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Xiao J, Sun S, Liu Z, Fan C, Zhu B, Zhang D. Analysis of key genes for the survival of Pantoea agglomerans under nutritional stress. Int J Biol Macromol 2023; 253:127059. [PMID: 37769756 DOI: 10.1016/j.ijbiomac.2023.127059] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 09/13/2023] [Accepted: 09/18/2023] [Indexed: 10/03/2023]
Abstract
The absolute amount of nutrients on plant leaves is usually low, and the growth of epiphytic bacteria is typically limited by nutrient content. Thus, is of great significance to study the survival mechanism of epiphytes under nutritional stress for plant disease control. In this paper, Pantoea agglomerans CHTF15 isolated from walnut leaves was used to detect the key genes for the survival of the bacterium under simulated nutrient stress in artificial medium. Genome sequencing was combined with transposon insertion sequencing (Tn-seq) for the detection technique. A total of 105 essential genes were screened from the whole genome. The genes were mainly related to the nucleotide metabolism, protein metabolism, biological oxidation and the gene repair of bacteria analyzed by gene ontology (GO) enrichment analysis. Volcano map analysis demonstrated that the functions of the 15 genes with the most significant differences were generally related to the synthesis of amino acids or proteins, the nucleotide metabolism and homologous recombination and repair. Competitive index analysis revealed that the deletion of the genes dksA and epmA regulating protein synthesis, the gene ribB involved in the nucleotide metabolism and the gene xerD involved in recombination repair induced a significant reduction in the survival ability of the corresponding mutants in the 0.10 % YEP medium and the walnut leaf surface. The results act as a foundation for further in-depth research on the infection process and the mechanisms of pathogenic bacteria.
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Affiliation(s)
- Jiawen Xiao
- College of Life Science, Hebei Agricultural University, Baoding, China; Hebei Provincial Engineering Research Center for Resource Utilization of Agricultural Wastes, Baoding, China
| | - Shangyi Sun
- College of Life Science, Hebei Agricultural University, Baoding, China; Hebei Provincial Engineering Research Center for Resource Utilization of Agricultural Wastes, Baoding, China
| | - Zhaosha Liu
- College of Life Science, Hebei Agricultural University, Baoding, China; Hebei Provincial Engineering Research Center for Resource Utilization of Agricultural Wastes, Baoding, China
| | - Chenxi Fan
- College of Life Science, Hebei Agricultural University, Baoding, China; Hebei Provincial Engineering Research Center for Resource Utilization of Agricultural Wastes, Baoding, China
| | - Baocheng Zhu
- College of Life Science, Hebei Agricultural University, Baoding, China; Hebei Provincial Engineering Research Center for Resource Utilization of Agricultural Wastes, Baoding, China
| | - Dongdong Zhang
- College of Life Science, Hebei Agricultural University, Baoding, China; Hebei Provincial Engineering Research Center for Resource Utilization of Agricultural Wastes, Baoding, China.
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Fernández-Vizarra E, López-Calcerrada S, Sierra-Magro A, Pérez-Pérez R, Formosa LE, Hock DH, Illescas M, Peñas A, Brischigliaro M, Ding S, Fearnley IM, Tzoulis C, Pitceathly RDS, Arenas J, Martín MA, Stroud DA, Zeviani M, Ryan MT, Ugalde C. Two independent respiratory chains adapt OXPHOS performance to glycolytic switch. Cell Metab 2022; 34:1792-1808.e6. [PMID: 36198313 DOI: 10.1016/j.cmet.2022.09.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 06/21/2022] [Accepted: 09/08/2022] [Indexed: 01/11/2023]
Abstract
The structural and functional organization of the mitochondrial respiratory chain (MRC) remains intensely debated. Here, we show the co-existence of two separate MRC organizations in human cells and postmitotic tissues, C-MRC and S-MRC, defined by the preferential expression of three COX7A subunit isoforms, COX7A1/2 and SCAFI (COX7A2L). COX7A isoforms promote the functional reorganization of distinct co-existing MRC structures to prevent metabolic exhaustion and MRC deficiency. Notably, prevalence of each MRC organization is reversibly regulated by the activation state of the pyruvate dehydrogenase complex (PDC). Under oxidative conditions, the C-MRC is bioenergetically more efficient, whereas the S-MRC preferentially maintains oxidative phosphorylation (OXPHOS) upon metabolic rewiring toward glycolysis. We show a link between the metabolic signatures converging at the PDC and the structural and functional organization of the MRC, challenging the widespread notion of the MRC as a single functional unit and concluding that its structural heterogeneity warrants optimal adaptation to metabolic function.
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Affiliation(s)
- Erika Fernández-Vizarra
- Medical Research Council, Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK; Veneto Institute of Molecular Medicine, 35129 Padova, Italy; Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy.
| | | | - Ana Sierra-Magro
- Instituto de Investigación Hospital 12 de Octubre, Madrid 28041, Spain
| | | | - Luke E Formosa
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, 3800 Melbourne, Australia
| | - Daniella H Hock
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 3052 Melbourne, Australia
| | - María Illescas
- Instituto de Investigación Hospital 12 de Octubre, Madrid 28041, Spain
| | - Ana Peñas
- Instituto de Investigación Hospital 12 de Octubre, Madrid 28041, Spain
| | | | - Shujing Ding
- Medical Research Council, Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK
| | - Ian M Fearnley
- Medical Research Council, Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK
| | - Charalampos Tzoulis
- Neuro-SysMed Center of Excellence for Clinical Research in Neurological Diseases, Department of Neurology, Haukeland University Hospital and Department of Clinical Medicine, University of Bergen, Pb 7804, 5020 Bergen, Norway
| | - Robert D S Pitceathly
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London WC1N 3BG, UK
| | - Joaquín Arenas
- Instituto de Investigación Hospital 12 de Octubre, Madrid 28041, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), U723 Madrid, Spain
| | - Miguel A Martín
- Instituto de Investigación Hospital 12 de Octubre, Madrid 28041, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), U723 Madrid, Spain
| | - David A Stroud
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 3052 Melbourne, Australia
| | - Massimo Zeviani
- Medical Research Council, Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK; Veneto Institute of Molecular Medicine, 35129 Padova, Italy; Department of Neurosciences, University of Padova, 35128 Padova, Italy
| | - Michael T Ryan
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, 3800 Melbourne, Australia
| | - Cristina Ugalde
- Instituto de Investigación Hospital 12 de Octubre, Madrid 28041, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), U723 Madrid, Spain.
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Al Khatib I, Deng J, Symes A, Kerr M, Zhang H, Huang SYN, Pommier Y, Khan A, Shutt TE. Functional characterization of two variants of mitochondrial topoisomerase TOP1MT that impact regulation of the mitochondrial genome. J Biol Chem 2022; 298:102420. [PMID: 36030054 PMCID: PMC9513266 DOI: 10.1016/j.jbc.2022.102420] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 08/02/2022] [Accepted: 08/03/2022] [Indexed: 11/21/2022] Open
Abstract
TOP1MT encodes a mitochondrial topoisomerase that is important for mtDNA regulation and is involved in mitochondrial replication, transcription, and translation. Two variants predicted to affect TOP1MT function (V1 - R198C and V2 - V338L) were identified by exome sequencing of a newborn with hypertrophic cardiomyopathy. As no pathogenic TOP1MT variants had been confirmed previously, we characterized these variants for their ability to rescue several TOP1MT functions in KO cells. Consistent with these TOP1MT variants contributing to the patient phenotype, our comprehensive characterization suggests that both variants had impaired activity. Critically, we determined neither variant was able to restore steady state levels of mitochondrial-encoded proteins nor to rescue oxidative phosphorylation when re-expressed in TOP1MT KO cells. However, we found the two variants behaved differently in some respects; while the V1 variant was more efficient in restoring transcript levels, the V2 variant showed better rescue of mtDNA copy number and replication. These findings suggest that the different TOP1MT variants affect distinct TOP1MT functions. Altogether, these findings begin to provide insight into the many roles that TOP1MT plays in the maintenance and expression of the mitochondrial genome and how impairments in this important protein may lead to human pathology.
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Affiliation(s)
- Iman Al Khatib
- Department of Biochemistry & Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Jingti Deng
- Department of Biochemistry & Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Andrew Symes
- Department of Geomatics Engineering, Schulich School of Engineering, University of Calgary, Calgary, Alberta, Canada
| | | | - Hongliang Zhang
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland, USA
| | - Shar-Yin Naomi Huang
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland, USA
| | - Yves Pommier
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland, USA
| | - Aneal Khan
- Discovery DNA, Calgary, Alberta, Canada; M.A.G.I.C. Clinic Ltd (Metabolics and Genetics in Calgary), Department of Pediatrics, Cumming School of Medicine, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada
| | - Timothy E Shutt
- Departments of Biochemistry & Molecular Biology and Medical Genetics, Cumming School of Medicine, Alberta Children's Hospital Research Institute, Hotchkiss Brain Institute, University of Calgary, Calgary, Alberta, Canada.
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Pinho SA, Costa CF, Deus CM, Pinho SLC, Miranda‐Santos I, Afonso G, Bagshaw O, Stuart JA, Oliveira PJ, Cunha‐Oliveira T. Mitochondrial and metabolic remodelling in human skin fibroblasts in response to glucose availability. FEBS J 2022; 289:5198-5217. [DOI: 10.1111/febs.16413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 02/01/2022] [Accepted: 02/24/2022] [Indexed: 11/29/2022]
Affiliation(s)
- Sónia A. Pinho
- CNC ‐ Center for Neuroscience and Cell Biology CIBB ‐ Centre for Innovative Biomedicine and Biotechnology University of Coimbra Portugal
- IIIUC ‐ Institute for Interdisciplinary Research University of Coimbra Portugal
- PhD Programme in Experimental Biology and Biomedicine (PDBEB) Institute for Interdisciplinary Research (IIIUC) University of Coimbra Portugal
| | - Cláudio F. Costa
- CNC ‐ Center for Neuroscience and Cell Biology CIBB ‐ Centre for Innovative Biomedicine and Biotechnology University of Coimbra Portugal
- IIIUC ‐ Institute for Interdisciplinary Research University of Coimbra Portugal
| | - Cláudia M. Deus
- CNC ‐ Center for Neuroscience and Cell Biology CIBB ‐ Centre for Innovative Biomedicine and Biotechnology University of Coimbra Portugal
- IIIUC ‐ Institute for Interdisciplinary Research University of Coimbra Portugal
| | - Sonia L. C. Pinho
- CNC ‐ Center for Neuroscience and Cell Biology CIBB ‐ Centre for Innovative Biomedicine and Biotechnology University of Coimbra Portugal
- IIIUC ‐ Institute for Interdisciplinary Research University of Coimbra Portugal
- CIVG‐ Vasco da Gama Research Center Vasco da Gama University School Portugal
| | - Inês Miranda‐Santos
- CNC ‐ Center for Neuroscience and Cell Biology CIBB ‐ Centre for Innovative Biomedicine and Biotechnology University of Coimbra Portugal
- IIIUC ‐ Institute for Interdisciplinary Research University of Coimbra Portugal
| | - Gonçalo Afonso
- CNC ‐ Center for Neuroscience and Cell Biology CIBB ‐ Centre for Innovative Biomedicine and Biotechnology University of Coimbra Portugal
- IIIUC ‐ Institute for Interdisciplinary Research University of Coimbra Portugal
| | - Olivia Bagshaw
- Department of Biological Sciences Brock University St. Catharines ON Canada
| | - Jeffrey A. Stuart
- Department of Biological Sciences Brock University St. Catharines ON Canada
| | - Paulo J. Oliveira
- CNC ‐ Center for Neuroscience and Cell Biology CIBB ‐ Centre for Innovative Biomedicine and Biotechnology University of Coimbra Portugal
- IIIUC ‐ Institute for Interdisciplinary Research University of Coimbra Portugal
| | - Teresa Cunha‐Oliveira
- CNC ‐ Center for Neuroscience and Cell Biology CIBB ‐ Centre for Innovative Biomedicine and Biotechnology University of Coimbra Portugal
- IIIUC ‐ Institute for Interdisciplinary Research University of Coimbra Portugal
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Faria-Pereira A, Temido-Ferreira M, Morais VA. BrainPhys Neuronal Media Support Physiological Function of Mitochondria in Mouse Primary Neuronal Cultures. Front Mol Neurosci 2022; 15:837448. [PMID: 35774868 PMCID: PMC9239074 DOI: 10.3389/fnmol.2022.837448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 05/02/2022] [Indexed: 11/28/2022] Open
Abstract
In vitro neuronal cultures are extensively used in the field of neurosciences as they represent an accessible experimental tool for neuronal genetic manipulation, time-lapse imaging, and drug screening. Optimizing the cultivation of rodent primary neuronal cultures led to the development of defined media that support the growth and maintenance of different neuronal types. Recently, a new neuronal medium, BrainPhys (BP), was formulated envisioning the mimicry of brain physiological conditions and suitability for cultured human iPSC-derived neurons and rat primary neurons. However, its advantages in mouse primary neuronal cultures and its effects in neuronal bioenergetics are yet to be demonstrated. In this study, we validated the beneficial use of BP in mouse primary neuronal cultures based on the observation that neuronal cultures in BP media showed enhanced ATP levels, which increased throughout neuronal maturation, a finding that correlates with higher mitochondrial activity and ATP production at later maturation stages, as well as an increased glycolysis response on mitochondrial inhibition and increased mitochondrial fuel flexibility. Taken together, our data demonstrate that BP medium promotes mitochondrial activity along with neuronal maturation of in vitro cultures.
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