1
|
Tec-Campos D, Posadas C, Tibocha-Bonilla JD, Thiruppathy D, Glonek N, Zuñiga C, Zepeda A, Zengler K. The genome-scale metabolic model for the purple non-sulfur bacterium Rhodopseudomonas palustris Bis A53 accurately predicts phenotypes under chemoheterotrophic, chemoautotrophic, photoheterotrophic, and photoautotrophic growth conditions. PLoS Comput Biol 2023; 19:e1011371. [PMID: 37556472 PMCID: PMC10441798 DOI: 10.1371/journal.pcbi.1011371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 08/21/2023] [Accepted: 07/18/2023] [Indexed: 08/11/2023] Open
Abstract
The purple non-sulfur bacterium Rhodopseudomonas palustris is recognized as a critical microorganism in the nitrogen and carbon cycle and one of the most common members in wastewater treatment communities. This bacterium is metabolically extremely versatile. It is capable of heterotrophic growth under aerobic and anaerobic conditions, but also able to grow photoautotrophically as well as mixotrophically. Therefore R. palustris can adapt to multiple environments and establish commensal relationships with other organisms, expressing various enzymes supporting degradation of amino acids, carbohydrates, nucleotides, and complex polymers. Moreover, R. palustris can degrade a wide range of pollutants under anaerobic conditions, e.g., aromatic compounds such as benzoate and caffeate, enabling it to thrive in chemically contaminated environments. However, many metabolic mechanisms employed by R. palustris to breakdown and assimilate different carbon and nitrogen sources under chemoheterotrophic or photoheterotrophic conditions remain unknown. Systems biology approaches, such as metabolic modeling, have been employed extensively to unravel complex mechanisms of metabolism. Previously, metabolic models have been reconstructed to study selected capabilities of R. palustris under limited experimental conditions. Here, we developed a comprehensive metabolic model (M-model) for R. palustris Bis A53 (iDT1294) consisting of 2,721 reactions, 2,123 metabolites, and comprising 1,294 genes. We validated the model using high-throughput phenotypic, physiological, and kinetic data, testing over 350 growth conditions. iDT1294 achieved a prediction accuracy of 90% for growth with various carbon and nitrogen sources and close to 80% for assimilation of aromatic compounds. Moreover, the M-model accurately predicts dynamic changes of growth and substrate consumption rates over time under nine chemoheterotrophic conditions and demonstrated high precision in predicting metabolic changes between photoheterotrophic and photoautotrophic conditions. This comprehensive M-model will help to elucidate metabolic processes associated with the assimilation of multiple carbon and nitrogen sources, anoxygenic photosynthesis, aromatic compound degradation, as well as production of molecular hydrogen and polyhydroxybutyrate.
Collapse
Affiliation(s)
- Diego Tec-Campos
- Facultad de Ingeniería Química, Universidad Autónoma de Yucatán, Mérida, Yucatán, México
- Department of Pediatrics, University of California, San Diego, La Jolla, California, United States of America
| | - Camila Posadas
- Facultad de Ingeniería Química, Universidad Autónoma de Yucatán, Mérida, Yucatán, México
| | - Juan D. Tibocha-Bonilla
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, California, United States of America
| | - Deepan Thiruppathy
- Department of Pediatrics, University of California, San Diego, La Jolla, California, United States of America
- Department of Bioengineering, University of California, San Diego, La Jolla California, United States of America
| | - Nathan Glonek
- Department of Pediatrics, University of California, San Diego, La Jolla, California, United States of America
| | - Cristal Zuñiga
- Department of Pediatrics, University of California, San Diego, La Jolla, California, United States of America
| | - Alejandro Zepeda
- Facultad de Ingeniería Química, Universidad Autónoma de Yucatán, Mérida, Yucatán, México
| | - Karsten Zengler
- Department of Pediatrics, University of California, San Diego, La Jolla, California, United States of America
- Department of Bioengineering, University of California, San Diego, La Jolla California, United States of America
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, California, United States of America
| |
Collapse
|
2
|
Hepatoprotective Effect of Grape Seed and Skin Extract Against Lithium Exposure Examined by the Window of Proteomics. Dose Response 2022; 20:15593258221141585. [DOI: 10.1177/15593258221141585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 11/07/2022] [Indexed: 11/23/2022] Open
Abstract
Context The liver is the organ by which the majority of substances are metabolized, including psychotropic drugs. Lithium (Li) used as drug for many neurological disorders such as bipolar disorders. Objective This study aims to assess lithium toxicity and to evaluate the hepatic-protective properties of a grape skin seed and extract (GSSE). Materials and methods Twenty-four male Wistar rats were exposed for 30 days to either various lithium concentrations, GSSE alone, or lithium supplemented with GSSE. The proteomic analysis revealed alterations of liver protein profiles after lithium treatments that were successfully identified by mass spectrometry. Results Lithium treatment induced an oxidative damage by the alteration of antioxidant enzymes activities such as superoxide dismutase, CAT, and Gpx. The regulated proteins are mainly involved in the respiratory electron transport chain, detoxification processes, ribosomal stress pathway, glycolysis, and cytoskeleton. Proteins were differentially expressed in a dose-dependent manner. Interestingly, GSSE reversed the situation and restored the level of liver proteins whose abundance was modified after lithium treatment, arguing for its protective activity. Conclusion Our data demonstrated the ability of proteomic analysis to underline the toxicity mechanisms of lithium in animal models. Based on these results, GSSE may be envisaged as a nutritional supplement to weaken the liver toxicity of lithium.
Collapse
|
3
|
Yankey R, Omoor INA, Karanja JK, Wang L, Urga RT, Fang CH, Dongmei L, Lin H, Okal JE, Datti IL, Nsanzinshuti A, Rensing C, Lin Z. Metabolic properties, gene functions, and biosafety analysis reveal the action of three rhizospheric plant growth-promoting bacteria of Jujuncao (Pennisetum giganteum). ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:38435-38449. [PMID: 35079973 DOI: 10.1007/s11356-021-17854-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 11/26/2021] [Indexed: 06/14/2023]
Abstract
This study aimed to identify the specific genes associated with plant growth promotion and cadmium tolerance in three bacteria strains associated with Pennisetum giganteum as well as to determine their biosafety levels in their potential use as biofertilizers for promoting plant growth and phytoremediation activities. The plant growth-promoting (PGP) abilities of Enterobacter cloacae strain RCB980 (A3), Klebsiella pneumonia strain kpa (A4), and Klebsiella sp. strain XT-2 (A7) were determined by a growth promotion trial and through testing for PGP traits such as 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase enzyme production, phosphorus solubilization, siderophore synthesis, and indole-3 acetic acid (IAA) production. The genes that potentially contribute to the beneficial activities of these three strains were identified through an analysis of their genomes. To establish the biosafety of the candidate PGPB, a pathological study was undertaken whereby 20 Kunming mice were injected intraperitoneally to study and analyze the effects of the strains on growth and lung paraffin sections of the mice. The strains had no obvious toxicity effect on the tested mice and were therefore not considered as highly virulent strains. These strains are thus considered non-toxic, safe, and highly recommended for use in environmental remediation strategies and agricultural production.
Collapse
Affiliation(s)
- Richard Yankey
- China National Engineering Research Center of Juncao Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.
- Department of Soil Science, College of Agriculture and Natural Sciences, University of Cape Coast, Cape Coast, Ghana.
| | - Ibrahim N A Omoor
- China National Engineering Research Center of Juncao Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Joseph K Karanja
- Center for Plant Water-Use and Nutrition Regulation, Joint International Research Laboratory of Water and Nutrient in Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Lifang Wang
- China National Engineering Research Center of Juncao Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Regassa Terefe Urga
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Chew Hui Fang
- China National Engineering Research Center of Juncao Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Lin Dongmei
- China National Engineering Research Center of Juncao Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Hui Lin
- China National Engineering Research Center of Juncao Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Jacob Eyalira Okal
- China National Engineering Research Center of Juncao Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Ibrahim Lawandi Datti
- China National Engineering Research Center of Juncao Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Aimable Nsanzinshuti
- China National Engineering Research Center of Juncao Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Christopher Rensing
- Institute of Environmental Microbiology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Zhanxi Lin
- China National Engineering Research Center of Juncao Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| |
Collapse
|
4
|
ITRAQ-Based Quantitative Proteomics Reveals the Proteome Profiles of Primary Duck Embryo Fibroblast Cells Infected with Duck Tembusu Virus. BIOMED RESEARCH INTERNATIONAL 2019; 2019:1582709. [PMID: 30809531 PMCID: PMC6369498 DOI: 10.1155/2019/1582709] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 11/26/2018] [Accepted: 12/13/2018] [Indexed: 11/18/2022]
Abstract
Outbreaks of duck Tembusu virus (DTMUV) have caused substantial economic losses in the major duck-producing regions of China since 2010. To improve our understanding of the host cellular responses to virus infection and the pathogenesis of DTMUV infection, we applied isobaric tags for relative and absolute quantification (iTRAQ) labeling coupled with multidimensional liquid chromatography-tandem mass spectrometry to detect the protein changes in duck embryo fibroblast cells (DEFs) infected and mock-infected with DTMUV. In total, 434 cellular proteins were differentially expressed, among which 116, 76, and 339 proteins were differentially expressed in the DTMUV-infected DEFs at 12, 24, and 42 hours postinfection, respectively. The Gene Ontology analysis indicated that the biological processes of the differentially expressed proteins were primarily related to cellular processes, metabolic processes, biological regulation, response to stimulus, and cellular organismal processes and that the molecular functions in which the differentially expressed proteins were mainly involved were binding and catalytic activity. Some selected proteins that were found to be differentially expressed in DTMUV-infected DEFs were further confirmed by real-time PCR. The results of this study provide valuable insight into DTMUV-host interactions. This could lead to a better understanding of DTMUV infection mechanisms.
Collapse
|
5
|
Structural basis for the magnesium-dependent activation of transketolase from Chlamydomonas reinhardtii. Biochim Biophys Acta Gen Subj 2017; 1861:2132-2145. [DOI: 10.1016/j.bbagen.2017.05.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 05/20/2017] [Accepted: 05/23/2017] [Indexed: 01/18/2023]
|
6
|
Chen YY, Chan KM. Differential effects of metal ions on TCDD-induced cytotoxicity and cytochrome P4501A1 gene expression in a zebrafish liver (ZFL) cell-line. Metallomics 2016; 8:236-51. [PMID: 26612010 DOI: 10.1039/c5mt00219b] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Trace metal ions and trace organic compounds are common co-contaminants in the environment that pose risks to human health. We evaluated the effects of four metal ions (As(3+), Cu(2+), Hg(2+), and Zn(2+)) on 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) induced cytotoxicity and the expression of the cytochrome P4501A1 gene (cyp1a1) in the zebrafish liver (ZFL) cell line. A metal accumulation study showed that Cu and Zn did not accumulate in ZFL cells. However, As and Hg did accumulate, which resulted in the inhibition of TCDD-mediated induction of cyp1a1 mRNA and protein expression, and 7-ethoxyresorufin O-deethylase activity. A luciferase assay showed that both As(3+) and Hg(2+) inhibited the TCDD-induced activity of gene constructs containing either synthetic 3XRE or a distal cyp1a1 promoter region, implying that the decreased levels of TCDD-induced cyp1a1 were due to transcriptional effects. A proteomic study showed that the toxic effects of As(3+) might be due to changes in cellular metabolic processes, the cellular stimulation response and the cellular redox state in ZFL cells.
Collapse
Affiliation(s)
- Ying Ying Chen
- School of Life Sciences, Chinese University, Sha Tin, Hong Kong SAR, China.
| | - King Ming Chan
- School of Life Sciences, Chinese University, Sha Tin, Hong Kong SAR, China.
| |
Collapse
|
7
|
Zhuang H, Gan Z, Jiang W, Zhang X, Hua ZC. Comparative proteomics analysis reveals roles for FADD in the regulation of energy metabolism and proteolysis pathway in mouse embryonic fibroblast. Proteomics 2013; 13:2398-413. [PMID: 23744592 DOI: 10.1002/pmic.201300017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Revised: 05/01/2013] [Accepted: 05/16/2013] [Indexed: 12/19/2022]
Abstract
Fas-associated death domain-containing protein (FADD) is a classical apoptotic pathway adaptor. Further studies revealed that it also plays essential roles in nonapoptotic processes, which is assumed to be regulated by its phosphorylation. However, the exact mechanisms are still poorly understood. To study the nonapoptotic effects of FADD, a comprehensive strategy of proteomics identification combined with bioinformatic analysis was undertaken to identify proteins differentially expressed in three cell lines containing FADD and its mutant, FADD-A and FADD-D. The cell lines were thought to bear wild-type FADD, unphosphorylated FADD mimic and constitutive phosphorylated FADD mimic, respectively. A total of 47 proteins were identified to be significantly changed due to FADD phosphorylation. Network analysis using MetaCore™ identified a number of changed proteins that were involved in cellular metabolic process, including lipid metabolism, fatty acid metabolism, glycolysis, and oxidative phosphorylation. The finding that FADD-D cell line showed an increase in fatty acid oxidation argues that it could contribute to the leaner phenotype of FADD-D mice as reported previously. In addition, six proteins related to the ubiquitin-proteasome pathway were also specifically overexpressed in FADD-D cell line. Finally, the c-Myc gene represents a convergent hub lying at the center of dysregulated pathways, and was upregulated in FADD-D cells. Taken together, these studies allowed us to conclude that impaired mitochondrial function and proteolysis might play pivotal roles in the dysfunction associated with FADD phosphorylation-induced disorders.
Collapse
Affiliation(s)
- Hongqin Zhuang
- The State Key Laboratory of Pharmaceutical Biotechnology, College of Life Science and School of Stomatology, Affiliated Stomatological Hospital, Nanjing University, Nanjing, PR China
| | | | | | | | | |
Collapse
|
8
|
Systems biology of meridians, acupoints, and chinese herbs in disease. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2012; 2012:372670. [PMID: 23118787 PMCID: PMC3483864 DOI: 10.1155/2012/372670] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Accepted: 09/26/2012] [Indexed: 02/07/2023]
Abstract
Meridians, acupoints, and Chinese herbs are important components of traditional Chinese medicine (TCM). They have been used for disease treatment and prevention and as alternative and complementary therapies. Systems biology integrates omics data, such as transcriptional, proteomic, and metabolomics data, in order to obtain a more global and complete picture of biological activity. To further understand the existence and functions of the three components above, we reviewed relevant research in the systems biology literature and found many recent studies that indicate the value of acupuncture and Chinese herbs. Acupuncture is useful in pain moderation and relieves various symptoms arising from acute spinal cord injury and acute ischemic stroke. Moreover, Chinese herbal extracts have been linked to wound repair, the alleviation of postmenopausal osteoporosis severity, and anti-tumor effects, among others. Different acupoints, variations in treatment duration, and herbal extracts can be used to alleviate various symptoms and conditions and to regulate biological pathways by altering gene and protein expression. Our paper demonstrates how systems biology has helped to establish a platform for investigating the efficacy of TCM in treating different diseases and improving treatment strategies.
Collapse
|