated their catalytic roles as β-amyrin 11-oxidases, sequentially converting β-amyrin to 11-oxo-β-amyrin via C-11 oxidation. Intriguingly, <em>MaCYP88A108</em> and <em>MaCYP88A164</em> exhibited dual functionality, participating not only in pentacyclic triterpene production but also in limonoid biosynthesis, suggesting their evolutionary recruitment for triterpenoid diversification. Phylogenetic reconstruction and structural modeling revealed that these CYP88A enzymes share close homology and conserved active-site architectures with <em>Glycyrrhiza uralensis</em> CYP88D6 (GuCYP88D6), a characterized β-amyrin 11-oxidase, despite lacking genomic synteny. This observation supports a paradigm of functional convergence driven by structural conservation rather than shared gene lineage. Furthermore, we characterized an oxidosqualene cyclase (<em>MaβAS1</em>) responsible for cyclizing 2,3-oxidosqualene to β-amyrin, thereby establishing the substrate pool for downstream oxidation. Our study uncovers a unique catalytic versatility in plant CYP88A P450s, demonstrating their capacity to coordinate two divergent triterpenoid branches. This functional plasticity, mediated by evolutionarily conserved structural frameworks, expands current paradigms of enzyme multifunctionality in plant specialized metabolism. The identified genes (<em>CYP88As</em> and <em>MaβAS1</em>) establish critical tools for synthetic biology platforms targeting heterologous production of pharmaceutically important triterpenoids, bridging mechanistic exploration of plant secondary metabolism with biotechnological applications.</div></div>","PeriodicalId":333,"journal":{"name":"International Journal of Biological Macromolecules","volume":"318 ","pages":"Article 145362"},"PeriodicalIF":7.7,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144322683","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Dong Li , Xumin Wang , Tiantian Liu , Yaping Song , Yujiao Song , Shuhan Yu , Xin Liu , Han Wang , Yingjie Wang , Jianchao Cui , Limin Wang , Da Zhang , Hongxia Zhang
{"title":"AtDIVARICATA1 promotes flowering through regulating flowering integrators and GA biosynthesis in Arabidopsis","authors":"Dong Li , Xumin Wang , Tiantian Liu , Yaping Song , Yujiao Song , Shuhan Yu , Xin Liu , Han Wang , Yingjie Wang , Jianchao Cui , Limin Wang , Da Zhang , Hongxia Zhang","doi":"10.1016/j.ijbiomac.2025.145316","DOIUrl":"10.1016/j.ijbiomac.2025.145316","url":null,"abstract":"<div><div>Arabidopsis R-R-type MYB-like transcription factors AtDIV1 and AtDIV2 (DIVARICATAs) act as critical participants in response to salinity stress. However, their functions in flowering transition are unknown. Here, we reported the function of AtDIV1 in flowering regulation. Protein sequence and 3D structure comparison showed that AtDIV1 was highly conserved, and contained two MYB-like DNA binding domains and one typical 'SHAQKYF/Y' motif. Expression pattern analyses exhibited that <em>AtDIV1</em> was highly expressed at the bolting stage in Arabidopsis. Overexpression of <em>AtDIV1</em> in Arabidopsis promoted the flowering of transgenic plants, whereas mutation of <em>AtDIV1</em> postponed the flowering of <em>div1-1</em> and <em>div1-2</em> mutants. Transcriptome analyses revealed that a number of plant hormone and flowering associated genes were up- or down-regulated in transgenic plants. ChIP and EMSA analyses demonstrated that AtDIV1 directly bound to the promoter regions of <em>TEM1</em>, <em>SOC1</em> and <em>GA3ox1</em>. Further growth experiments in <em>AtDIV1</em> transgenic plants and <em>div1-1</em> mutant demonstrated that the content of GA in them was respectively increased and decreased, and the promoted and postponed flowering of them could be respectively rescued with the exogenous application of GA<sub>3</sub> and GA biosynthesis inhibitor paclobutrazol. Our results provide insights into the regulatory mechanism of AtDIV1 mediated flowering via GA signalling pathway in Arabidopsis.</div></div>","PeriodicalId":333,"journal":{"name":"International Journal of Biological Macromolecules","volume":"318 ","pages":"Article 145316"},"PeriodicalIF":7.7,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144313954","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Ping Han , Fang Ma , Zhouping Wang , Xiang Zhou , Kai Zheng , Shiling Lu , Jingtao Sun , Juan Dong
{"title":"Characteristics of ultrasound-induced sesamol–soybean peptide composite particles (SSPPs) and SSPP-stabilized Pickering emulsions","authors":"Ping Han , Fang Ma , Zhouping Wang , Xiang Zhou , Kai Zheng , Shiling Lu , Jingtao Sun , Juan Dong","doi":"10.1016/j.ijbiomac.2025.145367","DOIUrl":"10.1016/j.ijbiomac.2025.145367","url":null,"abstract":"<div><div>To improve the properties of soybean peptide-based emulsifiers, non-covalent interactions between sesamol and soybean peptides were induced through ultrasound treatment. Accordingly, sesamol–soybean peptide composite particles (SSPPs) with excellent interfacial properties and antioxidant capacity were prepared to achieve the long-term stabilization of emulsion. In SSPPs, the secondary structure of the peptides was altered (increased β-sheet content) and the surface hydrophobicity was reduced owing to hydrophobic interactions and hydrogen bonding between sesamol and soybean peptides. Moreover, the SSPPs could effectively encapsulate sesamol. With the increase in sesamol concentration, the particle size of SSPPs gradually reduced, while their solubility and antioxidant activity increased. LC-MS/MS revealed that the addition of sesamol led to the generation of small peptides (length: 3–7 amino acids) in SSPPs. The proportion of hydrophobic amino acids at the N- and C-terminals of these peptides was >60 %, and the C-terminus was enriched with basic amino acids, which conferred strong antioxidant capacity to the SSPPs. The SSPPs could be effectively adsorbed and rearranged at the oil–water interface, forming an obvious interfacial barrier. Ultimately, Pickering emulsions stabilized by SSPP-1.5 showed the strongest resistance to droplet aggregation as well as lipid and protein oxidation during 30 days of storage.</div></div>","PeriodicalId":333,"journal":{"name":"International Journal of Biological Macromolecules","volume":"318 ","pages":"Article 145367"},"PeriodicalIF":7.7,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144321486","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Xiaomin Li , Tao Chen , Yujie Cai , Jingtao Zhang , Yuxin Wang , Jianjun Wang , Xueyuan Mao , Liancheng Xu , Dongdong Li , Yu Wang , Xiaoyan Wang
{"title":"CircSETD3 interrupts the bidirectional positive feedback of ErbB3 and Akt by sponging miR-4667-5p to inhibit colorectal cancer progression and cetuximab resistance","authors":"Xiaomin Li , Tao Chen , Yujie Cai , Jingtao Zhang , Yuxin Wang , Jianjun Wang , Xueyuan Mao , Liancheng Xu , Dongdong Li , Yu Wang , Xiaoyan Wang","doi":"10.1016/j.ijbiomac.2025.145352","DOIUrl":"10.1016/j.ijbiomac.2025.145352","url":null,"abstract":"<div><div>Circular RNAs play crucial roles in tumor progression and drug resistance. We previously reported that circSETD3 is downregulated in colorectal cancer (CRC) and correlates with tumor size and metastasis; however, the precise biological functions and underlying the mechanisms of action of circSETD3 in CRC remain unclear. Therefore, in the present study, we aimed to investigate the role of circSETD3 in CRC growth, metastasis, and cetuximab resistance using in vitro and in vivo functional assays. Our results demonstrated that circSETD3 acts as a tumor suppressor in CRC progression and cetuximab resistance. Mechanistically, RNA-seq, FISH, dual-luciferase reporter assays, and ChIP assays revealed that reduced circSETD3 expression in CRC activated ErbB3 and its downstream Akt pathway. Notably, we found that the Akt pathway upregulated ErbB3 transcription via HIF1A, indicating the presence of a novel positive feedback loop between ErbB3 and Akt pathway which reinforces CRC progression and drives cetuximab resistance. Furthermore, circSETD3 deficiency in CRC triggered a feedback loop through the miR-4667-5p–RASA4 axis which was effectively suppressed by exosomal circSETD3 supplementation. Thus, our findings highlight circSETD3 to be a promising therapeutic target for inhibiting CRC progression and overcoming cetuximab resistance.</div></div>","PeriodicalId":333,"journal":{"name":"International Journal of Biological Macromolecules","volume":"318 ","pages":"Article 145352"},"PeriodicalIF":7.7,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144314157","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Discovery, expression, and characterization of highly tolerant superoxide dismutases from extremophiles for potential industrial applications","authors":"Naying Zhang, Zefeng Ren, Dongsheng Wei, Meng Yang, Meng Niu, Chunxiao Shen, Xuanyan Jin, Maolin Wei, Jaehwan Choi, Myeongsam Park, Zhengqun Li","doi":"10.1016/j.ijbiomac.2025.145272","DOIUrl":"10.1016/j.ijbiomac.2025.145272","url":null,"abstract":"<div><div>Superoxide dismutases (SODs) are essential enzymes that protect cells by converting harmful superoxide radicals into oxygen and hydrogen peroxide. However, their application in industrial and medical settings is often limited by poor stability under extreme conditions such as high temperatures, extreme pH, and oxidative stress. In this study, we identified and characterized two highly stable manganese-dependent SODs from extremophiles. These enzymes remained highly active at temperatures up to 80 °C, across a broad pH range (3.0–12), and in the presence of oxidative agents and denaturing chemicals. Structural analysis revealed that their exceptional stability is attributed to tightly folded structures, strong hydrophobic cores, and robust metal-binding sites. Both <em>Os</em>SOD and <em>Gt</em>SOD demonstrated robust catalytic performance, with <em>k</em><sub><em>ca</em>t</sub><em>k</em><sub><em>m</em></sub> values of 2.29 × 10<sup>7</sup> and 1.06 × 10<sup>7</sup> M<sup>−1</sup>·s<sup>−1</sup>, respectively. In cell-based models, they effectively reduced oxidative stress and inflammation, indicating potential for antioxidant therapy. Additionally, their long-term stability supports their use in cosmetic and pharmaceutical formulations. Overall, these extremophile-derived SODs are highly stable and efficient enzymes with broad potential for industrial, medical, and cosmetic applications.</div></div>","PeriodicalId":333,"journal":{"name":"International Journal of Biological Macromolecules","volume":"319 ","pages":"Article 145272"},"PeriodicalIF":7.7,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144321201","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Thioctic acid driven chemical cross-linking of cellulose chains for fabricating high-performance cellulose films as food packaging","authors":"Youjie Gao , Guozhuo Chen , Chao Wu , Junjie Zhou , Guojun Jin , Hou-Yong Yu","doi":"10.1016/j.ijbiomac.2025.145076","DOIUrl":"10.1016/j.ijbiomac.2025.145076","url":null,"abstract":"<div><div>The widespread use of plastic packaging has improved convenience in daily life but has also led to serious environmental pollution. Therefore, an eco-friendly biodegradable material is needed to replace plastic packaging. In this study, the cellulose packaging materials were first time prepared by Thioctic acid (TA) driven chemical cross-linking with cellulose chains. Cellulose films with optimized concentrations of TA exhibited higher mechanical strength (126 MPa), hydrophobicity (99.7°), and barrier properties. The cross-linking of TA resulted in an orderly arrangement of cellulose molecules. Meanwhile, the cellulose film could effectively slow down evaporation of water from fruit (tomatoes) and extended food's shelf life for packaging applications, which is equivalent to commercial preservative film (polyethylene). This study presents a novel and scalable strategy for fabricating cellulose-based packaging materials with improved functional properties, offering a promising alternative to conventional plastic packaging.</div></div>","PeriodicalId":333,"journal":{"name":"International Journal of Biological Macromolecules","volume":"318 ","pages":"Article 145076"},"PeriodicalIF":7.7,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144321487","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Meng Zhang , Jing Wu , Yulan Wang , Yan Cao , Jingjing Liu , Quan Wang , Xiaofeng Song , Jian Zhao , Yixuan Wang
{"title":"Deep-m7G: A contrastive learning-based deep biological language model for identifying RNA N7-methylguanosine sites","authors":"Meng Zhang , Jing Wu , Yulan Wang , Yan Cao , Jingjing Liu , Quan Wang , Xiaofeng Song , Jian Zhao , Yixuan Wang","doi":"10.1016/j.ijbiomac.2025.145341","DOIUrl":"10.1016/j.ijbiomac.2025.145341","url":null,"abstract":"<div><div>N7-methylguanosine (m7G) is one of the most prevalent post-transcriptional modifications in RNA molecules, playing a pivotal role in regulating RNA metabolism and function. Given the complexity of canonical m7G cap-dependent protein synthesis, accurately predicting m7G modification sites facilitates further exploration of translation initiation mechanisms. Hence, we collected the most comprehensive single-nucleotide resolution m7G modification sites from the updated m7GHub v2.0 database. We subsequently developed Deep-m7G, a novel contrastive learning-enhanced deep biological language model, designed for both the full transcript and mature RNA datasets. Our methodological framework incorporates three key innovations: (1) implementation of a Most Distant undersampling strategy to mitigate class imbalance in training data; (2) integration of DNABERT-2 with a parallel convolutional neural network architecture for hierarchical feature extraction; and (3) introduction of a contrastive learning module to enhance feature discriminability and model generalizability. Systematic evaluation through 10-fold cross-validation demonstrated the critical contribution of our contrastive learning component. In rigorous benchmarking against existing tools, Deep-m7G achieved superior predictive performance (Full transcript: AUC = 0.960 vs 0.653–0.898 and Mature RNA: AUC = 0.845 vs 0.684–0.832) on independent test sets. Collectively, this computational advance provides a robust framework for the discovery of epitranscriptomics markers, thereby advancing mechanistic investigations of post-transcriptional regulation.</div></div>","PeriodicalId":333,"journal":{"name":"International Journal of Biological Macromolecules","volume":"318 ","pages":"Article 145341"},"PeriodicalIF":7.7,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144321492","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}