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Huang YY, Price MN, Hung A, Gal-Oz O, Tripathi S, Smith CW, Ho D, Carion H, Deutschbauer AM, Arkin AP. Barcoded overexpression screens in gut Bacteroidales identify genes with roles in carbon utilization and stress resistance. Nat Commun 2024; 15:6618. [PMID: 39103350 DOI: 10.1038/s41467-024-50124-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Accepted: 06/28/2024] [Indexed: 08/07/2024] Open
Abstract
A mechanistic understanding of host-microbe interactions in the gut microbiome is hindered by poorly annotated bacterial genomes. While functional genomics can generate large gene-to-phenotype datasets to accelerate functional discovery, their applications to study gut anaerobes have been limited. For instance, most gain-of-function screens of gut-derived genes have been performed in Escherichia coli and assayed in a small number of conditions. To address these challenges, we develop Barcoded Overexpression BActerial shotgun library sequencing (Boba-seq). We demonstrate the power of this approach by assaying genes from diverse gut Bacteroidales overexpressed in Bacteroides thetaiotaomicron. From hundreds of experiments, we identify new functions and phenotypes for 29 genes important for carbohydrate metabolism or tolerance to antibiotics or bile salts. Highlights include the discovery of a D-glucosamine kinase, a raffinose transporter, and several routes that increase tolerance to ceftriaxone and bile salts through lipid biosynthesis. This approach can be readily applied to develop screens in other strains and additional phenotypic assays.
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Affiliation(s)
- Yolanda Y Huang
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Department of Microbiology and Immunology, University at Buffalo, State University of New York, Buffalo, NY, USA.
| | - Morgan N Price
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Allison Hung
- Department of Molecular and Cell Biology, University of California-Berkeley, Berkeley, CA, USA
| | - Omree Gal-Oz
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Surya Tripathi
- Department of Plant and Microbial Biology, University of California-Berkeley, Berkeley, CA, USA
| | - Christopher W Smith
- Department of Microbiology and Immunology, University at Buffalo, State University of New York, Buffalo, NY, USA
| | - Davian Ho
- Department of Bioengineering, University of California-Berkeley, Berkeley, CA, USA
| | - Héloïse Carion
- Department of Bioengineering, University of California-Berkeley, Berkeley, CA, USA
| | - Adam M Deutschbauer
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Plant and Microbial Biology, University of California-Berkeley, Berkeley, CA, USA
| | - Adam P Arkin
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Department of Bioengineering, University of California-Berkeley, Berkeley, CA, USA.
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Lin WL, Huang H, Liu YQ, Liu HX, Wei Y, Zhao YQ, Wang YQ, Wu YY, Chen SJ, Li LH. Integrated 4D label-free proteomics and data mining to elucidate the effects of thermal processing on crisp grass carp protein profiles. Curr Res Food Sci 2024; 8:100681. [PMID: 38304000 PMCID: PMC10832373 DOI: 10.1016/j.crfs.2024.100681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 01/08/2024] [Accepted: 01/15/2024] [Indexed: 02/03/2024] Open
Abstract
The crisp grass carp (CGC; Ctenopharyngodon idellus C. et V.), known for its unique texture and flavour, is a culinary delicacy whose quality is significantly influenced by thermal processing. This study employed 4D label-free proteomics and data mining techniques to investigate the proteomic changes in CGC muscle tissue induced by various heating temperatures. CGC samples were subjected to a series of heat treatments at increasing temperatures from 20 °C to 90 °C. Proteins were extracted, digested, and analysed using high-resolution mass spectrometry. The proteomic data were then subjected to extensive bioinformatics analysis, including GO and KEGG pathway enrichment. We identified a total of 1085 proteins, 516 of which were shared across all the temperature treatments, indicating a core proteome responsible for CGC textural properties. Differential expression analysis revealed temperature-dependent changes, with significant alterations observed at 90 °C, suggesting denaturation or aggregation of proteins at higher temperatures. Functional enrichment analysis indicated that proteins involved in amino acid metabolism, glutathione metabolism, and nucleotide metabolism were particularly affected by heat. Textural analysis correlated these proteomic changes with alterations in CGC quality attributes, pinpointing 70 °C as the optimum temperature for maintaining the desired texture. A strong positive correlation between specific upregulated proteins was identified, such as the tubulin alpha chain and collagen alpha-1(IV) chain, and the improved textural properties of CGC during thermal processing, suggesting their potential as the potential biomarkers. This study offers a comprehensive proteomic view of the thermal stability and functionality of CGC proteins, delivering invaluable insights for both the culinary processing and scientific management of CGC. Our findings not only deepen the understanding of the molecular mechanisms underpinning the textural alterations in CGC during thermal processing but also furnish practical insights for the aquaculture industry. These insights could be leveraged to optimize cooking techniques, thereby enhancing the quality and consumer appeal of CGC products.
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Affiliation(s)
- Wan-ling Lin
- School of Life Sciences and Food Technology, Hanshan Normal University, Chaozhou, 521041, China
- Ministry of Agriculture Key Laboratory of Aquatic Products Processing, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, China
- Guangdong Provincial Key Laboratory of Functional Substances in Medicinal Edible Resources and Healthcare Products, Chaozhou, 521041, China
| | - Hui Huang
- Ministry of Agriculture Key Laboratory of Aquatic Products Processing, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, China
| | - Ya-qun Liu
- School of Life Sciences and Food Technology, Hanshan Normal University, Chaozhou, 521041, China
- Ministry of Agriculture Key Laboratory of Aquatic Products Processing, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, China
| | - Han-xu Liu
- School of Life Sciences and Food Technology, Hanshan Normal University, Chaozhou, 521041, China
| | - Ya Wei
- Ministry of Agriculture Key Laboratory of Aquatic Products Processing, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, China
| | - Yong-qiang Zhao
- Ministry of Agriculture Key Laboratory of Aquatic Products Processing, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, China
| | - Yue-qi Wang
- Ministry of Agriculture Key Laboratory of Aquatic Products Processing, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, China
| | - Yan-yan Wu
- Ministry of Agriculture Key Laboratory of Aquatic Products Processing, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, China
| | - Sheng-jun Chen
- Ministry of Agriculture Key Laboratory of Aquatic Products Processing, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, China
| | - Lai-hao Li
- Ministry of Agriculture Key Laboratory of Aquatic Products Processing, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, China
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