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Tripathi J, Gautam S. Unravelling the key steps impairing the metabolic state of Xanthomonas cells undergoing programmed cell death. Int Microbiol 2024; 27:1285-1296. [PMID: 38190087 DOI: 10.1007/s10123-023-00471-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 11/23/2023] [Accepted: 12/15/2023] [Indexed: 01/09/2024]
Abstract
Programmed cell death (PCD) has been reported in Xanthomonas axonopodis pv. glycines (Xag) wild type earlier and was indirectly shown to be induced by metabolic stress; however, deciphering the key proteins regulating the metabolic stress remained unrevealed. In this study, transcriptomic and proteomic analyses were performed to investigate the prominent pathways, having a role in the induction of metabolic stress in Xag cells undergoing PCD. A comprehensive analysis of transcriptome and proteome data revealed the major involvement of metabolic pathways related to branched chain amino acid degradation, such as acyl-CoA dehydrogenase and energy-yielding, ubiquinol:cytochrome c oxidoreductase complex, in Xag cells undergoing PCD. Consequently, oxidative stress response genes showed major upregulation in Xag cells in PCD-inducing medium; however, no such upregulation was observed at the protein level, indicative of depleted protein levels under excessive stress conditions. Activation of stress response and DNA repair proteins was also observed in Xag cells grown in PCD-inducing medium, which is indicative of excessive cellular damage. Thus, the findings indicate that programmed cell death in Xag is an outcome of metabolic stress in nutrient condition not suitable for a plant pathogen like Xanthomonas, which is more acclimatised with altogether a different nutritional requirement predominantly having an enriched carbohydrate source.
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Affiliation(s)
- Jyoti Tripathi
- Food Technology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, Maharashtra, 400085, India
- Homi Bhabha National Institute, Anushaktinagar, Mumbai, 400094, India
| | - Satyendra Gautam
- Food Technology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, Maharashtra, 400085, India.
- Homi Bhabha National Institute, Anushaktinagar, Mumbai, 400094, India.
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2
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Jamdar SN, Yadav P, Kulkarni BS, Sudesh, Kumar A, Makde RD. Crystal structure of a newly identified M61 family aminopeptidase with broad substrate specificity that is solely responsible for recycling acidic amino acids. FEBS J 2024; 291:3211-3232. [PMID: 38646733 DOI: 10.1111/febs.17133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 02/10/2024] [Accepted: 03/25/2024] [Indexed: 04/23/2024]
Abstract
Aminopeptidases with varied substrate specificities are involved in different crucial physiological processes of cellular homeostasis. They also have wide applications in food and pharma industries. Within the bacterial cell, broad specificity aminopeptidases primarily participate in the recycling of amino acids by degrading oligopeptides generated via primary proteolysis mediated by cellular ATP-dependent proteases. However, in bacteria, a truly broad specificity enzyme, which can cleave off acidic, basic, Gly and hydrophobic amino acid residues, is extremely rare. Here, we report structure-function of a putative glycyl aminopeptidase (M61xc) from Xanthomonas campestris pv campestris (Xcc) belonging to the M61 peptidase family. The enzyme exhibits broad specificity and cleaves Ala, Leu, Asp, Glu, Met, Ser, Phe, Tyr, Gly, Arg, and Lys at the N terminus, optimally of peptides with a length of 3-7 amino acids. Further, we report the high-resolution crystal structure of M61xc in the apo form (2.1 Å) and bestatin-bound form (1.95 Å), detailing its catalytic and substrate preference mechanisms. Comparative analysis of enzyme activity in crude cell extracts from both wild-type and m61xc-knockout mutant strains of Xcc has elucidated the unique intracellular role of M61xc. This study suggests that M61xc is the exclusive enzyme in these bacteria that is responsible for liberating Asp/Glu residues from the N-termini of peptides. Also, in view of its broad specificity and peptide degradation ability, it could be considered equivalent to M1 or other oligomeric peptidases from families like M17, M18, M42 or S9, who have an important auxiliary role in post-proteasomal protein degradation in prokaryotes.
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Affiliation(s)
- Sahayog N Jamdar
- Food Technology Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Pooja Yadav
- Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai, India
| | | | - Sudesh
- Food Technology Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Ashwani Kumar
- Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai, India
| | - Ravindra D Makde
- Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai, India
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Bandyopadhyay NC, Gautam S. Programmed cell death in Xanthomonas axonopodis pv. glycines is associated with modulation of gene expression resulting in altered states of motility, biofilm and virulence. Res Microbiol 2023; 174:104137. [PMID: 37716444 DOI: 10.1016/j.resmic.2023.104137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 09/06/2023] [Accepted: 09/07/2023] [Indexed: 09/18/2023]
Abstract
One of the foremost report of apoptosis-like programmed cell death (PCD) came from Xanthomonas axonopodis pv. glycines (Xag), which displayed rapid post-exponential cell death in PCD inducing media (PIM) but not in a non-inducing media (PNIM). The current study aims to decipher for the first time, the advantages of the existence of PCD in this phytopathogenic microorganism. Analysis of RNA-seq under inducing and non-inducing conditions, revealed differential expression of a number of genes related to key physiology of Xag, such as, motility, xanthan biosynthesis and export as well as virulence. A PCD negative mutant Xag M42 displayed diminished virulence and a contrasting transcriptome pattern. In vitro experiments revealed that under PCD inducing condition, Xag produced negligible xanthan gum as well as extracellular amylase, displayed enhanced swarming motility, released copious e-DNA and formed scanty biofilm. Lack of 'diffusible signalling factor' production was eliminated as possible reason for PCD-induction. Altogether, it appears that, in planta existence of the pathogen metabolically resembles PNIM, and on being transferred to PIM, the cells experience oxidative stress and circumvents it by adopting PCD as an altruistic response. Survival of the remaining population is encouraged by upregulating motility, detachment from the fragile biofilm to achieve dispersal.
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Affiliation(s)
- Nilantana C Bandyopadhyay
- Food Technology Division, Bhabha Atomic Research Centre, Mumbai, 400085, India; Homi Bhabha National Institute, Anushaktinagar, Mumbai, 400094, India
| | - Satyendra Gautam
- Food Technology Division, Bhabha Atomic Research Centre, Mumbai, 400085, India; Homi Bhabha National Institute, Anushaktinagar, Mumbai, 400094, India.
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Glutamine Homeostasis and Its Role in the Adaptive Strategies of the Blind Mole Rat, Spalax. Metabolites 2021; 11:metabo11110755. [PMID: 34822413 PMCID: PMC8620300 DOI: 10.3390/metabo11110755] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 10/26/2021] [Accepted: 10/30/2021] [Indexed: 12/20/2022] Open
Abstract
Oxidative metabolism is fine-tuned machinery that combines two tightly coupled fluxes of glucose and glutamine-derived carbons. Hypoxia interrupts the coordination between the metabolism of these two nutrients and leads to a decrease of the system efficacy and may eventually cause cell death. The subterranean blind mole rat, Spalax, is an underexplored, underground, hypoxia-tolerant mammalian group which spends its life under sharply fluctuating oxygen levels. Primary Spalax cells are an exceptional model to study the metabolic strategies that have evolved in mammals inhabiting low-oxygen niches. In this study we explored the metabolic frame of glutamine (Gln) homeostasis in Spalax skin cells under normoxic and hypoxic conditions and their impacts on the metabolism of rat cells. Targeted metabolomics employing liquid chromatography and mass spectrometry (LC-MS) was used to track the fate of heavy glutamine carbons (13C5 Gln) after 24 h under normoxia or hypoxia (1% O2). Our results indicated that large amounts of glutamine-originated carbons were detected as proline (Pro) and hydroxyproline (HPro) in normoxic Spalax cells with a further increase under hypoxia, suggesting a strategy for reduced Gln carbons storage in proteins. The intensity of the flux and the presence of HPro suggests collagen as a candidate protein that is most abundant in animals, and as the primary source of HPro. An increased conversion of αKG to 2 HG that was indicated in hypoxic Spalax cells prevents the degradation of hypoxia-inducible factor 1α (HIF-1α) and, consequently, maintains cytosolic and mitochondrial carbons fluxes that were uncoupled via inhibition of the pyruvate dehydrogenase complex. A strong antioxidant defense in Spalax cells can be attributed, at least in part, to the massive usage of glutamine-derived glutamate for glutathione (GSH) production. The present study uncovers additional strategies that have evolved in this unique mammal to support its hypoxia tolerance, and probably contribute to its cancer resistance, longevity, and healthy aging.
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Wadhawan S, Gautam S. Rescue of Escherichia coli cells from UV-induced death and filamentation by caspase-3 inhibitor. Int Microbiol 2019; 22:369-376. [DOI: 10.1007/s10123-019-00060-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 01/03/2019] [Accepted: 01/20/2019] [Indexed: 12/25/2022]
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Mouammine A, Eich K, Frandi A, Collier J. Control of proline utilization by the Lrp-like regulator PutR in Caulobacter crescentus. Sci Rep 2018; 8:14677. [PMID: 30279528 PMCID: PMC6168545 DOI: 10.1038/s41598-018-32660-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 09/11/2018] [Indexed: 11/09/2022] Open
Abstract
Cellular metabolism recently emerged as a central player modulating the bacterial cell cycle. The Alphaproteobacterium Caulobacter crescentus appears as one of the best models to study these connections, but its metabolism is still poorly characterized. Considering that it lives in oligotrophic environments, its capacity to use amino-acids is often critical for its growth. Here, we characterized the C. crescentus PutA bi-functional enzyme and showed that it is required for the utilization of proline as a carbon source. We also found that putA transcription and proline utilization by PutA are strictly dependent on the Lrp-like PutR activator. The activation of putA by PutR needs proline, which most likely acts as an effector molecule for PutR. Surprisingly, we also observed that an over-production of PutR leads to cell elongation in liquid medium containing proline, while it inhibits colony formation even in the absence of proline on solid medium. These cell division and growth defects were equally pronounced in a ΔputA mutant background, indicating that PutR can play other roles beyond the control of proline catabolism. Altogether, these findings suggest that PutR might connect central metabolism with cell cycle processes.
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Affiliation(s)
- Annabelle Mouammine
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Quartier UNIL/Sorge, Lausanne, CH, 1015, Switzerland
| | - Katharina Eich
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Quartier UNIL/Sorge, Lausanne, CH, 1015, Switzerland
| | - Antonio Frandi
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Quartier UNIL/Sorge, Lausanne, CH, 1015, Switzerland
| | - Justine Collier
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Quartier UNIL/Sorge, Lausanne, CH, 1015, Switzerland.
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Chen K, Pang Y, Zhang B, Feng J, Xu S, Wang X, Ouyang P. Process optimization for enhancing production of cis-4-hydroxy-L-proline by engineered Escherichia coli. Microb Cell Fact 2017; 16:210. [PMID: 29166916 PMCID: PMC5700529 DOI: 10.1186/s12934-017-0821-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 11/12/2017] [Indexed: 02/06/2023] Open
Abstract
Background Understanding the bioprocess limitations is critical for the efficient design of biocatalysts to facilitate process feasibility and improve process economics. In this study, a proline hydroxylation process with recombinant Escherichia coli expressing l-proline cis-4-hydroxylase (SmP4H) was investigated. The factors that influencing the metabolism of microbial hosts and process economics were focused on for the optimization of cis-4-hydroxy-l-proline (CHOP) production. Results In recombinant E. coli, SmP4H synthesis limitation was observed. After the optimization of expression system, CHOP production was improved in accordance with the enhanced SmP4H synthesis. Furthermore, the effects of the regulation of proline uptake and metabolism on whole-cell catalytic activity were investigated. The improved CHOP production by repressing putA gene responsible for l-proline degradation or overexpressing l-proline transporter putP on CHOP production suggested the important role of substrate uptake and metabolism on the whole-cell biocatalyst efficiency. Through genetically modifying these factors, the biocatalyst activity was significantly improved, and CHOP production was increased by twofold. Meanwhile, to further improve process economics, a two-strain coupling whole-cell system was established to supply co-substrate (α-ketoglutarate, α-KG) with a cheaper chemical l-glutamate as a starting material, and 13.5 g/L of CHOP was successfully produced. Conclusions In this study, SmP4H expression, and l-proline uptake and degradation, were uncovered as the hurdles for microbial production of CHOP. Accordingly, the whole-cell biocatalysts were metabolically engineered for enhancing CHOP production. Meanwhile, a two-strain biotransformation system for CHOP biosynthesis was developed aiming at supplying α-KG more economically. Our work provided valuable insights into the design of recombinant microorganism to improve the biotransformation efficiency that catalyzed by Fe(II)/α-KG-dependent dioxygenase. Electronic supplementary material The online version of this article (10.1186/s12934-017-0821-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kequan Chen
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, Jiangsu, China
| | - Yang Pang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, Jiangsu, China
| | - Bowen Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, Jiangsu, China
| | - Jiao Feng
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, Jiangsu, China
| | - Sheng Xu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, Jiangsu, China
| | - Xin Wang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, Jiangsu, China.
| | - Pingkai Ouyang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, Jiangsu, China
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Klemenčič M, Novinec M, Dolinar M. Orthocaspases are proteolytically active prokaryotic caspase homologues: the case of
M
icrocystis aeruginosa. Mol Microbiol 2015; 98:142-50. [DOI: 10.1111/mmi.13110] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/25/2015] [Indexed: 01/29/2023]
Affiliation(s)
- Marina Klemenčič
- Department of Chemistry and Biochemistry, Faculty of Chemistry and Chemical Technology University of Ljubljana Večna pot 113 SI‐1000 Ljubljana Slovenia
| | - Marko Novinec
- Department of Chemistry and Biochemistry, Faculty of Chemistry and Chemical Technology University of Ljubljana Večna pot 113 SI‐1000 Ljubljana Slovenia
| | - Marko Dolinar
- Department of Chemistry and Biochemistry, Faculty of Chemistry and Chemical Technology University of Ljubljana Večna pot 113 SI‐1000 Ljubljana Slovenia
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Andrukov BG, Somova LM, Timchenko NF. STRATEGY OF PROGRAMMED CELL DEATH IN PROKARYOTES. RUSSIAN JOURNAL OF INFECTION AND IMMUNITY 2015. [DOI: 10.15789/2220-7619-2015-1-15-26] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Programmed cell death (PCD) was first studied in eukaryotic organisms. This system also operates in the development life cycle of prokaryotes. The system PCD in microorganisms is activated a wide range of signals in response to the stresses associated with adverse environmental conditions or exposure to antibacterial agents. The results of numerous studies in the past decade allow considering the system PCD in prokaryotes as an evolutionary conservation of the species. These results significantly expanded understanding of the role of PCD in microorganisms and opened a number of important areas of research of the morphological and molecular genetic approaches to the study of death strategies for the survival in bacterial populations. The purpose of the review is to summarize the morphological and molecular genetic characteristics of PCD in prokaryotes which are real manifestations of the mechanisms of this phenomenon.
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Peter Y, Weingarten M, Akhavan N, Hanau J. A Place to Call Home: Bioengineering Pluripotential Stem Cell Cultures. AIMS BIOENGINEERING 2015. [DOI: 10.3934/bioeng.2015.2.15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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