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Mishra A, Chakraborty S, Jaiswal TP, Bhattacharjee S, Kesarwani S, Mishra AK, Singh SS. Untangling the adaptive strategies of thermophilic bacterium Anoxybacillus rupiensis TPH1 under low temperature. Extremophiles 2024; 28:31. [PMID: 39020126 DOI: 10.1007/s00792-024-01346-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 06/10/2024] [Indexed: 07/19/2024]
Abstract
The present study investigates the low temperature tolerance strategies of thermophilic bacterium Anoxybacillus rupiensis TPH1, which grows optimally at 55 °C , by subjecting it to a temperature down-shift of 10 °C (45 °C) for 4 and 6 h followed by studying its growth, morphophysiological, molecular and proteomic responses. Results suggested that although TPH1 experienced increased growth inhibition, ROS production, protein oxidation and membrane disruption after 4 h of incubation at 45 °C yet maintained its DNA integrity and cellular structure through the increased expression of DNA damage repair and cell envelop synthesizing proteins and also progressively alleviated growth inhibition by 20% within two hours i.e., 6 h, by inducing the expression of antioxidative enzymes, production of unsaturated fatty acids, capsular and released exopolysaccharides and forming biofilm along with chemotaxis proteins. Conclusively, the adaptation of Anoxybacillus rupiensis TPH1 to lower temperature is mainly mediated by the synthesis of large numbers of defense proteins and exopolysaccharide rich biofilm formation.
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Affiliation(s)
- Aditi Mishra
- Laboratory of Cyanobacterial Systematics and Stress Biology, Department of Botany, Banaras Hindu University, Varanasi, India
| | - Sindhunath Chakraborty
- Laboratory of Microbial Genetics, Department of Botany, Banaras Hindu University, Varanasi, India
| | - Tameshwar Prasad Jaiswal
- Laboratory of Cyanobacterial Systematics and Stress Biology, Department of Botany, Banaras Hindu University, Varanasi, India
| | - Samujjal Bhattacharjee
- Laboratory of Microbial Genetics, Department of Botany, Banaras Hindu University, Varanasi, India
| | - Shreya Kesarwani
- Laboratory of Cyanobacterial Systematics and Stress Biology, Department of Botany, Banaras Hindu University, Varanasi, India
| | - Arun Kumar Mishra
- Laboratory of Microbial Genetics, Department of Botany, Banaras Hindu University, Varanasi, India
| | - Satya Shila Singh
- Laboratory of Cyanobacterial Systematics and Stress Biology, Department of Botany, Banaras Hindu University, Varanasi, India.
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2
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Pires PM, Santos D, Calisto F, Pereira M. The monotopic quinone reductases from Staphylococcus aureus. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2024; 1865:149488. [PMID: 38950690 DOI: 10.1016/j.bbabio.2024.149488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 06/27/2024] [Indexed: 07/03/2024]
Abstract
Staphylococcus aureus, a Gram-positive bacterium, is an opportunistic pathogen and one of the most frequent causes for community acquired and nosocomial infections that has become a major public health threat due to the increased incidence of its drug resistance. Although being a prominent pathogen, its energetic metabolism is still underexplored, and its respiratory enzymes have been escaping attention. S. aureus can adapt to different environmental conditions by performing both aerobic and anaerobic respirations, which is particularly important as it frequently colonizes niches with different oxygen concentrations. This adaptability is derived from the composition of its respiratory chain, specifically from the presence of terminal electron acceptor reductases. The plasticity of S. aureus energy metabolism is enlarged by the ten quinone reductases encoded in its genome, eight of them being monotopic proteins. The role of these proteins is critical as they connect the different catabolic pathways to the respiratory chain. In this work, we identify, describe, and revise the monotopic quinone reductases present in S. aureus, providing an integrated view of its respiratory chain.
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Affiliation(s)
- Patrícia M Pires
- University of Lisbon, Faculty of Sciences, Department of Chemistry and Biochemistry and BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8, 1749-016 Lisboa, Portugal
| | - David Santos
- University of Lisbon, Faculty of Sciences, Department of Chemistry and Biochemistry and BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8, 1749-016 Lisboa, Portugal
| | - Filipa Calisto
- University of Lisbon, Faculty of Sciences, Department of Chemistry and Biochemistry and BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8, 1749-016 Lisboa, Portugal
| | - Manuela Pereira
- University of Lisbon, Faculty of Sciences, Department of Chemistry and Biochemistry and BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8, 1749-016 Lisboa, Portugal.
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3
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Oh S, Mai XL, Kim J, de Guzman ACV, Lee JY, Park S. Glycerol 3-phosphate dehydrogenases (1 and 2) in cancer and other diseases. Exp Mol Med 2024; 56:1066-1079. [PMID: 38689091 PMCID: PMC11148179 DOI: 10.1038/s12276-024-01222-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 02/05/2024] [Accepted: 02/18/2024] [Indexed: 05/02/2024] Open
Abstract
The glycerol 3-phosphate shuttle (GPS) is composed of two different enzymes: cytosolic NAD+-linked glycerol 3-phosphate dehydrogenase 1 (GPD1) and mitochondrial FAD-linked glycerol 3-phosphate dehydrogenase 2 (GPD2). These two enzymes work together to act as an NADH shuttle for mitochondrial bioenergetics and function as an important bridge between glucose and lipid metabolism. Since these genes were discovered in the 1960s, their abnormal expression has been described in various metabolic diseases and tumors. Nevertheless, it took a long time until scientists could investigate the causal relationship of these enzymes in those pathophysiological conditions. To date, numerous studies have explored the involvement and mechanisms of GPD1 and GPD2 in cancer and other diseases, encompassing reports of controversial and non-conventional mechanisms. In this review, we summarize and update current knowledge regarding the functions and effects of GPS to provide an overview of how the enzymes influence disease conditions. The potential and challenges of developing therapeutic strategies targeting these enzymes are also discussed.
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Affiliation(s)
- Sehyun Oh
- College of Pharmacy, Natural Products Research Institute, Seoul National University, Seoul, 08826, Korea
- Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02215, USA
| | - Xuan Linh Mai
- College of Pharmacy, Natural Products Research Institute, Seoul National University, Seoul, 08826, Korea
| | - Jiwoo Kim
- College of Pharmacy, Natural Products Research Institute, Seoul National University, Seoul, 08826, Korea
| | - Arvie Camille V de Guzman
- College of Pharmacy, Natural Products Research Institute, Seoul National University, Seoul, 08826, Korea
| | - Ji Yun Lee
- College of Pharmacy, Natural Products Research Institute, Seoul National University, Seoul, 08826, Korea.
| | - Sunghyouk Park
- College of Pharmacy, Natural Products Research Institute, Seoul National University, Seoul, 08826, Korea.
- School of Biological Sciences, Seoul National University, Seoul, 08826, Korea.
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Harrison GA, Wang ER, Cho K, Mreyoud Y, Sarkar S, Almqvist F, Patti GJ, Stallings CL. Inducing vulnerability to InhA inhibition restores isoniazid susceptibility in drug-resistant Mycobacterium tuberculosis. mBio 2024; 15:e0296823. [PMID: 38294237 PMCID: PMC10936210 DOI: 10.1128/mbio.02968-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 12/20/2023] [Indexed: 02/01/2024] Open
Abstract
Of the approximately 10 million cases of Mycobacterium tuberculosis (Mtb) infections each year, over 10% are resistant to the frontline antibiotic isoniazid (INH). INH resistance is predominantly caused by mutations that decrease the activity of the bacterial enzyme KatG, which mediates the conversion of the pro-drug INH to its active form INH-NAD. We previously discovered an inhibitor of Mtb respiration, C10, that enhances the bactericidal activity of INH, prevents the emergence of INH-resistant mutants, and re-sensitizes a collection of INH-resistant mutants to INH through an unknown mechanism. To investigate the mechanism of action of C10, we exploited the toxicity of high concentrations of C10 to select for resistant mutants. We discovered two mutations that confer resistance to the disruption of energy metabolism and allow for the growth of Mtb in high C10 concentrations, indicating that growth inhibition by C10 is associated with inhibition of respiration. Using these mutants as well as direct inhibitors of the Mtb electron transport chain, we provide evidence that inhibition of energy metabolism by C10 is neither sufficient nor necessary to potentiate killing by INH. Instead, we find that C10 acts downstream of INH-NAD synthesis, causing Mtb to become particularly sensitive to inhibition of the INH-NAD target, InhA, without changing the concentration of INH-NAD or the activity of InhA, the two predominant mechanisms of potentiating INH. Our studies revealed that there exists a vulnerability in Mtb that can be exploited to render Mtb sensitive to otherwise subinhibitory concentrations of InhA inhibitor.IMPORTANCEIsoniazid (INH) is a critical frontline antibiotic to treat Mycobacterium tuberculosis (Mtb) infections. INH efficacy is limited by its suboptimal penetration of the Mtb-containing lesion and by the prevalence of clinical INH resistance. We previously discovered a compound, C10, that enhances the bactericidal activity of INH, prevents the emergence of INH-resistant mutants, and re-sensitizes a set of INH-resistant mutants to INH. Resistance is typically mediated by katG mutations that decrease the activation of INH, which is required for INH to inhibit the essential enzyme InhA. Our current work demonstrates that C10 re-sensitizes INH-resistant katG-hypomorphs without enhancing the activation of INH. We furthermore show that C10 causes Mtb to become particularly vulnerable to InhA inhibition without compromising InhA activity on its own. Therefore, C10 represents a novel strategy to curtail the development of INH resistance and to sensitize Mtb to sub-lethal doses of INH, such as those achieved at the infection site.
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Affiliation(s)
- Gregory A. Harrison
- Department of Molecular Microbiology, Center for Women’s Infectious Disease Research, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Erin R. Wang
- Department of Molecular Microbiology, Center for Women’s Infectious Disease Research, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Kevin Cho
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
- Center for Metabolomics and Isotope Tracing, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Yassin Mreyoud
- Department of Molecular Microbiology, Center for Women’s Infectious Disease Research, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Souvik Sarkar
- Department of Chemistry, Umeå University, Umeå, Sweden
| | - Fredrik Almqvist
- Department of Chemistry, Umeå University, Umeå, Sweden
- Umeå Centre for Microbial Research, UCMR, Umeå University, Umeå, Sweden
| | - Gary J. Patti
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
- Center for Metabolomics and Isotope Tracing, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Christina L. Stallings
- Department of Molecular Microbiology, Center for Women’s Infectious Disease Research, Washington University School of Medicine, St. Louis, Missouri, USA
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Bozsó Z, Lapat V, Ott PG, Móricz ÁM. Disparate Effects of Two Clerodane Diterpenes of Giant Goldenrod ( Solidago gigantea Ait.) on Bacillus spizizenii. Int J Mol Sci 2024; 25:1531. [PMID: 38338810 PMCID: PMC10855248 DOI: 10.3390/ijms25031531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 01/21/2024] [Accepted: 01/22/2024] [Indexed: 02/12/2024] Open
Abstract
New substances with antimicrobial properties are needed to successfully treat emerging human, animal, or plant pathogens. Seven clerodane diterpenes, previously isolated from giant goldenrod (Solidago gigantea) root, were tested against Gram-positive Bacillus subtilis, Bacillus spizizenii and Rhodococcus fascians by measuring minimal bactericidal concentration (MBC), minimal inhibitory concentration (MIC) and half-maximal inhibitory concentration (IC50). Two of them, Sg3a (a dialdehyde) and Sg6 (solidagoic acid B), were proved to be the most effective and were selected for further study. Bacillus spizizenii was incubated with the two diterpenes for shorter (1 h) or longer (5 h) periods and then subjected to genome-wide transcriptional analyses. Only a limited number of common genes (28 genes) were differentially regulated after each treatment, and these were mainly related to the restoration of cell membrane integrity and to membrane-related transports. Changes in gene activity indicated that, among other things, K+ and Na+ homeostasis, pH and membrane electron transport processes may have been affected. Activated export systems can be involved in the removal of harmful molecules from the bacterial cells. Inhibition of bacterial chemotaxis and flagellar assembly, as well as activation of genes for the biosynthesis of secondary metabolites, were observed as a general response. Depending on the diterpenes and the duration of the treatments, down-regulation of the protein synthesis-related, oxidative phosphorylation, signal transduction and transcription factor genes was found. In other cases, up-regulation of the genes of oxidation-reduction processes, sporulation and cell wall modification could be detected. Comparison of the effect of diterpenes with the changes induced by different environmental and nutritional conditions revealed several overlapping processes with stress responses. For example, the Sg6 treatment seems to have caused a starvation-like condition. In summary, there were both common and diterpene-specific changes in the transcriptome, and these changes were also dependent on the length of treatments. The results also indicated that Sg6 exerted its effect more slowly than Sg3a, but ultimately its effect was greater.
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Affiliation(s)
| | | | | | - Ágnes M. Móricz
- Plant Protection Institute, HUN-REN Centre for Agricultural Research, Herman Ottó Str. 15, H-1022 Budapest, Hungary; (Z.B.); (P.G.O.)
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6
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Clarke RA, Govindaraju H, Beretta M, Olzomer E, Lawther AJ, Walker AK, Fang Z, Eapen V, Hyams TC, Killingsworth M, Bridge W, Turner N, Siddiqui KS. Immp2l Enhances the Structure and Function of Mitochondrial Gpd2 Dehydrogenase. Int J Mol Sci 2024; 25:990. [PMID: 38256063 PMCID: PMC10815762 DOI: 10.3390/ijms25020990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 12/25/2023] [Accepted: 12/28/2023] [Indexed: 01/24/2024] Open
Abstract
'Inner mitochondrial membrane peptidase 2 like' (IMMP2L) is a nuclear-encoded mitochondrial peptidase that has been conserved through evolutionary history, as has its target enzyme, 'mitochondrial glycerol phosphate dehydrogenase 2' (GPD2). IMMP2L is known to cleave the mitochondrial transit peptide from GPD2 and another nuclear-encoded mitochondrial respiratory-related protein, cytochrome C1 (CYC1). However, it is not known whether IMMP2L peptidase activates or alters the activity or respiratory-related functions of GPD2 or CYC1. Previous investigations found compelling evidence of behavioural change in the Immp2lKD-/- KO mouse, and in this study, EchoMRI analysis found that the organs of the Immp2lKD-/- KO mouse were smaller and that the KO mouse had significantly less lean mass and overall body weight compared with wildtype littermates (p < 0.05). Moreover, all organs analysed from the Immp2lKD-/- KO had lower relative levels of mitochondrial reactive oxygen species (mitoROS). The kidneys of the Immp2lKD-/- KO mouse displayed the greatest decrease in mitoROS levels that were over 50% less compared with wildtype litter mates. Mitochondrial respiration was also lowest in the kidney of the Immp2lKD-/- KO mouse compared with other tissues when using succinate as the respiratory substrate, whereas respiration was similar to the wildtype when glutamate was used as the substrate. When glycerol-3-phosphate (G3P) was used as the substrate for Gpd2, we observed ~20% and ~7% respective decreases in respiration in female and male Immp2lKD-/- KO mice over time. Together, these findings indicate that the respiratory-related functions of mGpd2 and Cyc1 have been compromised to different degrees in different tissues and genders of the Immp2lKD-/- KO mouse. Structural analyses using AlphaFold2-Multimer further predicted that the interaction between Cyc1 and mitochondrial-encoded cytochrome b (Cyb) in Complex III had been altered, as had the homodimeric structure of the mGpd2 enzyme within the inner mitochondrial membrane of the Immp2lKD-/- KO mouse. mGpd2 functions as an integral component of the glycerol phosphate shuttle (GPS), which positively regulates both mitochondrial respiration and glycolysis. Interestingly, we found that nonmitochondrial respiration (NMR) was also dramatically lowered in the Immp2lKD-/- KO mouse. Primary mouse embryonic fibroblast (MEF) cell lines derived from the Immp2lKD-/- KO mouse displayed a ~27% decrease in total respiration, comprising a ~50% decrease in NMR and a ~12% decrease in total mitochondrial respiration, where the latter was consistent with the cumulative decreases in substrate-specific mediated mitochondrial respiration reported here. This study is the first to report the role of Immp2l in enhancing Gpd2 structure and function, mitochondrial respiration, nonmitochondrial respiration, organ size and homeostasis.
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Affiliation(s)
- Raymond A. Clarke
- Discipline of Psychiatry, University of New South Wales, Sydney, NSW 2052, Australia; (A.K.W.); (V.E.)
- Ingham Institute for Applied Medical Research, Sydney, NSW 2170, Australia; (Z.F.); (T.C.H.); (M.K.)
- Academic Unit of Infant Child and Adolescent Services (AUCS), South Western Sydney Local Health District, Liverpool, NSW 2170, Australia
| | - Hemna Govindaraju
- Department of Pharmacology, School of Biomedical Sciences, University of New South Wales, Sydney, NSW 2052, Australia; (H.G.); (N.T.)
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia
| | - Martina Beretta
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia; (M.B.); (E.O.); (W.B.)
| | - Ellen Olzomer
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia; (M.B.); (E.O.); (W.B.)
| | - Adam J. Lawther
- Laboratory of ImmunoPsychiatry, Neuroscience Research Australia, Randwick, NSW 2031, Australia;
| | - Adam K. Walker
- Discipline of Psychiatry, University of New South Wales, Sydney, NSW 2052, Australia; (A.K.W.); (V.E.)
- Laboratory of ImmunoPsychiatry, Neuroscience Research Australia, Randwick, NSW 2031, Australia;
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Zhiming Fang
- Ingham Institute for Applied Medical Research, Sydney, NSW 2170, Australia; (Z.F.); (T.C.H.); (M.K.)
| | - Valsamma Eapen
- Discipline of Psychiatry, University of New South Wales, Sydney, NSW 2052, Australia; (A.K.W.); (V.E.)
- Ingham Institute for Applied Medical Research, Sydney, NSW 2170, Australia; (Z.F.); (T.C.H.); (M.K.)
- Academic Unit of Infant Child and Adolescent Services (AUCS), South Western Sydney Local Health District, Liverpool, NSW 2170, Australia
| | - Tzipi Cohen Hyams
- Ingham Institute for Applied Medical Research, Sydney, NSW 2170, Australia; (Z.F.); (T.C.H.); (M.K.)
| | - Murray Killingsworth
- Ingham Institute for Applied Medical Research, Sydney, NSW 2170, Australia; (Z.F.); (T.C.H.); (M.K.)
- NSW Health Pathology, Liverpool Hospital Campus, Liverpool, NSW 2107, Australia
| | - Wallace Bridge
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia; (M.B.); (E.O.); (W.B.)
| | - Nigel Turner
- Department of Pharmacology, School of Biomedical Sciences, University of New South Wales, Sydney, NSW 2052, Australia; (H.G.); (N.T.)
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia
| | - Khawar Sohail Siddiqui
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia; (M.B.); (E.O.); (W.B.)
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Syngkli S, Das B. Purification and characterization of human glycerol 3-phosphate dehydrogenases (mitochondrial and cytosolic) by NAD +/NADH redox method. Biochimie 2023; 214:199-215. [PMID: 37481063 DOI: 10.1016/j.biochi.2023.07.015] [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: 06/29/2023] [Accepted: 07/20/2023] [Indexed: 07/24/2023]
Abstract
Glycerol 3-phosphate (G3P) shuttle is composed of mGPDH and cGPDH and serves as the interface between carbohydrate- and lipid-metabolism. Recently, these metabolic enzymes have been implicated in type II diabetes mellitus but the detailed kinetic parameters and crystal structure of human mGPDH is unknown, though fewer studies on cGPDH are available. To characterize these enzymes, the human mGPDH and cGPDH genes were optimized and cloned into the pET-SUMO vector and pET-24a(+) vector, respectively, and over-expressed in Escherichia coli BL21 (DE3). However, SUMO-mGPDH was expressed as inclusion bodies. Hence, various culture parameters, solubilizing agents and expression vectors were used to solubilize the protein but they did not produce functional SUMO-mGPDH. Over-expression of SUMO-mGPDH along with molecular chaperone (pG-KJE8) produced a functional SUMO-mGPDH. The functional SUMO-mGPDH was purified and characterized using NAD+/NADH redox method. cGPDH was also over-expressed and purified for its characterization. DLS analysis and CD spectra of the purified proteins were performed. The mGPDH was a monomeric enzyme with MW of ∼74 kDa and displayed optimal activity in the Tris-HCl buffer (pH 7.4); while, cGPDH was a homodimer with a monomeric MW of ∼37 kDa and showed optimal activity in imidazole buffer (pH 8.0). The Kmapp was 0.475 mM for G3P, and 0.734 mM for DHAP. These methods may be used to characterize these enzymes to understand their role in metabolic disorders.
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Affiliation(s)
- Superior Syngkli
- Biological Chemistry Laboratory, Department of Zoology, North-Eastern Hill University, Shillong, 793022, India
| | - Bidyadhar Das
- Biological Chemistry Laboratory, Department of Zoology, North-Eastern Hill University, Shillong, 793022, India.
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8
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Broeks MH, Meijer NWF, Westland D, Bosma M, Gerrits J, German HM, Ciapaite J, van Karnebeek CDM, Wanders RJA, Zwartkruis FJT, Verhoeven-Duif NM, Jans JJM. The malate-aspartate shuttle is important for de novo serine biosynthesis. Cell Rep 2023; 42:113043. [PMID: 37647199 DOI: 10.1016/j.celrep.2023.113043] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 05/17/2023] [Accepted: 08/14/2023] [Indexed: 09/01/2023] Open
Abstract
The malate-aspartate shuttle (MAS) is a redox shuttle that transports reducing equivalents across the inner mitochondrial membrane while recycling cytosolic NADH to NAD+. We genetically disrupted each MAS component to generate a panel of MAS-deficient HEK293 cell lines in which we performed [U-13C]-glucose tracing. MAS-deficient cells have reduced serine biosynthesis, which strongly correlates with the lactate M+3/pyruvate M+3 ratio (reflective of the cytosolic NAD+/NADH ratio), consistent with the NAD+ dependency of phosphoglycerate dehydrogenase in the serine synthesis pathway. Among the MAS-deficient cells, those lacking malate dehydrogenase 1 (MDH1) show the most severe metabolic disruptions, whereas oxoglutarate-malate carrier (OGC)- and MDH2-deficient cells are less affected. Increasing the NAD+-regenerating capacity using pyruvate supplementation resolves most of the metabolic disturbances. Overall, we show that the MAS is important for de novo serine biosynthesis, implying that serine supplementation could be used as a therapeutic strategy for MAS defects and possibly other redox disorders.
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Affiliation(s)
- Melissa H Broeks
- Department of Genetics, Section Metabolic Diagnostics, University Medical Center Utrecht, Lundlaan 6, 3584 EA Utrecht, the Netherlands.
| | - Nils W F Meijer
- Department of Genetics, Section Metabolic Diagnostics, University Medical Center Utrecht, Lundlaan 6, 3584 EA Utrecht, the Netherlands
| | - Denise Westland
- Department of Genetics, Section Metabolic Diagnostics, University Medical Center Utrecht, Lundlaan 6, 3584 EA Utrecht, the Netherlands
| | - Marjolein Bosma
- Department of Genetics, Section Metabolic Diagnostics, University Medical Center Utrecht, Lundlaan 6, 3584 EA Utrecht, the Netherlands
| | - Johan Gerrits
- Department of Genetics, Section Metabolic Diagnostics, University Medical Center Utrecht, Lundlaan 6, 3584 EA Utrecht, the Netherlands
| | - Hannah M German
- Department of Genetics, Section Metabolic Diagnostics, University Medical Center Utrecht, Lundlaan 6, 3584 EA Utrecht, the Netherlands
| | - Jolita Ciapaite
- Department of Genetics, Section Metabolic Diagnostics, University Medical Center Utrecht, Lundlaan 6, 3584 EA Utrecht, the Netherlands
| | - Clara D M van Karnebeek
- Emma Center for Personalized Medicine, Departments of Pediatrics and Human Genetics, Amsterdam University Medical Center, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands; Departments of Pediatrics and Laboratory Medicine, Laboratory Genetic Metabolic Diseases, Amsterdam University Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
| | - Ronald J A Wanders
- Departments of Pediatrics and Laboratory Medicine, Laboratory Genetic Metabolic Diseases, Amsterdam University Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
| | - Fried J T Zwartkruis
- dLAB, Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands
| | - Nanda M Verhoeven-Duif
- Department of Genetics, Section Metabolic Diagnostics, University Medical Center Utrecht, Lundlaan 6, 3584 EA Utrecht, the Netherlands
| | - Judith J M Jans
- Department of Genetics, Section Metabolic Diagnostics, University Medical Center Utrecht, Lundlaan 6, 3584 EA Utrecht, the Netherlands.
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9
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Huang C, Pham HQ, Zhu L, Wang R, Law OK, Lin SL, Nie QC, Zhang L, Wang X, Lau TCK. Comparative Analysis of Transcriptome and Proteome Revealed the Common Metabolic Pathways Induced by Prevalent ESBL Plasmids in Escherichia coli. Int J Mol Sci 2023; 24:14009. [PMID: 37762311 PMCID: PMC10531281 DOI: 10.3390/ijms241814009] [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: 07/31/2023] [Revised: 09/11/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023] Open
Abstract
Antibiotic resistance has emerged as one of the most significant threats to global public health. Plasmids, which are highly efficient self-replicating genetic vehicles, play a critical role in the dissemination of drug-resistant genes. Previous studies have mainly focused on drug-resistant genes only, often neglecting the complete functional role of multidrug-resistant (MDR) plasmids in bacteria. In this study, we conducted a comprehensive investigation of the transcriptomes and proteomes of Escherichia coli J53 transconjugants harboring six major MDR plasmids of different incompatibility (Inc) groups, which were clinically isolated from patients. The RNA-seq analysis revealed that MDR plasmids influenced the gene expression in the bacterial host, in particular, the genes related to metabolic pathways. A proteomic analysis demonstrated the plasmid-induced regulation of several metabolic pathways including anaerobic respiration and the utilization of various carbon sources such as serine, threonine, sialic acid, and galactarate. These findings suggested that MDR plasmids confer a growth advantage to bacterial hosts in the gut, leading to the expansion of plasmid-carrying bacteria over competitors without plasmids. Moreover, this study provided insights into the versatility of prevalent MDR plasmids in moderating the cellular gene network of bacteria, which could potentially be utilized in therapeutics development for bacteria carrying MDR plasmids.
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Affiliation(s)
- Chuan Huang
- Department of Biomedical Sciences, College of Veterinary Medicine and Life Science, City University of Hong Kong, Hong Kong SAR, China; (C.H.); (H.-Q.P.); (L.Z.); (R.W.); (O.-K.L.); (S.-L.L.); (Q.-C.N.); (L.Z.)
- Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong SAR, China
| | - Hoa-Quynh Pham
- Department of Biomedical Sciences, College of Veterinary Medicine and Life Science, City University of Hong Kong, Hong Kong SAR, China; (C.H.); (H.-Q.P.); (L.Z.); (R.W.); (O.-K.L.); (S.-L.L.); (Q.-C.N.); (L.Z.)
- Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong SAR, China
| | - Lina Zhu
- Department of Biomedical Sciences, College of Veterinary Medicine and Life Science, City University of Hong Kong, Hong Kong SAR, China; (C.H.); (H.-Q.P.); (L.Z.); (R.W.); (O.-K.L.); (S.-L.L.); (Q.-C.N.); (L.Z.)
- Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong SAR, China
| | - Rui Wang
- Department of Biomedical Sciences, College of Veterinary Medicine and Life Science, City University of Hong Kong, Hong Kong SAR, China; (C.H.); (H.-Q.P.); (L.Z.); (R.W.); (O.-K.L.); (S.-L.L.); (Q.-C.N.); (L.Z.)
- Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong SAR, China
| | - Oi-Kwan Law
- Department of Biomedical Sciences, College of Veterinary Medicine and Life Science, City University of Hong Kong, Hong Kong SAR, China; (C.H.); (H.-Q.P.); (L.Z.); (R.W.); (O.-K.L.); (S.-L.L.); (Q.-C.N.); (L.Z.)
- Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong SAR, China
| | - Shu-Ling Lin
- Department of Biomedical Sciences, College of Veterinary Medicine and Life Science, City University of Hong Kong, Hong Kong SAR, China; (C.H.); (H.-Q.P.); (L.Z.); (R.W.); (O.-K.L.); (S.-L.L.); (Q.-C.N.); (L.Z.)
- Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong SAR, China
| | - Qi-Chang Nie
- Department of Biomedical Sciences, College of Veterinary Medicine and Life Science, City University of Hong Kong, Hong Kong SAR, China; (C.H.); (H.-Q.P.); (L.Z.); (R.W.); (O.-K.L.); (S.-L.L.); (Q.-C.N.); (L.Z.)
- Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong SAR, China
| | - Liang Zhang
- Department of Biomedical Sciences, College of Veterinary Medicine and Life Science, City University of Hong Kong, Hong Kong SAR, China; (C.H.); (H.-Q.P.); (L.Z.); (R.W.); (O.-K.L.); (S.-L.L.); (Q.-C.N.); (L.Z.)
- Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong SAR, China
| | - Xin Wang
- Department of Surgery, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China;
| | - Terrence Chi-Kong Lau
- Department of Biomedical Sciences, College of Veterinary Medicine and Life Science, City University of Hong Kong, Hong Kong SAR, China; (C.H.); (H.-Q.P.); (L.Z.); (R.W.); (O.-K.L.); (S.-L.L.); (Q.-C.N.); (L.Z.)
- Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong SAR, China
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10
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Jeelani G, Balogun EO, Husain A, Nozaki T. Glycerol biosynthetic pathway plays an essential role in proliferation and antioxidative defense in the human enteric protozoan parasite Entamoeba histolytica. Sci Rep 2023; 13:14596. [PMID: 37669981 PMCID: PMC10480196 DOI: 10.1038/s41598-023-40670-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 08/16/2023] [Indexed: 09/07/2023] Open
Abstract
Amebiasis is caused by the protozoan parasite Entamoeba histolytica. Treatment options other than metronidazole and its derivatives are few, and their low efficacy against asymptomatic cyst carriers, and experimental evidence of resistance in vitro justify the discovery/repurposing campaign for new drugs against amebiasis. Global metabolic responses to oxidative stress and cysteine deprivation by E. histolytica revealed glycerol metabolism may represent a rational target for drug development. In this study using 14C-labelled glucose, only 11% of the total glucose taken up by E. histolytica trophozoites is incorporated to lipids. To better understand the role of glycerol metabolism in this parasite, we focused on characterizing two important enzymes, glycerol kinase (GK) and glycerol 3-phosphate dehydrogenase (G3PDH). Recombinant GK was biochemically characterized in detail, while G3PDH was not due to failure of protein expression and purification. GK revealed novel characteristics and unprecedented kinetic properties in reverse reaction. Gene silencing revealed that GK is essential for optimum growth, whereas G3PDH is not. Gene silencing of G3PDH caused upregulated GK expression, while that of GK resulted in upregulation of antioxidant enzymes as shown by RNA-seq analysis. Although the precise molecular link between GK and the upregulation of antioxidant enzymes was not demonstrated, the observed increase in antioxidant enzyme expression upon GK gene silencing suggests a potential connection between GK and the cellular response to oxidative stress. Together, these results provide the first direct evidence of the biological importance and coordinated regulation of the glycerol metabolic pathways for proliferation and antioxidative defense in E. histolytica, justifying the exploitation of these enzymes as future drug targets.
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Affiliation(s)
- Ghulam Jeelani
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Emmanuel Oluwadare Balogun
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
- Department of Biochemistry, Ahmadu Bello University, Zaria, Nigeria
| | - Afzal Husain
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, India
| | - Tomoyoshi Nozaki
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
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11
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Mishra NN, de Paula Baptista R, Tran TT, Lapitan CK, Garcia-de-la-Maria C, Miró JM, Proctor RA, Bayer AS. Membrane Phenotypic, Metabolic and Genotypic Adaptations of Streptococcus oralis Strains Destined to Rapidly Develop Stable, High-Level Daptomycin Resistance during Daptomycin Exposures. Antibiotics (Basel) 2023; 12:1083. [PMID: 37508179 PMCID: PMC10376253 DOI: 10.3390/antibiotics12071083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 06/15/2023] [Accepted: 06/16/2023] [Indexed: 07/30/2023] Open
Abstract
The Streptococcus mitis-oralis subgroup of viridans group streptococci are important human pathogens. We previously showed that a substantial portion of S. mitis-oralis strains (>25%) are 'destined' to develop rapid, high-level, and stable daptomycin (DAP) resistance (DAP-R) during DAP exposures in vitro. Such DAP-R is often accompanied by perturbations in distinct membrane phenotypes and metabolic pathways. The current study evaluated two S. oralis bloodstream isolates, 73 and 205. Strain 73 developed stable, high-level DAP-R (minimum inhibitory concentration [MIC] > 256 µg/mL) within 2 days of in vitro DAP passage ("high level" DAP-R [HLDR]). In contrast, strain 205 evolved low-level and unstable DAP-R (MIC = 8 µg/mL) under the same exposure conditions in vitro ("non-HLDR"). Comparing the parental 73 vs. 73-D2 (HLDR) strain-pair, we observed the 73-D2 had the following major differences: (i) altered cell membrane (CM) phospholipid profiles, featuring the disappearance of phosphatidylglycerol (PG) and cardiolipin (CL), with accumulation of the PG-CL pathway precursor, phosphatidic acid (PA); (ii) enhanced CM fluidity; (iii) increased DAP surface binding; (iv) reduced growth rates; (v) decreased glucose utilization and lactate accumulation; and (vi) increased enzymatic activity within the glycolytic (i.e., lactate dehydrogenase [LDH]) and lipid biosynthetic (glycerol-3-phosphate dehydrogenase [GPDH]) pathways. In contrast, the 205 (non-HLDR) strain-pair did not show these same phenotypic or metabolic changes over the 2-day DAP exposure. WGS analyses confirmed the presence of mutations in genes involved in the above glycolytic and phospholipid biosynthetic pathways in the 73-D2 passage variant. These data suggest that S. oralis strains which are 'destined' to rapidly develop HLDR do so via a conserved cadre of genotypic, membrane phenotypic, and metabolic adaptations.
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Affiliation(s)
- Nagendra N Mishra
- Division of Infectious Diseases, The Lundquist Institute at Harbor-UCLA Medical Center, 1124 West Carson St. MRL Bldg. Room 224, Torrance, CA 90502, USA
- The David Geffen School of Medicine, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Rodrigo de Paula Baptista
- Center for Infectious Diseases, Houston Methodist Research Institute, Houston, TX 77030, USA
- Division of Infectious Diseases, Department of Medicine, Houston Methodist Hospital, Houston, TX 77030, USA
- Department of Medicine, Weill-Cornell Medical College, New York, NY 10065, USA
| | - Truc T Tran
- Center for Infectious Diseases, Houston Methodist Research Institute, Houston, TX 77030, USA
- Division of Infectious Diseases, Department of Medicine, Houston Methodist Hospital, Houston, TX 77030, USA
- Department of Medicine, Weill-Cornell Medical College, New York, NY 10065, USA
| | - Christian K Lapitan
- Division of Infectious Diseases, The Lundquist Institute at Harbor-UCLA Medical Center, 1124 West Carson St. MRL Bldg. Room 224, Torrance, CA 90502, USA
| | - Cristina Garcia-de-la-Maria
- Infectious Diseases Service, Hospital Clinic-IDIBAPS, University of Barcelona, 08036 Barcelona, Spain
- CIBERINFEC, Instituto de Salud Carlos III, 28220 Madrid, Spain
| | - Jose M Miró
- CIBERINFEC, Instituto de Salud Carlos III, 28220 Madrid, Spain
| | - Richard A Proctor
- The Department of Medicine, University of Wisconsin School of Medicine, Madison, WI 53705, USA
| | - Arnold S Bayer
- Division of Infectious Diseases, The Lundquist Institute at Harbor-UCLA Medical Center, 1124 West Carson St. MRL Bldg. Room 224, Torrance, CA 90502, USA
- The David Geffen School of Medicine, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
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12
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Sousa FM, Pires P, Barreto A, Refojo PN, Silva MS, Fernandes PB, Carapeto AP, Robalo TT, Rodrigues MS, Pinho MG, Cabrita EJ, Pereira MM. Unveiling the membrane bound dihydroorotate: Quinone oxidoreductase from Staphylococcus aureus. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2023; 1864:148948. [PMID: 36481274 DOI: 10.1016/j.bbabio.2022.148948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 11/23/2022] [Accepted: 11/28/2022] [Indexed: 12/12/2022]
Abstract
Staphylococcus aureus is an opportunistic pathogen and one of the most frequent causes for community acquired and nosocomial bacterial infections. Even so, its energy metabolism is still under explored and its respiratory enzymes have been vastly overlooked. In this work, we unveil the dihydroorotate:quinone oxidoreductase (DHOQO) from S. aureus, the first example of a DHOQO from a Gram-positive organism. This protein was shown to be a FMN containing menaquinone reducing enzyme, presenting a Michaelis-Menten behaviour towards the two substrates, which was inhibited by Brequinar, Leflunomide, Lapachol, HQNO, Atovaquone and TFFA with different degrees of effectiveness. Deletion of the DHOQO coding gene (Δdhoqo) led to lower bacterial growth rates, and effected in cell morphology and metabolism, most importantly in the pyrimidine biosynthesis, here systematized for S. aureus MW2 for the first time. This work unveils the existence of a functional DHOQO in the respiratory chain of the pathogenic bacterium S. aureus, enlarging the understanding of its energy metabolism.
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Affiliation(s)
- Filipe M Sousa
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157 Oeiras, Portugal; University of Lisbon, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8, 1749-016 Lisboa, Portugal
| | - Patrícia Pires
- University of Lisbon, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8, 1749-016 Lisboa, Portugal
| | - Andreia Barreto
- University of Lisbon, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8, 1749-016 Lisboa, Portugal
| | - Patrícia N Refojo
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157 Oeiras, Portugal
| | - Micael S Silva
- UCIBIO, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Pedro B Fernandes
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157 Oeiras, Portugal
| | - Ana P Carapeto
- University of Lisbon, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8, 1749-016 Lisboa, Portugal; Departamento de Física, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Tiago T Robalo
- University of Lisbon, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8, 1749-016 Lisboa, Portugal; Departamento de Física, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Mário S Rodrigues
- University of Lisbon, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8, 1749-016 Lisboa, Portugal; Departamento de Física, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Mariana G Pinho
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157 Oeiras, Portugal
| | - Eurico J Cabrita
- UCIBIO, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Manuela M Pereira
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157 Oeiras, Portugal; University of Lisbon, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8, 1749-016 Lisboa, Portugal.
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13
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McDowell JR, Bai G, Lasek-Nesselquist E, Eisele LE, Wu Y, Hurteau G, Johnson R, Bai Y, Chen Y, Chan J, McDonough KA. Mycobacterial phosphodiesterase Rv0805 is a virulence determinant and its cyclic nucleotide hydrolytic activity is required for propionate detoxification. Mol Microbiol 2023; 119:401-422. [PMID: 36760076 PMCID: PMC10315211 DOI: 10.1111/mmi.15030] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 01/15/2023] [Accepted: 01/21/2023] [Indexed: 02/11/2023]
Abstract
Cyclic AMP (cAMP) signaling is essential to Mycobacterium tuberculosis (Mtb) pathogenesis. However, the roles of phosphodiesterases (PDEs) Rv0805, and the recently identified Rv1339, in cAMP homeostasis and Mtb biology are unclear. We found that Rv0805 modulates Mtb growth within mice, macrophages and on host-associated carbon sources. Mycobacterium bovis BCG grown on a combination of propionate and glycerol as carbon sources showed high levels of cAMP and had a strict requirement for Rv0805 cNMP hydrolytic activity. Supplementation with vitamin B12 or spontaneous genetic mutations in the pta-ackA operon restored the growth of BCGΔRv0805 and eliminated propionate-associated cAMP increases. Surprisingly, reduction of total cAMP levels by ectopic expression of Rv1339 restored only 20% of growth, while Rv0805 complementation fully restored growth despite a smaller effect on total cAMP levels. Deletion of an Rv0805 localization domain also reduced BCG growth in the presence of propionate and glycerol. We propose that localized Rv0805 cAMP hydrolysis modulates activity of a specialized pathway associated with propionate metabolism, while Rv1339 has a broader role in cAMP homeostasis. Future studies will address the biological roles of Rv0805 and Rv1339, including their impacts on metabolism, cAMP signaling and Mtb pathogenesis.
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Affiliation(s)
- James R. McDowell
- Wadsworth Center, New York State Department of Health, Albany, NY 12208
- Department of Biomedical Sciences, School of Public Health, University at Albany, SUNY, Albany NY 12208
| | - Guangchun Bai
- Wadsworth Center, New York State Department of Health, Albany, NY 12208
- Department of Immunology and Microbial Disease, MC-151, Albany Medical College, Albany, NY 12208-3479
| | - Erica Lasek-Nesselquist
- Wadsworth Center, New York State Department of Health, Albany, NY 12208
- Department of Biomedical Sciences, School of Public Health, University at Albany, SUNY, Albany NY 12208
| | - Leslie E. Eisele
- Wadsworth Center, New York State Department of Health, Albany, NY 12208
| | - Yan Wu
- Wadsworth Center, New York State Department of Health, Albany, NY 12208
| | - Gregory Hurteau
- Wadsworth Center, New York State Department of Health, Albany, NY 12208
| | - Richard Johnson
- Wadsworth Center, New York State Department of Health, Albany, NY 12208
- Department of Biomedical Sciences, School of Public Health, University at Albany, SUNY, Albany NY 12208
| | - Yinlan Bai
- Department of Biomedical Sciences, School of Public Health, University at Albany, SUNY, Albany NY 12208
| | - Yong Chen
- Albert Einstein College of Medicine, Bronx, NY
| | - John Chan
- Albert Einstein College of Medicine, Bronx, NY
| | - Kathleen A. McDonough
- Wadsworth Center, New York State Department of Health, Albany, NY 12208
- Department of Biomedical Sciences, School of Public Health, University at Albany, SUNY, Albany NY 12208
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14
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Oh S, Jo S, Bajzikova M, Kim HS, Dao TTP, Rohlena J, Kim JM, Neuzil J, Park S. Non-bioenergetic roles of mitochondrial GPD2 promote tumor progression. Theranostics 2023; 13:438-457. [PMID: 36632231 PMCID: PMC9830446 DOI: 10.7150/thno.75973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 11/19/2022] [Indexed: 12/23/2022] Open
Abstract
Rationale: Despite growing evidence for mitochondria's involvement in cancer, the roles of specific metabolic components outside the respiratory complex have been little explored. We conducted metabolomic studies on mitochondrial DNA (mtDNA)-deficient (ρ0) cancer cells with lower proliferation rates to clarify the undefined roles of mitochondria in cancer growth. Methods and results: Despite extensive metabolic downregulation, ρ0 cells exhibited high glycerol-3-phosphate (G3P) level, due to low activity of mitochondrial glycerol-3-phosphate dehydrogenase (GPD2). Knockout (KO) of GPD2 resulted in cell growth suppression as well as inhibition of tumor progression in vivo. Surprisingly, this was unrelated to the conventional bioenergetic function of GPD2. Instead, multi-omics results suggested major changes in ether lipid metabolism, for which GPD2 provides dihydroxyacetone phosphate (DHAP) in ether lipid biosynthesis. GPD2 KO cells exhibited significantly lower ether lipid level, and their slower growth was rescued by supplementation of a DHAP precursor or ether lipids. Mechanistically, ether lipid metabolism was associated with Akt pathway, and the downregulation of Akt/mTORC1 pathway due to GPD2 KO was rescued by DHAP supplementation. Conclusion: Overall, the GPD2-ether lipid-Akt axis is newly described for the control of cancer growth. DHAP supply, a non-bioenergetic process, may constitute an important role of mitochondria in cancer.
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Affiliation(s)
- Sehyun Oh
- College of Pharmacy, Natural Product Research Institute, Seoul National University, Seoul 08826, Korea
| | - Sihyang Jo
- College of Pharmacy, Natural Product Research Institute, Seoul National University, Seoul 08826, Korea
| | - Martina Bajzikova
- School of Pharmacy and Medical Science, Griffith University, Southport, Qld, Australia
| | - Han Sun Kim
- College of Pharmacy, Natural Product Research Institute, Seoul National University, Seoul 08826, Korea
| | - Thien T. P. Dao
- College of Pharmacy, Natural Product Research Institute, Seoul National University, Seoul 08826, Korea
| | - Jakub Rohlena
- Institute of Physiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Jin-Mo Kim
- College of Pharmacy, Natural Product Research Institute, Seoul National University, Seoul 08826, Korea
| | - Jiri Neuzil
- School of Pharmacy and Medical Science, Griffith University, Southport, Qld, Australia.,Institute of Biotechnology, Czech Academy of Sciences, Prague-West, Czech Republic.,Faculty of Science, Charles University, Prague, Czech Republic.,✉ Corresponding authors: Sunghyouk Park, Natural Product Research Institute, College of Pharmacy, Seoul National University, Gwanak-Ro 1, Gwanak-gu, Seoul 08826, Republic of Korea, Tel: +82-2-880-7831; Fax: +82-2-880-7831; E-mail: ; Jiri Neuzil, School of Pharmacy and Medical Science, Griffith University, 1 Parklands Dr, Southport, Qld 4215, Australia, Tel: +61-(0)7-5552-9109; Fax: +61-(0)7-5552-9109; E-mail: or
| | - Sunghyouk Park
- College of Pharmacy, Natural Product Research Institute, Seoul National University, Seoul 08826, Korea.,✉ Corresponding authors: Sunghyouk Park, Natural Product Research Institute, College of Pharmacy, Seoul National University, Gwanak-Ro 1, Gwanak-gu, Seoul 08826, Republic of Korea, Tel: +82-2-880-7831; Fax: +82-2-880-7831; E-mail: ; Jiri Neuzil, School of Pharmacy and Medical Science, Griffith University, 1 Parklands Dr, Southport, Qld 4215, Australia, Tel: +61-(0)7-5552-9109; Fax: +61-(0)7-5552-9109; E-mail: or
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15
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Metabolic Mechanism and Physiological Role of Glycerol 3-Phosphate in Pseudomonas aeruginosa PAO1. mBio 2022; 13:e0262422. [PMID: 36218368 PMCID: PMC9765544 DOI: 10.1128/mbio.02624-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pseudomonas aeruginosa is an important opportunistic pathogen that is lethal to cystic fibrosis (CF) patients. Glycerol generated during the degradation of phosphatidylcholine, the major lung surfactant in CF patients, could be utilized by P. aeruginosa. Previous studies have indicated that metabolism of glycerol by this bacterium contributes to its adaptation to and persistence in the CF lung environment. Here, we investigated the metabolic mechanisms of glycerol and its important metabolic intermediate glycerol 3-phosphate (G3P) in P. aeruginosa PAO1. We found that G3P homeostasis plays an important role in the growth and virulence factor production of P. aeruginosa PAO1. The G3P accumulation caused by the mutation of G3P dehydrogenase (GlpD) and exogenous glycerol led to impaired growth and reductions in pyocyanin synthesis, motilities, tolerance to oxidative stress, and resistance to kanamycin. Transcriptomic analysis indicates that the growth retardation caused by G3P stress is associated with reduced glycolysis and adenosine triphosphate (ATP) generation. Furthermore, two haloacid dehalogenase-like phosphatases (PA0562 and PA3172) that play roles in the dephosphorylation of G3P in strain PAO1 were identified, and their enzymatic properties were characterized. Our findings reveal the importance of G3P homeostasis and indicate that GlpD, the key enzyme for G3P catabolism, is a potential therapeutic target for the prevention and treatment of infections by this pathogen. IMPORTANCE In view of the intrinsic resistance of Pseudomonas aeruginosa to antibiotics and its potential to acquire resistance to current antibiotics, there is an urgent need to develop novel therapeutic options for the treatment of infections caused by this bacterium. Bacterial metabolic pathways have recently become a focus of interest as potential targets for the development of new antibiotics. In this study, we describe the mechanism of glycerol utilization in P. aeruginosa PAO1, which is an available carbon source in the lung environment. Our results reveal that the homeostasis of glycerol 3-phosphate (G3P), a pivotal intermediate in glycerol catabolism, is important for the growth and virulence factor production of P. aeruginosa PAO1. The mutation of G3P dehydrogenase (GlpD) and the addition of glycerol were found to reduce the tolerance of P. aeruginosa PAO1 to oxidative stress and to kanamycin. The findings highlight the importance of G3P homeostasis and suggest that GlpD is a potential drug target for the treatment of P. aeruginosa infections.
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16
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Li J, Wang R, Zhao L, Wang M, Wang R, Guo D, Yang Y, Li Y, Guan N, Shi Y, Xia X, Shi C. Stress tolerance and transcriptomic response analysis of Yersinia enterocolitica adapted to Origanum vulgare L. essential oil. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.113930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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17
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KANG JB, KOH PO. Identification of changed proteins by retinoic acid in cerebral ischemic damage: a proteomic study. J Vet Med Sci 2022; 84:1194-1204. [PMID: 35831120 PMCID: PMC9523306 DOI: 10.1292/jvms.22-0119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 07/03/2022] [Indexed: 11/22/2022] Open
Abstract
Ischemic stroke is a severe neurodegenerative disease with a high mortality rate. Retinoic acid is a representative metabolite of vitamin A. It has many beneficial effects including anti-inflammatory, anti-apoptotic, and neuroprotective effects. The purpose of this study is to identify specific proteins that are regulated by retinoic acid in ischemic stroke. Middle cerebral artery occlusion (MCAO) was performed to induce focal cerebral ischemia. Retinoic acid (5 mg/kg) or vehicle was injected intraperitoneally into male rats for four days prior to MCAO operation. Neurobehavioral tests were performed 24 hr after MCAO and the cerebral cortex was collected for proteomic study. Retinoic acid alleviates neurobehavioral deficits and histopathological changes caused by MCAO. Furthermore, we identified various proteins that were altered by retinoic acid in MCAO damage. Among these identified proteins, adenosylhomocysteinase, isocitrate dehydrogenase [NAD+] subunit α, glycerol-3-phosphate dehydrogenase, Rab GDP dissociation inhibitor β, and apolipoprotein A1 were down-regulated in MCAO animals with vehicle treatment, whereas retinoic acid treatment alleviated these reductions. However, heat shock protein 60 was up-regulated in MCAO animals with vehicle, while retinoic acid treatment attenuated this increase. The changes in these expressions were confirmed by reverse transcription-PCR. These proteins regulate cell metabolism and mediate stress responses. Our results demonstrated that retinoic acid attenuates the neuronal damage by MCAO and regulates the various protein expressions that are involved in the survival of cells. Thus, we can suggest that retinoic acid exerts neuroprotective effects on focal cerebral ischemia by modulation of specific proteins.
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Affiliation(s)
- Ju-Bin KANG
- Department of Anatomy, College of Veterinary Medicine, Research Institute of Life Science, Gyeongsang National University, Jinju, South Korea
| | - Phil-Ok KOH
- Department of Anatomy, College of Veterinary Medicine, Research Institute of Life Science, Gyeongsang National University, Jinju, South Korea
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18
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Defining the Genes Required for Survival of Mycobacterium bovis in the Bovine Host Offers Novel Insights into the Genetic Basis of Survival of Pathogenic Mycobacteria. mBio 2022; 13:e0067222. [PMID: 35862770 PMCID: PMC9426507 DOI: 10.1128/mbio.00672-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This is the first report of the genetic requirements of an animal-adapted member of the
Mycobacterium tuberculosis
complex (MTBC) in a natural host.
M. bovis
has devastating impacts on cattle, and bovine tuberculosis is a considerable economic, animal welfare, and public health concern. The data highlight the importance of mycobacterial cholesterol catabolism and identify several new virulence factors.
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19
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Minjárez-Sáenz M, Martínez-Júlvez M, Yruela I, Medina M. Mining the Flavoproteome of Brucella ovis, the Brucellosis Causing Agent in Ovis aries. Microbiol Spectr 2022; 10:e0229421. [PMID: 35315701 PMCID: PMC9045290 DOI: 10.1128/spectrum.02294-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 02/19/2022] [Indexed: 11/20/2022] Open
Abstract
Flavoproteins are a diverse class of proteins that are mostly enzymes and contain as cofactors flavin mononucleotide (FMN) and/or flavin adenine dinucleotide (FAD), which enable them to participate in a wide range of physiological reactions. We have compiled 78 potential proteins building the flavoproteome of Brucella ovis (B. ovis), the causative agent of ovine brucellosis. The curated list of flavoproteins here reported is based on (i) the analysis of sequence, structure and function of homologous proteins, and their classification according to their structural domains, clans, and expected enzymatic functions; (ii) the constructed phylogenetic trees of enzyme functional classes using 19 Brucella strains and 26 pathogenic and/or biotechnological relevant alphaproteobacteria together with B. ovis; and (iii) the evaluation of the genetic context for each entry. Candidates account for ∼2.7% of the B. ovis proteome, and 75% of them use FAD as cofactor. Only 55% of these flavoproteins belong to the core proteome of Brucella and contribute to B. ovis processes involved in maintenance activities, survival and response to stress, virulence, and/or infectivity. Several of the predicted flavoproteins are highly divergent in Brucella genus from revised proteins and for them it is difficult to envisage a clear function. This might indicate modified catalytic activities or even divergent processes and mechanisms still not identified. We have also detected the lack of some functional flavoenzymes in B. ovis, which might contribute to it being nonzoonotic. Finally, potentiality of B. ovis flavoproteome as the source of antimicrobial targets or biocatalyst is discussed. IMPORTANCE Some microorganisms depend heavily on flavin-dependent activities, but others maintain them at a minimum. Knowledge about flavoprotein content and functions in different microorganisms will help to identify their metabolic requirements, as well as to benefit either industry or health. Currently, most flavoproteins from the sheep pathogen Brucella ovis are only automatically annotated in databases, and only two have been experimentally studied. Indeed, certain homologues with unknown function are not characterized, and they might relate to still not identified mechanisms or processes. Our research has identified 78 members that comprise its flavoproteome, 76 of them flavoenzymes, which mainly relate to bacteria survival, virulence, and/or infectivity. The list of flavoproteins here presented allows us to better understand the peculiarities of Brucella ovis and can be applied as a tool to search for candidates as new biocatalyst or antimicrobial targets.
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Affiliation(s)
- Martha Minjárez-Sáenz
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, Zaragoza, Spain
| | - Marta Martínez-Júlvez
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, Zaragoza, Spain
- Group of Biochemistry, Biophysics and Computational Biology “GBsC” (BIFI, Unizar) Joint Unit to CSIC, Zaragoza, Spain
| | - Inmaculada Yruela
- Estación Experimental de Aula Dei, CSIC, Zaragoza, Spain
- Group of Biochemistry, Biophysics and Computational Biology “GBsC” (BIFI, Unizar) Joint Unit to CSIC, Zaragoza, Spain
| | - Milagros Medina
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, Zaragoza, Spain
- Group of Biochemistry, Biophysics and Computational Biology “GBsC” (BIFI, Unizar) Joint Unit to CSIC, Zaragoza, Spain
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Wright JJ, Biner O, Chung I, Burger N, Bridges HR, Hirst J. Reverse Electron Transfer by Respiratory Complex I Catalyzed in a Modular Proteoliposome System. J Am Chem Soc 2022; 144:6791-6801. [PMID: 35380814 PMCID: PMC9026280 DOI: 10.1021/jacs.2c00274] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Indexed: 02/02/2023]
Abstract
Respiratory complex I is an essential metabolic enzyme that uses the energy from NADH oxidation and ubiquinone reduction to translocate protons across an energy transducing membrane and generate the proton motive force for ATP synthesis. Under specific conditions, complex I can also catalyze the reverse reaction, Δp-linked oxidation of ubiquinol to reduce NAD+ (or O2), known as reverse electron transfer (RET). Oxidative damage by reactive oxygen species generated during RET underpins ischemia reperfusion injury, but as RET relies on several converging metabolic pathways, little is known about its mechanism or regulation. Here, we demonstrate Δp-linked RET through complex I in a synthetic proteoliposome system for the first time, enabling complete kinetic characterization of RET catalysis. We further establish the capability of our system by showing how RET in the mammalian enzyme is regulated by the active-deactive transition and by evaluating RET by complex I from several species in which direct assessment has not been otherwise possible. We thus provide new insights into the reversibility of complex I catalysis, an important but little understood mechanistic and physiological feature.
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Affiliation(s)
- John J. Wright
- Medical Research Council
Mitochondrial Biology Unit, University of
Cambridge, Cambridge CB2 0XY, U.K.
| | | | - Injae Chung
- Medical Research Council
Mitochondrial Biology Unit, University of
Cambridge, Cambridge CB2 0XY, U.K.
| | | | - Hannah R. Bridges
- Medical Research Council
Mitochondrial Biology Unit, University of
Cambridge, Cambridge CB2 0XY, U.K.
| | - Judy Hirst
- Medical Research Council
Mitochondrial Biology Unit, University of
Cambridge, Cambridge CB2 0XY, U.K.
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21
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Lemieux H, Blier PU. Exploring Thermal Sensitivities and Adaptations of Oxidative Phosphorylation Pathways. Metabolites 2022; 12:metabo12040360. [PMID: 35448547 PMCID: PMC9025460 DOI: 10.3390/metabo12040360] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 04/08/2022] [Accepted: 04/11/2022] [Indexed: 12/20/2022] Open
Abstract
Temperature shifts are a major challenge to animals; they drive adaptations in organisms and species, and affect all physiological functions in ectothermic organisms. Understanding the origin and mechanisms of these adaptations is critical for determining whether ectothermic organisms will be able to survive when faced with global climate change. Mitochondrial oxidative phosphorylation is thought to be an important metabolic player in this regard, since the capacity of the mitochondria to produce energy greatly varies according to temperature. However, organism survival and fitness depend not only on how much energy is produced, but, more precisely, on how oxidative phosphorylation is affected and which step of the process dictates thermal sensitivity. These questions need to be addressed from a new perspective involving a complex view of mitochondrial oxidative phosphorylation and its related pathways. In this review, we examine the effect of temperature on the commonly measured pathways, but mainly focus on the potential impact of lesser-studied pathways and related steps, including the electron-transferring flavoprotein pathway, glycerophosphate dehydrogenase, dihydroorotate dehydrogenase, choline dehydrogenase, proline dehydrogenase, and sulfide:quinone oxidoreductase. Our objective is to reveal new avenues of research that can address the impact of temperature on oxidative phosphorylation in all its complexity to better portray the limitations and the potential adaptations of aerobic metabolism.
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Affiliation(s)
- Hélène Lemieux
- Faculty Saint-Jean, Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6C 4G9, Canada
- Correspondence: (H.L.); (P.U.B.)
| | - Pierre U. Blier
- Department Biologie, Université du Québec à Rimouski, Rimouski, QC G5L 3A1, Canada
- Correspondence: (H.L.); (P.U.B.)
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22
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Abstract
While most small, regulatory RNAs are thought to be “noncoding,” a few have been found to also encode a small protein. Here we describe a 164-nucleotide RNA that encodes a 28-amino acid, amphipathic protein, which interacts with aerobic glycerol-3-phosphate dehydrogenase and increases dehydrogenase activity but also base pairs with two mRNAs to reduce expression. The coding and base-pairing sequences overlap, and the two regulatory functions compete. Bacteria have evolved small RNAs (sRNAs) to regulate numerous biological processes and stress responses. While sRNAs generally are considered to be “noncoding,” a few have been found to also encode a small protein. Here we describe one such dual-function RNA that modulates carbon utilization in Escherichia coli. The 164-nucleotide RNA was previously shown to encode a 28-amino acid protein (denoted AzuC). We discovered the membrane-associated AzuC protein interacts with GlpD, the aerobic glycerol-3-phosphate dehydrogenase, and increases dehydrogenase activity. Overexpression of the RNA encoding AzuC results in a growth defect in glycerol and galactose medium. The defect in galactose medium was still observed for a stop codon mutant derivative, suggesting a second role for the RNA. Consistent with this observation, we found that cadA and galE are repressed by base pairing with the RNA (denoted AzuR). Interestingly, AzuC translation interferes with the observed repression of cadA and galE by the RNA and base pairing interferes with AzuC translation, demonstrating that the translation and base-pairing functions compete.
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Mansour MMF, Hassan FAS. How salt stress-responsive proteins regulate plant adaptation to saline conditions. PLANT MOLECULAR BIOLOGY 2022; 108:175-224. [PMID: 34964081 DOI: 10.1007/s11103-021-01232-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 12/06/2021] [Indexed: 05/20/2023]
Abstract
An overview is presented of recent advances in our knowledge of candidate proteins that regulate various physiological and biochemical processes underpinning plant adaptation to saline conditions. Salt stress is one of the environmental constraints that restrict plant distribution, growth and yield in many parts of the world. Increased world population surely elevates food demands all over the globe, which anticipates to add a great challenge to humanity. These concerns have necessitated the scientists to understand and unmask the puzzle of plant salt tolerance mechanisms in order to utilize various strategies to develop salt tolerant crop plants. Salt tolerance is a complex trait involving alterations in physiological, biochemical, and molecular processes. These alterations are a result of genomic and proteomic complement readjustments that lead to tolerance mechanisms. Proteomics is a crucial molecular tool that indicates proteins expressed by the genome, and also identifies the functions of proteins accumulated in response to salt stress. Recently, proteomic studies have shed more light on a range of promising candidate proteins that regulate various processes rendering salt tolerance to plants. These proteins have been shown to be involved in photosynthesis and energy metabolism, ion homeostasis, gene transcription and protein biosynthesis, compatible solute production, hormone modulation, cell wall structure modification, cellular detoxification, membrane stabilization, and signal transduction. These candidate salt responsive proteins can be therefore used in biotechnological approaches to improve tolerance of crop plants to salt conditions. In this review, we provided comprehensive updated information on the proteomic data of plants/genotypes contrasting in salt tolerance in response to salt stress. The roles of salt responsive proteins that are potential determinants for plant salt adaptation are discussed. The relationship between changes in proteome composition and abundance, and alterations observed in physiological and biochemical features associated with salt tolerance are also addressed.
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Affiliation(s)
| | - Fahmy A S Hassan
- Department of Horticulture, Faculty of Agriculture, Tanta University, Tanta, Egypt
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24
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Kou J, He C, Cui L, Zhang Z, Wang W, Tan L, Liu D, Zheng W, Gu W, Xia N. Discovery of Potential Biomarkers for Postmenopausal Osteoporosis Based on Untargeted GC/LC-MS. Front Endocrinol (Lausanne) 2022; 13:849076. [PMID: 35518930 PMCID: PMC9062097 DOI: 10.3389/fendo.2022.849076] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 03/17/2022] [Indexed: 12/12/2022] Open
Abstract
PURPOSE As an important public health problem, osteoporosis (OP) in China is also in an upward trend year by year. As a standard method for diagnosing OP, dual-energy X-ray absorptiometry (DXA) cannot analyze the pathological process but only see the results. It is difficult to evaluate the early diagnosis of OP. Our study was carried out through a serum metabolomic study of OP in Chinese postmenopausal women on untargeted gas chromatography (GC)/liquid chromatography (LC)-mass spectrometry (MS) to find possible diagnostic markers. MATERIALS AND METHODS 50 Chinese postmenopausal women with osteoporosis and 50 age-matched women were selected as normal controls. We first used untargeted GC/LC-MS to analyze the serum of these participants and then combined it with a large number of multivariate statistical analyses to analyze the data. Finally, based on a multidimensional analysis of the metabolites, the most critical metabolites were considered to be biomarkers of OP in postmenopausal women. Further, biomarkers identified relevant metabolic pathways, followed by a map of metabolic pathways found in the database. RESULTS We found that there may be metabolic pathway disorders like glucose metabolism, lipid metabolism, and amino acid metabolism in postmenopausal women with OP. 18 differential metabolites are considered to be potential biomarkers of OP in postmenopausal women which are a major factor in metabolism and bone physiological function. CONCLUSION These findings can be applied to clinical work through further validation studies. It also shows that metabonomic analysis has great potential in the application of early diagnosis and recurrence monitoring in postmenopausal OP women.
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Affiliation(s)
- Jun Kou
- College of Medicine, Southwest Jiaotong University, Chengdu, China
- Department of Orthopedics, General Hospital of Western Theater Command, Chengdu, China
| | - Chunyang He
- Department of Hyperbaric Oxygen, General Hospital of Western Theater Command, Chengdu, China
| | - Lin Cui
- Department of Orthopedics, General Hospital of Western Theater Command, Chengdu, China
| | - Zhengping Zhang
- Department of Spinal Surgery, Honghui Hospital, Xi’an Jiaotong University College of Medicine, Xi’an, China
| | - Wei Wang
- College of Medicine, Southwest Jiaotong University, Chengdu, China
- Department of Orthopedics, General Hospital of Western Theater Command, Chengdu, China
- *Correspondence: Wei Wang, ; Da Liu, ; Wei Zheng,
| | - Li Tan
- School of Automation, Chongqing University of Posts and Telecommunications Chongqing, Chongqing, China
| | - Da Liu
- Department of Orthopedics, General Hospital of Western Theater Command, Chengdu, China
- *Correspondence: Wei Wang, ; Da Liu, ; Wei Zheng,
| | - Wei Zheng
- Department of Orthopedics, General Hospital of Western Theater Command, Chengdu, China
- *Correspondence: Wei Wang, ; Da Liu, ; Wei Zheng,
| | - Wei Gu
- Department of Orthopedics, General Hospital of Western Theater Command, Chengdu, China
| | - Ning Xia
- Department of Orthopedics, General Hospital of Western Theater Command, Chengdu, China
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Shahbazi M, Tohidfar M, Azimzadeh Irani M. Identification of the key functional genes in salt-stress tolerance of Cyanobacterium Phormidium tenue using in silico analysis. 3 Biotech 2021; 11:503. [PMID: 34881166 PMCID: PMC8602552 DOI: 10.1007/s13205-021-03050-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 10/31/2021] [Indexed: 10/19/2022] Open
Abstract
The development of artificial biocrust using cyanobacterium Phormidium tenue has been suggested as an effective strategy to prevent soil degradation. Here, a combination of in silico approaches with growth rate, photosynthetic pigment, morphology, and transcript analysis was used to identify specific genes and their protein products in response to 500 mM NaCl in P. tenue. The results show that 500 mM NaCl induces the expression of genes encoding glycerol-3-phosphate dehydrogenase (glpD) as a Flavoprotein, ribosomal protein S12 methylthiotransferase (rimO), and a hypothetical protein (sll0939). The constructed co-expression network revealed a group of abiotic stress-responsive genes. Using the Basic Local Alignment Search Tool (BLAST), the homologous proteins of rimO, glpD, and sll0939 were identified in the P. tenue genome. Encoded proteins of glpD, rimO, and DUF1622 genes, respectively, contain (DAO and DAO C), (UPF0004, Radical SAM and TRAM 2), and (DUF1622) domains. The predicted ligand included 22B and MG for DUF1622, FS5 for rimO, and FAD for glpD protein. There was no direct disruption in ligand-binding sites of these proteins by Na+, Cl-, or NaCl. The growth rate, photosynthetic pigment, and morphology of P. tenue were investigated, and the result showed an acceptable tolerance rate of this microorganism under salt stress. The quantitative real-time polymerase chain reaction (qRT-PCR) results revealed the up-regulation of glpD, rimO, and DUF1622 genes under salt stress. This is the first report on computational and experimental analyses of the glpD, rimO, and DUF1622 genes in P. tenue under salt stress to the best of our knowledge. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-03050-w.
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Affiliation(s)
- Mehrdad Shahbazi
- Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, 1983969411 Tehran, Iran
| | - Masoud Tohidfar
- Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, 1983969411 Tehran, Iran
| | - Maryam Azimzadeh Irani
- Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, 1983969411 Tehran, Iran
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Frazee LJ, Rifkin J, Maheepala DC, Grant AG, Wright S, Kalisz S, Litt A, Spigler R. New genomic resources and comparative analyses reveal differences in floral gene expression in selfing and outcrossing Collinsia sister species. G3 (BETHESDA, MD.) 2021; 11:jkab177. [PMID: 34014319 PMCID: PMC8496223 DOI: 10.1093/g3journal/jkab177] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 05/11/2021] [Indexed: 11/14/2022]
Abstract
The evolutionary transition from outcross- to self-fertilization is one of the most common in angiosperms and is often associated with a parallel shift in floral morphological and developmental traits, such as reduced flower size and pollen to ovule ratios, known as the "selfing syndrome." How these convergent phenotypes arise, the extent to which they are shaped by selection, and the nature of their underlying genetic basis are unsettled questions in evolutionary biology. The genus Collinsia (Plantaginaceae) includes seven independent transitions from outcrossing or mixed mating to high selfing rates accompanied by selfing syndrome traits. Accordingly, Collinsia represents an ideal system for investigating this parallelism, but requires genomic resource development. We present a high quality de novo genome assembly for the highly selfing species Collinsia rattanii. To begin addressing the basis of selfing syndrome developmental shifts, we evaluate and contrast patterns of gene expression from floral transcriptomes across three stages of bud development for C. rattanii and its outcrossing sister species Collinsia linearis. Relative to C. linearis, total gene expression is less variable among individuals and bud stages in C. rattanii. In addition, there is a common pattern among differentially expressed genes: lower expression levels that are more constant across bud development in C. rattanii relative to C. linearis. Transcriptional regulation of enzymes involved in pollen formation specifically in early bud development may influence floral traits that distinguish selfing and outcrossing Collinsia species through pleiotropic functions. Future work will include additional Collinsia outcrossing-selfing species pairs to identify genomic signatures of parallel evolution.
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Affiliation(s)
- Lauren J Frazee
- Department of Biology, Temple University, Philadelphia, PA 19122, USA
| | - Joanna Rifkin
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S, Canada
| | - Dinusha C Maheepala
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA
| | - Alannie-Grace Grant
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Stephen Wright
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S, Canada
| | - Susan Kalisz
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Amy Litt
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA
| | - Rachel Spigler
- Department of Biology, Temple University, Philadelphia, PA 19122, USA
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Marito S, Keshari S, Traisaeng S, My DTT, Balasubramaniam A, Adi P, Hsieh MF, Herr DR, Huang CM. Electricity-producing Staphylococcus epidermidis counteracts Cutibacterium acnes. Sci Rep 2021; 11:12001. [PMID: 34099817 PMCID: PMC8184966 DOI: 10.1038/s41598-021-91398-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 05/10/2021] [Indexed: 12/19/2022] Open
Abstract
Staphylococcus epidermidis (S. epidermidis) ATCC 12228 was incubated with 2% polyethylene glycol (PEG)-8 Laurate to yield electricity which was measured by a voltage difference between electrodes. Production of electron was validated by a Ferrozine assay. The anti-Cutibacterium acnes (C. acnes) activity of electrogenic S. epidermidis was assessed in vitro and in vivo. The voltage change (~ 4.4 mV) reached a peak 60 min after pipetting S. epidermidis plus 2% PEG-8 Laurate onto anodes. The electricity produced by S. epidermidis caused significant growth attenuation and cell lysis of C. acnes. Intradermal injection of C. acnes and S. epidermidis plus PEG-8 Laurate into the mouse ear considerably suppressed the growth of C. acnes. This suppressive effect was noticeably reversed when cyclophilin A of S. epidermidis was inhibited, indicating the essential role of cyclophilin A in electricity production of S. epidermidis against C. acnes. In summary, we demonstrate for the first time that skin S. epidermidis, in the presence of PEG-8 Laurate, can mediate cyclophilin A to elicit an electrical current that has anti-C. acnes effects. Electricity generated by S. epidermidis may confer immediate innate immunity in acne lesions to rein in the overgrowth of C. acnes at the onset of acne vulgaris.
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Affiliation(s)
- Shinta Marito
- Department of Biomedical Sciences and Engineering, National Central University, Taoyuan, Taiwan
| | - Sunita Keshari
- Department of Life Sciences, National Central University, Taoyuan, Taiwan
| | | | - Do Thi Tra My
- Department of Biomedical Sciences and Engineering, National Central University, Taoyuan, Taiwan
| | - Arun Balasubramaniam
- Department of Biomedical Sciences and Engineering, National Central University, Taoyuan, Taiwan
| | - Prakoso Adi
- Department of Biomedical Sciences and Engineering, National Central University, Taoyuan, Taiwan
| | - Ming-Fa Hsieh
- Department of Biomedical Engineering, Chung Yuan Christian University, Taoyuan, Taiwan
| | | | - Chun-Ming Huang
- Department of Biomedical Sciences and Engineering, National Central University, Taoyuan, Taiwan.
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Jeucken A, Zhou M, Wösten MMSM, Brouwers JF. Control of n-Butanol Induced Lipidome Adaptations in E. coli. Metabolites 2021; 11:metabo11050286. [PMID: 33947169 PMCID: PMC8145963 DOI: 10.3390/metabo11050286] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/21/2021] [Accepted: 04/28/2021] [Indexed: 11/16/2022] Open
Abstract
The versatile compound n-butanol is one of the most promising biofuels for use in existing internal combustion engines, contributing to a smooth transition towards a clean energy society. Furthermore, n-butanol is a valuable resource to produce more complex molecules such as bioplastics. Microbial production of n-butanol from waste materials is hampered by the biotoxicity of n-butanol as it interferes with the proper functioning of lipid membranes. In this study we perform a large-scale investigation of the complete lipid-related enzyme machinery and its response to exposure to a sublethal concentration of n-butanol. We profiled, in triplicate, the growth characteristics and phospholipidomes of 116 different genetic constructs of E. coli, both in the presence and absence of 0.5% n-butanol (v/v). This led to the identification of 230 lipid species and subsequently to the reconstruction of the network of metabolites, enzymes and lipid properties driving the homeostasis of the E. coli lipidome. We were able to identify key lipids and biochemical pathways leading to altered n-butanol tolerance. The data led to new conceptual insights into the bacterial lipid metabolism which are discussed.
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Affiliation(s)
- Aike Jeucken
- Membrane Enzymology, Groningen Biomolecular and Biotechnology Institute (GBB), University of Groningen, 9747 AG Groningen, The Netherlands;
| | - Miaomiao Zhou
- Research Group Analysis Techniques in the Life Sciences, School of Life Sciences and Environmental Technology ATGM, Avans University of Applied Sciences, 4818 AJ Breda, The Netherlands;
| | - Marc M. S. M. Wösten
- Infection Biology, Department of Biomolecular Health Sciences, Utrecht University, 3584 CL Utrecht, The Netherlands;
| | - Jos F. Brouwers
- Research Group Analysis Techniques in the Life Sciences, School of Life Sciences and Environmental Technology ATGM, Avans University of Applied Sciences, 4818 AJ Breda, The Netherlands;
- Center for Molecular Medicine, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
- Correspondence: or
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Kim M, Lee J, Heo L, Lee SJ, Han SW. Proteomic and Phenotypic Analyses of a Putative Glycerol-3-Phosphate Dehydrogenase Required for Virulence in Acidovorax citrulli. THE PLANT PATHOLOGY JOURNAL 2021; 37:36-46. [PMID: 33551695 PMCID: PMC7847757 DOI: 10.5423/ppj.oa.12.2020.0221] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 12/28/2020] [Accepted: 12/29/2020] [Indexed: 05/05/2023]
Abstract
Acidovorax citrulli (Ac) is the causal agent of bacterial fruit blotch (BFB) in watermelon, a disease that poses a serious threat to watermelon production. Because of the lack of resistant cultivars against BFB, virulence factors or mechanisms need to be elucidated to control the disease. Glycerol-3-phosphate dehydrogenase is the enzyme involved in glycerol production from glucose during glycolysis. In this study, we report the functions of a putative glycerol-3-phosphate dehydrogenase in Ac (GlpdAc) using comparative proteomic analysis and phenotypic observation. A glpdAc knockout mutant, AcΔglpdAc(EV), lost virulence against watermelon in two pathogenicity tests. The putative 3D structure and amino acid sequence of GlpdAc showed high similarity with glycerol-3-phosphate dehydrogenases from other bacteria. Comparative proteomic analysis revealed that many proteins related to various metabolic pathways, including carbohydrate metabolism, were affected by GlpdAc. Although AcΔglpdAc(EV) could not use glucose as a sole carbon source, it showed growth in the presence of glycerol, indicating that GlpdAc is involved in glycolysis. AcΔglpdAc(EV) also displayed higher cell-to-cell aggregation than the wild-type bacteria, and tolerance to osmotic stress and ciprofloxacin was reduced and enhanced in the mutant, respectively. These results indicate that GlpdAc is involved in glycerol metabolism and other mechanisms, including virulence, demonstrating that the protein has pleiotropic effects. Our study expands the understanding of the functions of proteins associated with virulence in Ac.
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Affiliation(s)
- Minyoung Kim
- Department of Plant Science and Technology, Chung-Ang University, Anseong 7546, Korea
| | - Jongchan Lee
- Department of Plant Science and Technology, Chung-Ang University, Anseong 7546, Korea
| | - Lynn Heo
- Department of Plant Science and Technology, Chung-Ang University, Anseong 7546, Korea
| | - Sang Jun Lee
- Department of Systems Biotechnology, Chung-Ang University, Anseong 17546, Korea
- Co-corresponding authors. S. J. Lee, Phone) +82-31-670-3356, FAX) +82-2-675-3108, E-mail) , S.-W. Han, Phone) +82-31-670-3150, FAX) +82-2-670-8845, E-mail) , ORCID, Sang Jun Lee https://orcid.org/0000-0002-2803-753X, Sang-Wook Han https://orcid.org/0000-0002-0893-1438
| | - Sang-Wook Han
- Department of Plant Science and Technology, Chung-Ang University, Anseong 7546, Korea
- Co-corresponding authors. S. J. Lee, Phone) +82-31-670-3356, FAX) +82-2-675-3108, E-mail) , S.-W. Han, Phone) +82-31-670-3150, FAX) +82-2-670-8845, E-mail) , ORCID, Sang Jun Lee https://orcid.org/0000-0002-2803-753X, Sang-Wook Han https://orcid.org/0000-0002-0893-1438
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Amikacin and bacteriophage treatment modulates outer membrane proteins composition in Proteus mirabilis biofilm. Sci Rep 2021; 11:1522. [PMID: 33452316 PMCID: PMC7810710 DOI: 10.1038/s41598-020-80907-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 12/28/2020] [Indexed: 01/21/2023] Open
Abstract
Modification of outer membrane proteins (OMPs) is the first line of Gram-negative bacteria defence against antimicrobials. Here we point to Proteus mirabilis OMPs and their role in antibiotic and phage resistance. Protein profiles of amikacin (AMKrsv), phage (Brsv) and amikacin/phage (AMK/Brsv) resistant variants of P. mirabilis were compared to that obtained for a wild strain. In resistant variants there were identified 14, 1, 5 overexpressed and 13, 5, 1 downregulated proteins for AMKrsv, Brsv and AMK/Brsv, respectively. Application of phages with amikacin led to reducing the number of up- and downregulated proteins compared to single antibiotic treatment. Proteins isolated in AMKrsv are involved in protein biosynthesis, transcription and signal transduction, which correspond to well-known mechanisms of bacteria resistance to aminoglycosides. In isolated OMPs several cytoplasmic proteins, important in antibiotic resistance, were identified, probably as a result of environmental stress, e.g. elongation factor Tu, asparaginyl-tRNA and aspartyl-tRNA synthetases. In Brsv there were identified: NusA and dynamin superfamily protein which could play a role in bacteriophage resistance. In the resistant variants proteins associated with resistance mechanisms occurring in biofilm, e.g. polyphosphate kinase, flagella basal body rod protein were detected. These results indicate proteins important in the development of P. mirabilis antibiofilm therapies.
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Structural Characterization of Glycerol Kinase from the Thermophilic Fungus Chaetomium thermophilum. Int J Mol Sci 2020; 21:ijms21249570. [PMID: 33339113 PMCID: PMC7765489 DOI: 10.3390/ijms21249570] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 12/05/2020] [Accepted: 12/14/2020] [Indexed: 12/12/2022] Open
Abstract
Glycerol is an organic compound that can be utilized as an alternative source of carbon by various organisms. One of the ways to assimilate glycerol by the cell is the phosphorylative catabolic pathway in which its activation is catalyzed by glycerol kinase (GK) and glycerol-3-phosphate (G3P) is formed. To date, several GK crystal structures from bacteria, archaea, and unicellular eukaryotic parasites have been solved. Herein, we present a series of crystal structures of GK from Chaetomium thermophilum (CtGK) in apo and glycerol-bound forms. In addition, we show the feasibility of an ADP-dependent glucokinase (ADPGK)-coupled enzymatic assay to measure the CtGK activity. New structures described in our work provide structural insights into the GK catalyzed reaction in the filamentous fungus and set the foundation for understanding the glycerol metabolism in eukaryotes.
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Neves HI, Machado GT, Ramos TCDS, Yang HM, Yagil E, Spira B. Competition for nutritional resources masks the true frequency of bacterial mutants. BMC Biol 2020; 18:194. [PMID: 33317515 PMCID: PMC7737367 DOI: 10.1186/s12915-020-00913-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 11/03/2020] [Indexed: 12/02/2022] Open
Abstract
Background It is widely assumed that all mutant microorganisms present in a culture are able to grow and form colonies, provided that they express the features required for selection. Unlike wild-type Escherichia coli, PHO-constitutive mutants overexpress alkaline phosphatase and hence can hydrolyze glycerol-2-phosphate (G2P) to glycerol and form colonies on plates having G2P as the sole carbon source. These mutations mostly occur in the pst operon. However, the frequency of PHO-constitutive colonies on the G2P selective plate is exceptionally low. Results We show that the rate in which spontaneous PHO-constitutive mutations emerge is about 8.0 × 10−6/generation, a relatively high rate, but the growth of most existing mutants is inhibited by their neighboring wild-type cells. This inhibition is elicited only by non-mutant viable bacteria that can take up and metabolize glycerol formed by the mutants. Evidence indicates that the few mutants that do form colonies derive from microclusters of mutants on the selective plate. A mathematical model that describes the fate of the wild-type and mutant populations under these circumstances supports these results. Conclusion This scenario in which neither the wild-type nor the majority of the mutants are able to grow resembles an unavoidable “tragedy of the commons” case which results in the collapse of the majority of the population. Cooperation between rare adjacent mutants enables them to overcome the competition and eventually form mutant colonies. The inhibition of PHO-constitutive mutants provides an example of mutant frequency masked by orders of magnitude due to a competition between mutants and their ancestral wild-type cells. Similar “tragedy of the commons-like” cases may occur in other settings and should be taken into consideration while estimating true mutant frequencies and mutation rates. Supplementary Information The online version contains supplementary material available at (doi:10.1186/s12915-020-00913-1).
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Affiliation(s)
- Henrique Iglesias Neves
- Departamento de Microbiologia, Instituto de Ciências Biomédicas Universidade de São Paulo, São Paulo, SP, Brazil
| | - Gabriella Trombini Machado
- Departamento de Microbiologia, Instituto de Ciências Biomédicas Universidade de São Paulo, São Paulo, SP, Brazil
| | | | - Hyun Mo Yang
- Departamento de Matemática Aplicada, Instituto de Matemática, Estatística e Computação Científica, Campinas, SP, Brazil
| | - Ezra Yagil
- Departament of Biochemistry and Molecular Biology, Faculty of Life Sciences, Tel-Aviv University, Tel Aviv, Israel
| | - Beny Spira
- Departamento de Microbiologia, Instituto de Ciências Biomédicas Universidade de São Paulo, São Paulo, SP, Brazil.
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Yildiz I, Sizirici Yildiz B. Computational mechanistic study of human liver glycerol 3‐phosphate dehydrogenase using ONIOM method. J PHYS ORG CHEM 2020. [DOI: 10.1002/poc.4104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Pecinová A, Alán L, Brázdová A, Vrbacký M, Pecina P, Drahota Z, Houštěk J, Mráček T. Role of Mitochondrial Glycerol-3-Phosphate Dehydrogenase in Metabolic Adaptations of Prostate Cancer. Cells 2020; 9:cells9081764. [PMID: 32717855 PMCID: PMC7464303 DOI: 10.3390/cells9081764] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 07/14/2020] [Accepted: 07/22/2020] [Indexed: 12/26/2022] Open
Abstract
Prostate cancer is one of the most prominent cancers diagnosed in males. Contrasting with other cancer types, glucose utilization is not increased in prostate carcinoma cells as they employ different metabolic adaptations involving mitochondria as a source of energy and intermediates required for rapid cell growth. In this regard, prostate cancer cells were associated with higher activity of mitochondrial glycerol-3-phosphate dehydrogenase (mGPDH), the key rate limiting component of the glycerophosphate shuttle, which connects mitochondrial and cytosolic processes and plays significant role in cellular bioenergetics. Our research focused on the role of mGPDH biogenesis and regulation in prostate cancer compared to healthy cells. We show that the 42 amino acid presequence is cleaved from N-terminus during mGPDH biogenesis. Only the processed form is part of the mGPDH dimer that is the prominent functional enzyme entity. We demonstrate that mGPDH overexpression enhances the wound healing ability in prostate cancer cells. As mGPDH is at the crossroad of glycolysis, lipogenesis and oxidative metabolism, regulation of its activity by intramitochondrial processing might represent rapid means of cellular metabolic adaptations.
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Wang Y, Huang JM, Zhou YL, Almeida A, Finn RD, Danchin A, He LS. Phylogenomics of expanding uncultured environmental Tenericutes provides insights into their pathogenicity and evolutionary relationship with Bacilli. BMC Genomics 2020; 21:408. [PMID: 32552739 PMCID: PMC7301438 DOI: 10.1186/s12864-020-06807-4] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 06/05/2020] [Indexed: 12/28/2022] Open
Abstract
Background The metabolic capacity, stress response and evolution of uncultured environmental Tenericutes have remained elusive, since previous studies have been largely focused on pathogenic species. In this study, we expanded analyses on Tenericutes lineages that inhabit various environments using a collection of 840 genomes. Results Several environmental lineages were discovered inhabiting the human gut, ground water, bioreactors and hypersaline lake and spanning the Haloplasmatales and Mycoplasmatales orders. A phylogenomics analysis of Bacilli and Tenericutes genomes revealed that some uncultured Tenericutes are affiliated with novel clades in Bacilli, such as RF39, RFN20 and ML615. Erysipelotrichales and two major gut lineages, RF39 and RFN20, were found to be neighboring clades of Mycoplasmatales. We detected habitat-specific functional patterns between the pathogenic, gut and the environmental Tenericutes, where genes involved in carbohydrate storage, carbon fixation, mutation repair, environmental response and amino acid cleavage are overrepresented in the genomes of environmental lineages, perhaps as a result of environmental adaptation. We hypothesize that the two major gut lineages, namely RF39 and RFN20, are probably acetate and hydrogen producers. Furthermore, deteriorating capacity of bactoprenol synthesis for cell wall peptidoglycan precursors secretion is a potential adaptive strategy employed by these lineages in response to the gut environment. Conclusions This study uncovers the characteristic functions of environmental Tenericutes and their relationships with Bacilli, which sheds new light onto the pathogenicity and evolutionary processes of Mycoplasmatales.
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Affiliation(s)
- Yong Wang
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, No. 28, Luhuitou Road, Sanya, Hai Nan, P.R. China.
| | - Jiao-Mei Huang
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, No. 28, Luhuitou Road, Sanya, Hai Nan, P.R. China.,University of Chinese Academy of Sciences, Beijing, China
| | - Ying-Li Zhou
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, No. 28, Luhuitou Road, Sanya, Hai Nan, P.R. China.,University of Chinese Academy of Sciences, Beijing, China
| | - Alexandre Almeida
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK.,Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Robert D Finn
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
| | - Antoine Danchin
- Kodikos, Department of Infection, Immunity and Inflammation, Institut Cochin INSERM U1016 - CNRS UMR8104 - Université Paris Descartes, 24 rue du Faubourg Saint-Jacques, 75014, Paris, France.,Li Kashing Faculty of Medicine, School of Biomedical Sciences, University of Hong Kong, 21 Sassoon Road, Hong Kong, SAR, China
| | - Li-Sheng He
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, No. 28, Luhuitou Road, Sanya, Hai Nan, P.R. China
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36
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Zhang Q, Fang G, Chen W, Zhong X, Long Y, Qin H, Ye J. The molecular effects of ultrasound on the expression of cellular proteome. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 720:137439. [PMID: 32143036 DOI: 10.1016/j.scitotenv.2020.137439] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 02/18/2020] [Accepted: 02/18/2020] [Indexed: 06/10/2023]
Abstract
High frequency and low intensity, diagnostic ultrasound methods are recognized to be safe in epidemiology and pathology but the bioeffects of these methods on molecular and proteomic levels are unknown. As a representative organism that can directly reflect the molecular response to stresses, Escherichia coli was selected for exposure to ultrasound probes C1-5, M5s and 9 L for 10 min and 20 min. ITRAQ was used to measure the expression of the cellular proteome. The results showed that both the frequency and time of exposure to ultrasound affected the proteome expression. Fifty biological processes were affected and nineteen metabolic processes, including carbohydrate metabolism, asparagine metabolism and phosphate import were differentially regulated. Lower frequency ultrasound caused copper export and iron‑sulfur cluster biosynthesis upregulation. Nine proteins (GlpD, AsnB, TdcB, CopA, IscR, IscU, IscS, IscA, RecA) were key for the adaption to ultrasound. Accordingly, the results of the potential risks based on the calculation of the orthologous genome clarified that relevant pathways and potentially sensitive individuals were worthy of further study. These findings offer insights into reveal the bioeffects of ultrasound at the metabolic network and proteomic levels.
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Affiliation(s)
- Qinglin Zhang
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 510632, China
| | - Guiting Fang
- Department of Ultrasound, The First Affiliated Hospital of Jinan University, Guangzhou 510630, China
| | - Weijian Chen
- Department of Ultrasound, The First Affiliated Hospital of Jinan University, Guangzhou 510630, China
| | - Xing Zhong
- Department of Ultrasound, The First Affiliated Hospital of Jinan University, Guangzhou 510630, China
| | - Yan Long
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 510632, China
| | - Huaming Qin
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 510632, China
| | - Jinshao Ye
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 510632, China.
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Song M, Liu Y, Huang X, Ding S, Wang Y, Shen J, Zhu K. A broad-spectrum antibiotic adjuvant reverses multidrug-resistant Gram-negative pathogens. Nat Microbiol 2020; 5:1040-1050. [PMID: 32424338 DOI: 10.1038/s41564-020-0723-z] [Citation(s) in RCA: 213] [Impact Index Per Article: 53.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 04/14/2020] [Indexed: 12/13/2022]
Abstract
The rapid emergence and dissemination of multidrug-resistant (MDR) bacterial pathogens pose a serious threat to global healthcare. One particular concern is the carbapenem-resistant Enterobacteriaceae (CRE), a group of Gram-negative bacteria that have evolved resistance to all or nearly all available antibiotics. Coupled with the fact of barren antibiotic development pipeline nowadays, a critical approach is to revitalize existing antibiotics using antibiotic adjuvants. We found a short linear antibacterial peptide (SLAP)-S25 carrying four non-natural amino acids of 2,4-diaminobutanoic acid (Dab), which solely showed weak antibacterial activity but boosted the efficacy of antibiotics covering all major classes, including cefepime, colistin, ofloxacin, rifampicin, tetracycline and vancomycin, against MDR Gram-negative pathogens. Mechanistic studies showed that SLAP-S25 triggers membrane damage by binding to both lipopolysaccharide (LPS) in the outer membrane and phosphatidylglycerol (PG) in bacterial cytoplasmic membrane, to potentiate antibiotic efficacy through collaborative strategies. Lastly, SLAP-S25 effectively enhanced the activity of colistin against MDR Escherichia coli-associated infections in three animal models. Our findings provide a potential therapeutic option using existing antibiotics in combination with broad-spectrum antibiotic adjuvants, to address the prevalent infections caused by MDR Gram-negative pathogens worldwide.
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Affiliation(s)
- Meirong Song
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Yuan Liu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
| | - Xiaoyong Huang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Shuangyang Ding
- National Center for Veterinary Drug Safety Evaluation, College of Veterinary Medicine, China Agricultural University, Beijing, China.,Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety and Beijing Laboratory for Food Quality and Safety, China Agricultural University, Beijing, China
| | - Yang Wang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Jianzhong Shen
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, China. .,National Center for Veterinary Drug Safety Evaluation, College of Veterinary Medicine, China Agricultural University, Beijing, China. .,Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety and Beijing Laboratory for Food Quality and Safety, China Agricultural University, Beijing, China.
| | - Kui Zhu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, China. .,National Center for Veterinary Drug Safety Evaluation, College of Veterinary Medicine, China Agricultural University, Beijing, China.
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38
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Kim JW, Ko YS, Chae TU, Lee SY. High-level production of 3-hydroxypropionic acid from glycerol as a sole carbon source using metabolically engineered Escherichia coli. Biotechnol Bioeng 2020; 117:2139-2152. [PMID: 32227471 DOI: 10.1002/bit.27344] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Revised: 03/20/2020] [Accepted: 03/25/2020] [Indexed: 11/09/2022]
Abstract
As climate change is an important environmental issue, the conventional petrochemical-based processes to produce valuable chemicals are being shifted toward eco-friendly biological-based processes. In this study, 3-hydroxypropionic acid (3-HP), an industrially important three carbon (C3) chemical, was overproduced by metabolically engineered Escherichia coli using glycerol as a sole carbon source. As the first step to construct a glycerol-dependent 3-HP biosynthetic pathway, the dhaB1234 and gdrAB genes from Klebsiella pneumoniae encoding glycerol dehydratase and glycerol reactivase, respectively, were introduced into E. coli to convert glycerol into 3-hydroxypropionaldehyde (3-HPA). In addition, the ydcW gene from K. pneumoniae encoding γ-aminobutyraldehyde dehydrogenase, among five aldehyde dehydrogenases examined, was selected to further convert 3-HPA to 3-HP. Increasing the expression level of the ydcW gene enhanced 3-HP production titer and reduced 1,3-propanediol production. To enhance 3-HP production, fed-batch fermentation conditions were optimized by controlling dissolved oxygen (DO) level and employing different feeding strategies including intermittent feeding, pH-stat feeding, and continuous feeding strategies. Fed-batch culture of the final engineered E. coli strain with DO control and continuous feeding strategy produced 76.2 g/L of 3-HP with the yield and productivity of 0.457 g/g glycerol and 1.89 g·L-1 ·h-1 , respectively. To the best of our knowledge, this is the highest 3-HP productivity achieved by any microorganism reported to date.
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Affiliation(s)
- Je Woong Kim
- Metabolic and Biomolecular Engineering National Research Laboratory, Systems Metabolic Engineering and Systems Healthcare (SMESH) Cross-Generation Collaborative Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.,BioProcess Engineering Research Center, KAIST, Daejeon, Republic of Korea
| | - Yoo-Sung Ko
- Metabolic and Biomolecular Engineering National Research Laboratory, Systems Metabolic Engineering and Systems Healthcare (SMESH) Cross-Generation Collaborative Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.,BioProcess Engineering Research Center, KAIST, Daejeon, Republic of Korea
| | - Tong Un Chae
- Metabolic and Biomolecular Engineering National Research Laboratory, Systems Metabolic Engineering and Systems Healthcare (SMESH) Cross-Generation Collaborative Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.,BioProcess Engineering Research Center, KAIST, Daejeon, Republic of Korea
| | - Sang Yup Lee
- Metabolic and Biomolecular Engineering National Research Laboratory, Systems Metabolic Engineering and Systems Healthcare (SMESH) Cross-Generation Collaborative Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.,BioProcess Engineering Research Center, KAIST, Daejeon, Republic of Korea.,BioInformatics Research Center, KAIST, Daejeon, Republic of Korea
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Engineering of glycerol utilization in Pseudomonas chlororaphis GP72 for enhancing phenazine-1-carboxylic acid production. World J Microbiol Biotechnol 2020; 36:49. [PMID: 32157439 DOI: 10.1007/s11274-020-02824-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 02/29/2020] [Indexed: 12/25/2022]
Abstract
Glycerol is a by-product of biodiesel, and it has a great application prospect to be transformed to synthesize high value-added compounds. Pseudomonas chlororaphis GP72 isolated from the green pepper rhizosphere is a plant growth promoting rhizobacteria that can utilize amount of glycerol to synthesize phenazine-1-carboxylic acid (PCA). PCA has been commercially registered as "Shenqinmycin" in China due to its characteristics of preventing pepper blight and rice sheath blight. The aim of this study was to engineer glycerol utilization pathway in P. chlororaphis GP72. First, the two genes glpF and glpK from the glycerol metabolism pathway were overexpressed in GP72ANO separately. Then, the two genes were co-expressed in GP72ANO, improving PCA production from 729.4 mg/L to 993.4 mg/L at 36 h. Moreover, the shunt pathway was blocked to enhance glycerol utilization, resulting in 1493.3 mg/L PCA production. Additionally, we confirmed the inhibition of glpR on glycerol metabolism pathway in P. chlororaphis GP72. This study provides a good example for improving the utilization of glycerol to synthesize high value-added compounds in Pseudomonas.
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40
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Cronobacter sakazakii CICC 21544 responds to the combination of carvacrol and citral by regulating proton motive force. Lebensm Wiss Technol 2020. [DOI: 10.1016/j.lwt.2020.109040] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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41
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Zhou A, Cao Y, Zhou D, Hu S, Tan W, Xiao X, Yu Y, Li X. Global transcriptomic analysis of Cronobacter sakazakii CICC 21544 by RNA-seq under inorganic acid and organic acid stresses. Food Res Int 2019; 130:108963. [PMID: 32156398 DOI: 10.1016/j.foodres.2019.108963] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 12/23/2019] [Accepted: 12/25/2019] [Indexed: 01/07/2023]
Abstract
Cronobacter sakazakii is a common foodborne pathogen that can tolerate various stress conditions. Acidic environment is a common stress condition encountered by bacteria in food processing and gastrointestinal digestion, including both inorganic and organic acids. In order to elucidate the Acid Tolerance Response (ATR) of C. sakazakii, we performed high-throughput RNA-seq to compare gene expression under hydrochloric acid and citric acid stresses. In this study, 107 differentially expressed genes (DEGs) were identified in both acids, of which 85 DEGs were functionally related to the regulation of acid tolerance. Multiple layers of mechanisms may be applied by C. sakazakii in response to acid stress: Firstly, in order to reduce excessive intracellular protons, C. sakazakii pumps them out through trans-membrane proteins or consumes them through metabolic reactions. Secondly, under acidic conditions, a large amount of reactive oxygen species and hydroxyl radicals accumulate in the cells, resulting in oxidative damage. C. sakazakii protects cells by up-regulating the antioxidant stress genes such as soxS and madB. Thirdly, C. sakazakii chooses energy efficient metabolic pathways to reduce energy consumption and maintain necessary processes. Finally, genes involved in chemotaxis and motility were differentially expressed to respond to different acidic conditions. This study systematically analyzed the acid-resistant mechanism of C. sakazakii under the stress of organic and inorganic acids, and provided a theoretical basis for better control of its contamination in food.
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Affiliation(s)
- Ailian Zhou
- School of Food Sciences and Engineering, South China University of Technology, Guangzhou City, Guangdong Province 510640, China
| | - Yifang Cao
- School of Food Sciences and Engineering, South China University of Technology, Guangzhou City, Guangdong Province 510640, China
| | - Donggen Zhou
- Ningbo International Travel Healthcare Center. No. 336 Liuting Street, Haishu District, Ningbo City, Zhejiang Province 315012, China
| | - Shuangfang Hu
- Key Laboratory of Molecular Epidemiology of Shenzhen, Shenzhen Center for Disease Control and Prevention, Shenzhen City, Guangdong Province 518055, China
| | - Wanjing Tan
- School of Food Sciences and Engineering, South China University of Technology, Guangzhou City, Guangdong Province 510640, China
| | - Xinglong Xiao
- School of Food Sciences and Engineering, South China University of Technology, Guangzhou City, Guangdong Province 510640, China.
| | - Yigang Yu
- School of Food Sciences and Engineering, South China University of Technology, Guangzhou City, Guangdong Province 510640, China
| | - Xiaofeng Li
- State Key Laboratory of Pulp and Paper Engineering, College of Light Industry and Food Sciences, South China University of Technology, 381 Wusan Road, Tianhe District, Guangzhou City 510640, Guangdong Province, China.
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Povedano-Priego C, Jroundi F, Lopez-Fernandez M, Sánchez-Castro I, Martin-Sánchez I, Huertas FJ, Merroun ML. Shifts in bentonite bacterial community and mineralogy in response to uranium and glycerol-2-phosphate exposure. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 692:219-232. [PMID: 31349163 DOI: 10.1016/j.scitotenv.2019.07.228] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 07/15/2019] [Accepted: 07/15/2019] [Indexed: 06/10/2023]
Abstract
The multi-barrier deep geological repository system is currently considered as one of the safest option for the disposal of high-level radioactive wastes. Indigenous microorganisms of bentonites may affect the structure and stability of these clays through Fe-containing minerals biotransformation and radionuclides mobilization. The present work aimed to investigate the behavior of bentonite and its bacterial community in the case of a uranium leakage from the waste containers. Hence, bentonite microcosms were amended with uranyl nitrate (U) and glycerol-2-phosphate (G2P) and incubated aerobically for 6 months. Next generation 16S rRNA gene sequencing revealed that the bacterial populations of all treated microcosms were dominated by Actinobacteria and Proteobacteria, accounting for >50% of the community. Additionally, G2P and nitrate had a remarkable effect on the bacterial diversity of bentonites by the enrichment of bacteria involved in the nitrogen and carbon biogeochemical cycles (e.g. Azotobacter). A significant presence of sulfate-reducing bacteria such as Desulfonauticus and Desulfomicrobium were detected in the U-treated microcosms. The actinobacteria Amycolatopsis was enriched in G2P‑uranium amended bentonites. High-Angle Annular Dark-Field Scanning Transmission Electron Microscopy analyses showed the capacity of Amycolatopsis and a bentonite consortium formed by Bradyrhizobium-Rhizobium and Pseudomonas to precipitate U as U phosphate mineral phases, probably due to the phosphatase activity. The different amendments did not affect the mineralogy of the bentonite pointing to a high structural stability. These results would help to predict the impact of microbial processes on the biogeochemical cycles of elements (N and U) within the bentonite barrier under repository relevant conditions and to determine the changes in the microbial community induced by a uranium release.
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Affiliation(s)
- Cristina Povedano-Priego
- Department of Microbiology, University of Granada, Campus Fuentenueva s/n, 18071 Granada, Spain.
| | - Fadwa Jroundi
- Department of Microbiology, University of Granada, Campus Fuentenueva s/n, 18071 Granada, Spain.
| | - Margarita Lopez-Fernandez
- Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, 01328 Dresden, Germany.
| | - Iván Sánchez-Castro
- Department of Microbiology, University of Granada, Campus Fuentenueva s/n, 18071 Granada, Spain.
| | - Inés Martin-Sánchez
- Department of Microbiology, University of Granada, Campus Fuentenueva s/n, 18071 Granada, Spain.
| | - F Javier Huertas
- Instituto Andaluz de Ciencias de la Tierra, CSIC - University of Granada, 18100 Granada, Spain.
| | - Mohamed L Merroun
- Department of Microbiology, University of Granada, Campus Fuentenueva s/n, 18071 Granada, Spain.
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Tripartite Regulation of the glpFKD Operon Involved in Glycerol Catabolism by GylR, Crp, and SigF in Mycobacterium smegmatis. J Bacteriol 2019; 201:JB.00511-19. [PMID: 31570530 DOI: 10.1128/jb.00511-19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 09/26/2019] [Indexed: 11/20/2022] Open
Abstract
The glpD (MSMEG_6761) gene encoding glycerol-3-phosphate dehydrogenase was shown to be crucial for M. smegmatis to utilize glycerol as the sole carbon source. The glpD gene likely forms the glpFKD operon together with glpF and glpK, encoding a glycerol facilitator and glycerol kinase, respectively. The gylR (MSMEG_6757) gene, whose product belongs to the IclR family of transcriptional regulators, was identified 182 bp upstream of glpF It was demonstrated that GylR serves as a transcriptional activator and is involved in the induction of glpFKD expression in the presence of glycerol. Three GylR-binding sites with the consensus sequence (GKTCGRC-N3-GYCGAMC) were identified in the upstream region of glpF by DNase I footprinting analysis. The presence of glycerol-3-phosphate was shown to decrease the binding affinity of GylR to the glpF upstream region with changes in the quaternary structure of GylR from tetramer to dimer. Besides GylR, cAMP receptor protein (Crp) and an alternative sigma factor, SigF, are also implicated in the regulation of glpFKD expression. Crp functions as a repressor, while SigF induces expression of glpFKD under energy-limiting conditions. In conclusion, we suggest here that the glpFKD operon is under the tripartite control of GylR, SigF, and Crp, which enables M. smegmatis to integrate the availability of glycerol, cellular energy state, and cellular levels of cAMP to exquisitely control expression of the glpFKD operon involved in glycerol metabolism.IMPORTANCE Using genetic approaches, we first revealed that glycerol is catabolized through the glycolytic pathway after conversion to dihydroxyacetone phosphate in two sequential reactions catalyzed by glycerol kinase (GlpK) and flavin adenine dinucleotide (FAD)-containing glycerol-3-phosphate dehydrogenase (GlpD) in M. smegmatis Our study also revealed that in addition to the GylR transcriptional activator that mediates the induction of the glpFKD operon by glycerol, the operon is regulated by SigF and Crp, which reflect the cellular energy state and cAMP level, respectively.
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Wu Q, Lan Y, Cao X, Yao H, Qiao D, Xu H, Cao Y. Characterization and diverse evolution patterns of glycerol-3-phosphate dehydrogenase family genes in Dunaliella salina. Gene 2019; 710:161-169. [DOI: 10.1016/j.gene.2019.05.056] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 05/15/2019] [Accepted: 05/29/2019] [Indexed: 12/29/2022]
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Zhang T, Shi XC, Xia Y, Mai L, Tremblay PL. Escherichia coli adaptation and response to exposure to heavy atmospheric pollution. Sci Rep 2019; 9:10879. [PMID: 31350435 PMCID: PMC6659633 DOI: 10.1038/s41598-019-47427-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 07/16/2019] [Indexed: 12/30/2022] Open
Abstract
90% of the world population is exposed to heavy atmospheric pollution. This is a major public health issue causing 7 million death each year. Air pollution comprises an array of pollutants such as particulate matters, ozone and carbon monoxide imposing a multifactorial stress on living cells. Here, Escherichia coli was used as model cell and adapted for 390 generations to atmospheric pollution to assess its long-term effects at the genetic, transcriptomic and physiological levels. Over this period, E. coli evolved to grow faster and acquired an adaptive mutation in rpoB, which encodes the RNA polymerase β subunit. Transcriptomic and biochemical characterization showed alteration of the cell membrane composition resulting in lesser permeability after the adaptation process. A second significant change in the cell wall structure of the adapted strain was the greater accumulation of the exopolysaccharides colanic acid and cellulose in the extracellular fraction. Results also indicated that amino acids homeostasis was involved in E. coli response to atmospheric pollutants. This study demonstrates that adaptive mutation with transformative physiological impact can be fixed in genome after exposure to atmospheric pollution and also provides a comprehensive portrait of the cellular response mechanisms involved.
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Affiliation(s)
- Tian Zhang
- State Key Laboratory of Silicate Materials for Architectures, Wuhan University of Technology, Wuhan, P.R. China.,School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, Wuhan, P.R. China
| | - Xiao-Chen Shi
- State Key Laboratory of Silicate Materials for Architectures, Wuhan University of Technology, Wuhan, P.R. China.,School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, Wuhan, P.R. China
| | - Yangyang Xia
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, International School of Materials Science and Engineering, Wuhan University of Technology, Wuhan, P.R. China
| | - Liqiang Mai
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, International School of Materials Science and Engineering, Wuhan University of Technology, Wuhan, P.R. China
| | - Pier-Luc Tremblay
- State Key Laboratory of Silicate Materials for Architectures, Wuhan University of Technology, Wuhan, P.R. China. .,School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, Wuhan, P.R. China.
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Glycerol metabolism and its regulation in lactic acid bacteria. Appl Microbiol Biotechnol 2019; 103:5079-5093. [DOI: 10.1007/s00253-019-09830-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 04/02/2019] [Accepted: 04/04/2019] [Indexed: 01/09/2023]
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Effects of triethylamine on the expression patterns of two G3PDHs and lipid accumulation in Dunaliella tertiolecta. Enzyme Microb Technol 2019; 127:17-21. [PMID: 31088612 DOI: 10.1016/j.enzmictec.2019.04.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Revised: 03/20/2019] [Accepted: 04/04/2019] [Indexed: 12/17/2022]
Abstract
Glycerol-3-phosphate (G3P) is the important precursors for triacylglycerol synthesis, while glycerol-3-phosphate dehydrogenase (GPDH) determines the formation of G3P. In this study, two GDPH genes, Dtgdp1 and Dtgdp2 were isolated and identified from Dunaliella tertiolecta. The full-length Dtgdp1 and Dtgdp2 CDS were 2016 bp and 2094 bp, which encoded two putative protein sequences of 671 and 697 amino acids with predicted molecular weights of 73.64 kDa and 76.73 kDa, respectively. DtGDP1 and DtGDP2 both had a close relationship with those of algal and higher plants. DtGDP1 shared two conserved superfamily (A1 and A2) and four signature motifs (I-IV), and the DtGDP2 showed six signature domains (from motif I to VI) and DAO_C conserved family. Our previous work showed that the triethylamine intervention could greatly increase the triacylglycerol content (up to 80%) of D. tertiolecta. This study aims to investigate the effect of triethylamine on GPDH expression. Results showed that, when treated by triethylamine at 100 ppm and 150 ppm, the expression levels of Dtgdp1 and Dtgpd2 were increased to 5.121- and 56.964-fold compared with the control, respectively. Triethylamine seemed to enhance lipid metabolic flow by inducing the expressions of Dtgdp1 and Dtgdp2 to increase the lipid content, which provides a new insight into the desired pathway of lipid synthesis in algae through genetic engineering.
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48
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Poblete-Castro I, Wittmann C, Nikel PI. Biochemistry, genetics and biotechnology of glycerol utilization in Pseudomonas species. Microb Biotechnol 2019; 13:32-53. [PMID: 30883020 PMCID: PMC6922529 DOI: 10.1111/1751-7915.13400] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 02/17/2019] [Accepted: 02/23/2019] [Indexed: 11/30/2022] Open
Abstract
The use of renewable waste feedstocks is an environment‐friendly choice contributing to the reduction of waste treatment costs and increasing the economic value of industrial by‐products. Glycerol (1,2,3‐propanetriol), a simple polyol compound widely distributed in biological systems, constitutes a prime example of a relatively cheap and readily available substrate to be used in bioprocesses. Extensively exploited as an ingredient in the food and pharmaceutical industries, glycerol is also the main by‐product of biodiesel production, which has resulted in a progressive drop in substrate price over the years. Consequently, glycerol has become an attractive substrate in biotechnology, and several chemical commodities currently produced from petroleum have been shown to be obtained from this polyol using whole‐cell biocatalysts with both wild‐type and engineered bacterial strains. Pseudomonas species, endowed with a versatile and rich metabolism, have been adopted for the conversion of glycerol into value‐added products (ranging from simple molecules to structurally complex biopolymers, e.g. polyhydroxyalkanoates), and a number of metabolic engineering strategies have been deployed to increase the number of applications of glycerol as a cost‐effective substrate. The unique genetic and metabolic features of glycerol‐grown Pseudomonas are presented in this review, along with relevant examples of bioprocesses based on this substrate – and the synthetic biology and metabolic engineering strategies implemented in bacteria of this genus aimed at glycerol valorization.
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Affiliation(s)
- Ignacio Poblete-Castro
- Biosystems Engineering Laboratory, Center for Bioinformatics and Integrative Biology, Faculty of Natural Sciences, Universidad Andrés Bello, Santiago de Chile, Chile
| | - Christoph Wittmann
- Institute of Systems Biotechnology, Universität des Saarlandes, Saarbrücken, Germany
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs Lyngby, Denmark
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Sun J, Zhang C, Nan W, Li D, Ke D, Lu W. Glycerol improves heterologous biosynthesis of betulinic acid in engineered Yarrowia lipolytica. Chem Eng Sci 2019. [DOI: 10.1016/j.ces.2018.10.052] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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50
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Wang H, Zhang X, Wang X, Zhang B, Wang M, Yang X, Han X, Wang R, Ren S, Hu Y, Liu J. Comprehensive Analysis of the Global Protein Changes That Occur During Salivary Gland Degeneration in Female Ixodid Ticks Haemaphysalis longicornis. Front Physiol 2019; 9:1943. [PMID: 30723423 PMCID: PMC6349780 DOI: 10.3389/fphys.2018.01943] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 12/22/2018] [Indexed: 01/07/2023] Open
Abstract
Ticks are notorious blood-sucking arthropods that can spread a variety of pathogens and cause great harm to the health of humans, wildlife and domestic animals. The salivary glands of female ticks degenerate rapidly when the ticks reach critical weight or become engorged, which can be caused by hormones and by the synergistic effects of multiple proteins. To explore the complex molecular mechanisms of salivary gland degeneration in ticks, this study applies iTRAQ quantitative proteomic technology for the first time to study changes in protein expression in the salivary glands of female Haemaphysalis longicornis during the process of degeneration and to search for proteins that play an important role in salivary gland degeneration. It was found that the expression of some proteins associated with energy production was continuously down-regulated during salivary gland degeneration, while some proteins associated with DNA or protein degradation were consistently up-regulated. Furthermore, the expression of some proteins related to cell apoptosis or autophagy was also changed. These proteins were knocked down by RNAi to observe the phenotypic and physiological changes in female ticks. The results showed that the time required for engorgement and the mortality rates of the female ticks increased after RNAi of F0F1-type ATP synthase, NADH-ubiquinone oxidoreductase, cytochrome C, or apoptosis-inducing factor (AIF). The corresponding engorged weights, oviposition amounts, and egg hatching rates of the female ticks decreased after RNAi. Interference of the expression of AIF in engorged ticks by RNAi showed that the degeneration of salivary glands of female ticks was slowed down.
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Affiliation(s)
- Hui Wang
- Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Xiaoli Zhang
- Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Xiao Wang
- Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Baowen Zhang
- Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Minjing Wang
- Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Xiaolong Yang
- Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Xuying Han
- Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Rui Wang
- Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Shuguang Ren
- The Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Yuhong Hu
- Instrumental Analysis Center, Hebei Normal University, Shijiazhuang, China
| | - Jingze Liu
- Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
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