1
|
Li F, Thananusak R, Raethong N, Yang J, Wei M, Zhao X, Laoteng K, Song Y, Vongsangnak W. Dissecting Holistic Metabolic Acclimatization of Mucor circinelloides WJ11 Defective in Carotenoid Biosynthesis. Biology (Basel) 2024; 13:276. [PMID: 38666888 PMCID: PMC11048425 DOI: 10.3390/biology13040276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 04/15/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024]
Abstract
Mucor circinelloides WJ11 is a lipid-producing strain with industrial potential. A holistic approach using gene manipulation and bioprocessing development has improved lipid production and the strain's economic viability. However, the systematic regulation of lipid accumulation and carotenoid biosynthesis in M. circinelloides remains unknown. To dissect the metabolic mechanism underlying lipid and carotenoid biosynthesis, transcriptome analysis and reporter metabolites identification were implemented between the wild-type (WJ11) and ΔcarRP WJ11 strains of M. circinelloides. As a result, transcriptome analysis revealed 10,287 expressed genes, with 657 differentially expressed genes (DEGs) primarily involved in amino acid, carbohydrate, and energy metabolism. Integration with a genome-scale metabolic model (GSMM) identified reporter metabolites in the ΔcarRP WJ11 strain, highlighting metabolic pathways crucial for amino acid, energy, and nitrogen metabolism. Notably, the downregulation of genes associated with carotenoid biosynthesis and acetyl-CoA generation suggests a coordinated relationship between the carotenoid and fatty acid biosynthesis pathways. Despite disruptions in the carotenoid pathway, lipid production remains stagnant due to reduced acetyl-CoA availability, emphasizing the intricate metabolic interplay. These findings provide insights into the coordinated relationship between carotenoid and fatty acid biosynthesis in M. circinelloides that are valuable in applied research to design optimized strains for producing desired bioproducts through emerging technology.
Collapse
Affiliation(s)
- Fanyue Li
- Interdisciplinary Graduate Programs in Bioscience, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand;
- Colin Rateledge Center for Microbial Lipids, School of Agricultural Engineering and Food Science, Shandong University of Technology, 266 Xincun West Road, Zibo 255000, China
| | - Roypim Thananusak
- Omics Center for Agriculture, Bioresources, Food, and Health Kasetsart University (OmiKU), Bangkok 10900, Thailand;
| | - Nachon Raethong
- Institute of Nutrition, Mahidol University, Nakhon Pathom 73170, Thailand;
| | - Junhuan Yang
- Department of Food Sciences, College of Food Science and Engineering, Lingnan Normal University, Zhanjiang 524048, China;
| | - Mingyue Wei
- College of Ecology, Resources and Environment, Dezhou University, Dezhou 253000, China;
| | - Xingtang Zhao
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China;
| | - Kobkul Laoteng
- Industrial Bioprocess Technology Research Team, Functional Ingredient and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand;
| | - Yuanda Song
- Colin Rateledge Center for Microbial Lipids, School of Agricultural Engineering and Food Science, Shandong University of Technology, 266 Xincun West Road, Zibo 255000, China
| | - Wanwipa Vongsangnak
- Omics Center for Agriculture, Bioresources, Food, and Health Kasetsart University (OmiKU), Bangkok 10900, Thailand;
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| |
Collapse
|
2
|
Mok K, Poolsawat T, Somnuk S, Wanikorn B, Patumcharoenpol P, Nitisinprasert S, Vongsangnak W, Nakphaichit M. Preliminary characterization of gut mycobiome enterotypes reveals the correlation trends between host metabolic parameter and diet: a case study in the Thai Cohort. Sci Rep 2024; 14:5805. [PMID: 38461361 PMCID: PMC10924899 DOI: 10.1038/s41598-024-56585-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 03/08/2024] [Indexed: 03/11/2024] Open
Abstract
The association between the gut mycobiome and its potential influence on host metabolism in the Thai Cohort was assessed. Two distinct predominant enterotypes, Saccharomyces (Sa) and Aspergillus/Penicillium (Ap/Pe) showed differences in gut mycobiota diversity and composition. Notably, the Sa enterotype exhibited lower evenness and richness, likely due to the prevalence of Saccharomyces, while both enterotypes displayed unique metabolic behaviors related to nutrient metabolism and body composition. Fiber consumption was positively correlated with adverse body composition and fasting glucose levels in individuals with the Sa enterotype, whereas in the Ap/Pe enterotype it was positively correlated with fat and protein intake. The metabolic functional analysis revealed the Sa enterotype associated with carbohydrate metabolism, while the Ap/Pe enterotype involved in lipid metabolism. Very interestingly, the genes involved in the pentose and glucuronate interconversion pathway, such as polygalacturonase and L-arabinose-isomerase, were enriched in the Sa enterotype signifying a metabolic capacity for complex carbohydrate degradation and utilization of less common sugars as energy sources. These findings highlight the interplay between gut mycobiome composition, dietary habits, and metabolic outcomes within the Thai cohort studies.
Collapse
Affiliation(s)
- Kevin Mok
- Department of Biotechnology, Faculty of Agro-Industry, Kasetsart University, Bangkok, 10900, Thailand
- Specialized Research Unit: Probiotics and Prebiotics for Health, Faculty of Agro-Industry, Kasetsart University, Bangkok, 10900, Thailand
| | - Thitirat Poolsawat
- Department of Biotechnology, Faculty of Agro-Industry, Kasetsart University, Bangkok, 10900, Thailand
- Specialized Research Unit: Functional Food and Human Health Laboratory, Faculty of Agro-Industry, Kasetsart University, Bangkok, 10900, Thailand
| | - Surasawadee Somnuk
- Department of Sports and Health Sciences, Faculty of Sport Science, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom, 73140, Thailand
| | - Bandhita Wanikorn
- Department of Biotechnology, Faculty of Agro-Industry, Kasetsart University, Bangkok, 10900, Thailand
- Specialized Research Unit: Functional Food and Human Health Laboratory, Faculty of Agro-Industry, Kasetsart University, Bangkok, 10900, Thailand
| | - Preecha Patumcharoenpol
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
- Omics Center for Agriculture, Bioresources, Food, and Health, Kasetsart University (OmiKU), Bangkok, 10900, Thailand
| | - Sunee Nitisinprasert
- Department of Biotechnology, Faculty of Agro-Industry, Kasetsart University, Bangkok, 10900, Thailand
- Specialized Research Unit: Probiotics and Prebiotics for Health, Faculty of Agro-Industry, Kasetsart University, Bangkok, 10900, Thailand
| | - Wanwipa Vongsangnak
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
- Omics Center for Agriculture, Bioresources, Food, and Health, Kasetsart University (OmiKU), Bangkok, 10900, Thailand
| | - Massalin Nakphaichit
- Department of Biotechnology, Faculty of Agro-Industry, Kasetsart University, Bangkok, 10900, Thailand.
- Specialized Research Unit: Probiotics and Prebiotics for Health, Faculty of Agro-Industry, Kasetsart University, Bangkok, 10900, Thailand.
| |
Collapse
|
3
|
Soommat P, Raethong N, Ruengsang R, Thananusak R, Laomettachit T, Laoteng K, Saithong T, Vongsangnak W. Light-Exposed Metabolic Responses of Cordyceps militaris through Transcriptome-Integrated Genome-Scale Modeling. Biology (Basel) 2024; 13:139. [PMID: 38534409 DOI: 10.3390/biology13030139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 02/18/2024] [Accepted: 02/19/2024] [Indexed: 03/28/2024]
Abstract
The genome-scale metabolic model (GSMM) of Cordyceps militaris provides a comprehensive basis of carbon assimilation for cell growth and metabolite production. However, the model with a simple mass balance concept shows limited capability to probe the metabolic responses of C. militaris under light exposure. This study, therefore, employed the transcriptome-integrated GSMM approach to extend the investigation of C. militaris's metabolism under light conditions. Through the gene inactivity moderated by metabolism and expression (GIMME) framework, the iPS1474-tiGSMM model was furnished with the transcriptome data, thus providing a simulation that described reasonably well the metabolic responses underlying the phenotypic observation of C. militaris under the particular light conditions. The iPS1474-tiGSMM obviously showed an improved prediction of metabolic fluxes in correlation with the expressed genes involved in the cordycepin and carotenoid biosynthetic pathways under the sucrose culturing conditions. Further analysis of reporter metabolites suggested that the central carbon, purine, and fatty acid metabolisms towards carotenoid biosynthesis were the predominant metabolic processes responsible in light conditions. This finding highlights the key responsive processes enabling the acclimatization of C. militaris metabolism in varying light conditions. This study provides a valuable perspective on manipulating metabolic genes and fluxes towards the target metabolite production of C. militaris.
Collapse
Affiliation(s)
- Panyawarin Soommat
- Genetic Engineering and Bioinformatics Program, Graduate School, Kasetsart University, Bangkok 10900, Thailand
| | - Nachon Raethong
- Institute of Nutrition, Mahidol University, Nakhon Pathom 73170, Thailand
| | - Ratchaprapa Ruengsang
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology and School of Information Technology, King Mongkut's University of Technology Thonburi (Bang Khun Thian), Bangkok 10150, Thailand
| | - Roypim Thananusak
- Omics Center for Agriculture, Bioresources, Food, and Health, Kasetsart University (OmiKU), Bangkok 10900, Thailand
| | - Teeraphan Laomettachit
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology and School of Information Technology, King Mongkut's University of Technology Thonburi (Bang Khun Thian), Bangkok 10150, Thailand
| | - Kobkul Laoteng
- Industrial Bioprocess Technology Research Team, Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand
| | - Treenut Saithong
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology and School of Information Technology, King Mongkut's University of Technology Thonburi (Bang Khun Thian), Bangkok 10150, Thailand
- Center for Agricultural Systems Biology (CASB), Systems Biology and Bioinformatics Research Group, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi (Bang Khun Thian), Bangkok 10150, Thailand
| | - Wanwipa Vongsangnak
- Omics Center for Agriculture, Bioresources, Food, and Health, Kasetsart University (OmiKU), Bangkok 10900, Thailand
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| |
Collapse
|
4
|
Sukmak R, Suttinun C, Kovitvadhi U, Kovitvadhi A, Vongsangnak W. Uncovering nutrients and energy related gene functions of black soldier fly Hermetia illucens strain KUP. Gene 2024; 896:148045. [PMID: 38042219 DOI: 10.1016/j.gene.2023.148045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 11/18/2023] [Accepted: 11/28/2023] [Indexed: 12/04/2023]
Abstract
The black soldier fly (Hermetia illucens) has emerged as a significant insect species in the decomposition of organic waste for sustainable agricultural practices. Due to its remarkable characteristics and performance, H. illucens is increasingly utilised for insect farming, particularly for industrial-scale rearing throughout the world. In this study, we employed whole-genome sequencing to annotate the gene and protein functions of H. illucens and to explore the functional genomics related to nutrients and energy. As a result, a genome size of H. illucens strain KUP 1.68 Gb with a GC content of 42.13 % was achieved. Of the 14,036 coding sequences, we determined the function of 12,046 protein-coding genes. Based on metabolic functional assignment, we classified 4,218 protein-coding genes; the main category was metabolism (32.86 %). Comparative genomic analysis across the other H. illucens strain and insect species revealed that the major metabolic gene functions and pathways related to nutrient and energy sources of H. illucens KUP are involved in key amino acid metabolism (e.g., cysteine and methionine) as well as fatty acid biosynthesis and glycerolipid metabolism. These findings underscore the metabolic capability and versatility of H. illucens, which is regarded as a potential source of proteins and lipids. Our study contributes to the knowledge regarding the feed utilisation of H. illucens and offers insights into transforming waste into valuable products. H. illucens has the potential to create globally sustainable nutrients and environmentally friendly solutions, aligning with the goal of responsible resource utilisation.
Collapse
Affiliation(s)
- Rachrapee Sukmak
- Graduate Student in Animal Health and Biomedical Science Program, Faculty of Veterinary Medicine, Kasetsart University, Bangkok, Thailand
| | - Chanaporn Suttinun
- Department of Veterinary Biosciences and Veterinary Public Health, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Uthaiwan Kovitvadhi
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Attawit Kovitvadhi
- Department of Physiology, Faculty of Veterinary Medicine, Kasetsart University, Bangkok, Thailand.
| | - Wanwipa Vongsangnak
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok, Thailand; Omics Center for Agriculture, Bioresources, Food, and Health, Kasetsart University (OmiKU), Bangkok, Thailand.
| |
Collapse
|
5
|
Zhang Y, Xu M, Guo Y, Chen L, Vongsangnak W, Xu Q, Lu L. Programmed cell death and Salmonella pathogenesis: an interactive overview. Front Microbiol 2024; 14:1333500. [PMID: 38249488 PMCID: PMC10797706 DOI: 10.3389/fmicb.2023.1333500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 12/12/2023] [Indexed: 01/23/2024] Open
Abstract
Programmed cell death (PCD) is the collective term for the intrinsically regulated death of cells. Various types of cell death are triggered by their own programmed regulation during the growth and development of organisms, as well as in response to environmental and disease stresses. PCD encompasses apoptosis, pyroptosis, necroptosis, autophagy, and other forms. PCD plays a crucial role not only in the growth and development of organisms but also in serving as a component of the host innate immune defense and as a bacterial virulence strategy employed by pathogens during invasion. The zoonotic pathogen Salmonella has the ability to modulate multiple forms of PCD, including apoptosis, pyroptosis, necroptosis, and autophagy, within the host organism. This modulation subsequently impacts the bacterial infection process. This review aims to consolidate recent findings regarding the mechanisms by which Salmonella initiates and controls cell death signaling, the ways in which various forms of cell death can impede or restrict bacterial proliferation, and the interplay between cell death and innate immune pathways that can counteract Salmonella-induced suppression of host cell death. Ultimately, these insights may contribute novel perspectives for the diagnosis and treatment of clinical Salmonella-related diseases.
Collapse
Affiliation(s)
- Yu Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China
| | - Maodou Xu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China
| | - Yujiao Guo
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China
| | - Li Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Wanwipa Vongsangnak
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Qi Xu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China
| | - Lizhi Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| |
Collapse
|
6
|
Jeennor S, Anantayanon J, Panchanawaporn S, Chutrakul C, Vongsangnak W, Laoteng K. Efficient de novo production of bioactive cordycepin by Aspergillus oryzae using a food-grade expression platform. Microb Cell Fact 2023; 22:253. [PMID: 38071331 PMCID: PMC10710699 DOI: 10.1186/s12934-023-02261-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 11/29/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Cordycepin (3'-deoxyadenosine) is an important bioactive compound in medical and healthcare markets. The drawbacks of commercial cordycepin production using Cordyceps spp. include long cultivation periods and low cordycepin yields. To overcome these limitations and meet the increasing market demand, the efficient production of cordycepin by the GRAS-status Aspergillus oryzae strain using a synthetic biology approach was developed in this study. RESULTS An engineered strain of A. oryzae capable of cordycepin production was successfully constructed by overexpressing two metabolic genes (cns1 and cns2) involved in cordycepin biosynthesis under the control of constitutive promoters. Investigation of the flexibility of carbon utilization for cordycepin production by the engineered A. oryzae strain revealed that it was able to utilize C6-, C5-, and C12-sugars as carbon sources, with glucose being the best carbon source for cordycepin production. High cordycepin productivity (564.64 ± 9.59 mg/L/d) was acquired by optimizing the submerged fermentation conditions. CONCLUSIONS This study demonstrates a powerful production platform for bioactive cordycepin production by A. oryzae using a synthetic biology approach. An efficient and cost-effective fermentation process for cordycepin production using an engineered strain was established, offering a powerful alternative source for further upscaling.
Collapse
Affiliation(s)
- Sukanya Jeennor
- Industrial Bioprocess Technology Research Team, Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand.
| | - Jutamas Anantayanon
- Industrial Bioprocess Technology Research Team, Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
| | - Sarocha Panchanawaporn
- Industrial Bioprocess Technology Research Team, Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
| | - Chanikul Chutrakul
- Industrial Bioprocess Technology Research Team, Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
| | - Wanwipa Vongsangnak
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
- Omics Center for Agriculture, Bioresources, Food, and Health, Kasetsart University (OmiKU), Bangkok, 10900, Thailand
| | - Kobkul Laoteng
- Industrial Bioprocess Technology Research Team, Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
| |
Collapse
|
7
|
Prabhakaran P, Nazir MYM, Thananusak R, Hamid AA, Vongsangnak W, Song Y. Uncovering global lipid accumulation routes towards docosahexaenoic acid (DHA) production in Aurantiochytrium sp. SW1 using integrative proteomic analysis. Biochim Biophys Acta Mol Cell Biol Lipids 2023; 1868:159381. [PMID: 37625782 DOI: 10.1016/j.bbalip.2023.159381] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 08/15/2023] [Accepted: 08/22/2023] [Indexed: 08/27/2023]
Abstract
Aurantiochytrium sp., a marine thraustochytrid possesses a remarkable ability to produce lipid rich in polyunsaturated fatty acids (PUFAs), such as docosahexaenoic acid (DHA). Although gene regulation underlying lipid biosynthesis has been previously reported, proteomic analysis is still limited. In this study, high DHA accumulating strain Aurantiochytrium sp. SW1 has been used as a study model to elucidate the alteration in proteome profile under different cultivation phases i.e. growth, nitrogen-limitation and lipid accumulation. Of the total of 5146 identified proteins, 852 proteins were differentially expressed proteins (DEPs). The largest number of DEPs (488 proteins) was found to be uniquely expressed between lipid accumulating phase and growth phase. Interestingly, there were up-regulated proteins involved in glycolysis, glycerolipid, carotenoid and glutathione metabolism which were preferable metabolic routes towards lipid accumulation and DHA production as well as cellular oxidative defence. Integrated proteomic and transcriptomic data were also conducted to comprehend the gene and protein regulation underlying the lipid and DHA biosynthesis. A significant up-regulation of acetyl-CoA synthetase was observed which suggests alternative route of acetate metabolism for acetyl-CoA producer. This study presents the holistic routes underlying lipid accumulation and DHA production in Aurantiochytrium sp. SW1 and other relevant thraustochytrid.
Collapse
Affiliation(s)
- Pranesha Prabhakaran
- Colin Ratledge Centre for Microbial Lipids, School of Agriculture Engineering and Food Science, Shandong University of Technology, Zibo, China; Interdisciplinary Graduate Programs in Bioscience, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Mohamed Yusuf Mohamed Nazir
- Colin Ratledge Centre for Microbial Lipids, School of Agriculture Engineering and Food Science, Shandong University of Technology, Zibo, China; Department of Food Sciences, Faculty of Science and Technology, University Kebangsaan Malaysia, UKM, Bangi, Malaysia
| | - Roypim Thananusak
- Duckweed Holobiont Resource & Research Center (DHbRC), Faculty of Science, Kasetsart University, Bangkok, Thailand; Omics Center for Agriculture, Bioresources, Food, and Health, Kasetsart University (OmiKU), Bangkok, Thailand
| | - Aidil Abdul Hamid
- Department of Biological Science and Biotechnology, Faculty of Science and Technology, National University of Malaysia, Bangi, Malaysia.
| | - Wanwipa Vongsangnak
- Omics Center for Agriculture, Bioresources, Food, and Health, Kasetsart University (OmiKU), Bangkok, Thailand; Department of Zoology, Faculty of Science, Kasetsart University, Bangkok, Thailand.
| | - Yuanda Song
- Colin Ratledge Centre for Microbial Lipids, School of Agriculture Engineering and Food Science, Shandong University of Technology, Zibo, China.
| |
Collapse
|
8
|
Patumcharoenpol P, Kingkaw A, Nakphaichit M, Chatchatee P, Suratannon N, Panagiotou G, Vongsangnak W. Exploring Longitudinal Gut Microbiome towards Metabolic Functional Changes Associated in Atopic Dermatitis in Early Childhood. Biology (Basel) 2023; 12:1262. [PMID: 37759661 PMCID: PMC10525566 DOI: 10.3390/biology12091262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 09/14/2023] [Accepted: 09/18/2023] [Indexed: 09/29/2023]
Abstract
Atopic dermatitis (AD) is a prevalent inflammatory skin disease that has been associated with changes in gut microbial composition in early life. However, there are limited longitudinal studies examining the gut microbiome in AD. This study aimed to explore taxonomy and metabolic functions across longitudinal gut microbiomes associated with AD in early childhood from 9 to 30 months of age using integrative data analysis within the Thai population. Our analysis revealed that gut microbiome diversity was not different between healthy and AD groups; however, significant taxonomic differences were observed. Key gut bacteria with short-chain fatty acids (SCFAs) production potentials, such as Anaerostipes, Butyricicoccus, Ruminococcus, and Lactobacillus species, showed a higher abundance in the AD group. In addition, metabolic alterations between the healthy and AD groups associated with vitamin production and host immune response, such as biosynthesis of menaquinol, succinate, and (Kdo)2-lipid A, were observed. This study serves as the first framework for monitoring longitudinal microbial imbalances and metabolic functions associated with allergic diseases in Thai children during early childhood.
Collapse
Affiliation(s)
- Preecha Patumcharoenpol
- Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; (P.P.); (A.K.)
| | - Amornthep Kingkaw
- Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; (P.P.); (A.K.)
| | - Massalin Nakphaichit
- Department of Biotechnology, Faculty of Agro-Industry, Kasetsart University, Bangkok 10900, Thailand;
| | - Pantipa Chatchatee
- Center of Excellence for Allergy and Clinical Immunology, Division of Allergy, Immunology and Rheumatology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand;
- King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok 10330, Thailand
| | - Narissara Suratannon
- Center of Excellence for Allergy and Clinical Immunology, Division of Allergy, Immunology and Rheumatology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand;
- King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok 10330, Thailand
| | - Gianni Panagiotou
- Microbiome Dynamics, Leibniz Institute for Natural Product Research and Infection Biology–Hans Knöll Institute, 07745 Jena, Germany;
- Faculty of Biological Sciences, Friedrich Schiller University, 07743 Jena, Germany
- Department of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Wanwipa Vongsangnak
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Omics Center for Agriculture, Bioresources, Food, and Health, Kasetsart University (OmiKU), Bangkok 10900, Thailand
| |
Collapse
|
9
|
Liu X, Zhang H, Zhou Z, Prabhakaran P, Vongsangnak W, Hu G, Xiao F. Functional insight into Cordyceps militaris sugar transporters by structure modeling, network analysis and allosteric regulation. Phys Chem Chem Phys 2023; 25:14311-14323. [PMID: 37183444 DOI: 10.1039/d2cp05611a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Insights into the structures, functions and dynamics of Cordyceps militaris (C. militaris) sugar transporters are necessary for understanding their versatile metabolic capability for fungal growth. The sequence-function relationship study of 85 C. militaris sugar transporters showed that there is a gap between phylogenetic-based subfamily classification and their functions. Beyond protein sequences, structural modeling and principal component analysis of the structural ensemble revealed the different folds of the Car and Org subfamilies. Performing channel detection and network analysis found that the Alp and Hex subfamilies can be specifically distinguished from others by the betweenness of channel residues. Signature dynamics analysis further suggested that the Hex subfamily demonstrates different dynamics, with high flexibility at the H1 region in TM11. Furthermore, the H1 region as an allosteric site was examined by network parameter calculations that guided allosteric pathways between this region and the channel cavity. Together with gene expression data of C. militaris, e.g., Hex06741 in the Hex subfamily, it was promisingly expressed when sugar utilization was altered. This work demonstrates an in silico framework for investigating C. militaris sugar transporters as an example case study of the allosteric activity of the Hex subfamily and can facilitate sugar transporter engineering design that can further optimize the preferable sugar utilization and fermentation process of C. militaris.
Collapse
Affiliation(s)
- Xin Liu
- Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Suzhou Medical College of Soochow University, Suzhou 215123, China.
- Institute of Blood and Marrow Transplantation, Medical College of Soochow University, Jiangsu Institute of Hematology, The first Affiliated Hospital of Soochow University, Collaborative Innovation Center of Hematology, National Clinical Research Center for Hematologic Diseases, Soochow University, Suzhou 215123, China
| | - Hanyang Zhang
- Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Suzhou Medical College of Soochow University, Suzhou 215123, China.
| | - Ziyun Zhou
- Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Suzhou Medical College of Soochow University, Suzhou 215123, China.
- Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Soochow University, Suzhou, 215123, China
| | - Pranesha Prabhakaran
- Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Omics Center for Agriculture, Bioresources, Food, and Health, Kasetsart University (OmiKU), Bangkok 10900, Thailand
| | - Wanwipa Vongsangnak
- Omics Center for Agriculture, Bioresources, Food, and Health, Kasetsart University (OmiKU), Bangkok 10900, Thailand
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand.
| | - Guang Hu
- Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Suzhou Medical College of Soochow University, Suzhou 215123, China.
- Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Soochow University, Suzhou, 215123, China
| | - Fei Xiao
- Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Suzhou Medical College of Soochow University, Suzhou 215123, China.
| |
Collapse
|
10
|
Prabhakaran P, Raethong N, Thananusak R, Nazir MYM, Sapkaew C, Soommat P, Kingkaw A, Hamid AA, Vongsangnak W, Song Y. Revealing holistic metabolic responses associated with lipid and docosahexaenoic acid (DHA) production in Aurantiochytrium sp. SW1. Biochim Biophys Acta Mol Cell Biol Lipids 2023; 1868:159306. [PMID: 36907245 DOI: 10.1016/j.bbalip.2023.159306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 02/02/2023] [Accepted: 02/25/2023] [Indexed: 03/12/2023]
Abstract
Aurantiochytrium sp. SW1, a marine thraustochytrid, has been regarded as a potential candidate as a docosahexaenoic acid (DHA) producer. Even though the genomics of Aurantiochytrium sp. are available, the metabolic responses at a systems level are largely unknown. Therefore, this study aimed to investigate the global metabolic responses to DHA production in Aurantiochytrium sp. through transcriptome and genome-scale network-driven analysis. Of a total of 13,505 genes, 2527 differentially expressed genes (DEGs) were identified in Aurantiochytrium sp., unravelling the transcriptional regulations behinds lipid and DHA accumulation. The highest number of DEG were found for pairwise comparison between growth phase and lipid accumulating phase where a total of 1435 genes were down-regulated with 869 genes being up-regulated. These uncovered several metabolic pathways that contributing in DHA and lipid accumulation including amino acid and acetate metabolism which involve in the generation of crucial precursors. Upon applying network-driven analysis, hydrogen sulphide was found as potential reporter metabolite that could be associated with the genes related to acetyl-CoA synthesis for DHA production. Our findings suggest that the transcriptional regulation of these pathways is a ubiquitous feature in response to specific cultivation phases during DHA overproduction in Aurantiochytrium sp. SW1.
Collapse
Affiliation(s)
- Pranesha Prabhakaran
- Colin Ratledge Centre for Microbial Lipids, School of Agriculture Engineering and Food Science, Shandong University of Technology, Zibo, China; Interdisciplinary Graduate Programs in Bioscience, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Nachon Raethong
- Institute of Nutrition, Mahidol University, Nakhon Pathom, Thailand
| | - Roypim Thananusak
- Interdisciplinary Graduate Programs in Bioscience, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Mohamed Yusuf Mohamed Nazir
- Colin Ratledge Centre for Microbial Lipids, School of Agriculture Engineering and Food Science, Shandong University of Technology, Zibo, China; Department of Food Sciences, Faculty of Science and Technology, University Kebangsaan Malaysia, UKM, Bangi, Malaysia
| | - Chakkapan Sapkaew
- Interdisciplinary Graduate Programs in Bioscience, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; Department of Zoology, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Panyawarin Soommat
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok, Thailand; Genetic Engineering and Bioinformatic Program, Graduate School, Kasetsart University, Bangkok, Thailand
| | - Amornthep Kingkaw
- Interdisciplinary Graduate Programs in Bioscience, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Aidil Abdul Hamid
- Department of Biological Science and Biotechnology, Faculty of Science and Technology, National University of Malaysia, Bangi, Malaysia.
| | - Wanwipa Vongsangnak
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok, Thailand; Omics Center for Agriculture, Bioresources, Food, and Health, Kasetsart University (OmiKU), Bangkok, Thailand.
| | - Yuanda Song
- Colin Ratledge Centre for Microbial Lipids, School of Agriculture Engineering and Food Science, Shandong University of Technology, Zibo, China.
| |
Collapse
|
11
|
Raethong N, Thananusak R, Cheawchanlertfa P, Prabhakaran P, Rattanaporn K, Laoteng K, Koffas M, Vongsangnak W. Functional genomics and systems biology of Cordyceps species for biotechnological applications. Curr Opin Biotechnol 2023; 81:102939. [PMID: 37075529 DOI: 10.1016/j.copbio.2023.102939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 03/13/2023] [Accepted: 03/15/2023] [Indexed: 04/21/2023]
Abstract
The use of Cordyceps species for the manufacture of natural products has been established; however, the tremendous advances observed in recent years in genetic engineering and molecular biology have revolutionized the optimization of Cordyceps as cell factories and drastically expanded the biotechnological potential of these fungi. Here, we present a review of systems and synthetic biology studies of Cordyceps and their implications for fungal biology and industrial applications. We summarize the current status of synthetic biology for enhancing targeted metabolites in Cordyceps species, such as cordycepin, adenosine, polysaccharide, and pentostatin. Progress in the systems and synthetic biology of Cordyceps provides a strategy for comprehensively comprehensive controlling efficient cell factories of natural bioproducts and novel synthetic biology toolbox for targeted engineering.
Collapse
Affiliation(s)
- Nachon Raethong
- Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; Institute of Nutrition, Mahidol University, Nakhon Pathom 73170, Thailand
| | - Roypim Thananusak
- Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Pattsarun Cheawchanlertfa
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Pranesha Prabhakaran
- Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; Department of Zoology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Kittipong Rattanaporn
- Fermentation Technology Research Center (FTRC), Department of Biotechnology, Faculty of Agro-Industry, Kasetsart University, Bangkok 10900, Thailand
| | - Kobkul Laoteng
- Industrial Bioprocess Technology Research Team, Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology BIOTEC, National Science and Technology Development Agency NSTDA, Pathum Thani 12120, Thailand
| | - Mattheos Koffas
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA.
| | - Wanwipa Vongsangnak
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; Omics Center for Agriculture, Bioresources, Food, and Health, Kasetsart University (OmiKU), Bangkok 10900, Thailand.
| |
Collapse
|
12
|
Kruasuwan W, Lohmaneeratana K, Munnoch JT, Vongsangnak W, Jantrasuriyarat C, Hoskisson PA, Thamchaipenet A. Transcriptome Landscapes of Salt-Susceptible Rice Cultivar IR29 Associated with a Plant Growth Promoting Endophytic Streptomyces. Rice (N Y) 2023; 16:6. [PMID: 36739313 PMCID: PMC9899303 DOI: 10.1186/s12284-023-00622-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Accepted: 01/18/2023] [Indexed: 06/18/2023]
Abstract
Plant growth-promoting endophytic (PGPE) actinomycetes have been known to enhance plant growth and mitigate plant from abiotic stresses via their PGP-traits. In this study, PGPE Streptomyces sp. GKU 895 promoted growth and alleviated salt tolerance of salt-susceptible rice cultivar IR29 by augmentation of plant weight and declined ROS after irrigation with 150 mM NaCl in a pot experiment. Transcriptome analysis of IR29 exposed to the combination of strain GKU 895 and salinity demonstrated up and downregulated differentially expressed genes (DEGs) classified by gene ontology and plant reactome. Streptomyces sp. GKU 895 induced changes in expression of rice genes including transcription factors under salt treatment which involved in growth and development, photosynthesis, plant hormones, ROS scavenging, ion transport and homeostasis, and plant-microbe interactions regarding pathogenesis- and symbiosis-related proteins. Taken together, these data demonstrate that PGPE Streptomyces sp. GKU 895 colonized and enhanced growth of rice IR29 and triggered salt tolerance phenotype. Our findings suggest that utilisation of beneficial endophytes in the saline fields could allow for the use of such marginal soils for growing rice and possibly other crops.
Collapse
Affiliation(s)
- Worarat Kruasuwan
- Department of Genetics, Faculty of Sciences, Kasetsart University, Bangkok, Thailand
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK
- Siriraj Long-Read Lab (Si-LoL), Division of Medical Bioinformatics, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Karan Lohmaneeratana
- Department of Genetics, Faculty of Sciences, Kasetsart University, Bangkok, Thailand
| | - John T Munnoch
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK
| | - Wanwipa Vongsangnak
- Department of Zoology, Faculty of Sciences, Kasetsart University, Bangkok, Thailand
- Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Bangkok, Thailand
| | | | - Paul A Hoskisson
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK
| | - Arinthip Thamchaipenet
- Department of Genetics, Faculty of Sciences, Kasetsart University, Bangkok, Thailand.
- Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Bangkok, Thailand.
| |
Collapse
|
13
|
Chaiseksamphan O, Kittipongpattana P, Petchlorlian A, Vongsangnak W, Nakphaichit M, Patumcharoenpol P, Weerapakorn W, Nitisinprasert S, Poovorawan Y, Wanlapakorn N, Ngamphaiboon J, Nantanee R, Chatchatee P, Suratannon N. Longitudinal Analysis of Association Between Gut Microbiota and Atopic Dermatitis in Thai Children: A Birth Cohort Study. J Allergy Clin Immunol 2023. [DOI: 10.1016/j.jaci.2022.12.721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
|
14
|
Song L, Wu J, Weng K, Yao F, Vongsangnak W, Zhu G, Chen G, Zhang Y, Xu Q. The salmonella effector Hcp modulates infection response, and affects salmonella adhesion and egg contamination incidences in ducks. Front Cell Infect Microbiol 2022; 12:948237. [PMID: 36262184 PMCID: PMC9575552 DOI: 10.3389/fcimb.2022.948237] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 07/05/2022] [Indexed: 11/17/2022] Open
Abstract
Salmonella Entertidis (SE) often causes persistent infections and egg contamination in laying ducks. Hcp, the core structural and effector proteins of the Type VI Secretion System (T6SS) in SE, contributes to bacterial invasion, adhesion and virulence. However, little is known about the effect of Hcp on the host’s infection responses and egg contamination incidences in duck. Herein, we generated an hcp deletion mutant SE MY1△hcp and detected its ability to invade duck granulosa cells (dGCs) and contaminate eggs. In comparison with MY1-infected group, the SE adhesion decreased by 15.96% in MY1△hcp-infected dGCs, and the apoptosis in MY1△hcp-infected dGCs decreased by 26.58% and 30.99% at 3 and 6 hours postinfection, respectively. However, the expression levels of immunogenic genes TLR4, NOD1, TNFα, IL-1β and proinflammatory cytokines IL-6, IL-1β, TNF-α release were markedly lower in the dGCs inoculated with MY1△hcp than that of the wild type. Besides, the laying ducks were challenged with MY1 or MY1△hcp in vivo, respectively. The lower egg production and higher egg contamination were observed in MY1-infected ducks in comparison with MY1△hcp-infected birds. Furthermore, the host’s infection response of differentially abundant proteins (DAPs) to Salmonella effector Hcp was identified using quantitative proteomics. A total of 164 DAPs were identified between the MY1- and MY1△hcp-infected cells, which were mainly engaged in the immune, hormone synthesis, cell proliferation and cell apoptotic process. Among them, STAT3, AKT1, MAPK9, MAPK14, and CREBBP were the center of the regulatory network, which might serve as key host response regulators to bacterial Hcp. In conclusion, we demonstrated that effector Hcp contributed to not only SE invasion, induction of dGCs apoptosis, and trigger of immune responses, but also enhanced contamination incidences. Also, the STAT3, AKT1, MAPK9, MAPK14, and CREBBP were identified as host’s infection response regulators of bacterial Hcp in duck. Overall, these results not only offered a novel evidence of SE ovarian transmission but also identified some promising candidate regulators during SE infection.
Collapse
Affiliation(s)
- Lina Song
- Joint International Research Laboratory of Agriculture & Agri-Product Safety of Ministry of Education, Yangzhou University, Yangzhou, China
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Jia Wu
- Joint International Research Laboratory of Agriculture & Agri-Product Safety of Ministry of Education, Yangzhou University, Yangzhou, China
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Kaiqi Weng
- Joint International Research Laboratory of Agriculture & Agri-Product Safety of Ministry of Education, Yangzhou University, Yangzhou, China
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Fenghua Yao
- Joint International Research Laboratory of Agriculture & Agri-Product Safety of Ministry of Education, Yangzhou University, Yangzhou, China
| | - Wanwipa Vongsangnak
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Guoqiang Zhu
- Joint International Research Laboratory of Agriculture & Agri-Product Safety of Ministry of Education, Yangzhou University, Yangzhou, China
| | - Guohong Chen
- Joint International Research Laboratory of Agriculture & Agri-Product Safety of Ministry of Education, Yangzhou University, Yangzhou, China
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Yu Zhang
- Joint International Research Laboratory of Agriculture & Agri-Product Safety of Ministry of Education, Yangzhou University, Yangzhou, China
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
- *Correspondence: Yu Zhang,
| | - Qi Xu
- Joint International Research Laboratory of Agriculture & Agri-Product Safety of Ministry of Education, Yangzhou University, Yangzhou, China
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| |
Collapse
|
15
|
Prabhakaran P, Raethong N, Nazir Y, Halim H, Yang W, Vongsangnak W, Abdul Hamid A, Song Y. Whole Genome Analysis and Elucidation of Docosahexaenoic Acid (DHA) Biosynthetic Pathway in Aurantiochytrium sp. SW1. Gene 2022; 846:146850. [PMID: 36044942 DOI: 10.1016/j.gene.2022.146850] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 08/17/2022] [Accepted: 08/25/2022] [Indexed: 11/15/2022]
Abstract
Aurantiochytrium sp., a fungoid marine protist that belongs to Stramenophila has proven its potential in the production of polyunsaturated fatty acids (PUFAs), especially docosahexaenoic acids (DHA). In this study, genomic characterisation of a potential producer for commercial production of DHA, Aurantiochytrium sp. SW1 has been carried out via whole genome sequencing analysis. The genome size of this strain is 60.89 Mb, with a total of 11,588 protein-coding genes. Among these, 9,127 genes could be functionally annotated into a total of 7,248 (62.5%) from UniProt, 6,554 (56.6%) from KEGG and 8,643 (74.6%) genes from eggNOG protein database. The highest proportion of genes belongs to the protein family of metabolism were further assigned into 11 metabolic categories. The highest number of genes belonging to lipid metabolism (321 genes) followed by carbohydrate metabolism (290 genes), metabolism of cofactors and vitamins (197 genes) and amino acid metabolism (188 genes). Further analysis into the biosynthetic pathway for DHA showed evidence of all genes involved in PKS (polyketide synthase)-like PUFA synthase pathway and incomplete fatty acid synthase-elongase/desaturase pathway. Analysis of PUFA synthase showed the presence of up to ten tandem acyl carrier protein (ACP) domains which might have contributed to high DHA production in this organism. In addition, a hybrid system incorporating elements of FAS, Type I PKS and Type II PKS systems were found to be involved in the biosynthetic pathways of fatty acids in Aurantiochytrium sp. SW1. This study delivers an important reference for future research to enhance the lipid, especially DHA production in Aurantiochytrium sp, SW1 and establishment of this strain as an oleaginous thraustochytrid model.
Collapse
Affiliation(s)
- Pranesha Prabhakaran
- Colin Ratledge Center for Microbial Lipids, School of Agriculture Engineering and Food Science, Shandong University of Technology, Zibo, China; Interdisciplinary Graduate Programs in Bioscience, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Nachon Raethong
- Institute of Nutrition, Mahidol University, Nakhon Pathom, Thailand
| | - Yusuf Nazir
- Colin Ratledge Center for Microbial Lipids, School of Agriculture Engineering and Food Science, Shandong University of Technology, Zibo, China; Department of Food Sciences, Faculty of Science and Technology, University Kebangsaan Malaysia, UKM Bangi 43600, Malaysia
| | - Hafiy Halim
- Colin Ratledge Center for Microbial Lipids, School of Agriculture Engineering and Food Science, Shandong University of Technology, Zibo, China
| | - Wu Yang
- Colin Ratledge Center for Microbial Lipids, School of Agriculture Engineering and Food Science, Shandong University of Technology, Zibo, China
| | - Wanwipa Vongsangnak
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok, Thailand; Omics Center for Agriculture, Bioresources, Food, and Health, Kasetsart University (OmiKU), Bangkok 10900
| | - Aidil Abdul Hamid
- Department of Biological Science and Biotechnology, Faculty of Science and Technology, National University of Malaysia, Bangi, Malaysia.
| | - Yuanda Song
- Colin Ratledge Center for Microbial Lipids, School of Agriculture Engineering and Food Science, Shandong University of Technology, Zibo, China.
| |
Collapse
|
16
|
Cheawchanlertfa P, Chitcharoen S, Raethong N, Liu Q, Chumnanpuen P, Soommat P, Song Y, Koffas M, Laoteng K, Vongsangnak W. Enhancing Genome-Scale Model by Integrative Exometabolome and Transcriptome: Unveiling Carbon Assimilation towards Sphingolipid Biosynthetic Capability of Cordyceps militaris. J Fungi (Basel) 2022; 8:jof8080887. [PMID: 36012875 PMCID: PMC9409897 DOI: 10.3390/jof8080887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/15/2022] [Accepted: 08/19/2022] [Indexed: 11/16/2022] Open
Abstract
Cordyceps militaris is an industrially important fungus, which is often used in Asia as traditional medicine. There has been a published genome-scale metabolic model (GSMM) of C. militaris useful for predicting its growth behaviors; however, lipid metabolism, which plays a vital role in cellular functions, remains incomplete in the GSMM of C. militaris. A comprehensive study on C. militaris was thus performed by enhancing GSMM through integrative analysis of metabolic footprint and transcriptome data. Through the enhanced GSMM of C. militaris (called iPC1469), it contained 1469 genes, 1904 metabolic reactions and 1229 metabolites. After model evaluation, in silico growth simulation results agreed well with the experimental data of the fungal growths on different carbon sources. Beyond the model-driven integrative data analysis, interestingly, we found key metabolic responses in alteration of lipid metabolism in C. militaris upon different carbon sources. The sphingoid bases (e.g., sphinganine, sphingosine, and phytosphingosine) and ceramide were statistically significant accumulated in the xylose culture when compared with other cultures; this study suggests that the sphingolipid biosynthetic capability in C. militaris was dependent on the carbon source assimilated for cell growth; this finding provides a comprehensive basis for the sphingolipid biosynthesis in C. militaris that can help to further redesign its metabolic control for medicinal and functional food applications.
Collapse
Affiliation(s)
| | - Suwalak Chitcharoen
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand
| | - Nachon Raethong
- Institute of Nutrition, Mahidol University, Nakhon Pathom 73170, Thailand
| | - Qing Liu
- Colin Ratledge Center for Microbial Lipids, School of Agriculture Engineering and Food Sciences, Shandong University of Technology, Zibo 255000, China
| | - Pramote Chumnanpuen
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Omics Center for Agriculture, Bioresources, Food, and Health, Kasetsart University (OmiKU), Bangkok 10900, Thailand
| | - Panyawarin Soommat
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Genetic Engineering and Bioinformatics Program, Graduate School, Kasetsart University, Bangkok 10900, Thailand
| | - Yuanda Song
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Colin Ratledge Center for Microbial Lipids, School of Agriculture Engineering and Food Sciences, Shandong University of Technology, Zibo 255000, China
| | - Mattheos Koffas
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Kobkul Laoteng
- Industrial Bioprocess Technology Research Team, Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology BIOTEC, National Science and Technology Development Agency NSTDA, Pathum Thani 12120, Thailand
- Correspondence: (K.L.); (W.V.)
| | - Wanwipa Vongsangnak
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Omics Center for Agriculture, Bioresources, Food, and Health, Kasetsart University (OmiKU), Bangkok 10900, Thailand
- Correspondence: (K.L.); (W.V.)
| |
Collapse
|
17
|
Namrak T, Raethong N, Jatuponwiphat T, Nitisinprasert S, Vongsangnak W, Nakphaichit M. Probing Genome-Scale Model Reveals Metabolic Capability and Essential Nutrients for Growth of Probiotic Limosilactobacillus reuteri KUB-AC5. Biology (Basel) 2022; 11:biology11020294. [PMID: 35205160 PMCID: PMC8869380 DOI: 10.3390/biology11020294] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 02/10/2022] [Accepted: 02/10/2022] [Indexed: 12/14/2022]
Abstract
Limosilactobacillus reuteri KUB-AC5 displays the hallmark features of probiotic properties for food and feed industries. Optimization of cultivation condition for the industrial production is important to reach cell concentration and cost reduction. Considering the strain-specific growth physiology, metabolic capability, and essential nutrients of L. reuteri KUB-AC5, the genome-scale metabolic model (GSMM) of L. reuteri KUB-AC5 was developed. Hereby, the GSMM of iTN656 was successfully constructed which contained 656 genes, 831 metabolites, and 953 metabolic reactions. The iTN656 model could show a metabolic capability under various carbon sources and guide potentially 14 essential single nutrients (e.g., vitamin B complex and amino acids) and 2 essential double nutrients (pairwise glutamine-glutamate and asparagine-aspartate) for L. reuteri KUB-AC5 growth through single and double omission analysis. Promisingly, the iTN656 model was further integrated with transcriptome data suggesting that putative metabolic routes as preferable paths e.g., sucrose uptake, nucleotide biosynthesis, urea cycle, and glutamine transporter for L. reuteri KUB-AC5 growth. The developed GSMM offers a powerful tool for multi-level omics analysis, enabling probiotic strain optimization for biomass overproduction on an industrial scale.
Collapse
Affiliation(s)
- Thanawat Namrak
- Specialized Research Unit: Prebiotics and Probiotics for Health, Department of Biotechnology, Faculty of Agro-Industry, Kasetsart University, Bangkok 10900, Thailand; (T.N.); (S.N.)
| | - Nachon Raethong
- Institute of Nutrition, Mahidol University, Nakhon Pathom 73170, Thailand;
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Theeraphol Jatuponwiphat
- Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand;
| | - Sunee Nitisinprasert
- Specialized Research Unit: Prebiotics and Probiotics for Health, Department of Biotechnology, Faculty of Agro-Industry, Kasetsart University, Bangkok 10900, Thailand; (T.N.); (S.N.)
| | - Wanwipa Vongsangnak
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Omics Center for Agriculture, Bioresources, Food, and Health, Kasetsart University (OmiKU), Bangkok 10900, Thailand
- Correspondence: (W.V.); (M.N.)
| | - Massalin Nakphaichit
- Specialized Research Unit: Prebiotics and Probiotics for Health, Department of Biotechnology, Faculty of Agro-Industry, Kasetsart University, Bangkok 10900, Thailand; (T.N.); (S.N.)
- Correspondence: (W.V.); (M.N.)
| |
Collapse
|
18
|
In-on A, Thananusak R, Ruengjitchatchawalya M, Vongsangnak W, Laomettachit T. Construction of Light-Responsive Gene Regulatory Network for Growth, Development and Secondary Metabolite Production in Cordyceps militaris. Biology 2022; 11:biology11010071. [PMID: 35053069 PMCID: PMC8773263 DOI: 10.3390/biology11010071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 12/30/2021] [Accepted: 12/30/2021] [Indexed: 01/17/2023]
Abstract
Cordyceps militaris is an edible fungus that produces many beneficial compounds, including cordycepin and carotenoid. In many fungi, growth, development and secondary metabolite production are controlled by crosstalk between light-signaling pathways and other regulatory cascades. However, little is known about the gene regulation upon light exposure in C. militaris. This study aims to construct a gene regulatory network (GRN) that responds to light in C. militaris. First, a genome-scale GRN was built based on transcription factor (TF)-target gene interactions predicted from the Regulatory Sequence Analysis Tools (RSAT). Then, a light-responsive GRN was extracted by integrating the transcriptomic data onto the genome-scale GRN. The light-responsive network contains 2689 genes and 6837 interactions. From the network, five TFs, Snf21 (CCM_04586), an AT-hook DNA-binding motif TF (CCM_08536), a homeobox TF (CCM_07504), a forkhead box protein L2 (CCM_02646) and a heat shock factor Hsf1 (CCM_05142), were identified as key regulators that co-regulate a large group of growth and developmental genes. The identified regulatory network and expression profiles from our analysis suggested how light may induce the growth and development of C. militaris into a sexual cycle. The light-mediated regulation also couples fungal development with cordycepin and carotenoid production. This study leads to an enhanced understanding of the light-responsive regulation of growth, development and secondary metabolite production in the fungi.
Collapse
Affiliation(s)
- Ammarin In-on
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi, Bangkok 10150, Thailand; (A.I.-o.); (M.R.)
- School of Information Technology, King Mongkut’s University of Technology Thonburi, Bangkok 10150, Thailand
| | - Roypim Thananusak
- Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand;
| | - Marasri Ruengjitchatchawalya
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi, Bangkok 10150, Thailand; (A.I.-o.); (M.R.)
- Biotechnology Program, School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi, Bangkok 10150, Thailand
| | - Wanwipa Vongsangnak
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Bangkok 10900, Thailand
- Correspondence: (W.V.); (T.L.)
| | - Teeraphan Laomettachit
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi, Bangkok 10150, Thailand; (A.I.-o.); (M.R.)
- Theoretical and Computational Physics (TCP) Group, Center of Excellence in Theoretical and Computational Science (TaCS-CoE), King Mongkut’s University of Technology Thonburi, Bangkok 10150, Thailand
- Correspondence: (W.V.); (T.L.)
| |
Collapse
|
19
|
Jatuponwiphat T, Namrak T, Nitisinprasert S, Nakphaichit M, Vongsangnak W. Integrative growth physiology and transcriptome profiling of probiotic Limosilactobacillus reuteri KUB-AC5. PeerJ 2021; 9:e12226. [PMID: 34707932 PMCID: PMC8500091 DOI: 10.7717/peerj.12226] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 09/08/2021] [Indexed: 12/26/2022] Open
Abstract
Limosilactobacillus reuteri KUB-AC5 has been widely used as probiotic in chicken for Salmonella reduction. However, a preferable carbon source and growth phase is poorly characterized underlying metabolic responses on growth and inhibition effects of L. reuteri KUB-AC5. This study therefore aimed to investigate transcriptome profiling of L. reuteri KUB-AC5 revealing global metabolic responses when alteration of carbon sources and growth phases. Interestingly, L. reuteri KUB-AC5 grown under sucrose culture showed to be the best for fast growth and inhibition effects against Salmonella Enteritidis S003 growth. Towards the transcriptome profiling and reporter proteins/metabolites analysis, the results showed that amino acid transport via ABC systems as well as sucrose metabolism and transport are key metabolic responses at Logarithmic (L)-phase of L. reuteri KUB-AC5 growth. Considering the Stationary (S)-phase, we found the potential reporter proteins/metabolites involved in carbohydrate metabolism e.g., levansucrase and levan. Promisingly, levansucrase and levan were revealed to be candidates in relation to inhibition effects of L. reuteri KUB-AC5. Throughout this study, L. reuteri KUB-AC5 had a metabolic control in acclimatization to sucrose and energy pools through transcriptional co-regulation, which supported the cell growth and inhibition potentials. This study offers a perspective in optimizing fermentation condition through either genetic or physiological approaches for enhancing probiotic L. reuteri KUB-AC5 properties.
Collapse
Affiliation(s)
- Theeraphol Jatuponwiphat
- Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Thanawat Namrak
- Department of Biotechnology, Faculty of Agro-Industry, Kasetsart University, Bangkok, Thailand
| | - Sunee Nitisinprasert
- Department of Biotechnology, Faculty of Agro-Industry, Kasetsart University, Bangkok, Thailand
| | - Massalin Nakphaichit
- Department of Biotechnology, Faculty of Agro-Industry, Kasetsart University, Bangkok, Thailand
| | - Wanwipa Vongsangnak
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok, Thailand.,Omics Center for Agriculture, Bioresources, Food, and Health, Kasetsart University (OmiKU), Bangkok, Thailand
| |
Collapse
|
20
|
Mok K, Suratanon N, Roytrakul S, Charoenlappanit S, Patumcharoenpol P, Chatchatee P, Vongsangnak W, Nakphaichit M. ITS2 Sequencing and Targeted Meta-Proteomics of Infant Gut Mycobiome Reveal the Functional Role of Rhodotorula sp. during Atopic Dermatitis Manifestation. J Fungi (Basel) 2021; 7:jof7090748. [PMID: 34575786 PMCID: PMC8471346 DOI: 10.3390/jof7090748] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 09/04/2021] [Accepted: 09/08/2021] [Indexed: 12/12/2022] Open
Abstract
Association between the gut mycobiome and atopic dermatitis was investigated in 9-12-month-old infants using metagenomics. Two groups of atopic dermatitis infants were classified according to their symptom development as outgrown (recovered) and persisted (still undergoing). The evenness and diversity of the mycobiome in the persisted group were higher than in the healthy and outgrown groups. Dysbiosis of the microbiome in the persisted group was observed by a reduction in the Ascomycota/Basidiomycota ratio. Five fungi were selected as markers from each sample group. In the persisted group, Rhodotorula sp. abundance increased significantly, while Wickerhamomyces sp. and Kodamaea sp. abundance increased in the healthy group, and Acremonium sp. and Rhizopus sp. abundance increased considerably in the outgrown group. Metaproteomic analysis revealed that the persisted group had a high abundance of fungal proteins, particularly those from Rhodotorula sp. Unique proteins such as RAN-binding protein 1 and glycerol kinase from Rhodotorula sp. were hypothesized to be related to atopic dermatitis manifestation in infants.
Collapse
Affiliation(s)
- Kevin Mok
- Department of Biotechnology, Faculty of Agro-Industry, Kasetsart University, Bangkok 10900, Thailand;
- Specialized Research Unit: Probiotics and Prebiotics for Health, Faculty of Agro-Industry, Kasetsart University, Bangkok 10900, Thailand
| | - Narissara Suratanon
- Pediatric Allergy & Clinical Immunology Research Unit, Division of Allergy and Immunology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok 10330, Thailand; (N.S.); (P.C.)
| | - Sittiruk Roytrakul
- Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani 12120, Thailand; (S.R.); (S.C.)
| | - Sawanya Charoenlappanit
- Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani 12120, Thailand; (S.R.); (S.C.)
| | - Preecha Patumcharoenpol
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand;
- Omics Center for Agriculture, Bioresources, Food, and Health, Kasetsart University (OmiKU), Bangkok 10900, Thailand
| | - Pantipa Chatchatee
- Pediatric Allergy & Clinical Immunology Research Unit, Division of Allergy and Immunology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok 10330, Thailand; (N.S.); (P.C.)
| | - Wanwipa Vongsangnak
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand;
- Omics Center for Agriculture, Bioresources, Food, and Health, Kasetsart University (OmiKU), Bangkok 10900, Thailand
- Correspondence: (W.V.); (M.N.)
| | - Massalin Nakphaichit
- Department of Biotechnology, Faculty of Agro-Industry, Kasetsart University, Bangkok 10900, Thailand;
- Specialized Research Unit: Probiotics and Prebiotics for Health, Faculty of Agro-Industry, Kasetsart University, Bangkok 10900, Thailand
- Correspondence: (W.V.); (M.N.)
| |
Collapse
|
21
|
Zhang Y, Song L, Hou L, Cao Z, Vongsangnak W, Zhu G, Xu Q, Chen G. Dual Transcriptomic Analyses Unveil Host-Pathogen Interactions Between Salmonella enterica Serovar Enteritidis and Laying Ducks ( Anas platyrhynchos). Front Microbiol 2021; 12:705712. [PMID: 34421865 PMCID: PMC8374152 DOI: 10.3389/fmicb.2021.705712] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 07/13/2021] [Indexed: 12/13/2022] Open
Abstract
Salmonella enteritidis (SE) is a pathogen that can readily infect ovarian tissues and colonize the granulosa cell layer such that it can be transmitted via eggs from infected poultry to humans in whom it can cause food poisoning. Ducks are an important egg-laying species that are susceptible to SE infection, yet the host–pathogen interactions between SE and ducks have not been thoroughly studied to date. Herein, we performed dual RNA-sequencing analyses of these two organisms in a time-resolved infection model of duck granulosa cells (dGCs) by SE. In total, 10,510 genes were significantly differentially expressed in host dGCs, and 265 genes were differentially expressed in SE over the course of infection. These differentially expressed genes (DEGs) of dGCs were enriched in the cytokine–cytokine receptor interaction pathway via KEGG analyses, and the DEGs in SE were enriched in the two-component system, bacterial secretion system, and metabolism of pathogen factors pathways as determined. A subsequent weighted gene co-expression network analysis revealed that the cytokine–cytokine receptor interaction pathway is mostly enriched at 6 h post-infection (hpi). Moreover, a number of pathogenic factors identified in the pathogen–host interaction database (PHI-base) are upregulated in SE, including genes encoding the pathogenicity island/component, type III secretion, and regulators of systemic infection. Furthermore, an intracellular network associated with the regulation of SE infection in ducks was constructed, and 16 cytokine response-related dGCs DEGs (including IL15, CD40, and CCR7) and 17 pathogenesis-related factors (including sseL, ompR, and fliC) were identified, respectively. Overall, these results not only offer new insights into the mechanisms underlying host–pathogen interactions between SE and ducks, but they may also aid in the selection of potential targets for antimicrobial drug development.
Collapse
Affiliation(s)
- Yu Zhang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education, Yangzhou University, Yangzhou, China.,College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Lina Song
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education, Yangzhou University, Yangzhou, China.,College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Lie Hou
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Zhengfeng Cao
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Wanwipa Vongsangnak
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Guoqiang Zhu
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education, Yangzhou University, Yangzhou, China
| | - Qi Xu
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education, Yangzhou University, Yangzhou, China.,College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Guohong Chen
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education, Yangzhou University, Yangzhou, China.,College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| |
Collapse
|
22
|
Tesena P, Kingkaw A, Vongsangnak W, Pitikarn S, Phaonakrop N, Roytrakul S, Kovitvadhi A. Preliminary Study: Proteomic Profiling Uncovers Potential Proteins for Biomonitoring Equine Melanocytic Neoplasm. Animals (Basel) 2021; 11:1913. [PMID: 34199079 PMCID: PMC8300200 DOI: 10.3390/ani11071913] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 06/22/2021] [Accepted: 06/24/2021] [Indexed: 01/12/2023] Open
Abstract
Equine melanocytic neoplasm (EMN) is a cutaneous neoplasm and is mostly observed in aged grey horses. This preliminary study aimed to identify potential proteins to differentiate normal, mild and severe EMN from serum proteomic profiling. Serum samples were collected from 25 grey horses assigned to three groups: normal (free of EMN; n = 10), mild (n = 6) and severe EMN (n = 9). To explore the differences in proteins between groups, proteomic profiling and analysis were employed. Accordingly, 8241 annotated proteins out of 8725 total proteins were compared between normal and EMN groups and inspected based on differentially expressed proteins (DEPs). Through DEP analysis, 95 significant DEPs differed between normal and EMN groups. Among these DEPs, 41 significant proteins were categorised according to protein functions. Based on 41 significant proteins, 10 were involved in metabolism and 31 in non-metabolism. Interestingly, phospholipid phosphatase6 (PLPP6) and ATPase subunit alpha (Na+/K+-ATPase) were considered as potential proteins uniquely expressed in mild EMN and related to lipid and energy metabolism, respectively. Non-metabolism-related proteins (BRCA1, phosphorylase B kinase regulatory subunit: PHKA1, tyrosine-protein kinase receptor: ALK and rho-associated protein kinase: ROCK1) correlated to melanoma development differed among all groups. The results of our study provide a foundation for early EMN biomonitoring and prevention.
Collapse
Affiliation(s)
- Parichart Tesena
- Graduate Student in Animal Health and Biomedical Science Program, Faculty of Veterinary Medicine, Kasetsart University, Bangkok 10900, Thailand;
- Department of Clinical Science and Public Health, Faculty of Veterinary Science, Mahidol University, Salaya, Puttamonthon, Nakhon Pathom 73170, Thailand
| | - Amornthep Kingkaw
- Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand;
- Department of Zoology, Faculty of Sciences, Kasetsart University, Bangkok 10900, Thailand;
| | - Wanwipa Vongsangnak
- Department of Zoology, Faculty of Sciences, Kasetsart University, Bangkok 10900, Thailand;
- Omics Center for Agriculture, Bioresources, Food, and Health, Kasetsart University (OmiKU), Bangkok 10900, Thailand
| | - Surakiet Pitikarn
- Genetic Engineering and Bioinformatics Program, Graduate School, Kasetsart University, Bangkok 10900, Thailand;
| | - Narumon Phaonakrop
- Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani 12120, Thailand;
| | - Sittiruk Roytrakul
- Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani 12120, Thailand;
| | - Attawit Kovitvadhi
- Department of Physiology, Faculty of Veterinary Medicine, Kasetsart University, Bangkok 10900, Thailand
| |
Collapse
|
23
|
Zhang Y, Dong X, Hou L, Cao Z, Zhu G, Vongsangnak W, Xu Q, Chen G. Identification of Differentially Expressed Non-coding RNA Networks With Potential Immunoregulatory Roles During Salmonella Enteritidis Infection in Ducks. Front Vet Sci 2021; 8:692501. [PMID: 34222406 PMCID: PMC8242174 DOI: 10.3389/fvets.2021.692501] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 05/20/2021] [Indexed: 01/22/2023] Open
Abstract
Salmonella enterica serovar Enteritidis (S. Enteritidis) is a pathogen that can colonize the preovulatory follicles of poultry, thereby causing both reduced egg production and an elevated risk of foodborne salmonellosis in humans. Although a few studies have revealed S. Enteritidis preferentially invades the granulosa cell layer within these follicles, it can readily persist and proliferate through mechanisms that are not well-understood. In this study, we characterized competing endogenous RNA (ceRNA) regulatory networks within duck granulosa cells following time-course of S. Enteritidis challenge. The 8108 long non-coding RNAs (lncRNAs), 1545 circular RNAs (circRNAs), 542 microRNAs (miRNAs), and 4137 mRNAs (fold change ≥2; P < 0.01) were differentially expressed during S. Enteritidis challenge. Also, eight mRNAs, eight lncRNAs and five circRNAs were selected and the consistent expression trend was found between qRT-PCR detection and RNA-seq. Moreover, the target genes of these differentially expressed ncRNAs (including lncRNAs, circRNAs and miRNAs) were predicted, and significantly enriched in the innate immune response and steroidogenesis pathways. Then, the colocalization and coexpression analyses were conducted to investigate relationships between ncRNAs and mRNAs. The 16 differentially expressed miRNAs targeting 60 differentially expressed mRNAs were identified in granulosa cells at 3 and 6 h post-infection (hpi) and enriched in the MAPK, GnRH, cytokine-cytokine receptor interaction, Toll-like receptor, endocytosis, and oxidative phosphorylation signaling pathways. Additionally, underlying lncRNA-miRNA-mRNA and circRNA-miRNA-mRNA ceRNA networks were then constructed to further understand their interaction during S. Enteritidis infection. Lnc_012227 and novel_circ_0004892 were identified as ceRNAs, which could compete with miR-let-7g-5p and thereby indirectly modulating map3k8 expression to control S. Enteritidis infection. Together, our data thus identified promising candidate ncRNAs responsible for regulating S. Enteritidis infection in the preovulatory follicles of ducks, offering new insights regarding the ovarian transmission of this pathogen.
Collapse
Affiliation(s)
- Yu Zhang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education, Yangzhou University, Yangzhou, China.,Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China
| | - Xiaoqian Dong
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education, Yangzhou University, Yangzhou, China
| | - Lie Hou
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education, Yangzhou University, Yangzhou, China
| | - Zhengfeng Cao
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education, Yangzhou University, Yangzhou, China
| | - Guoqiang Zhu
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China
| | - Wanwipa Vongsangnak
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Qi Xu
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education, Yangzhou University, Yangzhou, China
| | - Guohong Chen
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education, Yangzhou University, Yangzhou, China
| |
Collapse
|
24
|
Raethong N, Nakphaichit M, Suratannon N, Sathitkowitchai W, Weerapakorn W, Keawsompong S, Vongsangnak W. Analysis of Human Gut Microbiome: Taxonomy and Metabolic Functions in Thai Adults. Genes (Basel) 2021; 12:genes12030331. [PMID: 33668840 PMCID: PMC7996147 DOI: 10.3390/genes12030331] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 02/20/2021] [Accepted: 02/21/2021] [Indexed: 02/07/2023] Open
Abstract
The gut microbiome plays a major role in the maintenance of human health. Characterizing the taxonomy and metabolic functions of the human gut microbiome is necessary for enhancing health. Here, we analyzed the metagenomic sequencing, assembly and construction of a meta-gene catalogue of the human gut microbiome with the overall aim of investigating the taxonomy and metabolic functions of the gut microbiome in Thai adults. As a result, the integrative analysis of 16S rRNA gene and whole metagenome shotgun (WMGS) sequencing data revealed that the dominant gut bacterial families were Lachnospiraceae and Ruminococcaceae of the Firmicutes phylum. Consistently, across 3.8 million (M) genes annotated from 163.5 gigabases (Gb) of WMGS sequencing data, a significant number of genes associated with carbohydrate metabolism of the dominant bacterial families were identified. Further identification of bacterial community-wide metabolic functions promisingly highlighted the importance of Roseburia and Faecalibacterium involvement in central carbon metabolism, sugar utilization and metabolism towards butyrate biosynthesis. This work presents an initial study of shotgun metagenomics in a Thai population-based cohort in a developing Southeast Asian country.
Collapse
Affiliation(s)
- Nachon Raethong
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand;
| | - Massalin Nakphaichit
- Department of Biotechnology, Faculty of Agro-Industry, Kasetsart University, Bangkok 10900, Thailand; (M.N.); (W.S.); (S.K.)
- Center for Advanced Studies for Agriculture and Food, Kasetsart University Institute for Advanced Studies, Kasetsart University, (CASAF, NRU-KU), Bangkok 10900, Thailand
| | - Narissara Suratannon
- Pediatric Allergy & Clinical Immunology Research Unit, Division of Allergy and Immunology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok 10330, Thailand; (N.S.); (W.W.)
| | - Witida Sathitkowitchai
- Department of Biotechnology, Faculty of Agro-Industry, Kasetsart University, Bangkok 10900, Thailand; (M.N.); (W.S.); (S.K.)
- Center for Advanced Studies for Agriculture and Food, Kasetsart University Institute for Advanced Studies, Kasetsart University, (CASAF, NRU-KU), Bangkok 10900, Thailand
- Microarray Research Team, National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Khlong Luang, Pathum Thani 12120, Thailand
| | - Wanlapa Weerapakorn
- Pediatric Allergy & Clinical Immunology Research Unit, Division of Allergy and Immunology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok 10330, Thailand; (N.S.); (W.W.)
| | - Suttipun Keawsompong
- Department of Biotechnology, Faculty of Agro-Industry, Kasetsart University, Bangkok 10900, Thailand; (M.N.); (W.S.); (S.K.)
- Center for Advanced Studies for Agriculture and Food, Kasetsart University Institute for Advanced Studies, Kasetsart University, (CASAF, NRU-KU), Bangkok 10900, Thailand
| | - Wanwipa Vongsangnak
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand;
- Omics Center for Agriculture, Bioresources, Food, and Health, Kasetsart University (OmiKU), Bangkok 10900, Thailand
- Correspondence:
| |
Collapse
|
25
|
Khuntawee W, Amornloetwattana R, Vongsangnak W, Namdee K, Yata T, Karttunen M, Wong-Ekkabut J. In silico and in vitro design of cordycepin encapsulation in liposomes for colon cancer treatment. RSC Adv 2021; 11:8475-8484. [PMID: 35423402 PMCID: PMC8695206 DOI: 10.1039/d1ra00038a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Accepted: 02/17/2021] [Indexed: 01/04/2023] Open
Abstract
Cordycepin or 3'-deoxyadenosine is an interesting anti-cancer drug candidate that is found in abundance in the fungus Cordyceps militaris. It inhibits cellular growth of many cancers including lung carcinoma, melanoma, bladder cancer, and colon cancer by inducing apoptosis, anti-proliferation, anti-metastasis and by arresting the cell cycle. Cordycepin has, however, poor stability and low solubility in water, resulting in loss of its bioactivity. Liposomes can be used to overcome these obstacles. Our aim is to improve cordycepin's anti-colon cancer activity by liposome encapsulation. Cordycepin-encapsulated liposomes were designed and fabricated based on a combination of theoretical and experimental studies. Molecular dynamics (MD) simulations and free energy calculations suggest that phosphatidylcholine (PC) lipid environment is favorable for cordycepin adsorption. Cordycepin passively permeates into PC lipid bilayers without membrane damage and strongly binds to the lipids' polar groups by flipping its deoxyribose sugar toward the bilayer center. Our fabricated liposomes containing 10 : 1 molar ratio of egg yolk PC : cholesterol showed encapsulation efficiency (%EE) of 99% using microfluidic hydrodynamic focusing (MHF) methods. In our in vitro study using the HT-29 colon cancer cell line, cordycepin was able to inhibit growth by induction of apoptosis. Cell viability was significantly decreased below 50% at 125 μg mL-1 dosage after 48 h treatment with non-encapsulated and encapsulated cordycepin. Importantly, encapsulation provided (1) a 2-fold improvement in the inhibition of cancer cell growth at 125 μg mL-1 dosage and (2) 4-fold increase in release time. These in silico and in vitro studies indicate that cordycepin-encapsulated liposomes could be a potent drug candidate for colon cancer therapy.
Collapse
Affiliation(s)
- Wasinee Khuntawee
- Department of Physics, Faculty of Science, Kasetsart University Bangkok 10900 Thailand
- Computational Biomodelling Laboratory for Agricultural Science and Technology (CBLAST), Faculty of Science, Kasetsart University Bangkok 10900 Thailand
- Thailand Center of Excellence in Physics (ThEP Center), Ministry of Higher Education, Science, Research and Innovation Bangkok 10400 Thailand
| | - Rawiporn Amornloetwattana
- Department of Physics, Faculty of Science, Kasetsart University Bangkok 10900 Thailand
- Computational Biomodelling Laboratory for Agricultural Science and Technology (CBLAST), Faculty of Science, Kasetsart University Bangkok 10900 Thailand
- Thailand Center of Excellence in Physics (ThEP Center), Ministry of Higher Education, Science, Research and Innovation Bangkok 10400 Thailand
| | - Wanwipa Vongsangnak
- Computational Biomodelling Laboratory for Agricultural Science and Technology (CBLAST), Faculty of Science, Kasetsart University Bangkok 10900 Thailand
- Department of Zoology, Faculty of Science, Kasetsart University Bangkok 10900 Thailand
| | - Katawut Namdee
- National Nanotechnology Centre (NANOTEC), National Science and Technology Development Agency 111 Thailand Science Park, Paholyothin Rd., Klong Luang Pathumthani 12120 Thailand
| | - Teerapong Yata
- Biochemistry Unit, Department of Physiology, Faculty of Veterinary Science, Chulalongkorn University Bangkok 10330 Thailand
- Natural Products and Nanoparticles Research Unit, Chulalongkorn University Bangkok 10330 Thailand
| | - Mikko Karttunen
- Department of Chemistry, The University of Western Ontario 1151 Richmond Street London Ontario N6A 3K7 Canada
- Department of Applied Mathematics, The University of Western Ontario London ON N6A 5B7 Canada
- The Center for Advanced Materials and Biomaterials Research, The University of Western Ontario London ON N6K 3K7 Canada
| | - Jirasak Wong-Ekkabut
- Department of Physics, Faculty of Science, Kasetsart University Bangkok 10900 Thailand
- Computational Biomodelling Laboratory for Agricultural Science and Technology (CBLAST), Faculty of Science, Kasetsart University Bangkok 10900 Thailand
- Thailand Center of Excellence in Physics (ThEP Center), Ministry of Higher Education, Science, Research and Innovation Bangkok 10400 Thailand
| |
Collapse
|
26
|
Patumcharoenpol P, Nakphaichit M, Panagiotou G, Senavonge A, Suratannon N, Vongsangnak W. MetGEMs Toolbox: Metagenome-scale models as integrative toolbox for uncovering metabolic functions and routes of human gut microbiome. PLoS Comput Biol 2021; 17:e1008487. [PMID: 33406089 PMCID: PMC7787440 DOI: 10.1371/journal.pcbi.1008487] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 11/03/2020] [Indexed: 12/20/2022] Open
Abstract
Investigating metabolic functional capability of a human gut microbiome enables the quantification of microbiome changes, which can cause a phenotypic change of host physiology and disease. One possible way to estimate the functional capability of a microbial community is through inferring metagenomic content from 16S rRNA gene sequences. Genome-scale models (GEMs) can be used as scaffold for functional estimation analysis at a systematic level, however up to date, there is no integrative toolbox based on GEMs for uncovering metabolic functions. Here, we developed the MetGEMs (metagenome-scale models) toolbox, an open-source application for inferring metabolic functions from 16S rRNA gene sequences to facilitate the study of the human gut microbiome by the wider scientific community. The developed toolbox was validated using shotgun metagenomic data and shown to be superior in predicting functional composition in human clinical samples compared to existing state-of-the-art tools. Therefore, the MetGEMs toolbox was subsequently applied for annotating putative enzyme functions and metabolic routes related in human disease using atopic dermatitis as a case study.
Collapse
Grants
- Kasetsart University Research and Development Institute (KURDI) at Kasetsart University
- Department of Zoology, Faculty of Science, Kasetsart University
- Omics Center for Agriculture, Bioresources, Food, and Health, Kasetsart University (OmiKU)
- Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University
- International Affairs Division (IAD), Kasetsart University
- National Science and Technology Development Agency
- Ratchadapisek Research Funds
- Chulalongkorn University
- Deutsche Forschungsgemeinschaft (DFG) CRC/Transregio 124 “Pathogenic fungi and their human host: Networks of interaction”, subprojects B5 and INF
Collapse
Affiliation(s)
- Preecha Patumcharoenpol
- Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Massalin Nakphaichit
- Department of Biotechnology, Faculty of Agro-Industry, Kasetsart University, Bangkok, Thailand
| | - Gianni Panagiotou
- Systems Biology & Bioinformatics Group, School of Biological Sciences, The University of Hong Kong, Hong Kong S.A.R., China
- Department of Medicine and State Key Laboratory of Pharmaceutical Biotechnology, The University of Hong Kong, Hong Kong S.A.R., China
- Systems Biology & Bioinformatics Unit, Leibniz Institute for Natural Product Research and Infection Biology–Hans Knöll Institute, Jena, Germany
| | - Anchalee Senavonge
- Pediatric Allergy & Clinical Immunology Research Unit, Division of Allergy and Immunology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok, Thailand
| | - Narissara Suratannon
- Pediatric Allergy & Clinical Immunology Research Unit, Division of Allergy and Immunology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok, Thailand
| | - Wanwipa Vongsangnak
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok, Thailand
- Omics Center for Agriculture, Bioresources, Food, and Health, Kasetsart University (OmiKU), Bangkok, Thailand
| |
Collapse
|
27
|
Kingkaw A, Nakphaichit M, Suratannon N, Nitisinprasert S, Wongoutong C, Chatchatee P, Krobthong S, Charoenlappanit S, Roytrakul S, Vongsangnak W. Analysis of the infant gut microbiome reveals metabolic functional roles associated with healthy infants and infants with atopic dermatitis using metaproteomics. PeerJ 2020; 8:e9988. [PMID: 33033661 PMCID: PMC7521340 DOI: 10.7717/peerj.9988] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 08/27/2020] [Indexed: 12/25/2022] Open
Abstract
The infant gut microbiome consists of a complex and diverse microbial community. Comprehensive taxonomic and metabolic functional knowledge about microbial communities supports medical and biological applications, such as fecal diagnostics. Among the omics approaches available for the investigation of microbial communities, metaproteomics-based analysis is a very powerful approach; under this method, the activity of microbial communities is explored by investigating protein expression within a sample. Through use of metaproteomics, this study aimed to investigate the microbial community composition of the infant gut to identify different key proteins playing metabolic functional roles in the microbiome of healthy infants and infants with atopic dermatitis in a Thai population-based birth cohort. Here, 18 fecal samples were analyzed by liquid chromatography-tandem mass spectrometry to conduct taxonomic, functional, and pathway-based protein annotation. Accordingly, 49,973 annotated proteins out of 68,232 total proteins were investigated in gut microbiome samples and compared between the healthy and atopic dermatitis groups. Through differentially expressed proteins (DEPs) analysis, 130 significant DEPs were identified between the healthy and atopic dermatitis groups. Among these DEPs, eight significant proteins were uniquely expressed in the atopic dermatitis group. For instance, triosephosphate isomerase (TPI) in Bifidobacteriaceae in the genus Alloscardovia and demethylmenaquinone methyltransferase (DMM) in Bacteroides were shown to potentially play metabolic functional roles related to disease. PPI network analysis revealed seven reporter proteins showing metabolic alterations between the healthy and disease groups associated with the biosynthesis of ubiquinone and other quinones as well as the energy supply. This study serves as a scaffold for microbial community-wide metabolic functional studies of the infant gut microbiome in relation to allergic disease.
Collapse
Affiliation(s)
- Amornthep Kingkaw
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Massalin Nakphaichit
- Department of Biotechnology, Faculty of Agro-Industry, Kasetsart University, Bangkok, Thailand
| | - Narissara Suratannon
- Pediatric Allergy & Clinical Immunology Research Unit, Division of Allergy and Immunology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, Thailand
| | - Sunee Nitisinprasert
- Department of Biotechnology, Faculty of Agro-Industry, Kasetsart University, Bangkok, Thailand
| | - Chantha Wongoutong
- Department of Statistics, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Pantipa Chatchatee
- Pediatric Allergy & Clinical Immunology Research Unit, Division of Allergy and Immunology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, Thailand
| | - Sucheewin Krobthong
- Proteomics Research Laboratory, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Sawanya Charoenlappanit
- Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Sittiruk Roytrakul
- Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Wanwipa Vongsangnak
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok, Thailand.,Omics Center for Agriculture, Bioresources, Food, and Health, Kasetsart University (OmiKU), Bangkok, Thailand
| |
Collapse
|
28
|
Thananusak R, Laoteng K, Raethong N, Zhang Y, Vongsangnak W. Metabolic Responses of Carotenoid and Cordycepin Biosynthetic Pathways in Cordyceps militaris under Light-Programming Exposure through Genome-Wide Transcriptional Analysis. Biology (Basel) 2020; 9:biology9090242. [PMID: 32825642 PMCID: PMC7576481 DOI: 10.3390/biology9090242] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 08/18/2020] [Accepted: 08/19/2020] [Indexed: 11/16/2022]
Abstract
Cordyceps militaris is currently exploited for commercial production of specialty products as its biomass constituents are enriched in bioactive compounds, such as cordycepin. The rational process development is important for economically feasible production of high quality bioproducts. Light is an abiotic factor affecting the cultivation process of this entomopathogenic fungus, particularly in its carotenoid formation. To uncover the cell response to light exposure, this study aimed to systematically investigate the metabolic responses of C. militaris strain TBRC6039 using integrative genome-wide transcriptome and genome-scale metabolic network (GSMN)-driven analysis. The genome-wide transcriptome analysis showed 8747 expressed genes in the glucose and sucrose cultures grown under light-programming and dark conditions. Of them, 689 differentially expressed genes were significant in response to the light-programming exposure. Through integration with the GSMN-driven analysis using the improved network (iRT1467), the reporter metabolites, e.g., adenosine-5′-monophosphate (AMP) and 2-oxoglutarate, were identified when cultivated under the carotenoid-producing condition controlled by light-programming exposure, linking to up-regulations of the metabolic genes involved in glyoxalase system, as well as cordycepin and carotenoid biosynthesis. These results indicated that C. militaris had a metabolic control in acclimatization to light exposure through transcriptional co-regulation, which supported the cell growth and cordycepin production in addition to the accumulation of carotenoid as a photo-protective bio-pigment. This study provides a perspective in manipulating the metabolic fluxes towards the target metabolites through either genetic or physiological approaches.
Collapse
Affiliation(s)
- Roypim Thananusak
- Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand;
| | - Kobkul Laoteng
- Industrial Bioprocess Technology Research Team, Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand
- Correspondence: (K.L.); (W.V.)
| | - Nachon Raethong
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand;
| | - Yu Zhang
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou 225009, China;
| | - Wanwipa Vongsangnak
- Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand;
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand;
- Omics Center for Agriculture, Bioresources, Food, and Health, Kasetsart University (OmiKU), Bangkok 10900, Thailand
- Correspondence: (K.L.); (W.V.)
| |
Collapse
|
29
|
Nguantad S, Chumnanpuen P, Thancharoen A, Vongsangnak W, Sriboonlert A. Identification of potential candidate genes involved in the sex determination cascade in an aquatic firefly, Sclerotia aquatilis (Coleoptera, Lampyridae). Genomics 2020; 112:2590-2602. [PMID: 32061895 DOI: 10.1016/j.ygeno.2020.01.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 01/13/2020] [Accepted: 01/23/2020] [Indexed: 12/27/2022]
Abstract
Sexual differentiation, dimorphism, and courtship behavior are the downstream developmental programs of the sex determination cascade. The sex determination cascade in arthropods often involves key genes, transformer (tra), doublesex (dsx), transformer-2 (tra2), and fruitless (fru). These genes are conserved among insect taxa; however, they have never been reported in fireflies. In this study, the candidate genes for these key genes were identified for the first time in an aquatic firefly, Sclerotia aquatilis using transcriptome analysis. A comparative protein-protein interaction (PPI) network of sex determination cascade was reconstructed for S. aquatilis based on a network of a model insect, Drosophila melanogaster. Subsequently, a sex determination cascade in S. aquatilis was proposed based on the amino acid sequence structures and expression profiles of these candidates. This study describes the first efforts toward understanding the molecular control of sex determination cascade in fireflies.
Collapse
Affiliation(s)
- Sarintip Nguantad
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Pramote Chumnanpuen
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok, Thailand; Omics Center for Agriculture, Bioresources, Food, and Health, Kasetsart University (OmiKU), Bangkok 10900, Thailand
| | - Anchana Thancharoen
- Department of Entomology, Faculty of Agriculture, Kasetsart University, Bangkok, Thailand
| | - Wanwipa Vongsangnak
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok, Thailand; Omics Center for Agriculture, Bioresources, Food, and Health, Kasetsart University (OmiKU), Bangkok 10900, Thailand.
| | - Ajaraporn Sriboonlert
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand.
| |
Collapse
|
30
|
Kittipongpattana P, Chatchatee P, Senavonge A, Vongsangnak W, Patumcharoenpol P, Weerapakorn W, Nitisinprasert S, Roytrakul S, Nakphaichit M, Suratannon N. Alteration of gut microbiota and microbial products in distinct allergic phenotypes: data from an Asian birth cohort study. J Allergy Clin Immunol 2020. [DOI: 10.1016/j.jaci.2019.12.725] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
31
|
Jatuponwiphat T, Namrak T, Supataragul A, Nitisinprasert S, Nakphaichit M, Vongsangnak W. Comparative genome analysis reveals metabolic traits associated with probiotics properties in Lactobacillus reuteri KUB-AC5. Gene Reports 2019. [DOI: 10.1016/j.genrep.2019.100536] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
|
32
|
Raethong N, Wang H, Nielsen J, Vongsangnak W. Optimizing cultivation of Cordyceps militaris for fast growth and cordycepin overproduction using rational design of synthetic media. Comput Struct Biotechnol J 2019; 18:1-8. [PMID: 31890138 PMCID: PMC6926140 DOI: 10.1016/j.csbj.2019.11.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 11/01/2019] [Accepted: 11/08/2019] [Indexed: 01/17/2023] Open
Abstract
Cordyceps militaris is an entomopathogenic fungus which is often used in Asia as a traditional medicine developed from age-old wisdom. Presently, cordycepin from C. militaris is a great interest in medicinal applications. However, cellular growth of C. militaris and the association with cordycepin production remain poorly understood. To explore the metabolism of C. militaris as potential cell factories in medical and biotechnology applications, this study developed a high-quality genome-scale metabolic model of C. militaris, iNR1329, based on its genomic content and physiological data. The model included a total of 1329 genes, 1821 biochemical reactions, and 1171 metabolites among 4 different cellular compartments. Its in silico growth simulation results agreed well with experimental data on different carbon sources. iNR1329 was further used for optimizing the growth and cordycepin overproduction using a novel approach, POPCORN, for rational design of synthetic media. In addition to the high-quality GEM iNR1329, the presented POPCORN approach was successfully used to rationally design an optimal synthetic medium with C:N ratio of 8:1 for enhancing 3.5-fold increase in cordycepin production. This study thus provides a novel insight into C. militaris physiology and highlights a potential GEM-driven method for synthetic media design and metabolic engineering application. The iNR1329 and the POPCORN approach are available at the GitHub repository: https://github.com/sysbiomics/Cordyceps_militaris-GEM.
Collapse
Affiliation(s)
- Nachon Raethong
- Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Hao Wang
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.,Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden.,National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Chalmers University of Technology, Gothenburg, Sweden
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Wanwipa Vongsangnak
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok, Thailand.,Omics Center for Agriculture, Bioresources, Food, and Health, Kasetsart University (OmiKU), Bangkok, Thailand.,Center for Systems Biology, School of Biology and Basic Medical Sciences, Soochow University, Suzhou, China
| |
Collapse
|
33
|
Zhang Y, Gu T, Chen Y, Zhu G, Vongsangnak W, Xu Q, Chen G. Screening and identification of SipC-interacting proteins in Salmonella enteritidis using Gal4 yeast two-hybrid system in duck. PeerJ 2019; 7:e7663. [PMID: 31565575 PMCID: PMC6746301 DOI: 10.7717/peerj.7663] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 08/12/2019] [Indexed: 11/29/2022] Open
Abstract
The zoonotic pathogen Salmonella not only reduces the production performance in ducks, but also poses a serious threat to human health through eggs and pollutes water bodies through feces. SipC, an effector protein of type III secretion systems (T3SS) in Salmonella, mediates translocation of effectors into the eukaryotic host. However, the precise role of SipC effectors remains unknown in ducks. In this study, the SipC from duck granulosa cells (dGCs) was selected as bait, and the SipC-interacting proteins in Salmonella enteritidis (SE) were screened using Gal4 yeast two-hybrid system in duck. Twelve SipC-interacting proteins were identified. Among those, the p53-effector related to PMP-22 (PERP) and TGF-β activated kinase 1-binding protein 2 (TAB2) were selected to further confirm the function by GST pull-down in vitro. Over-expression of PERP resulted in not only increasing SE adhesion and invasion but also triggering the production of IL-1β and IFN-α in SE infected dGCs, while knock-down PERP showed the opposite tendency (P < 0.01). In addition, TAB2 significantly induced the production of IL-6, IL-1β, IFN-α, and INF-γ in SE infected dGCs (P < 0.05), but did not cause obvious changes in SE adhesion and invasion. When the sipC in SE was deleted, the activities of duck PERP and TAB2 were abolished because they could not bind to SipC. Taken together, although the protein of PERP and TAB2 can interact with SipC, their mechanisms were different in duck challenged by SE. Therefore, PERP was involved in SE invasion and inflammatory response of dGC ovaries, and TAB2 only contributed to dGCs inflammatory response, which provided critical insights about the mechanism in host- bacterium protein interactions during Salmonella invasion in duck.
Collapse
Affiliation(s)
- Yu Zhang
- Joint International Research Laboratory of Agriculture & Agri-Product Safety of Ministry of Education, Yangzhou University, Yangzhou, China.,Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China
| | - Tiantian Gu
- Joint International Research Laboratory of Agriculture & Agri-Product Safety of Ministry of Education, Yangzhou University, Yangzhou, China
| | - Yang Chen
- Joint International Research Laboratory of Agriculture & Agri-Product Safety of Ministry of Education, Yangzhou University, Yangzhou, China
| | - Guoqiang Zhu
- Joint International Research Laboratory of Agriculture & Agri-Product Safety of Ministry of Education, Yangzhou University, Yangzhou, China
| | - Wanwipa Vongsangnak
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Qi Xu
- Joint International Research Laboratory of Agriculture & Agri-Product Safety of Ministry of Education, Yangzhou University, Yangzhou, China
| | - Guohong Chen
- Joint International Research Laboratory of Agriculture & Agri-Product Safety of Ministry of Education, Yangzhou University, Yangzhou, China
| |
Collapse
|
34
|
Chanchay P, Vongsangnak W, Thancharoen A, Sriboonlert A. Reconstruction of insect hormone pathways in an aquatic firefly, Sclerotia aquatilis (Coleoptera: Lampyridae), using RNA-seq. PeerJ 2019; 7:e7428. [PMID: 31396456 PMCID: PMC6681800 DOI: 10.7717/peerj.7428] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Accepted: 07/07/2019] [Indexed: 01/19/2023] Open
Abstract
Insect hormones: ecdysteroids and juvenile hormones have crucial functions during the regulation of different developmental pathways in insects. Insect metamorphosis is one of the primary pathways regulated by these hormones. The insect hormone biosynthetic pathway is conserved among arthropods, including insects, with some variations in the form of hormones used among each group of insects. In this study, the candidate genes involved in the insect hormone pathways and their functional roles were assessed in an aquatic firefly, Sclerotia aquatilis using a high-throughput RNA sequencing technique. Illumina next-generation sequencing (NGS) was used to generate transcriptome data for the different developmental stages (i.e., larva, pupa, and adult) of S. aquatilis. A total of 82,022 unigenes were generated across all different developmental stages. Functional annotation was performed for each gene, based on multiple biological databases, generating 46,230 unigenes. These unigenes were subsequently mapped using KEGG pathways. Accordingly, 221 protein-encoding genes involved in the insect hormone pathways were identified, including, JHAMT, CYP15A1, JHE, and Halloween family genes. Twenty potential gene candidates associated with the biosynthetic and degradation pathways for insect hormones were subjected to real-time PCR, reverse transcriptase PCR (RT-PCR) and sequencing analyses. The real-time PCR results showed similar expression patterns as those observed for transcriptome expression profiles for most of the examined genes. RT-PCR and Sanger sequencing confirmed the expressed coding sequences of these gene candidates. This study is the first to examine firefly insect hormone pathways, facilitating a better understanding of firefly growth and development.
Collapse
Affiliation(s)
- Pornchanan Chanchay
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Wanwipa Vongsangnak
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok, Thailand.,Omics Center for Agriculture, Bioresources, Food, and Health, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Anchana Thancharoen
- Department of Entomology, Faculty of Agriculture, Kasetsart University, Bangkok, Thailand
| | | |
Collapse
|
35
|
Kongsema M, Wongkhieo S, Khongkow M, Lam EWF, Boonnoy P, Vongsangnak W, Wong-Ekkabut J. Molecular mechanism of Forkhead box M1 inhibition by thiostrepton in breast cancer cells. Oncol Rep 2019; 42:953-962. [PMID: 31322278 PMCID: PMC6667886 DOI: 10.3892/or.2019.7225] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 07/03/2019] [Indexed: 12/16/2022] Open
Abstract
Breast cancer is the most common type of malignancies in women worldwide, and genotoxic chemotherapeutic drugs are effective by causing DNA damage in cancer cells. However, >90% of patients with metastatic cancer are resistant to chemotherapy. The Forkhead box M1 (FOXM1) transcription factor plays a pivotal role in the resistance of breast cancer cells to chemotherapy by promoting DNA damage repair following genotoxic drug treatment. The aim of the present study was to investigate the inhibition of the FOXM1 protein by thiostrepton, a natural antibiotic produced by the Streptomyces species. Experimental studies were designed to examine the effectiveness of thiostrepton in downregulating FOXM1 mRNA expression and activity, leading to senescence and apoptosis of breast cancer cells. The cytotoxicity of thiostrepton in breast cancer was determined using cell viability assay. Additionally, thiostrepton treatment decreased the mRNA expression of cyclin B1 (CCNB1), a downstream target of FOXM1. The present results indicated that thiostrepton inhibited FOXM1 mRNA expression and its effect on CCNB1. Molecular dynamic simulations were performed to study the interactions between FOXM1-DNA and thiostrepton after molecular docking. The results revealed that the possible mechanism underlying the inhibitory effect of thiostrepton on FOXM1 function was by forming a tight complex with the DNA and FOXM1 via its binding domain. Collectively, these results indicated that thiostrepton is a specific and direct inhibitor of the FOXM1 protein in breast cancer. The findings of the present study may lead to the development of novel therapeutic strategies for breast cancer and help overcome resistance to conventional chemotherapeutic drugs.
Collapse
Affiliation(s)
- Mesayamas Kongsema
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Sudtirak Wongkhieo
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Mattaka Khongkow
- National Nanotechnology Centre (NANOTEC), National Science and Technology Development Agency, Pathum Thani 12120, Thailand
| | - Eric W-F Lam
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, London W12 0NN, UK
| | - Phansiri Boonnoy
- Computational Biomodelling Laboratory for Agricultural Science and Technology (CBLAST), Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Wanwipa Vongsangnak
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Jirasak Wong-Ekkabut
- Computational Biomodelling Laboratory for Agricultural Science and Technology (CBLAST), Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| |
Collapse
|
36
|
Isarankura Na Ayudhya N, Laoteng K, Song Y, Meechai A, Vongsangnak W. Metabolic traits specific for lipid-overproducing strain of Mucor circinelloides WJ11 identified by genome-scale modeling approach. PeerJ 2019; 7:e7015. [PMID: 31316868 PMCID: PMC6613434 DOI: 10.7717/peerj.7015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 04/20/2019] [Indexed: 01/02/2023] Open
Abstract
The genome-scale metabolic model of a lipid-overproducing strain of Mucor circinelloides WJ11 was developed. The model (iNI1159) contained 1,159 genes, 648 EC numbers, 1,537 metabolites, and 1,355 metabolic reactions, which were localized in different compartments of the cell. Using flux balance analysis (FBA), the iNI1159 model was validated by predicting the specific growth rate. The metabolic traits investigated by phenotypic phase plane analysis (PhPP) showed a relationship between the nutrient uptake rate, cell growth, and the triacylglycerol production rate, demonstrating the strength of the model. A putative set of metabolic reactions affecting the lipid-accumulation process was identified when the metabolic flux distributions under nitrogen-limited conditions were altered by performing fast flux variability analysis (fastFVA) and relative flux change. Comparative analysis of the metabolic models of the lipid-overproducing strain WJ11 (iNI1159) and the reference strain CBS277.49 (iWV1213) using both fastFVA and coordinate hit-and-run with rounding (CHRR) showed that the flux distributions between these two models were significantly different. Notably, a higher flux distribution through lipid metabolisms such as lanosterol, zymosterol, glycerolipid and fatty acids biosynthesis in iNI1159 was observed, leading to an increased lipid production when compared to iWV1213. In contrast, iWV1213 exhibited a higher flux distribution across carbohydrate and amino acid metabolisms and thus generated a high flux for biomass production. This study demonstrated that iNI1159 is an effective predictive tool for the pathway engineering of oleaginous strains for the production of diversified oleochemicals with industrial relevance.
Collapse
Affiliation(s)
- Nattapat Isarankura Na Ayudhya
- Department of Chemical Engineering, Faculty of Engineering, King Mongkut's Institute of Technology Thonburi, Bangkok, Thailand
| | - Kobkul Laoteng
- Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Sciences and Technology Development Agency (NSTDA), Khong Luang, Pathum Thani, Thailand
| | - Yuanda Song
- Colin Ratledge Center for Microbial Lipids, School of Agriculture Engineering and Food Sciences, Shandong University of Technology, Shandong, China
| | - Asawin Meechai
- Department of Chemical Engineering, Faculty of Engineering, King Mongkut's Institute of Technology Thonburi, Bangkok, Thailand
| | - Wanwipa Vongsangnak
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok, Thailand.,Omics Center for Agriculture, Bioresources, Food, and Health, Faculty of Science, Kasetsart University (OmiKU), Bangkok, Thailand
| |
Collapse
|
37
|
Wongsa B, Raethong N, Chumnanpuen P, Wong-Ekkabut J, Laoteng K, Vongsangnak W. Alternative metabolic routes in channeling xylose to cordycepin production of Cordyceps militaris identified by comparative transcriptome analysis. Genomics 2019; 112:629-636. [PMID: 31022437 DOI: 10.1016/j.ygeno.2019.04.015] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 04/14/2019] [Accepted: 04/21/2019] [Indexed: 12/12/2022]
Abstract
The responsive mechanism of C. militaris TBRC7358 on xylose utilization was investigated by comparative analysis of transcriptomes, growth kinetics and cordycepin productions. The result showed that the culture grown on xylose exhibited high production yield of cordycepin on dry biomass. Comparing xylose to other carbon sources, a set of significantly up-regulated genes in xylose were enriched in pentose and glucuronate interconversion, and cordycepin biosynthesis. After validating up-regulated genes using quantitative real-time PCR, interestingly, putative alternative 3'-AMP-associated metabolic route on cordycepin biosynthesis was identified. Through reporter metabolites analysis of C. militaris, significant metabolites (e.g., AMP, glycine and L-glutamate) were identified guiding involvement of growth and cordycepin production. These findings suggested that there was a cooperative mechanism in transcriptional control of the supplying precursors pool directed towards the cordycepin biosynthesis through main and putative alternative metabolic routes for leverage of cell growth and cordycepin production on xylose of C. militaris strain TBRC7358.
Collapse
Affiliation(s)
- Boontariga Wongsa
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Nachon Raethong
- Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Pramote Chumnanpuen
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; Computational Biomodelling Laboratory for Agricultural Science and Technology (CBLAST), Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Jirasak Wong-Ekkabut
- Computational Biomodelling Laboratory for Agricultural Science and Technology (CBLAST), Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; Department of Physics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Kobkul Laoteng
- Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand.
| | - Wanwipa Vongsangnak
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; Omics Center for Agriculture, Bioresources, Food, and Health, Faculty of Science, Kasetsart University (OmiKU), Bangkok 10900, Thailand.
| |
Collapse
|
38
|
Yang J, Li S, Kabir Khan MA, Garre V, Vongsangnak W, Song Y. Increased Lipid Accumulation in Mucor circinelloides by Overexpression of Mitochondrial Citrate Transporter Genes. Ind Eng Chem Res 2019. [DOI: 10.1021/acs.iecr.8b05564] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Junhuan Yang
- Colin Ratledge Center for Microbial Lipids, School of Agriculture Engineering and Food Sciences, Shandong University of Technology, Shandong zibo 255049, P. R. China
| | - Shaoqi Li
- Colin Ratledge Center for Microbial Lipids, School of Agriculture Engineering and Food Sciences, Shandong University of Technology, Shandong zibo 255049, P. R. China
| | - Md. Ahsanul Kabir Khan
- Colin Ratledge Center for Microbial Lipids, School of Agriculture Engineering and Food Sciences, Shandong University of Technology, Shandong zibo 255049, P. R. China
| | - Victoriano Garre
- Departmento de Genética y Microbiología (Unidad Asociada al Instituto de Química Física Rocasolano, Consejo Superior de Investigaciones Científicas), Facultad de Biología, Universidad de Murcia, Murcia 30100, Spain
| | - Wanwipa Vongsangnak
- Omics Center for Agriculture, Bioresources, Food and Health, Faculty of Science, Kasetsart University (OmiKU), Bangkok 10900, Thailand
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Yuanda Song
- Colin Ratledge Center for Microbial Lipids, School of Agriculture Engineering and Food Sciences, Shandong University of Technology, Shandong zibo 255049, P. R. China
| |
Collapse
|
39
|
Nakphaichit M, Sobanbua S, Siemuang S, Vongsangnak W, Nakayama J, Nitisinprasert S. Protective effect of Lactobacillus reuteri KUB-AC5 against Salmonella Enteritidis challenge in chickens. Benef Microbes 2018; 10:43-54. [PMID: 30406695 DOI: 10.3920/bm2018.0034] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Poultry is an important high-quality food and protein source for humans. However, chicken is considered a primary source of foodborne diseases, especially Salmonella Enteritidis infection. Reducing Salmonella contamination in live poultry will thus lower the risk to consumers. Our previous studies reported that Lactobacillus reuteri KUB-AC5 can produce a substance with antimicrobial activity against pathogenic bacteria, especially Salmonella. In vivo testing revealed that this strain greatly influenced the ileal microbiota by improving chicken gastrointestinal health and inhibiting certain pathogenic bacteria. However, its activity against Salmonella in chicken is unknown. This study investigated the effects of the probiotic L. reuteri KUB-AC5 at various concentrations against Salmonella and the microbiota status in the gastrointestinal tract of broiler chickens. Four treatments groups were used: negative-control group (no Salmonella challenge), positive-control group (Salmonella challenge), and 5 or 7 log cfu probiotic supplementation to Salmonella-challenged chickens. The resultant microbial diversities at the growing and finisher stages were not significantly different among the groups (P>0.05). However, a high dosage of KUB-AC5 maintained similar microbial diversity in Salmonella-challenged chickens as observed in the non-challenged group in the early stage. The exposure Salmonella can affect the microbial diversity that consequently contributes to the disease progression in chicken. Low and high dosages of KUB-AC5 eliminated S. Enteritidis from the ileum and caecum at 14, 21 and 35 days of age. A high-dose of KUB-AC5 also enhanced Lactobacillaceae levels in the growing stage in both the ileum and caecum and suppressed Enterobacteriaceae levels in the finisher stage on day 35, whereas these effects were not observed in the low dose of KUB-AC5 or control groups. These results support the potential value of high-dose L. reuteri KUB-AC5 supplementation for three days after hatching in preventing Salmonella infection in chickens.
Collapse
Affiliation(s)
- M Nakphaichit
- 1 Department of Biotechnology, Faculty of Agro-Industry, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - S Sobanbua
- 1 Department of Biotechnology, Faculty of Agro-Industry, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - S Siemuang
- 2 Research and development center, Betagro group, 136 Moo 9, Klong Nueng, Klong Luang Pathumthani 12120, Thailand
| | - W Vongsangnak
- 3 Department of Zoology, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand.,4 Computational Biomodelling Laboratory for Agricultural Science and Technology (CBLAST), Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - J Nakayama
- 5 Laboratory of Microbial Technology, Division of Applied Molecular Microbiology and Biomass Chemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, Higashi-ku, Fukuoka 812-8581, Japan
| | - S Nitisinprasert
- 1 Department of Biotechnology, Faculty of Agro-Industry, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| |
Collapse
|
40
|
Raethong N, Laoteng K, Vongsangnak W. Uncovering global metabolic response to cordycepin production in Cordyceps militaris through transcriptome and genome-scale network-driven analysis. Sci Rep 2018; 8:9250. [PMID: 29915355 PMCID: PMC6006141 DOI: 10.1038/s41598-018-27534-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 06/05/2018] [Indexed: 01/09/2023] Open
Abstract
The cellular metabolic adaptations of Cordyceps militaris have been progressively studied. In particular, the cordycepin pathway is of interest in medicinal applications. Even though the metabolic pathways for cordycepin production are known to be related to different carbon sources, the regulatory mechanisms at a systems level are poorly characterized. To explore the regulatory mechanisms, this study therefore aimed to investigate the global metabolic response to cordycepin production in C. militaris through transcriptome analysis and genome-scale network-driven analysis. Here, transcriptome analysis of 16,805 expressed genes in C. militaris strain TBRC6039 grown on different carbon sources was performed. Of these genes, 2,883 were significantly differentially expressed genes, uncovering sucrose- and glucose-mediated changes in the transcriptional regulation of central carbon metabolism in C. militaris, which was shown using the CmSNF1 mechanism as an example. After applying genome-scale metabolic network-driven analysis, reporter metabolites and key metabolic subnetworks involving adenosine, cordycepin and methionine were proposed through the up-regulation of cordycepin biosynthetic genes. Our findings suggest that the transcriptional regulation of these pathways is a ubiquitous feature in response to specific culture conditions during cordycepin overproduction.
Collapse
Affiliation(s)
- Nachon Raethong
- Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Kobkul Laoteng
- Bioprocess Technology Laboratory, Food Biotechnology Research Unit, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand
| | - Wanwipa Vongsangnak
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand. .,Computational Biomodelling Laboratory for Agricultural Science and Technology (CBLAST), Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand.
| |
Collapse
|
41
|
Vongsangnak W, Chumnanpuen P, Sriboonlert A. Transcriptome analysis reveals candidate genes involved in luciferin metabolism in Luciola aquatilis (Coleoptera: Lampyridae). PeerJ 2016; 4:e2534. [PMID: 27761329 PMCID: PMC5068357 DOI: 10.7717/peerj.2534] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Accepted: 09/06/2016] [Indexed: 12/31/2022] Open
Abstract
Bioluminescence, which living organisms such as fireflies emit light, has been studied extensively for over half a century. This intriguing reaction, having its origins in nature where glowing insects can signal things such as attraction or defense, is now widely used in biotechnology with applications of bioluminescence and chemiluminescence. Luciferase, a key enzyme in this reaction, has been well characterized; however, the enzymes involved in the biosynthetic pathway of its substrate, luciferin, remains unsolved at present. To elucidate the luciferin metabolism, we performed a de novo transcriptome analysis using larvae of the firefly species, Luciola aquatilis. Here, a comparative analysis is performed with the model coleopteran insect Tribolium casteneum to elucidate the metabolic pathways in L. aquatilis. Based on a template luciferin biosynthetic pathway, combined with a range of protein and pathway databases, and various prediction tools for functional annotation, the candidate genes, enzymes, and biochemical reactions involved in luciferin metabolism are proposed for L. aquatilis. The candidate gene expression is validated in the adult L. aquatilis using reverse transcription PCR (RT-PCR). This study provides useful information on the bio-production of luciferin in the firefly and will benefit to future applications of the valuable firefly bioluminescence system.
Collapse
Affiliation(s)
- Wanwipa Vongsangnak
- Department of Zoology, Kasetsart University, Bangkok, Thailand; Computational Biomodelling Laboratory for Agricultural Science and Technology (CBLAST), Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Pramote Chumnanpuen
- Department of Zoology, Kasetsart University, Bangkok, Thailand; Computational Biomodelling Laboratory for Agricultural Science and Technology (CBLAST), Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Ajaraporn Sriboonlert
- Department of Genetics, Kasetsart University, Bangkok, Thailand; Centre for Advanced Studies in Tropical Natural Resources, Kasetsart University, Bangkok, Thailand
| |
Collapse
|
42
|
Vongsangnak W, Klanchui A, Tawornsamretkit I, Tatiyaborwornchai W, Laoteng K, Meechai A. Genome-scale metabolic modeling of Mucor circinelloides and comparative analysis with other oleaginous species. Gene 2016; 583:121-129. [DOI: 10.1016/j.gene.2016.02.028] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 12/31/2015] [Accepted: 02/08/2016] [Indexed: 11/29/2022]
|
43
|
Patumcharoenpol P, Doungpan N, Meechai A, Shen B, Chan JH, Vongsangnak W. An integrated text mining framework for metabolic interaction network reconstruction. PeerJ 2016; 4:e1811. [PMID: 27019783 PMCID: PMC4806637 DOI: 10.7717/peerj.1811] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 02/24/2016] [Indexed: 11/20/2022] Open
Abstract
Text mining (TM) in the field of biology is fast becoming a routine analysis for the extraction and curation of biological entities (e.g., genes, proteins, simple chemicals) as well as their relationships. Due to the wide applicability of TM in situations involving complex relationships, it is valuable to apply TM to the extraction of metabolic interactions (i.e., enzyme and metabolite interactions) through metabolic events. Here we present an integrated TM framework containing two modules for the extraction of metabolic events (Metabolic Event Extraction module—MEE) and for the construction of a metabolic interaction network (Metabolic Interaction Network Reconstruction module—MINR). The proposed integrated TM framework performed well based on standard measures of recall, precision and F-score. Evaluation of the MEE module using the constructed Metabolic Entities (ME) corpus yielded F-scores of 59.15% and 48.59% for the detection of metabolic events for production and consumption, respectively. As for the testing of the entity tagger for Gene and Protein (GP) and metabolite with the test corpus, the obtained F-score was greater than 80% for the Superpathway of leucine, valine, and isoleucine biosynthesis. Mapping of enzyme and metabolite interactions through network reconstruction showed a fair performance for the MINR module on the test corpus with F-score >70%. Finally, an application of our integrated TM framework on a big-scale data (i.e., EcoCyc extraction data) for reconstructing a metabolic interaction network showed reasonable precisions at 69.93%, 70.63% and 46.71% for enzyme, metabolite and enzyme–metabolite interaction, respectively. This study presents the first open-source integrated TM framework for reconstructing a metabolic interaction network. This framework can be a powerful tool that helps biologists to extract metabolic events for further reconstruction of a metabolic interaction network. The ME corpus, test corpus, source code, and virtual machine image with pre-configured software are available at www.sbi.kmutt.ac.th/ preecha/metrecon.
Collapse
Affiliation(s)
- Preecha Patumcharoenpol
- Systems Biology and Bioinformatics Laboratory, King Mongkut's University of Technology Thonburi, Bangkok, Thailand.,Center for Systems Biology, Soochow University, Suzhou, China
| | - Narumol Doungpan
- School of Information Technology, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Asawin Meechai
- Systems Biology and Bioinformatics Laboratory, King Mongkut's University of Technology Thonburi, Bangkok, Thailand.,Department of Chemical Engineering, Faculty of Engineering, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Bairong Shen
- Center for Systems Biology, Soochow University, Suzhou, China
| | - Jonathan H Chan
- Systems Biology and Bioinformatics Laboratory, King Mongkut's University of Technology Thonburi, Bangkok, Thailand.,School of Information Technology, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Wanwipa Vongsangnak
- Center for Systems Biology, Soochow University, Suzhou, China.,Department of Zoology, Faculty of Science, Kasetsart University, Bangkok, Thailand
| |
Collapse
|
44
|
Kittichotirat W, Engchuan W, Vongsangnak W, Meechai A. Preface to selected papers from the 6th International Conference on Computational Systems-Biology and Bioinformatics (CSBio2015). J Bioinform Comput Biol 2016; 14:1602001. [PMID: 26762476 DOI: 10.1142/s0219720016020017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
| | | | | | - Asawin Meechai
- 1 King Mongkut's University of Technology Thonburi, Thailand
| |
Collapse
|
45
|
Klanchui A, Raethong N, Prommeenate P, Vongsangnak W, Meechai A. Cyanobacterial Biofuels: Strategies and Developments on Network and Modeling. Adv Biochem Eng Biotechnol 2016; 160:75-102. [PMID: 27783135 DOI: 10.1007/10_2016_42] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Cyanobacteria, the phototrophic microorganisms, have attracted much attention recently as a promising source for environmentally sustainable biofuels production. However, barriers for commercial markets of cyanobacteria-based biofuels concern the economic feasibility. Miscellaneous strategies for improving the production performance of cyanobacteria have thus been developed. Among these, the simple ad hoc strategies resulting in failure to optimize fully cell growth coupled with desired product yield are explored. With the advancement of genomics and systems biology, a new paradigm toward systems metabolic engineering has been recognized. In particular, a genome-scale metabolic network reconstruction and modeling is a crucial systems-based tool for whole-cell-wide investigation and prediction. In this review, the cyanobacterial genome-scale metabolic models, which offer a system-level understanding of cyanobacterial metabolism, are described. The main process of metabolic network reconstruction and modeling of cyanobacteria are summarized. Strategies and developments on genome-scale network and modeling through the systems metabolic engineering approach are advanced and employed for efficient cyanobacterial-based biofuels production.
Collapse
Affiliation(s)
- Amornpan Klanchui
- Biological Engineering Program, Faculty of Engineering, King Mongkut's University of Technology Thonburi, Bangkok, 10140, Thailand
| | - Nachon Raethong
- Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Peerada Prommeenate
- Biochemical Engineering and Pilot Plant Research and Development (BEC) Unit, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Wanwipa Vongsangnak
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand.,Computational Biomodelling Laboratory for Agricultural Science and Technology (CBLAST), Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Asawin Meechai
- Department of Chemical Engineering, Faculty of Engineering, King Mongkut's University of Technology Thonburi, Bangkok, 10140, Thailand.
| |
Collapse
|
46
|
Hu G, Xiao F, Li Y, Li Y, Vongsangnak W. Protein-Protein Interface and Disease: Perspective from Biomolecular Networks. Adv Biochem Eng Biotechnol 2016; 160:57-74. [PMID: 27928579 DOI: 10.1007/10_2016_40] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Protein-protein interactions are involved in many important biological processes and molecular mechanisms of disease association. Structural studies of interfacial residues in protein complexes provide information on protein-protein interactions. Characterizing protein-protein interfaces, including binding sites and allosteric changes, thus pose an imminent challenge. With special focus on protein complexes, approaches based on network theory are proposed to meet this challenge. In this review we pay attention to protein-protein interfaces from the perspective of biomolecular networks and their roles in disease. We first describe the different roles of protein complexes in disease through several structural aspects of interfaces. We then discuss some recent advances in predicting hot spots and communication pathway analysis in terms of amino acid networks. Finally, we highlight possible future aspects of this area with respect to both methodology development and applications for disease treatment.
Collapse
Affiliation(s)
- Guang Hu
- Center for Systems Biology, School of Electronic and Information Engineering, Soochow University, Suzhou, 215006, China.
| | - Fei Xiao
- School of Basic Medicine and Biological Sciences, Medical College of Soochow University, Suzhou, 215123, China
| | - Yuqian Li
- School of Electronic Engineering, University of Electronic Science and Technology of China, Chengdu, 611731, China
| | - Yuan Li
- Center for Systems Biology, School of Electronic and Information Engineering, Soochow University, Suzhou, 215006, China
| | - Wanwipa Vongsangnak
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand.
- Computational Biomodelling Laboratory for Agricultural Science and Technology (CBLAST), Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand.
| |
Collapse
|
47
|
Xiao F, Yang M, Xu Y, Vongsangnak W. Comparisons of Prostate Cancer Inhibitors Abiraterone and TOK-001 Binding with CYP17A1 through Molecular Dynamics. Comput Struct Biotechnol J 2015; 13:520-7. [PMID: 26682016 PMCID: PMC4652021 DOI: 10.1016/j.csbj.2015.10.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Revised: 10/25/2015] [Accepted: 10/26/2015] [Indexed: 12/19/2022] Open
Abstract
Cytochrome P450 17A1 (CYP17A1) is associated in the steroid hormone biosynthesis in human. As cell proliferation of prostate cancer in response to androgen steroid, an inhibition of CYP17A1 becomes an alternative approach to inhibit biosynthesis of androgen and support treatment of prostate cancer. However, biology-driven inhibitor development of prostate cancer is poorly elucidated. The aims of this study are to address structural differences at atomic-level between CYP17A1 and inhibitors i.e., abiraterone and TOK-001, and further investigate the effect of point mutation of CYP17A1 on the active site stability and the local interactions that are hydrophobic interaction and hydrogen bonding throughout molecular dynamics (MD) simulation. After performing multiple comparisons among four different complexes across CYP17A1 and inhibitors, interestingly TOK-001 oriented toward the active pocket and formed larger volume with I-helix of CYP17A1 than abiraterone, whereas abiraterone showed tighter binding and more active site stability. Considering on the effect of hydrophobic interaction and hydrogen bonding between abiraterone and CYP17A1, the key residues of Phe114, Ile371, Val482, and Asn202 were identified. This contributes into tight binding interactions; however abiraterone is effectively weakened along with the global conformation mobility increased in A105L mutation. Surprisingly, overall conformation of the CYP17A1 remained stable when bound to TOK-001. This basic knowledge can guide future experiments on design of efficient inhibitors for CYP17A1, which provides theoretical basis of androgen-dependent disease therapy.
Collapse
Affiliation(s)
- Fei Xiao
- School of Biology and Basic Medical Sciences, Medical College of Soochow University, 199 Ren ai Road, China-Singapore Industrial Park, Suzhou, JiangSu 215123, China
- Corresponding authors.
| | - Maohua Yang
- School of Biology and Basic Medical Sciences, Medical College of Soochow University, 199 Ren ai Road, China-Singapore Industrial Park, Suzhou, JiangSu 215123, China
| | - Youjun Xu
- School of Biology and Basic Medical Sciences, Medical College of Soochow University, 199 Ren ai Road, China-Singapore Industrial Park, Suzhou, JiangSu 215123, China
| | - Wanwipa Vongsangnak
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Corresponding authors.
| |
Collapse
|
48
|
Li Y, Vongsangnak W, Chen L, Shen B. Integrative analysis reveals disease-associated genes and biomarkers for prostate cancer progression. BMC Med Genomics 2014; 7 Suppl 1:S3. [PMID: 25080090 PMCID: PMC4110715 DOI: 10.1186/1755-8794-7-s1-s3] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
|
49
|
Huang ML, Wattanachaisaereekul S, Han YJ, Vongsangnak W. In silico analysis of plant and animal transposable elements. Int J Bioinform Res Appl 2014; 10:297-306. [PMID: 24794071 DOI: 10.1504/ijbra.2014.060763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Transposable Elements (TEs) play important roles in the evolution of eukaryotic organisms. TEs widely distribute depending on their properties present in the genome. This study elucidated the molecular characteristics of TEs in land plants and animals using bioinformatics and in silico mutational approach. We discovered that the GC-rich class I TEs is the predominant class of TEs in animal, but the AT-rich class II TEs is prevalent in plants. The GC-rich class I TEs appears to be evolved within the animals. On contrary, the preserved in AT-rich in class II TEs is believed to be contributed in host defence systems.
Collapse
Affiliation(s)
- Mo-Li Huang
- Center for Systems Biology, Soochow University, Suzhou 215006, China
| | - Songsak Wattanachaisaereekul
- Pilot Plant Development and Training Institute, King Mongkut's University of Technology, Thonburi, Bangkhunthian, Bangkok 10150, Thailand
| | - Yu-Jun Han
- Center for Human Genome Variation, Duke University School of Medicine, Durham, NC 27708, USA
| | | |
Collapse
|
50
|
Jiang J, Cui W, Vongsangnak W, Hu G, Shen B. Post genome-wide association studies functional characterization of prostate cancer risk loci. BMC Genomics 2013; 14 Suppl 8:S9. [PMID: 24564736 PMCID: PMC4042239 DOI: 10.1186/1471-2164-14-s8-s9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Background Over the last decade, genome-wide association studies (GWAS) have discovered many risk associated single nucleotide polymorphisms (SNPs) of prostate cancer (PCa). However, the majority of the associated PCa SNPs, including those in linkage disequilibrium (LD) blocks, are generally not located in protein coding regions. The systematical investigation of the functional roles of these SNPs, especially the non-coding SNPs, becomes very necessary and helpful to the understanding of the molecular mechanism of PCa. Results In this work, we proposed a comprehensive framework at network level to integrate the SNP annotation, target gene assignment, gene ontology (GO) classification, pathway enrichment analysis and regulatory network reconstruction to illustrate the molecular functions of PCa associated SNPs. By LD expansion, we first identified 1828 LD SNPs using 49 reported GWAS SNPs as a start. We carefully annotated these 1828 LD SNPs via either UCSC known genes, UCSC regulation elements, or expression Quantitative Trait Loci (eQTL) data. As a result, we found 1154 SNPs were functionally annotated and obtained 205 unique PCa genes for further enrichment analysis. The enriched GO biological processes and pathways were found mainly related to regulation of cell death, apoptosis, cell proliferation, and metabolic process, which have been proved essential to cancer development. We constructed PCa genes specific transcription regulatory networks, finding several important genetic regulators for PCa, such as IGF-1/IGF-2 receptors, SP1, CREB1, and androgen receptor (AR). Conclusions A comprehensive framework was proposed for integrative and systematic analysis of PCa SNPs, the analysis can provide essential information for the understanding of the regulatory function of GWAS SNPs in PCa, and will facilitate the discovery of novel candidate biomarkers for diagnosis and prognosis of PCa.
Collapse
|