Development of a computational whole model of Lacticaseibacillus casei ATCC 393

IF 0.9 Q4 GENETICS & HEREDITY

Gene Reports Pub Date : 2025-09-10 DOI:10.1016/j.genrep.2025.102335

Kanganwiro Mugwanda , Mutsa Takundwa , Leon M.T. Dicks , Deepak B. Thimiri Govinda Raj

引用次数: 0

Abstract

Genome-scale metabolic models (GEMs) are important tools for predicting the metabolic behaviour of microorganisms, including probiotics, under diverse environmental conditions and assessing the impact of genome modifications. In this study, a draft genome-scale metabolic model for Lacticaseibacillus casei ATCC 393 was constructed using the ModelSEED pipeline. The draft model was validated through simulations in OptFlux 3. The resulting ilcaseidsm20011 model includes 555 genes, 73 metabolic pathways, 950 reactions, and 1095 compounds. This model provides a foundational framework for understanding L. casei ATCC 393 metabolism, serving as a valuable resource for further studies on probiotic functionality and rational metabolic engineering.

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干酪乳杆菌ATCC 393计算整体模型的建立

基因组尺度代谢模型（GEMs）是预测微生物（包括益生菌）在不同环境条件下代谢行为和评估基因组修饰影响的重要工具。本研究利用ModelSEED管道构建了干酪乳杆菌ATCC 393的基因组尺度代谢模型草图。通过OptFlux 3的仿真验证了草稿模型的有效性。由此产生的ilcaseidsm20011模型包括555个基因，73个代谢途径，950个反应和1095个化合物。该模型为理解干酪乳杆菌ATCC 393代谢提供了基础框架，为进一步研究益生菌功能和合理代谢工程提供了宝贵的资源。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Gene Reports Biochemistry, Genetics and Molecular Biology-Genetics

CiteScore

3.30

自引率

7.70%

发文量

246

审稿时长

49 days

期刊介绍： Gene Reports publishes papers that focus on the regulation, expression, function and evolution of genes in all biological contexts, including all prokaryotic and eukaryotic organisms, as well as viruses. Gene Reports strives to be a very diverse journal and topics in all fields will be considered for publication. Although not limited to the following, some general topics include: DNA Organization, Replication & Evolution -Focus on genomic DNA (chromosomal organization, comparative genomics, DNA replication, DNA repair, mobile DNA, mitochondrial DNA, chloroplast DNA). Expression & Function - Focus on functional RNAs (microRNAs, tRNAs, rRNAs, mRNA splicing, alternative polyadenylation) Regulation - Focus on processes that mediate gene-read out (epigenetics, chromatin, histone code, transcription, translation, protein degradation). Cell Signaling - Focus on mechanisms that control information flow into the nucleus to control gene expression (kinase and phosphatase pathways controlled by extra-cellular ligands, Wnt, Notch, TGFbeta/BMPs, FGFs, IGFs etc.) Profiling of gene expression and genetic variation - Focus on high throughput approaches (e.g., DeepSeq, ChIP-Seq, Affymetrix microarrays, proteomics) that define gene regulatory circuitry, molecular pathways and protein/protein networks. Genetics - Focus on development in model organisms (e.g., mouse, frog, fruit fly, worm), human genetic variation, population genetics, as well as agricultural and veterinary genetics. Molecular Pathology & Regenerative Medicine - Focus on the deregulation of molecular processes in human diseases and mechanisms supporting regeneration of tissues through pluripotent or multipotent stem cells.