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Bakr S, Brennan K, Mukherjee P, Argemi J, Hernaez M, Gevaert O. Identifying key multifunctional components shared by critical cancer and normal liver pathways via SparseGMM. CELL REPORTS METHODS 2023; 3:100392. [PMID: 36814838 PMCID: PMC9939431 DOI: 10.1016/j.crmeth.2022.100392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 09/16/2022] [Accepted: 12/21/2022] [Indexed: 01/19/2023]
Abstract
Despite the abundance of multimodal data, suitable statistical models that can improve our understanding of diseases with genetic underpinnings are challenging to develop. Here, we present SparseGMM, a statistical approach for gene regulatory network discovery. SparseGMM uses latent variable modeling with sparsity constraints to learn Gaussian mixtures from multiomic data. By combining coexpression patterns with a Bayesian framework, SparseGMM quantitatively measures confidence in regulators and uncertainty in target gene assignment by computing gene entropy. We apply SparseGMM to liver cancer and normal liver tissue data and evaluate discovered gene modules in an independent single-cell RNA sequencing (scRNA-seq) dataset. SparseGMM identifies PROCR as a regulator of angiogenesis and PDCD1LG2 and HNF4A as regulators of immune response and blood coagulation in cancer. Furthermore, we show that more genes have significantly higher entropy in cancer compared with normal liver. Among high-entropy genes are key multifunctional components shared by critical pathways, including p53 and estrogen signaling.
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Affiliation(s)
- Shaimaa Bakr
- Department of Electrical Engineering, Stanford University, Stanford, CA 94305, USA
- Stanford Center for Biomedical Informatics Research, Department of Medicine and Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
- Department of Radiology, Stanford University, Stanford, CA 94305, USA
| | - Kevin Brennan
- Stanford Center for Biomedical Informatics Research, Department of Medicine and Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Pritam Mukherjee
- Stanford Center for Biomedical Informatics Research, Department of Medicine and Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Josepmaria Argemi
- Liver Unit, Clinica Universidad de Navarra, Hepatology Program, Center for Applied Medical Research, 31008 Pamplona, Navarra, Spain
| | - Mikel Hernaez
- Center for Applied Medical Research, University of Navarra, 31009 Pamplona, Navarra, Spain
| | - Olivier Gevaert
- Stanford Center for Biomedical Informatics Research, Department of Medicine and Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
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Diao M, Wu Y, Yang J, Liu C, Xu J, Jin H, Wang J, Zhang J, Gao F, Jin C, Tian H, Xu J, Ou Q, Li Y, Xu G, Lu L. Identification of Novel Key Molecular Signatures in the Pathogenesis of Experimental Diabetic Kidney Disease. Front Endocrinol (Lausanne) 2022; 13:843721. [PMID: 35432190 PMCID: PMC9005898 DOI: 10.3389/fendo.2022.843721] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Accepted: 02/28/2022] [Indexed: 11/15/2022] Open
Abstract
Diabetic kidney disease (DKD) is a long-term major microvascular complication of uncontrolled hyperglycemia and one of the leading causes of end-stage renal disease (ESDR). The pathogenesis of DKD has not been fully elucidated, and effective therapy to completely halt DKD progression to ESDR is lacking. This study aimed to identify critical molecular signatures and develop novel therapeutic targets for DKD. This study enrolled 10 datasets consisting of 93 renal samples from the National Center of Biotechnology Information (NCBI) Gene Expression Omnibus (GEO). Networkanalyst, Enrichr, STRING, and Cytoscape were used to conduct the differentially expressed genes (DEGs) analysis, pathway enrichment analysis, protein-protein interaction (PPI) network construction, and hub gene screening. The shared DEGs of type 1 diabetic kidney disease (T1DKD) and type 2 diabetic kidney disease (T2DKD) datasets were performed to identify the shared vital pathways and hub genes. Strepotozocin-induced Type 1 diabetes mellitus (T1DM) rat model was prepared, followed by hematoxylin & eosin (HE) staining, and Oil Red O staining to observe the lipid-related morphological changes. The quantitative reverse transcription-polymerase chain reaction (qRT-PCR) was conducted to validate the key DEGs of interest from a meta-analysis in the T1DKD rat. Using meta-analysis, 305 shared DEGs were obtained. Among the top 5 shared DEGs, Tmem43, Mpv17l, and Slco1a1, have not been reported relevant to DKD. Ketone body metabolism ranked in the top 1 in the KEGG enrichment analysis. Coasy, Idi1, Fads2, Acsl3, Oxct1, and Bdh1, as the top 10 down-regulated hub genes, were first identified to be involved in DKD. The qRT-PCR verification results of the novel hub genes were mostly consistent with the meta-analysis. The positive Oil Red O staining showed that the steatosis appeared in tubuloepithelial cells at 6 w after DM onset. Taken together, abnormal ketone body metabolism may be the key factor in the progression of DKD. Targeting metabolic abnormalities of ketone bodies may represent a novel therapeutic strategy for DKD. These identified novel molecular signatures in DKD merit further clinical investigation.
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Affiliation(s)
- Meng Diao
- Department of Ophthalmology, Shanghai Tongji Hospital of Tongji University, Laboratory of Clinical Visual Science of Tongji Eye Institute, School of Medicine, Tongji University, Shanghai, China
| | - Yimu Wu
- Department of Ophthalmology, Shanghai Tongji Hospital of Tongji University, Laboratory of Clinical Visual Science of Tongji Eye Institute, School of Medicine, Tongji University, Shanghai, China
| | - Jialu Yang
- Department of Ophthalmology, Shanghai Tongji Hospital of Tongji University, Laboratory of Clinical Visual Science of Tongji Eye Institute, School of Medicine, Tongji University, Shanghai, China
| | - Caiying Liu
- Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai, China
| | - Jinyuan Xu
- Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai, China
| | - Hongchao Jin
- Business School and Science School, University of Auckland, Auckland, New Zealand
| | - Juan Wang
- Department of Human Genetics, Tongji University School of Medicine, Shanghai, China
| | - Jieping Zhang
- Department of Pharmacology, Tongji University School of Medicine, Shanghai, China
| | - Furong Gao
- Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai, China
| | - Caixia Jin
- Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai, China
| | - Haibin Tian
- Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai, China
| | - Jingying Xu
- Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai, China
| | - Qingjian Ou
- Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai, China
| | - Ying Li
- Department of Endocrinology, Tongji Hospital of Tongji University, Shanghai, China
- *Correspondence: Lixia Lu, ; Guotong Xu, ; Ying Li,
| | - Guotong Xu
- Department of Ophthalmology, Shanghai Tongji Hospital of Tongji University, Laboratory of Clinical Visual Science of Tongji Eye Institute, School of Medicine, Tongji University, Shanghai, China
- Department of Pharmacology, Tongji University School of Medicine, Shanghai, China
- *Correspondence: Lixia Lu, ; Guotong Xu, ; Ying Li,
| | - Lixia Lu
- Department of Ophthalmology, Shanghai Tongji Hospital of Tongji University, Laboratory of Clinical Visual Science of Tongji Eye Institute, School of Medicine, Tongji University, Shanghai, China
- Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai, China
- *Correspondence: Lixia Lu, ; Guotong Xu, ; Ying Li,
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A new ELISA plate based microtiter well assay for mycobacterial topoisomerase I for the direct screening of enzyme inhibitory monoclonal antibody supernatants. J Immunol Methods 2010; 357:26-32. [DOI: 10.1016/j.jim.2010.03.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2009] [Revised: 03/06/2010] [Accepted: 03/09/2010] [Indexed: 11/18/2022]
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Frelet-Barrand A, Boutigny S, Moyet L, Deniaud A, Seigneurin-Berny D, Salvi D, Bernaudat F, Richaud P, Pebay-Peyroula E, Joyard J, Rolland N. Lactococcus lactis, an alternative system for functional expression of peripheral and intrinsic Arabidopsis membrane proteins. PLoS One 2010; 5:e8746. [PMID: 20098692 PMCID: PMC2808337 DOI: 10.1371/journal.pone.0008746] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2009] [Accepted: 12/18/2009] [Indexed: 11/19/2022] Open
Abstract
Background Despite their functional and biotechnological importance, the study of membrane proteins remains difficult due to their hydrophobicity and their low natural abundance in cells. Furthermore, into established heterologous systems, these proteins are frequently only produced at very low levels, toxic and mis- or unfolded. Lactococcus lactis, a Gram-positive lactic bacterium, has been traditionally used in food fermentations. This expression system is also widely used in biotechnology for large-scale production of heterologous proteins. Various expression vectors, based either on constitutive or inducible promoters, are available for this system. While previously used to produce bacterial and eukaryotic membrane proteins, the ability of this system to produce plant membrane proteins was until now not tested. Methodology/Principal Findings The aim of this work was to test the expression, in Lactococcus lactis, of either peripheral or intrinsic Arabidopsis membrane proteins that could not be produced, or in too low amount, using more classical heterologous expression systems. In an effort to easily transfer genes from Gateway-based Arabidopsis cDNA libraries to the L. lactis expression vector pNZ8148, we first established a cloning strategy compatible with Gateway entry vectors. Interestingly, the six tested Arabidopsis membrane proteins could be produced, in Lactococcus lactis, at levels compatible with further biochemical analyses. We then successfully developed solubilization and purification processes for three of these proteins. Finally, we questioned the functionality of a peripheral and an intrinsic membrane protein, and demonstrated that both proteins were active when produced in this system. Conclusions/Significance Altogether, these data suggest that Lactococcus lactis might be an attractive system for the efficient and functional production of difficult plant membrane proteins.
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Affiliation(s)
- Annie Frelet-Barrand
- CNRS, Laboratoire de Physiologie Cellulaire Végétale, UMR5168, Grenoble, France
- CEA, DSV, iRTSV, LPCV, Grenoble, France
- INRA, Laboratoire de Physiologie Cellulaire Végétale, UMR1200, Grenoble, France
- Université Joseph Fourier, Laboratoire de Physiologie Cellulaire Végétale, Grenoble, France
| | - Sylvain Boutigny
- CNRS, Laboratoire de Physiologie Cellulaire Végétale, UMR5168, Grenoble, France
- CEA, DSV, iRTSV, LPCV, Grenoble, France
- INRA, Laboratoire de Physiologie Cellulaire Végétale, UMR1200, Grenoble, France
- Université Joseph Fourier, Laboratoire de Physiologie Cellulaire Végétale, Grenoble, France
| | - Lucas Moyet
- CNRS, Laboratoire de Physiologie Cellulaire Végétale, UMR5168, Grenoble, France
- CEA, DSV, iRTSV, LPCV, Grenoble, France
- INRA, Laboratoire de Physiologie Cellulaire Végétale, UMR1200, Grenoble, France
- Université Joseph Fourier, Laboratoire de Physiologie Cellulaire Végétale, Grenoble, France
| | - Aurélien Deniaud
- CEA, IBS Institut de Biologie Structurale Jean-Pierre Ebel, Grenoble, France
- CNRS, IBS Institut de Biologie Structurale Jean-Pierre Ebel, Grenoble, France
- Université Joseph Fourier, IBS Institut de Biologie Structurale Jean-Pierre Ebel, Grenoble, France
| | - Daphné Seigneurin-Berny
- CNRS, Laboratoire de Physiologie Cellulaire Végétale, UMR5168, Grenoble, France
- CEA, DSV, iRTSV, LPCV, Grenoble, France
- INRA, Laboratoire de Physiologie Cellulaire Végétale, UMR1200, Grenoble, France
- Université Joseph Fourier, Laboratoire de Physiologie Cellulaire Végétale, Grenoble, France
- * E-mail:
| | - Daniel Salvi
- CNRS, Laboratoire de Physiologie Cellulaire Végétale, UMR5168, Grenoble, France
- CEA, DSV, iRTSV, LPCV, Grenoble, France
- INRA, Laboratoire de Physiologie Cellulaire Végétale, UMR1200, Grenoble, France
- Université Joseph Fourier, Laboratoire de Physiologie Cellulaire Végétale, Grenoble, France
| | - Florent Bernaudat
- CEA, IBS Institut de Biologie Structurale Jean-Pierre Ebel, Grenoble, France
- CNRS, IBS Institut de Biologie Structurale Jean-Pierre Ebel, Grenoble, France
- Université Joseph Fourier, IBS Institut de Biologie Structurale Jean-Pierre Ebel, Grenoble, France
| | - Pierre Richaud
- CEA, DSV, iBEB, Laboratoire des Echanges Membranaires et Signalisation, St Paul les Durance, France
- CNRS, UMR 6191, St Paul les Durance, France
- Université Aix-Marseille, St Paul les Durance, France
| | - Eva Pebay-Peyroula
- CEA, IBS Institut de Biologie Structurale Jean-Pierre Ebel, Grenoble, France
- CNRS, IBS Institut de Biologie Structurale Jean-Pierre Ebel, Grenoble, France
- Université Joseph Fourier, IBS Institut de Biologie Structurale Jean-Pierre Ebel, Grenoble, France
| | - Jacques Joyard
- CNRS, Laboratoire de Physiologie Cellulaire Végétale, UMR5168, Grenoble, France
- CEA, DSV, iRTSV, LPCV, Grenoble, France
- INRA, Laboratoire de Physiologie Cellulaire Végétale, UMR1200, Grenoble, France
- Université Joseph Fourier, Laboratoire de Physiologie Cellulaire Végétale, Grenoble, France
| | - Norbert Rolland
- CNRS, Laboratoire de Physiologie Cellulaire Végétale, UMR5168, Grenoble, France
- CEA, DSV, iRTSV, LPCV, Grenoble, France
- INRA, Laboratoire de Physiologie Cellulaire Végétale, UMR1200, Grenoble, France
- Université Joseph Fourier, Laboratoire de Physiologie Cellulaire Végétale, Grenoble, France
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Chigri F, Hörmann F, Stamp A, Stammers DK, Bölter B, Soll J, Vothknecht UC. Calcium regulation of chloroplast protein translocation is mediated by calmodulin binding to Tic32. Proc Natl Acad Sci U S A 2006; 103:16051-6. [PMID: 17035502 PMCID: PMC1635125 DOI: 10.1073/pnas.0607150103] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2006] [Indexed: 11/18/2022] Open
Abstract
The import of nuclear-encoded proteins into chloroplasts is tightly controlled on both sides of the envelope membranes. Regulatory circuits include redox-control as well as calcium-regulation, with calmodulin being the likely mediator of the latter. Using affinity-chromatography on calmodulin-agarose, we could identify the inner envelope translocon component Tic32 as the predominant calmodulin-binding protein of this membrane. Calmodulin-binding assays corroborate the interaction for heterologously expressed as well as native Tic32. The interaction is calcium-dependent and is mediated by a calmodulin-binding domain between Leu-296 and Leu-314 close to the C-proximal end of the pea Tic32. We furthermore could establish Tic32 as a bona fide NADPH-dependent dehydrogenase. NADPH but not NADH or NADP(+) affects the interaction of Tic110 with Tic32 as well as Tic62. At the same time, dehydrogenase activity of Tic32 is affected by calmodulin. In particular, binding of NADPH and calmodulin to Tic32 appear to be mutually exclusive. These results suggest that redox modulation and calcium regulation of chloroplast protein import convene at the Tic translocon and that both could be mediated by Tic32.
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Affiliation(s)
- Fatima Chigri
- *Department of Biology I, Ludwig-Maximilians-Universität, Menzinger Strasse 67, D-80638 München, Germany; and
| | - Friederike Hörmann
- *Department of Biology I, Ludwig-Maximilians-Universität, Menzinger Strasse 67, D-80638 München, Germany; and
| | - Anna Stamp
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - David K. Stammers
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Bettina Bölter
- *Department of Biology I, Ludwig-Maximilians-Universität, Menzinger Strasse 67, D-80638 München, Germany; and
| | - Jürgen Soll
- *Department of Biology I, Ludwig-Maximilians-Universität, Menzinger Strasse 67, D-80638 München, Germany; and
| | - Ute C. Vothknecht
- *Department of Biology I, Ludwig-Maximilians-Universität, Menzinger Strasse 67, D-80638 München, Germany; and
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Loeb-Hennard C, McIntyre JO. (R)-3-hydroxybutyrate dehydrogenase: selective phosphatidylcholine binding by the C-terminal domain. Biochemistry 2000; 39:11928-38. [PMID: 11009606 DOI: 10.1021/bi000425y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
(R)-3-Hydroxybutyrate dehydrogenase (BDH) is a lipid-requiring mitochondrial enzyme that has a specific requirement of phosphatidylcholine (PC) for function. The C-terminal domain (CTBDH) of human heart BDH (residues 195-297) has now been expressed in Escherichia coli as a chimera with a soluble protein, glutathione S-transferase (GST), yielding GST-CTBDH, a novel fusion protein that has been purified and shown to selectively bind to PC vesicles. Both recombinant human heart BDH (HH-Histag-BDH) and GST-CTBDH (but not GST) form well-defined protein-lipid complexes with either PC or phosphatidylethanolamine (PE)/diphosphatidylglycerol (DPG) vesicles (but not with digalactosyl diglyceride vesicles) as demonstrated by flotation in sucrose gradients. The protein-PC complexes are stable to 0.5 M NaCl, but complexes of either HH-Histag-BDH or GST-CTBDH with PE/DPG vesicles are dissociated by salt treatment. Thrombin cleavage of GST-CTBDH, either before or after reconstitution with PC vesicles, yields CTBDH (12 111 Da by MALDI mass spectrometry) which retains lipid binding without attached GST. The BDH activator, 1-palmitoyl-2-(1-pyrenyl)decanoyl-PC (pyrenyl-PC), at <2.5% of total phospholipid in vesicles, efficiently quenches a fraction (0.36 and 0.47, respectively) of the tryptophan fluorescence of both HH-Histag-BDH and GST-CTBDH with effective Stern-Volmer quenching constants, (K(Q))(eff), of 11 and 9.3 (%)(-)(1), respectively (half-maximal quenching at approximately 0.1% pyrenyl-PC). Maximal quenching by pyrenyl-PC obtains at approximately stoichiometric pyrenyl-PC to protein ratios, reflecting high-affinity interaction of pyrenyl-PC with both HH-Histag-BDH and GST-CTBDH. The analogous pyrenyl-PE effects a similar maximal quenching of tryptophan fluorescence for both proteins but with approximately 15-fold lower (K(Q))(eff) (half-maximal quenching at approximately 1.5% pyrenyl-PE) referable to nonspecific interaction of pyrenyl-PE with HH-Histag-BDH or GST-CTBDH. Thus, the 103-residue CTBDH constitutes a PC-selective lipid binding domain of the PC-requiring BDH.
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Affiliation(s)
- C Loeb-Hennard
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37235, USA
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Chelius D, Loeb-Hennard C, Fleischer S, McIntyre JO, Marks AR, De S, Hahn S, Jehl MM, Moeller J, Philipp R, Wise JG, Trommer WE. Phosphatidylcholine activation of human heart (R)-3-hydroxybutyrate dehydrogenase mutants lacking active center sulfhydryls: site-directed mutagenesis of a new recombinant fusion protein. Biochemistry 2000; 39:9687-97. [PMID: 10933785 DOI: 10.1021/bi000274z] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
(R)-3-Hydroxybutyrate dehydrogenase (BDH) is a lipid-requiring mitochondrial enzyme with a specific requirement of phosphatidylcholine (PC) for function. A plasmid has been constructed to express human heart (HH) BDH in Escherichia coli as a hexahistidine-tagged fusion protein (HH-Histag-BDH). A rapid two-step affinity purification yields active HH-Histag-BDH (and six mutants) with high specific activity ( approximately 130 micromol of NAD(+) reduced.min(-1).mg(-1)). HH-Histag-BDH has no activity in the absence of phospholipid and exhibits a specific requirement of PC for function. The HH-Histag-BDH-PC complex (and HH-BDH derived therefrom by enterokinase cleavage) has apparent Michaelis constants (K(m) values) for NAD(+), NADH, (R)-3-hydroxybutyrate (HOB), and acetoacetate (AcAc) similar to those for bovine heart or rat liver BDH. A computed structural model of HH-BDH predicts the two active center sulfhydryls to be C69 (near the adenosine moiety of NAD) and C242. With both sulfhydryls derivatized, BDH has minimal activity, but site-directed mutagenesis of C69 and/or C242 now shows that neither of these cysteines is required for PC activation or catalysis (the double mutant, C69A/C242A, is highly active with essentially normal kinetic parameters). Six cysteine mutants each have an increased K(m)(NADH) (2-6-fold) but an unchanged K(m)(NAD)+. The C242S and C69A/C242S enzymes (but not the analogous C242A mutants nor the C69A or C69S mutants) exhibit approximately 10-fold increases in K(m)(HOB) and K(m)(AcAc), reflecting an altered substrate binding site. Thus, although C242 (in the C-terminal lipid binding domain of BDH) is close to the active site, it appears to be in a hydrophobic environment and only indirectly defines the substrate binding site at the catalytic center of BDH.
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Affiliation(s)
- D Chelius
- Fachbereich Chemie, Universität Kaiserslautern, Erwin-Schroedinger-Strasse, D-67663 Kaiserslautern, Germany
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Aneja P, Charles TC. Poly-3-hydroxybutyrate degradation in Rhizobium (Sinorhizobium) meliloti: isolation and characterization of a gene encoding 3-hydroxybutyrate dehydrogenase. J Bacteriol 1999; 181:849-57. [PMID: 9922248 PMCID: PMC93451 DOI: 10.1128/jb.181.3.849-857.1999] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We have cloned and sequenced the 3-hydroxybutyrate dehydrogenase-encoding gene (bdhA) from Rhizobium (Sinorhizobium) meliloti. The gene has an open reading frame of 777 bp that encodes a polypeptide of 258 amino acid residues (molecular weight 27,177, pI 6.07). The R. meliloti Bdh protein exhibits features common to members of the short-chain alcohol dehydrogenase superfamily. bdhA is the first gene transcribed in an operon that also includes xdhA, encoding xanthine oxidase/dehydrogenase. Transcriptional start site analysis by primer extension identified two transcription starts. S1, a minor start site, was located 46 to 47 nucleotides upstream of the predicted ATG start codon, while S2, the major start site, was mapped 148 nucleotides from the start codon. Analysis of the sequence immediately upstream of either S1 or S2 failed to reveal the presence of any known consensus promoter sequences. Although a sigma54 consensus sequence was identified in the region between S1 and S2, a corresponding transcript was not detected, and a rpoN mutant of R. meliloti was able to utilize 3-hydroxybutyrate as a sole carbon source. The R. meliloti bdhA gene is able to confer upon Escherichia coli the ability to utilize 3-hydroxybutyrate as a sole carbon source. An R. meliloti bdhA mutant accumulates poly-3-hydroxybutyrate to the same extent as the wild type and shows no symbiotic defects. Studies with a strain carrying a lacZ transcriptional fusion to bdhA demonstrated that gene expression is growth phase associated.
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Affiliation(s)
- P Aneja
- Department of Natural Resource Sciences, McGill University, Ste-Anne-de-Bellevue, Quebec, Canada H9X 3V9
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Green D, Marks AR, Fleischer S, McIntyre JO. Wild type and mutant human heart (R)-3-hydroxybutyrate dehydrogenase expressed in insect cells. Biochemistry 1996; 35:8158-65. [PMID: 8679568 DOI: 10.1021/bi952807n] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
(R)-3-Hydroxybutyrate dehydrogenase (BDH) is a lipid-requiring mitochondrial enzyme with a specific requirement of phosphatidylcholine (PC) for function. PC is an allosteric activator that enhances NAD(H) binding to BDH. The enzyme serves as a paradigm to study specific lipid-protein interactions in membranes. Analysis of the primary sequence of BDH, as determined by molecular cloning, predicts that lipid binding and substrate specificity are contributed by the C-terminal third of the protein [Marks, A. R., McIntyre, J. O., Duncan, T. M., Erdjument-Bromage, H., Tempst, P., & Fleischer, S. (1992) J. Biol. Chem. 267, 15459-15463]. The mature form of human heart BDH has now been expressed in catalytically active form in insect cells (Sf9, Spodoptera frugiperda) transfected with BDH-cDNA in baculovirus. Endogenous PC in the insect cells fulfills the lipid requirement for the expressed BDH since enzymatic activity is lost upon digestion with phospholipase A2 and restored selectively by reconstitution with PC vesicles. The K(m)s for NAD+ and (R)-3-hydroxybutyrate (R-HOB) of expressed BDH are similar to those for bovine heart or rat liver BDH in mitochondria. Replacing Cys242 (the only cysteine in the C-terminal domain) with serine by site-directed mutagenesis resulted in a 10-fold increase in K(m) for R-HOB with no change in the K(m) for NAD+, indicating a role for Cys242 in substrate binding. Carboxypeptidase cleavage studies had indicated a requirement of the C-terminal for catalysis and a role in lipid binding [Adami, P., Duncan, T. M., McIntyre, J. O., Carter, C. E., Fu, C., Melin, M., Latruffe, N., & Fleischer, S. (1993) Biochem J. 292, 863-872]. We now show that deletion of twelve C-terminal amino acids to form a truncated BDH mutant results in loss of enzymic function. The expression in Sf 9 cells of the constitutively active full-length mature form of human heart BDH and the first expression and characterization of BDH mutants validate this system for structure-function studies of BDH.
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Affiliation(s)
- D Green
- Brookdale Center for Molecular Biology Mount Sinai School of Medicine, New York, New York 10032 USA
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