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Chen M, Feng X, Liu J, Wang J, Yang X, Yu X, Kong W, Sun B, Wu H. Prokaryote-derived phosphorylated Tau epitope vaccine is immunogenic and non-T-cell activated in the mice model. Vaccine 2024; 42:1211-1219. [PMID: 38331660 DOI: 10.1016/j.vaccine.2023.12.072] [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: 09/29/2023] [Revised: 12/11/2023] [Accepted: 12/21/2023] [Indexed: 02/10/2024]
Abstract
Accumulation of phosphorylated Tau protein is a prominent pathological hallmark of Alzheimer's disease (AD). However, current vaccines targeting phosphorylation sites are primarily modified using chemical reactions, which exhibit low efficiency in terms of linking to the vaccine carrier. Despite the identification of over 2000 phosphorylation sites on approximately 20% of E. coli proteins through proteomic studies, it remains unclear whether recombinant Tau proteins expressed in bacteria undergo direct phosphorylation. Additionally, limited information is available regarding the immunogenicity and safety profiles of prokaryotic-derived pTau epitope vaccines. Our study discovered that the prokaryotic system can induce phosphorylation on four residues (T181, T205, S262, and S396) of the full-length Tau protein. Based on this finding, we developed a prokaryotic-modified phosphorylated Tau protein vaccine and immunized wild-type mice, resulting in enhanced immunogenicity and a favorable safety profile.
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Affiliation(s)
- Mo Chen
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Xuejian Feng
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Jiaxin Liu
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Jianan Wang
- Changchun BCHT Biotechnology, 1260 Huoju Road, Changchun High-tech Zone, Changchun, Jilin, China
| | - Xu Yang
- Chemistry Room, Jilin Institute for Drug Control, No. 657, Zhanjiang Road, Changchun, Jilin, China
| | - Xianghui Yu
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, China; Key Laboratory for Molecular Enzymology and Engineering, The Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Wei Kong
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, China; Key Laboratory for Molecular Enzymology and Engineering, The Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Bo Sun
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, China; Key Laboratory for Molecular Enzymology and Engineering, The Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China.
| | - Hui Wu
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, China; Key Laboratory for Molecular Enzymology and Engineering, The Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China.
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Sarkhel R, Priyadarsini S, Mahawar M. Nutrient limitation and oxidative stress induce the promoter of acetate operon in Salmonella Typhimurium. Arch Microbiol 2024; 206:126. [PMID: 38411730 DOI: 10.1007/s00203-024-03863-2] [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: 12/22/2023] [Revised: 01/22/2024] [Accepted: 01/23/2024] [Indexed: 02/28/2024]
Abstract
Glyoxylate shunt is an important pathway for microorganisms to survive under multiple stresses. One of its enzymes, malate synthase (encoded by aceB gene), has been widely speculated for its contribution to both the pathogenesis and virulence of various microorganisms. We have previously demonstrated that malate synthase (MS) is required for the growth of Salmonella Typhimurium (S. Typhimurium) under carbon starvation and survival under oxidative stress conditions. The aceB gene is encoded by the acetate operon in S. Typhimurium. We attempted to study the activity of acetate promoter under both the starvation and oxidative stress conditions in a heterologous system. The lac promoter of the pUC19 plasmid was substituted with the putative promoter sequence of the acetate operon of S. Typhimurium upstream to the lacZ gene and transformed the vector construct into E. coli NEBα cells. The transformed cells were subjected to the stress conditions mentioned above. We observed a fourfold increase in the β-galactosidase activity in these cells resulting from the upregulation of the lacZ gene in the stationary phase of cell growth (nutrient deprived) as compared to the mid-log phase. Following exposure of stationary phase cells to hypochlorite-induced oxidative stress, we further observed a 1.6-fold increase in β galactosidase activity. These data suggest the induction of promoter activity of the acetate operon under carbon starvation and oxidative stress conditions. Thus, these observations corroborate our previous findings regarding the upregulation of aceB expression under stressful environments.
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Affiliation(s)
- Ratanti Sarkhel
- ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Swagatika Priyadarsini
- ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India.
- Indian Council of Agricultural Research- National Research Centre on Camel, Bikaner, Rajasthan, India.
| | - Manish Mahawar
- ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India.
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Sarkhel R, Apoorva S, Priyadarsini S, Sridhar HB, Bhure SK, Mahawar M. Malate synthase contributes to the survival of Salmonella Typhimurium against nutrient and oxidative stress conditions. Sci Rep 2022; 12:15979. [PMID: 36155623 PMCID: PMC9510125 DOI: 10.1038/s41598-022-20245-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 09/12/2022] [Indexed: 11/09/2022] Open
Abstract
To survive and replicate in the host, S. Typhimurium have evolved several metabolic pathways. The glyoxylate shunt is one such pathway that can utilize acetate for the synthesis of glucose and other biomolecules. This pathway is a bypass of the TCA cycle in which CO2 generating steps are omitted. Two enzymes involved in the glyoxylate cycle are isocitrate lyase (ICL) and malate synthase (MS). We determined the contribution of MS in the survival of S. Typhimurium under carbon limiting and oxidative stress conditions. The ms gene deletion strain (∆ms strain) grew normally in LB media but failed to grow in M9 minimal media supplemented with acetate as a sole carbon source. However, the ∆ms strain showed hypersensitivity (p < 0.05) to hypochlorite. Further, ∆ms strain has been significantly more susceptible to neutrophils. Interestingly, several folds induction of ms gene was observed following incubation of S. Typhimurium with neutrophils. Further, ∆ms strain showed defective colonization in poultry spleen and liver. In short, our data demonstrate that the MS contributes to the virulence of S. Typhimurium by aiding its survival under carbon starvation and oxidative stress conditions.
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Rangwala AM, Mingione VR, Georghiou G, Seeliger MA. Kinases on Double Duty: A Review of UniProtKB Annotated Bifunctionality within the Kinome. Biomolecules 2022; 12:biom12050685. [PMID: 35625613 PMCID: PMC9138534 DOI: 10.3390/biom12050685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/03/2022] [Accepted: 05/09/2022] [Indexed: 01/27/2023] Open
Abstract
Phosphorylation facilitates the regulation of all fundamental biological processes, which has triggered extensive research of protein kinases and their roles in human health and disease. In addition to their phosphotransferase activity, certain kinases have evolved to adopt additional catalytic functions, while others have completely lost all catalytic activity. We searched the Universal Protein Resource Knowledgebase (UniProtKB) database for bifunctional protein kinases and focused on kinases that are critical for bacterial and human cellular homeostasis. These kinases engage in diverse functional roles, ranging from environmental sensing and metabolic regulation to immune-host defense and cell cycle control. Herein, we describe their dual catalytic activities and how they contribute to disease pathogenesis.
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5
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Advances in microbial production of feed amino acid. ADVANCES IN APPLIED MICROBIOLOGY 2022; 119:1-33. [DOI: 10.1016/bs.aambs.2022.05.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Enhanced glycolic acid yield through xylose and cellobiose utilization by metabolically engineered Escherichia coli. Bioprocess Biosyst Eng 2021; 44:1081-1091. [PMID: 33527231 DOI: 10.1007/s00449-020-02502-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 12/24/2020] [Indexed: 12/11/2022]
Abstract
Microbial biorefinery is a promising route toward sustainable production of glycolic acid (GA), a valuable raw material for various industries. However, inherent microbial GA production has limited substrate consumption using either D-xylose or D-glucose as carbon catabolite repression (CCR) averts their co-utilization. To bypass CCR, a GA-producing strain using D-xylose via Dahms pathway was engineered to allow cellobiose uptake. Unlike glucose, cellobiose was assimilated and intracellularly degraded without repressing D-xylose uptake. The final GA-producing E. coli strain (CLGA8) has an overexpressed cellobiose phosphorylase (cep94A) from Saccharophagus degradans 2-40 and an activated glyoxylate shunt pathway. Expression of cep94A improved GA production reaching the maximum theoretical yield (0.51 g GA g-1 xylose), whereas activation of glyoxylate shunt pathway enabled GA production from cellobiose, which further increased the GA titer (2.25 g GA L-1). To date, this is the highest reported GA yield from D-xylose through Dahms pathway in an engineered E. coli with cellobiose as co-substrate.
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Sun P, Liu Y, Ma T, Ding J. Structure and allosteric regulation of human NAD-dependent isocitrate dehydrogenase. Cell Discov 2020; 6:94. [PMID: 33349631 PMCID: PMC7752914 DOI: 10.1038/s41421-020-00220-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 09/24/2020] [Accepted: 09/25/2020] [Indexed: 11/09/2022] Open
Abstract
Human NAD-dependent isocitrate dehydrogenase or HsIDH3 catalyzes the decarboxylation of isocitrate into α-ketoglutarate in the TCA cycle. HsIDH3 exists and functions as a heterooctamer composed of the αβ and αγ heterodimers, and is regulated allosterically and/or competitively by numerous metabolites including CIT, ADP, ATP, and NADH. In this work, we report the crystal structure of HsIDH3 containing a β mutant in apo form. In the HsIDH3 structure, the αβ and αγ heterodimers form the α2βγ heterotetramer via their clasp domains, and two α2βγ heterotetramers form the (α2βγ)2 heterooctamer through insertion of the N-terminus of the γ subunit of one heterotetramer into the back cleft of the β subunit of the other heterotetramer. The functional roles of the key residues at the allosteric site, the pseudo allosteric site, the heterodimer and heterodimer-heterodimer interfaces, and the N-terminal of the γ subunit are validated by mutagenesis and kinetic studies. Our structural and biochemical data together demonstrate that the allosteric site plays an important role but the pseudo allosteric site plays no role in the allosteric activation of the enzyme; the activation signal from the allosteric site is transmitted to the active sites of both αβ and αγ heterodimers via the clasp domains; and the N-terminal of the γ subunit plays a critical role in the formation of the heterooctamer to ensure the optimal activity of the enzyme. These findings reveal the molecular mechanism of the assembly and allosteric regulation of HsIDH3.
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Affiliation(s)
- Pengkai Sun
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Yan Liu
- School of Life Science and Technology, ShanghaiTech University, 393 Huaxia Zhong Road, Shanghai 201210, China
| | - Tengfei Ma
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Jianping Ding
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China. .,School of Life Science and Technology, ShanghaiTech University, 393 Huaxia Zhong Road, Shanghai 201210, China. .,School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, 1 Xiangshan Road, Hangzhou, Zhejiang 310024, China.
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Madikonda AK, Shaikh A, Khanra S, Yakkala H, Yellaboina S, Lin-Chao S, Siddavattam D. Metabolic remodeling in Escherichia coli MG1655. A prophage e14-encoded small RNA, co293, post-transcriptionally regulates transcription factors HcaR and FadR. FEBS J 2020; 287:4767-4782. [PMID: 32061118 DOI: 10.1111/febs.15247] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 10/10/2019] [Accepted: 02/12/2020] [Indexed: 11/26/2022]
Abstract
In previous studies, we have shown the existence of metabolic remodeling in glucose-grown Escherichia coli MG1655 cells expressing the esterase Orf306 from the opd island of Sphingobium fuliginis. We now show that Orf306-dependent metabolic remodeling is due to regulation of a novel small RNA (sRNA). Endogenous propionate, produced due to the esterase/lipase activity of Orf306, repressed expression of a novel E. coli sRNA, co293. This sRNA post-transcriptionally regulates expression of the transcription factors HcaR and FadR either by inhibiting translation or by destabilizing their transcripts. Hence, repression of co293 expression elevates the levels of HcaR and FadR with consequent activation of alternative carbon catabolic pathways. HcaR activates the hca and MHP operons leading to upregulation of the phenyl propionate and hydroxy phenyl propionate (HPP) degradation pathways. Similarly, FadR stimulates the expression of the transcription factor IclR which negatively regulates the glyoxylate bypass pathway genes, aceBAK.
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Affiliation(s)
- Ashok Kumar Madikonda
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, India
| | - Akbarpasha Shaikh
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, India
| | - Sonali Khanra
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, India
| | - Harshita Yakkala
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, India
| | - Sailu Yellaboina
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, India
| | - Sue Lin-Chao
- Institute of Molecular Biology, Academia Sinica, Nangang, Taiwan
| | - Dayananda Siddavattam
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, India
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Sun P, Ma T, Zhang T, Zhu H, Zhang J, Liu Y, Ding J. Molecular basis for the function of the αβ heterodimer of human NAD-dependent isocitrate dehydrogenase. J Biol Chem 2019; 294:16214-16227. [PMID: 31515270 PMCID: PMC6827300 DOI: 10.1074/jbc.ra119.010099] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 08/21/2019] [Indexed: 01/07/2023] Open
Abstract
Mammalian mitochondrial NAD-dependent isocitrate dehydrogenase (NAD-IDH) catalyzes the decarboxylation of isocitrate into α-ketoglutarate in the tricarboxylic acid cycle. It exists as the α2βγ heterotetramer composed of the αβ and αγ heterodimers. Different from the αγ heterodimer that can be allosterically activated by CIT and ADP, the αβ heterodimer cannot be allosterically regulated by the activators; however, the molecular mechanism is unclear. We report here the crystal structures of the αβ heterodimer of human NAD-IDH with the α subunit in apo form and in Ca2+-bound, NAD-bound, and NADH-bound forms. Structural analyses and comparisons reveal that the αβ heterodimer has a similar yet more compact overall structure compared with the αγ heterodimer and contains a pseudo-allosteric site that is structurally different from the allosteric site. In particular, the β3-α3 and β12-α8 loops of the β subunit at the pseudo-allosteric site adopt significantly different conformations from those of the γ subunit at the allosteric site and hence impede the binding of the activators, explaining why the αβ heterodimer cannot be allosterically regulated by the activators. The structural data also show that NADH can compete with NAD to bind to the active site and inhibits the activity of the αβ heterodimer. These findings together with the biochemical data reveal the molecular basis for the function of the αβ heterodimer of human NAD-IDH.
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Affiliation(s)
- Pengkai Sun
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China
| | - Tengfei Ma
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China
| | - Tianlong Zhang
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China
| | - Hanwen Zhu
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China
| | - Jianyang Zhang
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China
| | - Yabing Liu
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China
| | - Jianping Ding
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China, To whom correspondence should be addressed:
State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China. Tel.:
86-21-5492-1619; E-mail:
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Zhang X, Shen Q, Lei Z, Wang Q, Zheng J, Jia Z. Characterization of metal binding of bifunctional kinase/phosphatase AceK and implication in activity modulation. Sci Rep 2019; 9:9198. [PMID: 31235769 PMCID: PMC6591243 DOI: 10.1038/s41598-019-45704-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 06/11/2019] [Indexed: 12/20/2022] Open
Abstract
A unique bifunctional enzyme, isocitrate dehydrogenase kinase/phosphatase (AceK) regulates isocitrate dehydrogenase (IDH) by phosphorylation and dephosphorylation in response to nutrient availability. Herein we report the crystal structure of AceK in complex with ADP and Mn2+ ions. Although the overall structure is similar to the previously reported structures which contain only one Mg2+ ion, surprisingly, two Mn2+ ions are found in the catalytic center of the AceK-Mn2+ structure. Our enzymatic assays demonstrate that AceK-Mn2+ showed higher phosphatase activity than AceK-Mg2+, whereas the kinase activity was relatively unaffected. We created mutants of AceK for all metal-coordinating residues. The phosphatase activities of these mutants were significantly impaired, suggesting the pivotal role of the binuclear (M1-M2) core in AceK phosphatase catalysis. Moreover, we have studied the interactions of Mn2+ and Mg2+ with wild-type and mutant AceK and found that the number of metal ions bound to AceK is in full agreement with the crystal structures. Combined with the enzymatic results, we demonstrate that AceK exhibits phosphatase activity in the presence of two, but not one, Mn2+ ions, similar to PPM phosphatases. Taken together, we suggest that metal ions help AceK to balance and fine tune its kinase and phosphatase activities.
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Affiliation(s)
- Xiaoying Zhang
- College of Chemistry, Beijing Normal University, Beijing, 100875, China
| | - Qingya Shen
- College of Chemistry, Beijing Normal University, Beijing, 100875, China
| | - Zhen Lei
- College of Chemistry, Beijing Normal University, Beijing, 100875, China
| | - Qianyi Wang
- College of Chemistry, Beijing Normal University, Beijing, 100875, China
| | - Jimin Zheng
- College of Chemistry, Beijing Normal University, Beijing, 100875, China.
| | - Zongchao Jia
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, K7L3N6, Canada.
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11
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Studies on the activation of isocitrate dehydrogenase kinase/phosphatase (AceK) by Mn 2+ and Mg 2. Biometals 2018; 31:991-1002. [PMID: 30311020 DOI: 10.1007/s10534-018-0144-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 09/22/2018] [Indexed: 10/28/2022]
Abstract
Isocitrate dehydrogenase kinase/phosphatase (AceK) is a bifunctional enzyme with both kinase and phosphatase activities that are activated by Mg2+. We have studied the interactions of Mn2+and Mg2+ with AceK using isothermal titration calorimetry (ITC) combined with molecular docking simulations and show for the first time that Mn2+ also activates the enzyme activities. However, Mn2+ and Mg2+ exert their effects by different mechanisms. Although they have similar binding constants (of 1.11 × 105 and 0.98 × 105 M-1, respectively) for AceK and induce conformational changes of the enzyme, they do not compete for the same binding site. Instead Mn2+ appears to bind to the regulatory domain of AceK, and its effect is transmitted to the active site of the enzyme by the conformational change that it induces. The information in this study should be very useful for understanding the molecular mechanism underlying the interaction between AceK and metal ions, especially Mn2+ and Mg2+.
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12
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Zhao H, Fang Y, Wang X, Zhao L, Wang J, Li Y. Increasing L-threonine production in Escherichia coli by engineering the glyoxylate shunt and the L-threonine biosynthesis pathway. Appl Microbiol Biotechnol 2018; 102:5505-5518. [PMID: 29713792 DOI: 10.1007/s00253-018-9024-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Revised: 03/20/2018] [Accepted: 04/13/2018] [Indexed: 11/29/2022]
Abstract
L-threonine is an important amino acid that can be added in food, medicine, or feed. Here, the influence of glyoxylate shunt on an L-threonine producing strain Escherichia coli TWF001 has been studied. The gene iclR was deleted, and the native promoter of the aceBA operon was replaced by the trc promoter in the chromosome of TWF001, the resulting strainTWF004 could produce 0.39 g L-threonine from1 g glucose after 36-h flask cultivation. Further replacing the native promoter of aspC by the trc promoter in the chromosome of TWF004 resulted in the strain TWF006. TWF006 could produce 0.42 g L-threonine from 1 g glucose after 36-h flask cultivation. Three key genes in the biosynthetic pathway of L-threonine, thrA * (a mutated thrA), thrB, and thrC were overexpressed in TWF006, resulting the strain TWF006/pFW01-thrA * BC. TWF006/pFW01-thrA * BC could produce 0.49 g L-threonine from 1 g glucose after 36-h flask cultivation. Next, the genes asd, rhtA, rhtC, or thrE were inserted into the plasmid TWF006/pFW01-thrA * BC, and TWF006 was transformed with these plasmids, resulting the strains TWF006/pFW01-thrA * BC-asd, TWF006/pFW01-thrA * BC-rhtA, TWF006/pFW01-thrA * BC-rhtC, and TWF006/pFW01-thrA * BC-thrE, respectively. These four strains could produce more L-threonine than the control strain, and the highest yield was produced by TWF006/pFW01-thrA * BC-asd; after 36-h flask cultivation, TWF006/pFW01-thrA * BC-asd could produce 15.85 g/l L-threonine, i.e., 0.53 g L-threonine per 1 g glucose, which is a 70% increase relative to the control strain TWF001. The results suggested that the combined engineering of glyoxylate shunt and L-threonine biosynthesis pathway could significantly increase the L-threonine production in E. coli.
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Affiliation(s)
- Hui Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Yu Fang
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Xiaoyuan Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China. .,Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China. .,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China.
| | - Lei Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Jianli Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Ye Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China
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Huang LY, Wang SC, Cheng TJR, Wong CH. Undecaprenyl Phosphate Phosphatase Activity of Undecaprenol Kinase Regulates the Lipid Pool in Gram-Positive Bacteria. Biochemistry 2017; 56:5417-5427. [PMID: 28872301 DOI: 10.1021/acs.biochem.7b00603] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Bacteria cell walls contain many repeating glycan structures, such as peptidoglycans, lipopolysaccharides, teichoic acids, and capsular polysaccharides. Their synthesis starts in the cytosol, and they are constructed from a glycan lipid carrier, undecaprenyl phosphate (C55P), which is essential for cell growth and survival. The lipid derivative undecaprenol (C55OH) is predominant in many Gram-positive bacteria but has not been detected in Gram-negative bacteria; its origin and role have thus remained unknown. Recently, a homologue of diacylglycerol kinase (DgkA) in Escherichia coli (E. coli) was demonstrated to be an undecaprenol kinase (UK) in the Gram-positive bacterium Streptococcus mutans (S. mutans). In this study, we found that S. mutans UK was not only an undecaprenol kinase but also a Mg-ADP-dependent undecaprenyl phosphate phosphatase (UpP), catalyzing the hydrolysis of C55P to C55OH and a free inorganic phosphate. Furthermore, the naturally undetectable C55OH was observed in E. coli cells expressing S. mutans dgkA, supporting the phosphatase activity of UK/UpP in vivo. These two activities were indispensable to each other and utilized identical essential residues binding to their substrates, suggesting that both activities share the same active site and might involve a direct phosphoryl transfer mechanism. This study revealed a unique membrane enzyme displaying bifunctional activities determined by substrate binding and C55OH production. The reciprocal conversion of C55P and the undecaprenol pool efficiently regulate cell wall synthesis, especially in Gram-positive bacteria.
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Affiliation(s)
- Lin-Ya Huang
- Genomics Research Center, Academia Sinica , Taipei 115, Taiwan
| | - Shih-Chi Wang
- Genomics Research Center, Academia Sinica , Taipei 115, Taiwan.,Institute of Biochemistry and Molecular Biology, National Yang-Ming University , Taipei 112, Taiwan
| | | | - Chi-Huey Wong
- Genomics Research Center, Academia Sinica , Taipei 115, Taiwan.,Institute of Biochemistry and Molecular Biology, National Yang-Ming University , Taipei 112, Taiwan
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14
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Nguyen HA, El Khoury T, Guiral S, Laaberki MH, Candusso MP, Galisson F, Foucher AE, Kesraoui S, Ballut L, Vallet S, Orelle C, Zucchini L, Martin J, Page A, Attieh J, Aghajari N, Grangeasse C, Jault JM. Expanding the Kinome World: A New Protein Kinase Family Widely Conserved in Bacteria. J Mol Biol 2017; 429:3056-3074. [PMID: 28890133 DOI: 10.1016/j.jmb.2017.08.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 08/20/2017] [Accepted: 08/21/2017] [Indexed: 12/31/2022]
Abstract
Fine tuning of signaling pathways is essential for cells to cope with sudden environmental variations. This delicate balance is maintained in particular by protein kinases that control the activity of target proteins by reversible phosphorylation. In addition to homologous eukaryotic enzymes, bacteria have evolved some specific Ser/Thr/Tyr protein kinases without any structural resemblance to their eukaryotic counterparts. Here, we show that a previously identified family of ATPases, broadly conserved among bacteria, is in fact a new family of protein kinases with a Ser/Thr/Tyr kinase activity. A prototypic member of this family, YdiB from Bacillus subtilis, is able to autophosphorylate and to phosphorylate a surrogate substrate, the myelin basic protein. Two crystal structures of YdiB were solved (1.8 and 2.0Å) that display a unique ATP-binding fold unrelated to known protein kinases, although a conserved HxD motif is reminiscent of that found in Hanks-type protein kinases. The effect of mutations of conserved residues further highlights the unique nature of this new protein kinase family that we name ubiquitous bacterial kinase. We investigated the cellular role of YdiB and showed that a ∆ydiB mutant was more sensitive to paraquat treatment than the wild type, with ~13% of cells with an aberrant morphology. In addition, YdiE, which is known to participate with both YdiC and YdiB in an essential chemical modification of some specific tRNAs, is phosphorylated in vitro by YdiB. These results expand the boundaries of the bacterial kinome and support the involvement of YdiB in protein translation and resistance to oxidative stress in B. subtilis.
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Affiliation(s)
- Hien-Anh Nguyen
- Institut de Biologie Structurale, Université Joseph Fourier Grenoble 1, UMR5075 CNRS/CEA/UJF, 41 rue Jules Horowitz, 38027 Grenoble Cedex 1, France
| | - Takla El Khoury
- Institut de Biologie Structurale, Université Joseph Fourier Grenoble 1, UMR5075 CNRS/CEA/UJF, 41 rue Jules Horowitz, 38027 Grenoble Cedex 1, France; University of Lyon, CNRS, UMR5086 "Molecular Microbiology and Structural Biochemistry," 7 Passage du Vercors, F-69367 Lyon, France; Department of Biology, Faculty of Sciences, University of Balamand, Lebanon
| | - Sébastien Guiral
- University of Lyon, CNRS, UMR5086 "Molecular Microbiology and Structural Biochemistry," 7 Passage du Vercors, F-69367 Lyon, France
| | - Maria-Halima Laaberki
- Institut de Biologie Structurale, Université Joseph Fourier Grenoble 1, UMR5075 CNRS/CEA/UJF, 41 rue Jules Horowitz, 38027 Grenoble Cedex 1, France
| | - Marie-Pierre Candusso
- University of Lyon, CNRS, UMR5086 "Molecular Microbiology and Structural Biochemistry," 7 Passage du Vercors, F-69367 Lyon, France
| | - Frédéric Galisson
- University of Lyon, CNRS, UMR5086 "Molecular Microbiology and Structural Biochemistry," 7 Passage du Vercors, F-69367 Lyon, France
| | - Anne-Emmanuelle Foucher
- Institut de Biologie Structurale, Université Joseph Fourier Grenoble 1, UMR5075 CNRS/CEA/UJF, 41 rue Jules Horowitz, 38027 Grenoble Cedex 1, France
| | - Salsabil Kesraoui
- University of Lyon, CNRS, UMR5086 "Molecular Microbiology and Structural Biochemistry," 7 Passage du Vercors, F-69367 Lyon, France
| | - Lionel Ballut
- University of Lyon, CNRS, UMR5086 "Molecular Microbiology and Structural Biochemistry," 7 Passage du Vercors, F-69367 Lyon, France
| | - Sylvain Vallet
- University of Lyon, CNRS, UMR5086 "Molecular Microbiology and Structural Biochemistry," 7 Passage du Vercors, F-69367 Lyon, France
| | - Cédric Orelle
- University of Lyon, CNRS, UMR5086 "Molecular Microbiology and Structural Biochemistry," 7 Passage du Vercors, F-69367 Lyon, France
| | - Laure Zucchini
- University of Lyon, CNRS, UMR5086 "Molecular Microbiology and Structural Biochemistry," 7 Passage du Vercors, F-69367 Lyon, France
| | - Juliette Martin
- University of Lyon, CNRS, UMR5086 "Molecular Microbiology and Structural Biochemistry," 7 Passage du Vercors, F-69367 Lyon, France
| | - Adeline Page
- Protein Science Facility, SFR BioSciences CNRS UMS3444, Inserm US8, UCBL, ENS de Lyon, 50 Avenue Tony Garnier, 69007 Lyon, France
| | - Jihad Attieh
- Department of Biology, Faculty of Sciences, University of Balamand, Lebanon
| | - Nushin Aghajari
- University of Lyon, CNRS, UMR5086 "Molecular Microbiology and Structural Biochemistry," 7 Passage du Vercors, F-69367 Lyon, France
| | - Christophe Grangeasse
- University of Lyon, CNRS, UMR5086 "Molecular Microbiology and Structural Biochemistry," 7 Passage du Vercors, F-69367 Lyon, France
| | - Jean-Michel Jault
- University of Lyon, CNRS, UMR5086 "Molecular Microbiology and Structural Biochemistry," 7 Passage du Vercors, F-69367 Lyon, France.
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15
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Ma T, Peng Y, Huang W, Ding J. Molecular mechanism of the allosteric regulation of the αγ heterodimer of human NAD-dependent isocitrate dehydrogenase. Sci Rep 2017; 7:40921. [PMID: 28098230 PMCID: PMC5241874 DOI: 10.1038/srep40921] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 12/13/2016] [Indexed: 11/12/2022] Open
Abstract
Human NAD-dependent isocitrate dehydrogenase catalyzes the decarboxylation of isocitrate (ICT) into α-ketoglutarate in the Krebs cycle. It exists as the α2βγ heterotetramer composed of the αβ and αγ heterodimers. Previously, we have demonstrated biochemically that the α2βγ heterotetramer and αγ heterodimer can be allosterically activated by citrate (CIT) and ADP. In this work, we report the crystal structures of the αγ heterodimer with the γ subunit bound without or with different activators. Structural analyses show that CIT, ADP and Mg2+ bind adjacent to each other at the allosteric site. The CIT binding induces conformational changes at the allosteric site, which are transmitted to the active site through the heterodimer interface, leading to stabilization of the ICT binding at the active site and thus activation of the enzyme. The ADP binding induces no further conformational changes but enhances the CIT binding through Mg2+-mediated interactions, yielding a synergistic activation effect. ICT can also bind to the CIT-binding subsite, which induces similar conformational changes but exhibits a weaker activation effect. The functional roles of the key residues are verified by mutagenesis, kinetic and structural studies. Our structural and functional data together reveal the molecular mechanism of the allosteric regulation of the αγ heterodimer.
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Affiliation(s)
- Tengfei Ma
- National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Yingjie Peng
- National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Wei Huang
- National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Jianping Ding
- National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
- School of Life Science and Technology, ShanghaiTech University, 100 Haike Road, Shanghai 201210, China
- Shanghai Science Research Center, Chinese Academy of Sciences, 333 Haike Road, Shanghai 201210, China
- Collaborative Innovation Center for Genetics and Development, Fudan University, 2005 Songhu Road, Shanghai 200438, China
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16
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Murima P, Zimmermann M, Chopra T, Pojer F, Fonti G, Dal Peraro M, Alonso S, Sauer U, Pethe K, McKinney JD. A rheostat mechanism governs the bifurcation of carbon flux in mycobacteria. Nat Commun 2016; 7:12527. [PMID: 27555519 PMCID: PMC4999502 DOI: 10.1038/ncomms12527] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2015] [Accepted: 07/11/2016] [Indexed: 11/30/2022] Open
Abstract
Fatty acid metabolism is an important feature of the pathogenicity of Mycobacterium tuberculosis during infection. Consumption of fatty acids requires regulation of carbon flux bifurcation between the oxidative TCA cycle and the glyoxylate shunt. In Escherichia coli, flux bifurcation is regulated by phosphorylation-mediated inhibition of isocitrate dehydrogenase (ICD), a paradigmatic example of post-translational mechanisms governing metabolic fluxes. Here, we demonstrate that, in contrast to E. coli, carbon flux bifurcation in mycobacteria is regulated not by phosphorylation but through metabolic cross-activation of ICD by glyoxylate, which is produced by the glyoxylate shunt enzyme isocitrate lyase (ICL). This regulatory circuit maintains stable partitioning of fluxes, thus ensuring a balance between anaplerosis, energy production, and precursor biosynthesis. The rheostat-like mechanism of metabolite-mediated control of flux partitioning demonstrates the importance of allosteric regulation during metabolic steady-state. The sensitivity of this regulatory mechanism to perturbations presents a potentially attractive target for chemotherapy. Microbes survive in dynamic environments by modulating their intracellular metabolism. Here, the authors reveal that mycobacteria employ a rheostat-like mechanism to regulate carbon flux between the oxidative TCA cycle and the glyoxylate shunt during glucose-acetate diauxic shift.
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Affiliation(s)
- Paul Murima
- School of Life Sciences, Swiss Federal Institute of Technology in Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Michael Zimmermann
- Institute of Molecular Systems Biology, Swiss Federal Institute of Technology in Zürich (ETHZ), CH-8093 Zürich, Switzerland
| | - Tarun Chopra
- School of Life Sciences, Swiss Federal Institute of Technology in Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Florence Pojer
- Protein Crystallography Platform, Swiss Federal Institute of Technology in Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Giulia Fonti
- School of Life Sciences, Swiss Federal Institute of Technology in Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Matteo Dal Peraro
- School of Life Sciences, Swiss Federal Institute of Technology in Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Sylvie Alonso
- Department of Microbiology, Yong Loo Lin School of Medicine and Immunology Programme, Life Sciences Institute, National University of Singapore, Singapore 117456, Singapore
| | - Uwe Sauer
- Institute of Molecular Systems Biology, Swiss Federal Institute of Technology in Zürich (ETHZ), CH-8093 Zürich, Switzerland
| | - Kevin Pethe
- Lee Kong Chian School of Medicine and School of Biological Sciences, Nanyang Technological University, 59 Nanyang Drive, Singapore 636 921, Singapore
| | - John D McKinney
- School of Life Sciences, Swiss Federal Institute of Technology in Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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17
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Yin Y, Li S, Gao Y, Tong L, Zheng J, Jia Z, Jiang G, Wei Q. Loopβ3αC plays an important role in the structure and function of isocitrate dehydrogenase kinase/phosphatase. FEBS Lett 2016; 590:3144-54. [PMID: 27528271 DOI: 10.1002/1873-3468.12355] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 08/02/2016] [Accepted: 08/08/2016] [Indexed: 11/08/2022]
Abstract
This work aims to investigate the role of the loopβ3αC amino acids in the structure and function of isocitrate dehydrogenase kinase/phosphatase (AceK). The results demonstrate that the precise configuration of loopβ3αC is very important for AceK structure and function: structural changes alter the affinity of the enzyme for the isocitrate dehydrogenase (ICDH), which modifies enzyme activity. Intriguingly, D340 is significant for the retention of kinase and phosphatase activities, for the conformational stability of AceK and for binding ICDH. The deletion Δ341-345 increases enzyme activity by increasing the maximum velocity and affinity for ICDH. The β3αC loop is thus critical for the structure and function of AceK.
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Affiliation(s)
- Yanxia Yin
- Department of Biochemistry and Molecular Biology, Beijing Normal University, Beijing Key Laboratory, China
| | - Shanze Li
- Department of Biochemistry and Molecular Biology, Beijing Normal University, Beijing Key Laboratory, China
| | - Yadan Gao
- Department of Biochemistry and Molecular Biology, Beijing Normal University, Beijing Key Laboratory, China
| | - Li Tong
- Department of Biochemistry and Molecular Biology, Beijing Normal University, Beijing Key Laboratory, China
| | - Jimin Zheng
- College of Chemistry, Beijing Normal University, China
| | - Zongchao Jia
- College of Chemistry, Beijing Normal University, China
| | - Guohua Jiang
- Department of Biochemistry and Molecular Biology, Beijing Normal University, Beijing Key Laboratory, China.
| | - Qun Wei
- Department of Biochemistry and Molecular Biology, Beijing Normal University, Beijing Key Laboratory, China.
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18
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Wessels HJCT, de Almeida NM, Kartal B, Keltjens JT. Bacterial Electron Transfer Chains Primed by Proteomics. Adv Microb Physiol 2016; 68:219-352. [PMID: 27134025 DOI: 10.1016/bs.ampbs.2016.02.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Electron transport phosphorylation is the central mechanism for most prokaryotic species to harvest energy released in the respiration of their substrates as ATP. Microorganisms have evolved incredible variations on this principle, most of these we perhaps do not know, considering that only a fraction of the microbial richness is known. Besides these variations, microbial species may show substantial versatility in using respiratory systems. In connection herewith, regulatory mechanisms control the expression of these respiratory enzyme systems and their assembly at the translational and posttranslational levels, to optimally accommodate changes in the supply of their energy substrates. Here, we present an overview of methods and techniques from the field of proteomics to explore bacterial electron transfer chains and their regulation at levels ranging from the whole organism down to the Ångstrom scales of protein structures. From the survey of the literature on this subject, it is concluded that proteomics, indeed, has substantially contributed to our comprehending of bacterial respiratory mechanisms, often in elegant combinations with genetic and biochemical approaches. However, we also note that advanced proteomics offers a wealth of opportunities, which have not been exploited at all, or at best underexploited in hypothesis-driving and hypothesis-driven research on bacterial bioenergetics. Examples obtained from the related area of mitochondrial oxidative phosphorylation research, where the application of advanced proteomics is more common, may illustrate these opportunities.
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Affiliation(s)
- H J C T Wessels
- Nijmegen Center for Mitochondrial Disorders, Radboud Proteomics Centre, Translational Metabolic Laboratory, Radboud University Medical Center, Nijmegen, The Netherlands
| | - N M de Almeida
- Institute of Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - B Kartal
- Institute of Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands; Laboratory of Microbiology, Ghent University, Ghent, Belgium
| | - J T Keltjens
- Institute of Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands.
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19
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Qin J, Tan H, Li X, Chen G, Zheng J, Wang Y, Ma J, Jia Z. Theoretical studies of the function switch and mechanism of AceK as a highly active ATPase. RSC Adv 2016. [DOI: 10.1039/c6ra11873a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
As a multi-function enzyme, AceK integrates kinase, phosphatase and ATPase activities in a single active site and these functions are delicately regulated..
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Affiliation(s)
- Jiajia Qin
- College of Chemistry
- Beijing Normal University
- 100875 Beijing
- China
| | - Hongwei Tan
- College of Chemistry
- Beijing Normal University
- 100875 Beijing
- China
| | - Xichen Li
- College of Chemistry
- Beijing Normal University
- 100875 Beijing
- China
| | - Guangju Chen
- College of Chemistry
- Beijing Normal University
- 100875 Beijing
- China
| | - Jimin Zheng
- College of Chemistry
- Beijing Normal University
- 100875 Beijing
- China
| | - Ye Wang
- College of Chemistry
- Beijing Normal University
- 100875 Beijing
- China
| | - Jianqiu Ma
- College of Chemistry
- Beijing Normal University
- 100875 Beijing
- China
| | - Zongchao Jia
- College of Chemistry
- Beijing Normal University
- 100875 Beijing
- China
- Department of Biomedical and Molecular Sciences
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20
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Metabolic responses of Rhodococcus erythropolis PR4 grown on diesel oil and various hydrocarbons. Appl Microbiol Biotechnol 2015; 99:9745-59. [DOI: 10.1007/s00253-015-6936-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Revised: 08/07/2015] [Accepted: 08/11/2015] [Indexed: 10/23/2022]
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21
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Wang S, Shen Q, Chen G, Zheng J, Tan H, Jia Z. The phosphatase mechanism of bifunctional kinase/phosphatase AceK. Chem Commun (Camb) 2015; 50:14117-20. [PMID: 25272278 DOI: 10.1039/c4cc05375c] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
We have revealed that bifunctional AceK kinase/phosphatase utilizes a stepwise addition-elimination mechanism in its dephosphorylation reaction. This work explains how AceK enables opposite kinase and phosphatase activities with Asp477 and a single Mg(2+) ion.
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Affiliation(s)
- Shu Wang
- College of Chemistry, Beijing Normal University, Beijing, 100875, China.
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22
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Li Q, Zheng J, Tan H, Li X, Chen G, Jia Z. Unique kinase catalytic mechanism of AceK with a single magnesium ion. PLoS One 2013; 8:e72048. [PMID: 23977203 PMCID: PMC3747045 DOI: 10.1371/journal.pone.0072048] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Accepted: 07/06/2013] [Indexed: 11/26/2022] Open
Abstract
Isocitrate dehydrogenase kinase/phosphatase (AceK) is the founding member of the protein phosphorylation system in prokaryotes. Based on the novel and unique structural characteristics of AceK recently uncovered, we sought to understand its kinase reaction mechanism, along with other features involved in the phosphotransfer process. Herein we report density functional theory QM calculations of the mechanism of the phosphotransfer reaction catalysed by AceK. The transition states located by the QM calculations indicate that the phosphorylation reaction, catalysed by AceK, follows a dissociative mechanism with Asp457 serving as the catalytic base to accept the proton delivered by the substrate. Our results also revealed that AceK prefers a single Mg2+-containing active site in the phosphotransfer reaction. The catalytic roles of conserved residues in the active site are discussed.
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Affiliation(s)
- Quanjie Li
- College of Chemistry, Beijing Normal University, Beijing, People’s Republic of China
| | - Jimin Zheng
- College of Chemistry, Beijing Normal University, Beijing, People’s Republic of China
| | - Hongwei Tan
- College of Chemistry, Beijing Normal University, Beijing, People’s Republic of China
- * E-mail: (HT); (GC)
| | - Xichen Li
- College of Chemistry, Beijing Normal University, Beijing, People’s Republic of China
| | - Guangju Chen
- College of Chemistry, Beijing Normal University, Beijing, People’s Republic of China
- * E-mail: (HT); (GC)
| | - Zongchao Jia
- College of Chemistry, Beijing Normal University, Beijing, People’s Republic of China
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, Ontario, Canada
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23
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Tonks NK. Protein tyrosine phosphatases--from housekeeping enzymes to master regulators of signal transduction. FEBS J 2013; 280:346-78. [PMID: 23176256 DOI: 10.1111/febs.12077] [Citation(s) in RCA: 340] [Impact Index Per Article: 30.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Revised: 11/13/2012] [Accepted: 11/15/2012] [Indexed: 12/12/2022]
Abstract
There are many misconceptions surrounding the roles of protein phosphatases in the regulation of signal transduction, perhaps the most damaging of which is the erroneous view that these enzymes exert their effects merely as constitutively active housekeeping enzymes. On the contrary, the phosphatases are critical, specific regulators of signalling in their own right and serve an essential function, in a coordinated manner with the kinases, to determine the response to a physiological stimulus. This review is a personal perspective on the development of our understanding of the protein tyrosine phosphatase family of enzymes. I have discussed various aspects of the structure, regulation and function of the protein tyrosine phosphatase family, which I hope will illustrate the fundamental importance of these enzymes in the control of signal transduction.
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Affiliation(s)
- Nicholas K Tonks
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724-2208, USA.
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