1
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Gaschignard G, Millet M, Bruley A, Benzerara K, Dezi M, Skouri-Panet F, Duprat E, Callebaut I. AlphaFold2-guided description of CoBaHMA, a novel family of bacterial domains within the heavy-metal-associated superfamily. Proteins 2024; 92:776-794. [PMID: 38258321 DOI: 10.1002/prot.26668] [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: 09/28/2023] [Revised: 12/22/2023] [Accepted: 01/01/2024] [Indexed: 01/24/2024]
Abstract
Three-dimensional (3D) structure information, now available at the proteome scale, may facilitate the detection of remote evolutionary relationships in protein superfamilies. Here, we illustrate this with the identification of a novel family of protein domains related to the ferredoxin-like superfold, by combining (i) transitive sequence similarity searches, (ii) clustering approaches, and (iii) the use of AlphaFold2 3D structure models. Domains of this family were initially identified in relation with the intracellular biomineralization of calcium carbonates by Cyanobacteria. They are part of the large heavy-metal-associated (HMA) superfamily, departing from the latter by specific sequence and structural features. In particular, most of them share conserved basic amino acids (hence their name CoBaHMA for Conserved Basic residues HMA), forming a positively charged surface, which is likely to interact with anionic partners. CoBaHMA domains are found in diverse modular organizations in bacteria, existing in the form of monodomain proteins or as part of larger proteins, some of which are membrane proteins involved in transport or lipid metabolism. This suggests that the CoBaHMA domains may exert a regulatory function, involving interactions with anionic lipids. This hypothesis might have a particular resonance in the context of the compartmentalization observed for cyanobacterial intracellular calcium carbonates.
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Affiliation(s)
- Geoffroy Gaschignard
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Maxime Millet
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Apolline Bruley
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Karim Benzerara
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Manuela Dezi
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Feriel Skouri-Panet
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Elodie Duprat
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Isabelle Callebaut
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
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2
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Kimura T, Kimura AK, Epand RM. Systematic crosstalk in plasmalogen and diacyl lipid biosynthesis for their differential yet concerted molecular functions in the cell. Prog Lipid Res 2023; 91:101234. [PMID: 37169310 DOI: 10.1016/j.plipres.2023.101234] [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: 03/03/2023] [Revised: 04/29/2023] [Accepted: 05/05/2023] [Indexed: 05/13/2023]
Abstract
Plasmalogen is a major phospholipid of mammalian cell membranes. Recently it is becoming evident that the sn-1 vinyl-ether linkage in plasmalogen, contrasting to the ester linkage in the counterpart diacyl glycerophospholipid, yields differential molecular characteristics for these lipids especially related to hydrocarbon-chain order, so as to concertedly regulate biological membrane processes. A role played by NMR in gaining information in this respect, ranging from molecular to tissue levels, draws particular attention. We note here that a broad range of enzymes in de novo synthesis pathway of plasmalogen commonly constitute that of diacyl glycerophospholipid. This fact forms the basis for systematic crosstalk that not only controls a quantitative balance between these lipids, but also senses a defect causing loss of lipid in either pathway for compensation by increase of the counterpart lipid. However, this inherent counterbalancing mechanism paradoxically amplifies imbalance in differential effects of these lipids in a diseased state on membrane processes. While sharing of enzymes has been recognized, it is now possible to overview the crosstalk with growing information for specific enzymes involved. The overview provides a fundamental clue to consider cell and tissue type-dependent schemes in regulating membrane processes by plasmalogen and diacyl glycerophospholipid in health and disease.
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Affiliation(s)
- Tomohiro Kimura
- Department of Chemistry & Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas 66506, USA.
| | - Atsuko K Kimura
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Richard M Epand
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4K1, Canada
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3
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Aulakh SS, Bozelli JC, Epand RM. Exploring the AlphaFold Predicted Conformational Properties of Human Diacylglycerol Kinases. J Phys Chem B 2022; 126:7172-7183. [PMID: 36041230 DOI: 10.1021/acs.jpcb.2c04533] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Diacylglycerol kinases (DGKs) are important enzymes in molecular membrane biology, as they can lower the concentration of diacylglycerol through phosphorylation while at the same time producing phosphatidic acid. Dysfunction of DGK is linked with multiple diseases including cancer and autoimmune disorders. Currently, the high-resolution structures have not been determined for any of the 10 human DGK paralogs, which has made it difficult to gain a more complete understanding of the enzyme's mechanism of action and regulation. In the present study, we have taken advantage of the significant developments in protein structural prediction technology by artificial intelligence (i.e., Alphafold 2.0), to conduct a comprehensive investigation on the properties of all 10 human DGK paralogs. Structural alignment of the predictions reveals that the C1, catalytic, and accessory domains are conserved in their spatial arrangement relative to each other, across all paralogs. This suggests a critical role played by this domain architecture in DGK function. Moreover, docking studies corroborate the existence of a conserved ATP-binding site between the catalytic and accessory domains. Interestingly, the ATP bound to the interdomain cleft was also found to be in proximity of the conserved glycine-rich motif, which in protein kinases has been suggested to function in ATP binding. Lastly, the spatial arrangement of DGK, with respect to the membrane, reveals that most paralogs possess a more energetically favorable interaction with curved membranes. In conclusion, AlphaFold predictions of human DGKs provide novel insights into the enzyme's structural and functional properties while also paving the way for future experimentation.
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Affiliation(s)
- Sukhvershjit S Aulakh
- Department of Biochemistry and Biomedical Sciences, Health Sciences Centre, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - José Carlos Bozelli
- Department of Biochemistry and Biomedical Sciences, Health Sciences Centre, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Richard M Epand
- Department of Biochemistry and Biomedical Sciences, Health Sciences Centre, McMaster University, Hamilton, ON L8S 4K1, Canada
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de Kok NAW, Driessen AJM. The catalytic and structural basis of archaeal glycerophospholipid biosynthesis. Extremophiles 2022; 26:29. [PMID: 35976526 PMCID: PMC9385802 DOI: 10.1007/s00792-022-01277-w] [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: 03/21/2022] [Accepted: 08/02/2022] [Indexed: 12/03/2022]
Abstract
Archaeal glycerophospholipids are the main constituents of the cytoplasmic membrane in the archaeal domain of life and fundamentally differ in chemical composition compared to bacterial phospholipids. They consist of isoprenyl chains ether-bonded to glycerol-1-phosphate. In contrast, bacterial glycerophospholipids are composed of fatty acyl chains ester-bonded to glycerol-3-phosphate. This largely domain-distinguishing feature has been termed the “lipid-divide”. The chemical composition of archaeal membranes contributes to the ability of archaea to survive and thrive in extreme environments. However, ether-bonded glycerophospholipids are not only limited to extremophiles and found also in mesophilic archaea. Resolving the structural basis of glycerophospholipid biosynthesis is a key objective to provide insights in the early evolution of membrane formation and to deepen our understanding of the molecular basis of extremophilicity. Many of the glycerophospholipid enzymes are either integral membrane proteins or membrane-associated, and hence are intrinsically difficult to study structurally. However, in recent years, the crystal structures of several key enzymes have been solved, while unresolved enzymatic steps in the archaeal glycerophospholipid biosynthetic pathway have been clarified providing further insights in the lipid-divide and the evolution of early life.
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Affiliation(s)
- Niels A W de Kok
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747AG, Groningen, The Netherlands
| | - Arnold J M Driessen
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747AG, Groningen, The Netherlands.
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5
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Ma Q, Srinivasan L, Gabelli SB, Raben DM. Elusive structure of mammalian DGKs. Adv Biol Regul 2022; 83:100847. [PMID: 34922895 PMCID: PMC8858910 DOI: 10.1016/j.jbior.2021.100847] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 11/29/2021] [Accepted: 11/30/2021] [Indexed: 01/03/2023]
Abstract
Mammalian diacylglycerol kinases (DGKs) are a group of enzymes that catalyze the ATP-dependent phosphorylation of diacylglycerol (DAG) to produce phosphatidic acid (PtdOH). In doing so, they modulate the levels of these two important signaling lipids. Currently, ten mammalian DGKs are organized into five classes that vary with respect to domain organization, regulation, and cellular/subcellular distribution. As lipids play critical roles in cells, it is not surprising that there is increasing interest in understanding the mechanism underlying the catalysis and regulation of lipid modulating enzymes such as DGKs. However, there are no solved 3D structures for any of the eukaryotic DGKs. In this review, we summarize what is known and the current challenges in determining the structures of these important enzymes. In addition to gain critical insights into their mechanisms of catalysis and regulation, DGK structures will provide a platform for the design of isoform specific inhibitors.
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Affiliation(s)
- Qianqian Ma
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore Maryland
| | - Lakshmi Srinivasan
- Department of Biophysics and Biophysical Chemistry, The Johns Hopkins University School of Medicine, Baltimore Maryland
| | - Sandra B. Gabelli
- Department of Biophysics and Biophysical Chemistry, The Johns Hopkins University School of Medicine, Baltimore Maryland,Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore Maryland,Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore Maryland,Corresponding author: Sandra B. Gabelli (), Daniel M. Raben ()
| | - Daniel M. Raben
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore Maryland,Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore Maryland,Corresponding author: Sandra B. Gabelli (), Daniel M. Raben ()
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6
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Sakane F, Hoshino F, Ebina M, Sakai H, Takahashi D. The Roles of Diacylglycerol Kinase α in Cancer Cell Proliferation and Apoptosis. Cancers (Basel) 2021; 13:cancers13205190. [PMID: 34680338 PMCID: PMC8534027 DOI: 10.3390/cancers13205190] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 10/14/2021] [Accepted: 10/14/2021] [Indexed: 02/02/2023] Open
Abstract
Simple Summary Diacylglycerol (DG) kinase (DGK) phosphorylates DG to generate phosphatidic acid (PA). DGKα is highly expressed in several refractory cancer cells, including melanoma, hepatocellular carcinoma, and glioblastoma cells, attenuates apoptosis, and promotes proliferation. In cancer cells, PA produced by DGKα plays an important role in proliferation/antiapoptosis. In addition to cancer cells, DGKα is highly abundant in T cells and induces a nonresponsive state (anergy), representing the main mechanism by which advanced cancers avoid immune action. In T cells, DGKα induces anergy through DG consumption. Therefore, a DGKα-specific inhibitor is expected to be a dual effective anticancer treatment that inhibits cancer cell proliferation and simultaneously activates T cell function. Moreover, the inhibition of DGKα synergistically enhances the anticancer effects of programmed cell death-1/programmed cell death ligand 1 blockade. Taken together, DGKα inhibition provides a promising new treatment strategy for refractory cancers. Abstract Diacylglycerol (DG) kinase (DGK) phosphorylates DG to generate phosphatidic acid (PA). The α isozyme is activated by Ca2+ through its EF-hand motifs and tyrosine phosphorylation. DGKα is highly expressed in several refractory cancer cells including melanoma, hepatocellular carcinoma, and glioblastoma cells. In melanoma cells, DGKα is an antiapoptotic factor that activates nuclear factor-κB (NF-κB) through the atypical protein kinase C (PKC) ζ-mediated phosphorylation of NF-κB. DGKα acts as an enhancer of proliferative activity through the Raf–MEK–ERK pathway and consequently exacerbates hepatocellular carcinoma progression. In glioblastoma and melanoma cells, DGKα attenuates apoptosis by enhancing the phosphodiesterase (PDE)-4A1–mammalian target of the rapamycin pathway. As PA activates PKCζ, Raf, and PDE, it is likely that PA generated by DGKα plays an important role in the proliferation/antiapoptosis of cancer cells. In addition to cancer cells, DGKα is highly abundant in T cells and induces a nonresponsive state (anergy), which represents the main mechanism by which advanced cancers escape immune action. In T cells, DGKα attenuates the activity of Ras-guanyl nucleotide-releasing protein, which is activated by DG and avoids anergy through DG consumption. Therefore, a DGKα-specific inhibitor is expected to be a dual effective anticancer treatment that inhibits cancer cell proliferation and simultaneously enhances T cell functions. Moreover, the inhibition of DGKα synergistically enhances the anticancer effects of programmed cell death-1/programmed cell death ligand 1 blockade. Taken together, DGKα inhibition provides a promising new treatment strategy for refractory cancers.
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Affiliation(s)
- Fumio Sakane
- Department of Chemistry, Graduate School of Science, Chiba University, Chiba 263-8522, Japan; (F.H.); (M.E.)
- Correspondence: ; Tel.: +81-43-290-3695
| | - Fumi Hoshino
- Department of Chemistry, Graduate School of Science, Chiba University, Chiba 263-8522, Japan; (F.H.); (M.E.)
| | - Masayuki Ebina
- Department of Chemistry, Graduate School of Science, Chiba University, Chiba 263-8522, Japan; (F.H.); (M.E.)
| | - Hiromichi Sakai
- Department of Biosignaling and Radioisotope Experiment, Interdisciplinary Center for Science Research, Organization for Research and Academic Information, Shimane University, Izumo 693-8501, Japan;
| | - Daisuke Takahashi
- Department of Pharmaceutical Health Care and Sciences, Kyushu University, Fukuoka 812-8582, Japan;
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7
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The Lactococcal dgkB ( yecE) and dxsA Genes for Lipid Metabolism Are Involved in the Resistance to Cell Envelope-Acting Antimicrobials. Int J Mol Sci 2021; 22:ijms22031014. [PMID: 33498351 PMCID: PMC7864038 DOI: 10.3390/ijms22031014] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 01/18/2021] [Accepted: 01/18/2021] [Indexed: 01/01/2023] Open
Abstract
The emergence of antibiotic-resistant bacteria led to an urgent need for next-generation antimicrobial agents with novel mechanisms of action. The use of positively charged antimicrobial peptides that target cytoplasmic membrane is an especially promising strategy since essential functions and the conserved structure of the membrane hinder the development of bacterial resistance. Aureocin A53- and enterocin L50-like bacteriocins are highly cationic, membrane-targeting antimicrobial peptides that have potential as next-generation antibiotics. However, the mechanisms of resistance to these bacteriocins and cross-resistance against antibiotics must be examined before application to ensure their safe use. Here, in the model bacterium Lactococcus lactis, we studied the development of resistance to selected aureocin A53- and enterocin L50-like bacteriocins and its correlation with antibiotics. First, to generate spontaneous resistant mutants, L.lactis was exposed to bacteriocin BHT-B. Sequencing of their genomes revealed single nucleotide polymorphisms (SNPs) in the dgkB (yecE) and dxsA genes encoding diacylglycerol kinase and 1-deoxy-D-xylulose 5-phosphate synthase, respectively. Then, selected mutants underwent susceptibility tests with a wide array of bacteriocins and antibiotics. The highest alterations in the sensitivity of studied mutants were seen in the presence of cytoplasmic membrane targeting bacteriocins (K411, Ent7, EntL50, WelM, SalC, nisin) and antibiotics (daptomycin and gramicidin) as well as lipid II cycle-blocking bacteriocins (nisin and Lcn972) and antibiotics (bacitracin). Interestingly, decreased via the SNPs accumulation sensitivity to membrane-active bacteriocins and antibiotics resulted in the concurrently increased vulnerability to bacitracin, carbenicillin, or chlortetracycline. It is suspected that SNPs may result in alterations to the efficiency of the nascent enzymes rather than a total loss of their function as neither deletion nor overexpression of dxsA restored the phenotype observed in spontaneous mutants.
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8
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Spontaneously Arising Streptococcus mutans Variants with Reduced Susceptibility to Chlorhexidine Display Genetic Defects and Diminished Fitness. Antimicrob Agents Chemother 2019; 63:AAC.00161-19. [PMID: 31036688 DOI: 10.1128/aac.00161-19] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 04/20/2019] [Indexed: 01/10/2023] Open
Abstract
Chlorhexidine (CHX) has been used to control dental caries caused by acid-tolerant bacteria such as Streptococcus mutans since the 1970s. Repeat CHX exposure for other bacterial species results in the development of variants with reduced susceptibility that also become more resistant to other antimicrobials. It has not been tested if such variants arise when streptococci are exposed to CHX. Here, we passaged S. mutans in increasing concentrations of CHX and isolated spontaneously arising reduced susceptibility variants (RSVs) from separate lineages that have MICs that are up to 3-fold greater than the parental strain. The RSVs have increased growth rates at neutral pH and under acidic conditions in the presence of CHX but accumulate less biomass in biofilms. RSVs display higher MICs for daptomycin and clindamycin but increased sensitivity to dental-relevant antimicrobials triclosan and sodium fluoride. Plate-based assays for competition with health-associated oral streptococci revealed decreased bacteriocin production by the RSVs, increased sensitivity to hydrogen peroxide, and diminished competitive fitness in a human-derived ex vivo biofilm consortium. Whole-genome sequencing identified common single nucleotide polymorphisms (SNPs) within a diacylglycerol kinase homolog and a glycolipid synthesis enzyme, which could alter the accumulation of lipoteichoic acids and other envelope constituents, as well as a variety of mutations in other genes. Collectively, these findings confirm that S. mutans and likely other streptococci can develop tolerance to CHX but that increased tolerance comes at a fitness cost, such that CHX-induced variants that spontaneously arise in the human oral cavity may not persist.
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9
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Seif Y, Monk JM, Mih N, Tsunemoto H, Poudel S, Zuniga C, Broddrick J, Zengler K, Palsson BO. A computational knowledge-base elucidates the response of Staphylococcus aureus to different media types. PLoS Comput Biol 2019; 15:e1006644. [PMID: 30625152 PMCID: PMC6326480 DOI: 10.1371/journal.pcbi.1006644] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 11/14/2018] [Indexed: 12/15/2022] Open
Abstract
S. aureus is classified as a serious threat pathogen and is a priority that guides the discovery and development of new antibiotics. Despite growing knowledge of S. aureus metabolic capabilities, our understanding of its systems-level responses to different media types remains incomplete. Here, we develop a manually reconstructed genome-scale model (GEM-PRO) of metabolism with 3D protein structures for S. aureus USA300 str. JE2 containing 854 genes, 1,440 reactions, 1,327 metabolites and 673 3-dimensional protein structures. Computations were in 85% agreement with gene essentiality data from random barcode transposon site sequencing (RB-TnSeq) and 68% agreement with experimental physiological data. Comparisons of computational predictions with experimental observations highlight: 1) cases of non-essential biomass precursors; 2) metabolic genes subject to transcriptional regulation involved in Staphyloxanthin biosynthesis; 3) the essentiality of purine and amino acid biosynthesis in synthetic physiological media; and 4) a switch to aerobic fermentation upon exposure to extracellular glucose elucidated as a result of integrating time-course of quantitative exo-metabolomics data. An up-to-date GEM-PRO thus serves as a knowledge-based platform to elucidate S. aureus’ metabolic response to its environment. Environmental perturbations (e.g., antibiotic stress, nutrient starvation, oxidative stress) induce systems-level perturbations of bacterial cells that vary depending on the growth environment. The generation of omics data is aimed at capturing a complete view of the organism’s response under different conditions. Genome-scale models (GEMs) of metabolism represent a knowledge-based platform for the contextualization and integration of multi-omic measurements and can serve to offer valuable insights of system-level responses. This work provides the most up to date reconstruction effort integrating recent advances in the knowledge of S. aureus molecular biology with previous annotations resulting in the first quantitatively and qualitatively validated S. aureus GEM. GEM guided predictions obtained from model analysis provided insights into the effects of medium composition on metabolic flux distribution and gene essentiality. The model can also serve as a platform to guide network reconstructions for other Staphylococci as well as direct hypothesis generation following the integration of omics data sets, including transcriptomics, proteomics, metabolomics, and multi-strain genomic data.
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Affiliation(s)
- Yara Seif
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States of America
| | - Jonathan M. Monk
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States of America
| | - Nathan Mih
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States of America
| | - Hannah Tsunemoto
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, United States of America
| | - Saugat Poudel
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States of America
| | - Cristal Zuniga
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States of America
| | - Jared Broddrick
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States of America
| | - Karsten Zengler
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States of America
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, United States of America
| | - Bernhard O. Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States of America
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, United States of America
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, United States of America
- * E-mail:
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10
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Ma Q, Gabelli SB, Raben DM. Diacylglycerol kinases: Relationship to other lipid kinases. Adv Biol Regul 2019; 71:104-110. [PMID: 30348515 PMCID: PMC6347529 DOI: 10.1016/j.jbior.2018.09.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 09/24/2018] [Accepted: 09/25/2018] [Indexed: 04/17/2023]
Abstract
Lipid kinases regulate a wide variety of cellular functions and have emerged as one the most promising targets for drug design. Diacylglycerol kinases (DGKs) are a family of enzymes that catalyze the ATP-dependent phosphorylation of diacylglycerol (DAG) to phosphatidic acid (PtdOH). Despite the critical role in lipid biosynthesis, both DAG and PtdOH have been shown as bioactive lipids mediating a number of signaling pathways. Although there is increasing recognition of their role in signaling systems, our understanding of the key enzyme which regulate the balance of these two lipid messages remain limited. Solved structures provide a wealth of information for understanding the function and regulation of these enzymes. Solving the structures of mammalian DGKs by traditional NMR and X-ray crystallography approaches have been challenging and so far, there are still no three-dimensional structures of these DGKs. Despite this, some insights may be gained by examining the similarities and differences between prokaryotic DGKs and other mammalian lipid kinases. This review focuses on summarizing and comparing the structure of prokaryotic and mammalian DGKs as well as two other lipid kinases: sphingosine kinase and phosphatidylinositol-3-kinase. How these known lipid kinases structures relate to mammalian DGKs will also be discussed.
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Affiliation(s)
- Qianqian Ma
- The Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Sandra B Gabelli
- The Department of Biophysics, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Daniel M Raben
- The Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
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Merida I, Arranz-Nicolás J, Torres-Ayuso P, Ávila-Flores A. Diacylglycerol Kinase Malfunction in Human Disease and the Search for Specific Inhibitors. Handb Exp Pharmacol 2019; 259:133-162. [PMID: 31227890 DOI: 10.1007/164_2019_221] [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] [Indexed: 12/17/2022]
Abstract
The diacylglycerol kinases (DGKs) are master regulator kinases that control the switch from diacylglycerol (DAG) to phosphatidic acid (PA), two lipids with important structural and signaling properties. Mammalian DGKs distribute into five subfamilies that regulate local availability of DAG and PA pools in a tissue- and subcellular-restricted manner. Pharmacological manipulation of DGK activity holds great promise, given the critical contribution of specific DGK subtypes to the control of membrane structure, signaling complexes, and cell-cell communication. The latest advances in the DGK field have unveiled the differential contribution of selected isoforms to human disease. Defects in the expression/activity of individual DGK isoforms contribute substantially to cognitive impairment, mental disorders, insulin resistance, and vascular pathologies. Abnormal DGK overexpression, on the other hand, confers the acquisition of malignant traits including invasion, chemotherapy resistance, and inhibition of immune attack on tumors. Translation of these findings into therapeutic approaches will require development of methods to pharmacologically modulate DGK functions. In particular, inhibitors that target the DGKα isoform hold particular promise in the fight against cancer, on their own or in combination with immune-targeting therapies.
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Affiliation(s)
- Isabel Merida
- Department of Immunology and Oncology, National Center of Biotechnology (CNB-CSIC), Madrid, Spain.
| | - Javier Arranz-Nicolás
- Department of Immunology and Oncology, National Center of Biotechnology (CNB-CSIC), Madrid, Spain
| | - Pedro Torres-Ayuso
- Laboratory of Cell and Developmental Signaling, National Cancer Institute (NCI-NIH), Frederick, MD, USA
| | - Antonia Ávila-Flores
- Department of Immunology and Oncology, National Center of Biotechnology (CNB-CSIC), Madrid, Spain
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12
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Takahashi D, Sakane F. Expression and purification of human diacylglycerol kinase α from baculovirus-infected insect cells for structural studies. PeerJ 2018; 6:e5449. [PMID: 30128205 PMCID: PMC6089211 DOI: 10.7717/peerj.5449] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 07/26/2018] [Indexed: 02/02/2023] Open
Abstract
Diacylglycerol kinases (DGKs) are lipid kinases that modulate the levels of lipid second messengers, diacylglycerol and phosphatidic acid. Recently, increasing attention has been paid to its α isozyme (DGKα) as a potential target for cancer immunotherapy. DGKα consists of the N-terminal regulatory domains including EF-hand motifs and C1 domains, and the C-terminal catalytic domain (DGKα-CD). To date, however, no structures of mammalian DGKs including their CDs have yet been reported, impeding our understanding on the catalytic mechanism of DGKs and the rational structure-based drug design. Here we attempted to produce DGKα-CD or a full-length DGKα using bacterial and baculovirus-insect cell expression system for structural studies. While several DGKα-CD constructs produced using both bacterial and insect cells formed insoluble or soluble aggregates, the full-length DGKα expressed in insect cells remained soluble and was purified to near homogeneity as a monomer with yields (1.3 mg/mL per one L cell culture) feasible for protein crystallization. Following enzymatic characterization showed that the purified DGKα is in fully functional state. We further demonstrated that the purified enzyme could be concentrated without any significant aggregation, and characterized its secondary structure by circular dichroism. Taken together, these results suggest that the presence of N-terminal regulatory domains suppress protein aggregation likely via their intramolecular interactions with DGKα-CD, and demonstrate that the baculovirus-insect cell expression of the full-length form of DGKα, not DGKα-CD alone, represents a promising approach to produce protein sample for structural studies of DGKα. Thus, our study will encourage future efforts to determine the crystal structure of DGK, which has not been determined since it was first identified in 1959.
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Affiliation(s)
- Daisuke Takahashi
- Department of Chemistry, Graduate School of Science, Chiba University, Chiba, Japan
| | - Fumio Sakane
- Department of Chemistry, Graduate School of Science, Chiba University, Chiba, Japan
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13
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Ganesh BP, Hall A, Ayyaswamy S, Nelson JW, Fultz R, Major A, Haag A, Esparza M, Lugo M, Venable S, Whary M, Fox JG, Versalovic J. Diacylglycerol kinase synthesized by commensal Lactobacillus reuteri diminishes protein kinase C phosphorylation and histamine-mediated signaling in the mammalian intestinal epithelium. Mucosal Immunol 2018; 11:380-393. [PMID: 28745328 PMCID: PMC5785580 DOI: 10.1038/mi.2017.58] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 05/21/2017] [Indexed: 02/04/2023]
Abstract
Lactobacillus reuteri 6475 (Lr) of the human microbiome synthesizes histamine and can suppress inflammation via type 2 histamine receptor (H2R) activation in the mammalian intestine. Gut microbes such as Lr promote H2R signaling and may suppress H1R proinflammatory signaling pathways in parallel by unknown mechanisms. In this study, we identified a soluble bacterial enzyme known as diacylglycerol kinase (Dgk) from Lr that is secreted into the extracellular milieu and presumably into the intestinal lumen. DgK diminishes diacylglycerol (DAG) quantities in mammalian cells by promoting its metabolic conversion and causing reduced protein kinase C phosphorylation (pPKC) as a net effect in mammalian cells. We demonstrated that histamine synthesized by gut microbes (Lr) activates both mammalian H1R and H2R, but Lr-derived Dgk suppresses the H1R signaling pathway. Phospho-PKC and IκBα were diminished within the intestinal epithelium of mice and humans treated by wild-type (WT) Lr, but pPKC and IκBα were not decreased in treatment with ΔdgkA Lr. Mucosal IL-6 and systemic interleukin (IL)-1α, eotaxin, and granulocyte colony-stimulating factor (G-CSF) were suppressed in WT Lr, but not in ΔdgkA Lr colonized mice. Collectively, the commensal microbe Lr may act as a "microbial antihistamine" by suppressing intestinal H1R-mediated proinflammatory responses via diminished pPKC-mediated mammalian cell signaling.
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Affiliation(s)
- Bhanu Priya Ganesh
- Departments of Pathology & Immunology, Baylor College of Medicine, Houston, TX, USA
- Department of Pathology, Texas Children’s Hospital, Houston, TX, USA
- Division of Comparative Medicine, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Anne Hall
- Departments of Pathology & Immunology, Baylor College of Medicine, Houston, TX, USA
- Department of Pathology, Texas Children’s Hospital, Houston, TX, USA
| | - Sriram Ayyaswamy
- Departments of Pathology & Immunology, Baylor College of Medicine, Houston, TX, USA
- Department of Pathology, Texas Children’s Hospital, Houston, TX, USA
| | - James Willard Nelson
- Graduate Program in Integrative Molecular and Biomedical Sciences, Baylor College of Medicine, Houston, TX, USA
| | - Robert Fultz
- Department of Pathology, Texas Children’s Hospital, Houston, TX, USA
- Graduate Program in Integrative Molecular and Biomedical Sciences, Baylor College of Medicine, Houston, TX, USA
| | - Angela Major
- Departments of Pathology & Immunology, Baylor College of Medicine, Houston, TX, USA
- Department of Pathology, Texas Children’s Hospital, Houston, TX, USA
| | - Anthony Haag
- Department of Pathology, Texas Children’s Hospital, Houston, TX, USA
| | - Magdalena Esparza
- Departments of Pathology & Immunology, Baylor College of Medicine, Houston, TX, USA
- Department of Pathology, Texas Children’s Hospital, Houston, TX, USA
| | - Monica Lugo
- Departments of Pathology & Immunology, Baylor College of Medicine, Houston, TX, USA
- Department of Pathology, Texas Children’s Hospital, Houston, TX, USA
| | - Susan Venable
- Departments of Pathology & Immunology, Baylor College of Medicine, Houston, TX, USA
- Department of Pathology, Texas Children’s Hospital, Houston, TX, USA
| | - Mark Whary
- Division of Comparative Medicine, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - James G. Fox
- Division of Comparative Medicine, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - James Versalovic
- Departments of Pathology & Immunology, Baylor College of Medicine, Houston, TX, USA
- Department of Pathology, Texas Children’s Hospital, Houston, TX, USA
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14
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Gupta RS, Epand RM. Phylogenetic analysis of the diacylglycerol kinase family of proteins and identification of multiple highly-specific conserved inserts and deletions within the catalytic domain that are distinctive characteristics of different classes of DGK homologs. PLoS One 2017; 12:e0182758. [PMID: 28829789 PMCID: PMC5567653 DOI: 10.1371/journal.pone.0182758] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 07/24/2017] [Indexed: 01/01/2023] Open
Abstract
Diacylglycerol kinase (DGK) family of proteins, which phosphorylates diacylglycerol into phosphatidic acid, play important role in controlling diverse cellular processes in eukaryotic organisms. Most vertebrate species contain 10 different DGK isozymes, which are grouped into 5 different classes based on the presence or absence of specific functional domains. However, the relationships among different DGK isozymes or how they have evolved from a common ancestor is unclear. The catalytic domain constitutes the single largest sequence element within the DGK proteins that is commonly and uniquely shared by all family members, but there is limited understanding of the overall function of this domain. In this work, we have used the catalytic domain sequences to construct a phylogenetic tree for the DGK family members from representatives of the main vertebrate classes and have also examined the distributions of various DGK isozymes in eukaryotic phyla. In a tree based on catalytic domain sequences, the DGK homologs belonging to different classes formed strongly supported clusters which were separated by long branches, and the different isozymes within each class also generally formed monophyletic groupings. Further, our analysis of the sequence alignments of catalytic domains has identified >10 novel sequence signatures consisting of conserved signature indels (inserts or deletions, CSIs) that are distinctive characteristics of either particular classes of DGK isozymes, or are commonly shared by members of two or more classes of DGK isozymes. The conserved indels in protein sequences are known to play important functional roles in the proteins/organisms where they are found. Thus, our identification of multiple highly specific CSIs that are distinguishing characteristics of different classes of DGK homologs points to the existence of important differences in the catalytic domain function among the DGK isozymes. The identified CSIs in conjunction with the results of blast searches on species distribution of DGK isozymes also provide useful insights into the evolutionary relationships among the DGK family of proteins.
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Affiliation(s)
- Radhey S. Gupta
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- * E-mail:
| | - Richard M. Epand
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
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15
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Robertson RM, Yao J, Gajewski S, Kumar G, Martin EW, Rock CO, White SW. A two-helix motif positions the lysophosphatidic acid acyltransferase active site for catalysis within the membrane bilayer. Nat Struct Mol Biol 2017; 24:666-671. [PMID: 28714993 DOI: 10.1038/nsmb.3436] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 06/15/2017] [Indexed: 11/09/2022]
Abstract
Phosphatidic acid (PA), the central intermediate in membrane phospholipid synthesis, is generated by two acyltransferases in a pathway conserved in all life forms. The second step in this pathway is catalyzed by 1-acyl-sn-glycerol-3-phosphate acyltransferase, called PlsC in bacteria. Here we present the crystal structure of PlsC from Thermotoga maritima, revealing an unusual hydrophobic/aromatic N-terminal two-helix motif linked to an acyltransferase αβ-domain that contains the catalytic HX4D motif. PlsC dictates the acyl chain composition of the 2-position of phospholipids, and the acyl chain selectivity 'ruler' is an appropriately placed and closed hydrophobic tunnel. We confirmed this by site-directed mutagenesis and membrane composition analysis of Escherichia coli cells that expressed mutant PlsC. Molecular dynamics (MD) simulations showed that the two-helix motif represents a novel substructure that firmly anchors the protein to one leaflet of the membrane. This binding mode allows the PlsC active site to acylate lysophospholipids within the membrane bilayer by using soluble acyl donors.
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Affiliation(s)
- Rosanna M Robertson
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Jiangwei Yao
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Stefan Gajewski
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Gyanendra Kumar
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Erik W Martin
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Charles O Rock
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Stephen W White
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
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16
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Franks CE, Campbell ST, Purow BW, Harris TE, Hsu KL. The Ligand Binding Landscape of Diacylglycerol Kinases. Cell Chem Biol 2017; 24:870-880.e5. [PMID: 28712745 DOI: 10.1016/j.chembiol.2017.06.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 05/15/2017] [Accepted: 06/16/2017] [Indexed: 11/17/2022]
Abstract
Diacylglycerol kinases (DGKs) are integral components of signal transduction cascades that regulate cell biology through ATP-dependent phosphorylation of the lipid messenger diacylglycerol. Methods for direct evaluation of DGK activity in native biological systems are lacking and needed to study isoform-specific functions of these multidomain lipid kinases. Here, we utilize ATP acyl phosphate activity-based probes and quantitative mass spectrometry to define, for the first time, ATP and small-molecule binding motifs of representative members from all five DGK subtypes. We use chemical proteomics to discover an unusual binding mode for the DGKα inhibitor, ritanserin, including interactions at the atypical C1 domain distinct from the ATP binding region. Unexpectedly, deconstruction of ritanserin yielded a fragment compound that blocks DGKα activity through a conserved binding mode and enhanced selectivity against the kinome. Collectively, our studies illustrate the power of chemical proteomics to profile protein-small molecule interactions of lipid kinases for fragment-based lead discovery.
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Affiliation(s)
- Caroline E Franks
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA
| | - Sean T Campbell
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA; Department of Pathology, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Benjamin W Purow
- Department of Neurology, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Thurl E Harris
- Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Ku-Lung Hsu
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA; Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, VA 22908, USA.
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17
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Miner GE, Starr ML, Hurst LR, Fratti RA. Deleting the DAG kinase Dgk1 augments yeast vacuole fusion through increased Ypt7 activity and altered membrane fluidity. Traffic 2017; 18:315-329. [PMID: 28276191 DOI: 10.1111/tra.12479] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 03/06/2017] [Accepted: 03/06/2017] [Indexed: 12/20/2022]
Abstract
Diacylglycerol (DAG) is a fusogenic lipid that can be produced through phospholipase C activity on phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2 ], or through phosphatidic acid (PA) phosphatase activity. The fusion of Saccharomyces cerevisiae vacuoles requires DAG, PA and PI(4,5)P2 , and the production of these lipids is thought to provide temporally specific stoichiometries that are critical for each stage of fusion. Furthermore, DAG and PA can be interconverted by the DAG kinase Dgk1 and the PA phosphatase Pah1. Previously we found that pah1 Δ vacuoles were fragmented, blocked in SNARE priming and showed arrested endosomal maturation. In other pathways the effects of deleting PAH1 can be compensated for by additionally deleting DGK1 ; however, deleting both genes did not rescue the pah1 Δ vacuolar defects. Deleting DGK1 alone caused a marked increase in vacuole fusion that was attributed to elevated DAG levels. This was accompanied by a gain in resistance to the inhibitory effects of PA as well as inhibitors of Ypt7 activity. Together these data show that Dgk1 function can act as a negative regulator of vacuole fusion through the production of PA at the cost of depleting DAG and reducing Ypt7 activity.
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Affiliation(s)
- Gregory E Miner
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Matthew L Starr
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Logan R Hurst
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Rutilio A Fratti
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois.,Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois
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18
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Jennings W, Doshi S, Hota PK, Prodeus A, Black S, Epand RM. Expression, Purification, and Properties of a Human Arachidonoyl-Specific Isoform of Diacylglycerol Kinase. Biochemistry 2017; 56:1337-1347. [PMID: 28199087 DOI: 10.1021/acs.biochem.6b01193] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Diacylglycerol kinase ε (DGKε) catalyzes the phosphorylation of diacylglycerol, producing phosphatidic acid. DGKε demonstrates exquisite specificity for the acyl chains of diacylglycerol. This contributes to the enrichment of particular acyl chains within the lipids of the phosphatidylinositol cycle. Phosphatidylinositol is highly enriched with 1-stearoyl-2-arachidonoyl, which is important for maintaining cellular health. Dysregulation of DGKε perturbs lipid signaling and biosynthesis, which has been linked to epilepsy, Huntington's disease, and heart disease. Recessive loss-of-function mutations in the DGKε gene cause atypical hemolytic uremic syndrome. Because DGKε has never been purified, little is known about its molecular properties. We expressed human DGKε and a truncated version lacking the first 40 residues (DGKεΔ40) and purified both proteins to near homogeneity using nickel affinity chromatography. Kinase activity measurements showed that both purified constructs retained their acyl chain specificity for diacylglycerol with an activity level comparable to that of N-terminally FLAG epitope-tagged forms of these proteins expressed in COS7 cells. Both constructs lost activity upon being stored, particularly upon freezing and thawing, which was minimized by the addition of glycerol. Circular dichroism revealed that DGKε and DGKεΔ40 both contain significant amounts of α-helical and β structure and exhibit biphasic thermal denaturations. The loss of secondary structure upon heating was irreversible for both constructs, with relatively little effect of added dioleoylphosphatidylcholine. The addition of 50% glycerol stabilized both constructs and facilitated refolding of their secondary structures after heating. This is the first successful purification and characterization of DGKε's enzymatic and conformational properties. The purification of DGKε permits detailed analyses of this unique enzyme and will improve our understanding of DGKε-related diseases.
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Affiliation(s)
- William Jennings
- Department of Biochemistry and Biomedical Sciences, McMaster University , 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Sejal Doshi
- Department of Biochemistry and Biomedical Sciences, McMaster University , 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Prasanta Kumar Hota
- Department of Biochemistry and Biomedical Sciences, McMaster University , 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Aaron Prodeus
- Department of Biochemistry and Biomedical Sciences, McMaster University , 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Stephanie Black
- Department of Biochemistry and Biomedical Sciences, McMaster University , 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Richard M Epand
- Department of Biochemistry and Biomedical Sciences, McMaster University , 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
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19
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Epand RM, So V, Jennings W, Khadka B, Gupta RS, Lemaire M. Diacylglycerol Kinase-ε: Properties and Biological Roles. Front Cell Dev Biol 2016; 4:112. [PMID: 27803897 PMCID: PMC5067486 DOI: 10.3389/fcell.2016.00112] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 09/27/2016] [Indexed: 12/20/2022] Open
Abstract
In mammals there are at least 10 isoforms of diacylglycerol kinases (DGK). All catalyze the phosphorylation of diacylglycerol (DAG) to phosphatidic acid (PA). Among DGK isoforms, DGKε has several unique features. It is the only DGK isoform with specificity for a particular species of DAG, i.e., 1-stearoyl-2-arachidonoyl glycerol. The smallest of all known DGK isoforms, DGKε, is also the only DGK devoid of a regulatory domain. DGKε is the only DGK isoform that has a hydrophobic segment that is predicted to form a transmembrane helix. As the only membrane-bound, constitutively active DGK isoform with exquisite specificity for particular molecular species of DAG, the functional overlap between DGKε and other DGKs is predicted to be minimal. DGKε exhibits specificity for DAG containing the same acyl chains as those found in the lipid intermediates of the phosphatidylinositol-cycle. It has also been shown that DGKε affects the acyl chain composition of phosphatidylinositol in whole cells. It is thus likely that DGKε is responsible for catalyzing one step in the phosphatidylinositol-cycle. Steps of this cycle take place in both the plasma membrane and the endoplasmic reticulum membrane. DGKε is likely present in both of these membranes. DGKε is the only DGK isoform that is associated with a human disease. Indeed, recessive loss-of-function mutations in DGKε cause atypical hemolytic-uremic syndrome (aHUS). This condition is characterized by thrombosis in the small vessels of the kidney. It causes acute renal insufficiency in infancy and most patients develop end-stage renal failure before adulthood. Disease pathophysiology is poorly understood and there is no therapy. There are also data suggesting that DGKε may play a role in epilepsy and Huntington disease. Thus, DGKε has many unique molecular and biochemical properties when compared to all other DGK isoforms. DGKε homologs also contain a number of conserved sequence features that are distinctive characteristics of either the rodents or specific groups of primate homologs. How cells, tissues and organisms harness DGKε's catalytic prowess remains unclear. The discovery of DGKε's role in causing aHUS will hopefully boost efforts to unravel the mechanisms by which DGKε dysfunction causes disease.
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Affiliation(s)
- Richard M Epand
- Department of Biochemistry and Biomedical Sciences, McMaster University Health Sciences Centre Hamilton, ON, Canada
| | - Vincent So
- Department of Biochemistry and Biomedical Sciences, McMaster University Health Sciences CentreHamilton, ON, Canada; Nephrology Division and Cell Biology Program, Hospital for Sick ChildrenToronto, ON, Canada
| | - William Jennings
- Department of Biochemistry and Biomedical Sciences, McMaster University Health Sciences Centre Hamilton, ON, Canada
| | - Bijendra Khadka
- Department of Biochemistry and Biomedical Sciences, McMaster University Health Sciences Centre Hamilton, ON, Canada
| | - Radhey S Gupta
- Department of Biochemistry and Biomedical Sciences, McMaster University Health Sciences Centre Hamilton, ON, Canada
| | - Mathieu Lemaire
- Nephrology Division and Cell Biology Program, Hospital for Sick ChildrenToronto, ON, Canada; Department of Biochemistry, University of TorontoToronto, ON, Canada; Institute of Medicine, University of TorontoToronto, ON, Canada
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20
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Epand RM, So V, Jennings W, Khadka B, Gupta RS, Lemaire M. Diacylglycerol Kinase-ε: Properties and Biological Roles. Front Cell Dev Biol 2016. [PMID: 27803897 DOI: 10.3389/fcell.2016.00112)] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
In mammals there are at least 10 isoforms of diacylglycerol kinases (DGK). All catalyze the phosphorylation of diacylglycerol (DAG) to phosphatidic acid (PA). Among DGK isoforms, DGKε has several unique features. It is the only DGK isoform with specificity for a particular species of DAG, i.e., 1-stearoyl-2-arachidonoyl glycerol. The smallest of all known DGK isoforms, DGKε, is also the only DGK devoid of a regulatory domain. DGKε is the only DGK isoform that has a hydrophobic segment that is predicted to form a transmembrane helix. As the only membrane-bound, constitutively active DGK isoform with exquisite specificity for particular molecular species of DAG, the functional overlap between DGKε and other DGKs is predicted to be minimal. DGKε exhibits specificity for DAG containing the same acyl chains as those found in the lipid intermediates of the phosphatidylinositol-cycle. It has also been shown that DGKε affects the acyl chain composition of phosphatidylinositol in whole cells. It is thus likely that DGKε is responsible for catalyzing one step in the phosphatidylinositol-cycle. Steps of this cycle take place in both the plasma membrane and the endoplasmic reticulum membrane. DGKε is likely present in both of these membranes. DGKε is the only DGK isoform that is associated with a human disease. Indeed, recessive loss-of-function mutations in DGKε cause atypical hemolytic-uremic syndrome (aHUS). This condition is characterized by thrombosis in the small vessels of the kidney. It causes acute renal insufficiency in infancy and most patients develop end-stage renal failure before adulthood. Disease pathophysiology is poorly understood and there is no therapy. There are also data suggesting that DGKε may play a role in epilepsy and Huntington disease. Thus, DGKε has many unique molecular and biochemical properties when compared to all other DGK isoforms. DGKε homologs also contain a number of conserved sequence features that are distinctive characteristics of either the rodents or specific groups of primate homologs. How cells, tissues and organisms harness DGKε's catalytic prowess remains unclear. The discovery of DGKε's role in causing aHUS will hopefully boost efforts to unravel the mechanisms by which DGKε dysfunction causes disease.
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Affiliation(s)
- Richard M Epand
- Department of Biochemistry and Biomedical Sciences, McMaster University Health Sciences Centre Hamilton, ON, Canada
| | - Vincent So
- Department of Biochemistry and Biomedical Sciences, McMaster University Health Sciences CentreHamilton, ON, Canada; Nephrology Division and Cell Biology Program, Hospital for Sick ChildrenToronto, ON, Canada
| | - William Jennings
- Department of Biochemistry and Biomedical Sciences, McMaster University Health Sciences Centre Hamilton, ON, Canada
| | - Bijendra Khadka
- Department of Biochemistry and Biomedical Sciences, McMaster University Health Sciences Centre Hamilton, ON, Canada
| | - Radhey S Gupta
- Department of Biochemistry and Biomedical Sciences, McMaster University Health Sciences Centre Hamilton, ON, Canada
| | - Mathieu Lemaire
- Nephrology Division and Cell Biology Program, Hospital for Sick ChildrenToronto, ON, Canada; Department of Biochemistry, University of TorontoToronto, ON, Canada; Institute of Medicine, University of TorontoToronto, ON, Canada
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21
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Tu-Sekine B, Goldschmidt HL, Raben DM. DGK-θ: Structure, Enzymology, and Physiological Roles. Front Cell Dev Biol 2016; 4:101. [PMID: 27683659 PMCID: PMC5021689 DOI: 10.3389/fcell.2016.00101] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 08/29/2016] [Indexed: 12/13/2022] Open
Abstract
Diacylglycerol kinases (DGKs) are a family of enzymes that catalyze the ATP-dependent phosphorylation of diacylglycerol (DAG) to phosphatidic acid (PtdOH). The recognition of the importance of these enzymes has been increasing ever since it was determined that they played a role in the phosphatidylinositol (PtdIns) cycle and a number of excellent reviews have already been written [(see van Blitterswijk and Houssa, 2000; Kanoh et al., 2002; Mérida et al., 2008; Tu-Sekine and Raben, 2009, 2011; Shulga et al., 2011; Tu-Sekine et al., 2013) among others]. We now know there are ten mammalian DGKs that are organized into five classes. DGK-θ is the lone member of the Type V class of DGKs and remains as one of the least studied. This review focuses on our current understanding of the structure, enzymology, regulation, and physiological roles of this DGK and suggests some future areas of research to understand this DGK isoform.
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Affiliation(s)
- Becky Tu-Sekine
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine Baltimore, MD, USA
| | - Hana L Goldschmidt
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine Baltimore, MD, USA
| | - Daniel M Raben
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine Baltimore, MD, USA
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22
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Sphingosine Kinases: Emerging Structure-Function Insights. Trends Biochem Sci 2016; 41:395-409. [PMID: 27021309 DOI: 10.1016/j.tibs.2016.02.007] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 02/08/2016] [Accepted: 02/17/2016] [Indexed: 12/15/2022]
Abstract
Sphingosine kinases (SK1 and SK2) catalyse the conversion of sphingosine into sphingosine 1-phosphate and control fundamental cellular processes, including cell survival, proliferation, differentiation, migration, and immune function. In this review, we highlight recent breakthroughs in the structural and functional characterisation of SK1 and these are contextualised by analysis of crystal structures for closely related prokaryotic lipid kinases. We identify a putative dimerisation interface and propose novel regulatory mechanisms governing structural plasticity induced by phosphorylation and interaction with phospholipids and proteins. Our analysis suggests that the catalytic function and regulation of the enzymes might be dependent on conformational mobility and it provides a roadmap for future interrogation of SK1 function and its role in physiology and disease.
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23
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Pyne S, Adams DR, Pyne NJ. Sphingosine 1-phosphate and sphingosine kinases in health and disease: Recent advances. Prog Lipid Res 2016; 62:93-106. [PMID: 26970273 DOI: 10.1016/j.plipres.2016.03.001] [Citation(s) in RCA: 141] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 03/07/2016] [Accepted: 03/08/2016] [Indexed: 12/24/2022]
Abstract
Sphingosine kinases (isoforms SK1 and SK2) catalyse the formation of a bioactive lipid, sphingosine 1-phosphate (S1P). S1P is a well-established ligand of a family of five S1P-specific G protein coupled receptors but also has intracellular signalling roles. There is substantial evidence to support a role for sphingosine kinases and S1P in health and disease. This review summarises recent advances in the area in relation to receptor-mediated signalling by S1P and novel intracellular targets of this lipid. New evidence for a role of each sphingosine kinase isoform in cancer, the cardiovascular system, central nervous system, inflammation and diabetes is discussed. There is continued research to develop isoform selective SK inhibitors, summarised here. Analysis of the crystal structure of SK1 with the SK1-selective inhibitor, PF-543, is used to identify residues that could be exploited to improve selectivity in SK inhibitor development for future therapeutic application.
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Affiliation(s)
- Susan Pyne
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral St, Glasgow, G4 0RE, Scotland, UK.
| | - David R Adams
- School of Engineering & Physical Sciences, Heriot-Watt University, Edinburgh EH14 4AS, Scotland, UK.
| | - Nigel J Pyne
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral St, Glasgow, G4 0RE, Scotland, UK.
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Molecular properties of diacylglycerol kinase-epsilon in relation to function. Chem Phys Lipids 2015; 192:100-108. [PMID: 26134136 DOI: 10.1016/j.chemphyslip.2015.06.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 06/21/2015] [Indexed: 01/12/2023]
Abstract
The epsilon isoform of mammalian diacylglycerol kinase (DGKϵ) is an enzyme that associates strongly with membranes and acts on a lipid substrate, diacylglycerol. The protein has one segment that is predicted to be a transmembrane helix, but appears to interconvert between a transmembrane helix and a re-entrant helix. Despite the hydrophobicity of this segment and the fact that the lipid substrate is also hydrophobic, removal of this hydrophobic segment by truncating the protein at the amino terminus has no effect on its enzymatic activity. The amino acid sequence of the catalytic segment of DGKϵ is highly homologous to that of a bacterial DGK, DgkB. This has allowed us to predict a conformation of DGKϵ based on the known crystal structure of DgkB. An important property of DGKϵ is that it is specific for diacylglycerol species containing an arachidonoyl group. The region of DGKϵ that interacts with this group is found within the accessory domain of the protein and not in the active site nor in the hydrophobic amino terminus. The nature of the acyl chain specificity of the enzyme indicates that DGKϵ is associated with the synthesis of phosphatidylinositol. Defects or deletion of the enzyme give rise to several disease states.
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25
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Kuhn S, Slavetinsky CJ, Peschel A. Synthesis and function of phospholipids in Staphylococcus aureus. Int J Med Microbiol 2014; 305:196-202. [PMID: 25595024 DOI: 10.1016/j.ijmm.2014.12.016] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Abstract
Phospholipids are the major components of bacterial membranes, and changes in phospholipid composition affect important cellular processes such as metabolism, stress response, antimicrobial resistance, and virulence. The most prominent phospholipids in Staphylococcus aureus are phosphatidylglycerol, lysyl-phosphatidylglycerol, and cardiolipin, whose biosynthesis is mediated by a complex protein machinery. Phospholipid composition of the staphylococcal membrane has to be continuously adjusted to changing external conditions, which is achieved by a series of transcriptional and biochemical regulatory mechanisms. This mini-review outlines the current state of knowledge concerning synthesis, regulation, and function of the major staphylococcal phospholipids.
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Affiliation(s)
- Sebastian Kuhn
- University of Tübingen, Interfaculty Institute of Microbiology and Infection Medicine, Cellular and Molecular Microbiology Division, Elfriede-Aulhorn-Strasse 6, 72076 Tübingen, Germany
| | - Christoph J Slavetinsky
- University of Tübingen, Interfaculty Institute of Microbiology and Infection Medicine, Cellular and Molecular Microbiology Division, Elfriede-Aulhorn-Strasse 6, 72076 Tübingen, Germany
| | - Andreas Peschel
- University of Tübingen, Interfaculty Institute of Microbiology and Infection Medicine, Cellular and Molecular Microbiology Division, Elfriede-Aulhorn-Strasse 6, 72076 Tübingen, Germany.
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26
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Percy MG, Gründling A. Lipoteichoic Acid Synthesis and Function in Gram-Positive Bacteria. Annu Rev Microbiol 2014; 68:81-100. [DOI: 10.1146/annurev-micro-091213-112949] [Citation(s) in RCA: 266] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Matthew G. Percy
- Section of Microbiology and MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, SW7 2AZ UK; ,
| | - Angelika Gründling
- Section of Microbiology and MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, SW7 2AZ UK; ,
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Abstract
Sphingosine-1-phosphate is a potent sphingolipid mediator, and the kinase that produces it, sphingosine kinase 1 (SphK1), has been implicated in cancer progression, inflammation, and cardiovascular diseases. In this issue of Structure, Wang and colleagues provide the scientific community with the long awaited structure of SphK1.
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Wu WL, Liao JH, Lin GH, Lin MH, Chang YC, Liang SY, Yang FL, Khoo KH, Wu SH. Phosphoproteomic analysis reveals the effects of PilF phosphorylation on type IV pilus and biofilm formation in Thermus thermophilus HB27. Mol Cell Proteomics 2013; 12:2701-13. [PMID: 23828892 DOI: 10.1074/mcp.m113.029330] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Thermus thermophilus HB27 is an extremely thermophilic eubacteria with a high frequency of natural competence. This organism is therefore often used as a thermophilic model to investigate the molecular basis of type IV pili-mediated functions, such as the uptake of free DNA, adhesion, twitching motility, and biofilm formation, in hot environments. In this study, the phosphoproteome of T. thermophilus HB27 was analyzed via a shotgun approach and high-accuracy mass spectrometry. Ninety-three unique phosphopeptides, including 67 in vivo phosphorylated sites on 53 phosphoproteins, were identified. The distribution of Ser/Thr/Tyr phosphorylation sites was 57%/36%/7%. The phosphoproteins were mostly involved in central metabolic pathways and protein/cell envelope biosynthesis. According to this analysis, the ATPase motor PilF, a type IV pili-related component, was first found to be phosphorylated on Thr-368 and Ser-372. Through the point mutation of PilF, mimic phosphorylated mutants T368D and S372E resulted in nonpiliated and nontwitching phenotypes, whereas nonphosphorylated mutants T368V and S372A displayed piliation and twitching motility. In addition, mimic phosphorylated mutants showed elevated biofilm-forming abilities with a higher initial attachment rate, caused by increasing exopolysaccharide production. In summary, the phosphorylation of PilF might regulate the pili and biofilm formation associated with exopolysaccharide production.
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Affiliation(s)
- Wan-Ling Wu
- Institute of Biochemical Sciences, College of Life Sciences, National Taiwan University, Taipei 106, Taiwan
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29
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Parsons JB, Rock CO. Bacterial lipids: metabolism and membrane homeostasis. Prog Lipid Res 2013; 52:249-76. [PMID: 23500459 PMCID: PMC3665635 DOI: 10.1016/j.plipres.2013.02.002] [Citation(s) in RCA: 298] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Revised: 02/27/2013] [Accepted: 02/28/2013] [Indexed: 11/29/2022]
Abstract
Membrane lipid homeostasis is a vital facet of bacterial cell physiology. For decades, research in bacterial lipid synthesis was largely confined to the Escherichia coli model system. This basic research provided a blueprint for the biochemistry of lipid metabolism that has largely defined the individual steps in bacterial fatty acid and phospholipids synthesis. The advent of genomic sequencing has revealed a surprising amount of diversity in the genes, enzymes and genetic organization of the components responsible for bacterial lipid synthesis. Although the chemical steps in fatty acid synthesis are largely conserved in bacteria, there are surprising differences in the structure and cofactor requirements for the enzymes that perform these reactions in Gram-positive and Gram-negative bacteria. This review summarizes how the explosion of new information on the diversity of biochemical and genetic regulatory mechanisms has impacted our understanding of bacterial lipid homeostasis. The potential and problems of developing therapeutics that block pathogen phospholipid synthesis are explored and evaluated. The study of bacterial lipid metabolism continues to be a rich source for new biochemistry that underlies the variety and adaptability of bacterial life styles.
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Affiliation(s)
- Joshua B Parsons
- Department of Infectious Diseases, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
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30
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Wang Z, Min X, Xiao SH, Johnstone S, Romanow W, Meininger D, Xu H, Liu J, Dai J, An S, Thibault S, Walker N. Molecular basis of sphingosine kinase 1 substrate recognition and catalysis. Structure 2013; 21:798-809. [PMID: 23602659 DOI: 10.1016/j.str.2013.02.025] [Citation(s) in RCA: 144] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Revised: 02/05/2013] [Accepted: 02/28/2013] [Indexed: 11/24/2022]
Abstract
Sphingosine kinase 1 (SphK1) is a lipid kinase that catalyzes the conversion of sphingosine to sphingosine-1-phosphate (S1P), which has been shown to play a role in lymphocyte trafficking, angiogenesis, and response to apoptotic stimuli. As a central enzyme in modulating the S1P levels in cells, SphK1 emerges as an important regulator for diverse cellular functions and a potential target for drug discovery. Here, we present the crystal structures of human SphK1 in the apo form and in complexes with a substrate sphingosine-like lipid, ADP, and an inhibitor at 2.0-2.3 Å resolution. The SphK1 structures reveal a two-domain architecture in which its catalytic site is located in the cleft between the two domains and a hydrophobic lipid-binding pocket is buried in the C-terminal domain. Comparative analysis of these structures with mutagenesis and kinetic studies provides insight into how SphK1 recognizes the lipid substrate and catalyzes ATP-dependent phosphorylation.
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Affiliation(s)
- Zhulun Wang
- Department of Molecular Structure and Characterization, Amgen, Inc., 1120 Veterans Boulevard, South San Francisco, CA 94080, USA.
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31
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Petro EJ, Raben DM. Bacterial expression strategies for several Sus scrofa diacylglycerol kinase alpha constructs: solubility challenges. Sci Rep 2013; 3:1609. [PMID: 23558375 PMCID: PMC3617429 DOI: 10.1038/srep01609] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Accepted: 03/19/2013] [Indexed: 01/27/2023] Open
Abstract
We pursued several strategies for expressing either full-length Sus scrofa diacylglycerol kinase (DGK) alpha or the catalytic domain (alphacat) in Escherichia coli. Alphacat could be extracted, refolded, and purified from inclusion bodies, but when subjected to analytical gel filtration chromatography, it elutes in the void volume, in what we conclude are microscopic aggregates unsuitable for x-ray crystallography. Adding glutathione S-transferase, thioredoxin, or maltose binding protein as N-terminal fusion tags did not improve alphacat's solubility. Coexpressing with bacterial chaperones increased the yield of alphacat in the supernatant after high-speed centrifugation, but the protein still elutes in the void upon analytical gel filtration chromatography. We believe our work will be of interest to those interested in the structure of eukaryotic DGKs, so that they know which expression strategies have already been tried, as well as to those interested in protein folding and those interested in chaperone/target-protein interactions.
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Affiliation(s)
- Elizabeth J. Petro
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD
| | - Daniel M. Raben
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD
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32
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The basis of the substrate specificity of the epsilon isoform of human diacylglycerol kinase is not a consequence of competing hydrolysis of ATP. Chem Phys Lipids 2012; 166:26-30. [PMID: 23261795 DOI: 10.1016/j.chemphyslip.2012.11.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Revised: 11/08/2012] [Accepted: 11/21/2012] [Indexed: 01/11/2023]
Abstract
The diacylglycerol kinase from E. coli transfers some of the γ-phosphate of ATP to water as well as to diacylglycerol. We also demonstrate that glycerol can act as an acceptor for the phosphate of ATP. We have compared this behavior with that of the only mammalian isoform of diacylglycerol kinase that exhibits acyl chain specificity, i.e. DGKɛ. The purpose of the study was to determine if differences in the competition between ATPase activity and lipid phosphorylation could contribute to the observed acyl chain specificity with different diacylglycerols. Neither with the highly specific substrate of DGKɛ, 1-stearoyl-2-arachidonoyl glycerol, nor with a less specific substrate, 1-stearoyl-2-linoleoyl glycerol, is there any evidence for ATP hydrolysis accompanying substrate phosphorylation. Thus, at least for this isoform of diacylglycerol kinase, water does not compete with diacylglycerol as an acceptor of the γ-phosphate of ATP. The results demonstrate that the substrate specificity of mammalian DGKɛ is not a consequence of different degrees of ATP hydrolysis in the presence of different species of diacylglycerol.
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33
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Tu-Sekine B, Goldschmidt H, Petro E, Raben DM. Diacylglycerol kinase θ: regulation and stability. Adv Biol Regul 2012; 53:118-26. [PMID: 23266086 DOI: 10.1016/j.jbior.2012.09.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Accepted: 09/10/2012] [Indexed: 10/27/2022]
Abstract
Given the well-established roles of diacylglycerol (DAG) and phosphatidic acid (PtdOH) in a variety of signaling cascades, it is not surprising that there is an increasing interest in understanding their physiological roles and mechanisms that regulate their cellular levels. One class of enzymes capable of coordinately regulating the levels of these two lipids is the diacylglycerol kinases (DGKs). These enzymes catalyze the transfer of the γ-phosphate of ATP to the hydroxyl group of DAG, which generates PtdOH while reducing DAG. As these enzymes reciprocally modulate the relative levels of these two signaling lipids, it is essential to understand the regulation and roles of these enzymes in various tissues. One system where these enzymes play important roles is the nervous system. Of the ten mammalian DGKs, eight of them are readily detected in the mammalian central nervous system (CNS): DGK-α, DGK-β, DGK-γ, DGK-η, DGK-ζ, DGK-ι, DGK-ε, and DGK-θ. Despite the increasing interest in DGKs, little is known about their regulation. We have focused some attention on understanding the enzymology and regulation of one of these DGK isoforms, DGK-θ. We recently showed that DGK-θ is regulated by an accessory protein containing polybasic regions. We now report that this accessory protein is required for the previously reported broadening of the pH profile observed in cell lysates in response to phosphatidylserine (PtdSer). Our data further reveal DGK-θ is regulated by magnesium and zinc, and sensitive to the known DGK inhibitor R599022. These data outline new parameters involved in regulating DGK-θ.
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Affiliation(s)
- Becky Tu-Sekine
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205-2185, USA
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34
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Baker DL, Pham TCT, Sparks MA. Structure and catalytic function of sphingosine kinases: analysis by site-directed mutagenesis and enzyme kinetics. Biochim Biophys Acta Mol Cell Biol Lipids 2012; 1831:139-46. [PMID: 23000541 DOI: 10.1016/j.bbalip.2012.09.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Revised: 09/12/2012] [Accepted: 09/13/2012] [Indexed: 12/17/2022]
Abstract
Sphingosine kinases 1 and 2 (SK1 and SK2) generate the bioactive lipid mediator sphingosine 1-phosphate and as such play a significant role in cell fate and in human health and disease. Despite significant interest in and examination of the role played by SK enzymes in disease, comparatively little is currently known about the three-dimensional structure and catalytic mechanisms of these enzymes. To date, limited numbers of studies have used site directed mutagenesis and activity determinations to examine the roles of individual SK residues in substrate, calmodulin, and membrane binding, as well as activation via phosphorylation. Assays are currently available that allow for both single and bisubstrate kinetic analysis of mutant proteins that show normal, lowered and enhanced activity as compared to wild type controls. Additional studies will be required to build on this foundation to completely understand SK mediated substrate binding and phosphoryl group transfer. A deeper understanding of the SK catalytic mechanism, as well as SK interactions with potential small molecule inhibitors will be invaluable to the future design and identification of SK activity modulators as research tools and potential therapeutics. This article is part of a Special Issue entitled Advances in Lysophospholipid Research.
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Affiliation(s)
- Daniel L Baker
- Department of Chemistry, University of Memphis, Memphis, TN 38152, USA.
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35
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Phosphatidic acid synthesis in bacteria. Biochim Biophys Acta Mol Cell Biol Lipids 2012; 1831:495-502. [PMID: 22981714 DOI: 10.1016/j.bbalip.2012.08.018] [Citation(s) in RCA: 124] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2012] [Revised: 08/21/2012] [Accepted: 08/23/2012] [Indexed: 12/15/2022]
Abstract
Membrane phospholipid synthesis is a vital facet of bacterial physiology. Although the spectrum of phospholipid headgroup structures produced by bacteria is large, the key precursor to all of these molecules is phosphatidic acid (PtdOH). Glycerol-3-phosphate derived from the glycolysis via glycerol-phosphate synthase is the universal source for the glycerol backbone of PtdOH. There are two distinct families of enzymes responsible for the acylation of the 1-position of glycerol-3-phosphate. The PlsB acyltransferase was discovered in Escherichia coli, and homologs are present in many eukaryotes. This protein family primarily uses acyl-acyl carrier protein (ACP) endproducts of fatty acid synthesis as acyl donors, but may also use acyl-CoA derived from exogenous fatty acids. The second protein family, PlsY, is more widely distributed in bacteria and utilizes the unique acyl donor, acyl-phosphate, which is produced from acyl-ACP by the enzyme PlsX. The acylation of the 2-position is carried out by members of the PlsC protein family. All PlsCs use acyl-ACP as the acyl donor, although the PlsCs of the γ-proteobacteria also may use acyl-CoA. Phospholipid headgroups are precursors in the biosynthesis of other membrane-associated molecules and the diacylglycerol product of these reactions is converted to PtdOH by one of two distinct families of lipid kinases. The central importance of the de novo and recycling pathways to PtdOH in cell physiology suggest that these enzymes are suitable targets for the development of antibacterial therapeutics in Gram-positive pathogens. This article is part of a Special Issue entitled Phospholipids and Phospholipid Metabolism.
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36
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Crystal structure of LpxK, the 4'-kinase of lipid A biosynthesis and atypical P-loop kinase functioning at the membrane interface. Proc Natl Acad Sci U S A 2012; 109:12956-61. [PMID: 22826246 DOI: 10.1073/pnas.1206072109] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
In Gram-negative bacteria, the hydrophobic anchor of the outer membrane lipopolysaccharide is lipid A, a saccharolipid that plays key roles in both viability and pathogenicity of these organisms. The tetraacyldisaccharide 4'-kinase (LpxK) of the diverse P-loop-containing nucleoside triphosphate hydrolase superfamily catalyzes the sixth step in the biosynthetic pathway of lipid A, and is the only known P-loop kinase to act upon a lipid substrate at the membrane. Here, we report the crystal structures of apo- and ADP/Mg(2+)-bound forms of Aquifex aeolicus LpxK to a resolution of 1.9 Å and 2.2 Å, respectively. LpxK consists of two α/β/α sandwich domains connected by a two-stranded β-sheet linker. The N-terminal domain, which has most structural homology to other family members, is responsible for catalysis at the P-loop and positioning of the disaccharide-1-phosphate substrate for phosphoryl transfer on the inner membrane. The smaller C-terminal domain, a substructure unique to LpxK, helps bind the nucleotide substrate and Mg(2+) cation using a 25° hinge motion about its base. Activity was severely reduced in alanine point mutants of conserved residues D138 and D139, which are not directly involved in ADP or Mg(2+) binding in our structures, indicating possible roles in phosphoryl acceptor positioning or catalysis. Combined structural and kinetic studies have led to an increased understanding of the enzymatic mechanism of LpxK and provided the framework for structure-based antimicrobial design.
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Lim KG, Tonelli F, Berdyshev E, Gorshkova I, Leclercq T, Pitson SM, Bittman R, Pyne S, Pyne NJ. Inhibition kinetics and regulation of sphingosine kinase 1 expression in prostate cancer cells: functional differences between sphingosine kinase 1a and 1b. Int J Biochem Cell Biol 2012; 44:1457-64. [PMID: 22634604 DOI: 10.1016/j.biocel.2012.05.012] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2012] [Revised: 05/02/2012] [Accepted: 05/15/2012] [Indexed: 11/24/2022]
Abstract
Sphingosine kinase 1 catalyses the formation of the bioactive lipid, sphingosine 1-phosphate and is a target for anti-cancer agents. We demonstrate here that 2-(p-hydroxyanilino)-4-(p-chlorophenyl)thiazole (SKi, also referred to as SKI-II), FTY720 (Fingolimod), and (S)-FTY720 vinylphosphonate inhibit sphingosine kinase 1 activity with distinct kinetics, indicating that these compounds exhibit different binding modalities with sphingosine kinase 1. Thus, SKi is a mixed inhibitor of sphingosine and ATP binding, whereas FTY720 is competitive with sphingosine and uncompetitive with ATP, and (S)-FTY720 vinylphosphonate is uncompetitive with sphingosine and is a mixed inhibitor with respect to ATP. A novel 'see-saw' model is proposed for the binding of inhibitor to catalytic and allosteric sites, the latter dependent on substrate binding, that provides an explanation for the different inhibitor kinetics. In addition, we demonstrate that the expression level and properties unique to an N-terminal 86 amino-acid isoform variant of sphingosine kinase 1 (SK1b) in prostate cancer cells reduce its sensitivity to SKi-induced proteasomal degradation in comparison to SK1a, i.e. these two N-terminal variants of sphingosine kinase 1 (SK1a and SK1b) have different properties. The reduced sensitivity of SK1b to proteasomal degradation in response to SKi is translated into specific changes in ceramide and S1P levels that leads to apoptosis of androgen-sensitive but not androgen-independent LNCaP prostate cancer cells. Therefore, our proposed 'see-saw' model might be usefully employed in the design of sphingosine kinase inhibitors to promote apoptosis of chemotherapeutic resistant cancer cells.
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Affiliation(s)
- Keng Gat Lim
- Strathclyde Institute of Pharmacy and Biomedical Science, University of Strathclyde, Glasgow, UK
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38
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Abstract
Prokaryotic diacylglycerol kinase (DAGK) and undecaprenol kinase (UDPK) are the lone members of a family of multispan membrane enzymes that are very small, lack relationships to any other family of proteins-including water soluble kinases-and exhibit an unusual structure and active site architecture. Escherichia coli DAGK plays an important role in recycling diacylglycerol produced as a by-product of biosynthesis of molecules located in the periplasmic space. UDPK seems to play an analogous role in gram-positive bacteria, where its importance is evident because UDPK is essential for biofilm formation by the oral pathogen Streptococcus mutans. DAGK has also long served as a model system for studies of membrane protein biocatalysis, folding, stability, and structure. This review explores our current understanding of the microbial physiology, enzymology, structural biology, and folding of the prokaryotic DAGK family, which is based on over 40 years of studies.
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Affiliation(s)
- Wade D Van Horn
- Department of Biochemistry and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232, USA
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39
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Shaping up the membrane: diacylglycerol coordinates spatial orientation of signaling. Trends Biochem Sci 2011; 36:593-603. [PMID: 21798744 DOI: 10.1016/j.tibs.2011.06.005] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2011] [Revised: 06/21/2011] [Accepted: 06/23/2011] [Indexed: 11/23/2022]
Abstract
Diacylglycerol signals by binding and activating C1 domain-containing proteins expressed principally in neuronal and immune tissues. This restricted expression profile suggests that diacylglycerol-regulated signals are particularly relevant in cell-cell communication processes in which active endocytosis and exocytosis take place. Not surprisingly, various experimental approaches have demonstrated a crucial role for diacylglycerol effectors and metabolizing enzymes in the control of immune responses, neuron communication and phagocytosis. Current research delineates a scenario in which coordinated decoding of diacylglycerol signals is translated into complex biological responses such as neuronal plasticity, T cell development or cytolytic killing. Diacylglycerol functions reach maximal diversity in these highly specialized systems in which signal intensity directly regulates distinct biological outcomes. This review brings together the most recent studies, emphasizing the contribution of compartmentalized DAG metabolism to orientated signaling events.
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40
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Kennedy AJ, Mathews TP, Kharel Y, Field SD, Moyer ML, East JE, Houck JD, Lynch KR, Macdonald TL. Development of amidine-based sphingosine kinase 1 nanomolar inhibitors and reduction of sphingosine 1-phosphate in human leukemia cells. J Med Chem 2011; 54:3524-48. [PMID: 21495716 DOI: 10.1021/jm2001053] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Sphingosine 1-phosphate (S1P) is a bioactive lipid that has been identified as an accelerant of cancer progression. The sphingosine kinases (SphKs) are the sole producers of S1P, and thus, SphK inhibitors may prove effective in cancer mitigation and chemosensitization. Of the two SphKs, SphK1 overexpression has been observed in a myriad of cancer cell lines and tissues and has been recognized as the presumptive target over that of the poorly characterized SphK2. Herein, we present the design and synthesis of amidine-based nanomolar SphK1 subtype-selective inhibitors. A homology model of SphK1, trained with this library of amidine inhibitors, was then used to predict the activity of additional, more potent, inhibitors. Lastly, select amidine inhibitors were validated in human leukemia U937 cells, where they significantly reduced endogenous S1P levels at nanomolar concentrations.
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Affiliation(s)
- Andrew J Kennedy
- Department of Chemistry, University of Virginia, McCormick Road, Charlottesville, Virginia 22904, United States.
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41
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Pitson SM. Regulation of sphingosine kinase and sphingolipid signaling. Trends Biochem Sci 2011; 36:97-107. [DOI: 10.1016/j.tibs.2010.08.001] [Citation(s) in RCA: 217] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2010] [Revised: 08/16/2010] [Accepted: 08/16/2010] [Indexed: 01/09/2023]
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Ramboarina S, Garnett JA, Zhou M, Li Y, Peng Z, Taylor JD, Lee WC, Bodey A, Murray JW, Alguel Y, Bergeron J, Bardiaux B, Sawyer E, Isaacson R, Tagliaferri C, Cota E, Nilges M, Simpson P, Ruiz T, Wu H, Matthews S. Structural insights into serine-rich fimbriae from Gram-positive bacteria. J Biol Chem 2010; 285:32446-57. [PMID: 20584910 PMCID: PMC2952246 DOI: 10.1074/jbc.m110.128165] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2010] [Revised: 06/25/2010] [Indexed: 11/06/2022] Open
Abstract
The serine-rich repeat family of fimbriae play important roles in the pathogenesis of streptococci and staphylococci. Despite recent attention, their finer structural details and precise adhesion mechanisms have yet to be determined. Fap1 (Fimbriae-associated protein 1) is the major structural subunit of serine-rich repeat fimbriae from Streptococcus parasanguinis and plays an essential role in fimbrial biogenesis, adhesion, and the early stages of dental plaque formation. Combining multidisciplinary, high resolution structural studies with biological assays, we provide new structural insight into adhesion by Fap1. We propose a model in which the serine-rich repeats of Fap1 subunits form an extended structure that projects the N-terminal globular domains away from the bacterial surface for adhesion to the salivary pellicle. We also uncover a novel pH-dependent conformational change that modulates adhesion and likely plays a role in survival in acidic environments.
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Affiliation(s)
- Stéphanie Ramboarina
- From the Department of Biological Sciences, Centre for Structural Biology, Imperial College London, South Kensington, London SW7 2AZ, United Kingdom
| | - James A. Garnett
- From the Department of Biological Sciences, Centre for Structural Biology, Imperial College London, South Kensington, London SW7 2AZ, United Kingdom
| | - Meixian Zhou
- the Department of Pediatric Dentistry, University of Alabama at Birmingham, Birmingham, Alabama 35294-0007
| | - Yuebin Li
- the Department of Pediatric Dentistry, University of Alabama at Birmingham, Birmingham, Alabama 35294-0007
| | - Zhixiang Peng
- the Department of Pediatric Dentistry, University of Alabama at Birmingham, Birmingham, Alabama 35294-0007
| | - Jonathan D. Taylor
- From the Department of Biological Sciences, Centre for Structural Biology, Imperial College London, South Kensington, London SW7 2AZ, United Kingdom
| | - Wei-chao Lee
- From the Department of Biological Sciences, Centre for Structural Biology, Imperial College London, South Kensington, London SW7 2AZ, United Kingdom
| | - Andrew Bodey
- From the Department of Biological Sciences, Centre for Structural Biology, Imperial College London, South Kensington, London SW7 2AZ, United Kingdom
| | - James W. Murray
- From the Department of Biological Sciences, Centre for Structural Biology, Imperial College London, South Kensington, London SW7 2AZ, United Kingdom
| | - Yilmaz Alguel
- From the Department of Biological Sciences, Centre for Structural Biology, Imperial College London, South Kensington, London SW7 2AZ, United Kingdom
| | - Julien Bergeron
- From the Department of Biological Sciences, Centre for Structural Biology, Imperial College London, South Kensington, London SW7 2AZ, United Kingdom
- the Department of Infectious Diseases, King's College London School of Medicine, London SE1 9RT, United Kingdom
| | - Benjamin Bardiaux
- the Structural Biology Unit, Leibniz Institute for Molecular Pharmacology, FMP Robert-Rossle Strasse 10, 13125 Berlin, Germany
| | - Elizabeth Sawyer
- From the Department of Biological Sciences, Centre for Structural Biology, Imperial College London, South Kensington, London SW7 2AZ, United Kingdom
| | - Rivka Isaacson
- From the Department of Biological Sciences, Centre for Structural Biology, Imperial College London, South Kensington, London SW7 2AZ, United Kingdom
| | - Camille Tagliaferri
- From the Department of Biological Sciences, Centre for Structural Biology, Imperial College London, South Kensington, London SW7 2AZ, United Kingdom
| | - Ernesto Cota
- From the Department of Biological Sciences, Centre for Structural Biology, Imperial College London, South Kensington, London SW7 2AZ, United Kingdom
| | - Michael Nilges
- the Institut Pasteur Unité de Bioinformatique Structurale, 25-28 Rue du Dr Roux, F-75724 Paris Cedex 15, France, and
| | - Peter Simpson
- From the Department of Biological Sciences, Centre for Structural Biology, Imperial College London, South Kensington, London SW7 2AZ, United Kingdom
| | - Teresa Ruiz
- the Department of Molecular Physiology and Biophysics, University of Vermont, Burlington, Vermont 05405
| | - Hui Wu
- the Department of Pediatric Dentistry, University of Alabama at Birmingham, Birmingham, Alabama 35294-0007
| | - Stephen Matthews
- From the Department of Biological Sciences, Centre for Structural Biology, Imperial College London, South Kensington, London SW7 2AZ, United Kingdom
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Mérida I, Avila-Flores A, García J, Merino E, Almena M, Torres-Ayuso P. Diacylglycerol kinase alpha, from negative modulation of T cell activation to control of cancer progression. ACTA ACUST UNITED AC 2009; 49:174-88. [PMID: 19534031 DOI: 10.1016/j.advenzreg.2009.01.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Isabel Mérida
- Department of Immunology and Oncology, Centro Nacional de Biotecnología/CSIC, Darwin 3, Campus de Cantoblanco, E-28049 Madrid, Spain.
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Van Horn WD, Kim HJ, Ellis CD, Hadziselimovic A, Sulistijo ES, Karra MD, Tian C, Sönnichsen FD, Sanders CR. Solution nuclear magnetic resonance structure of membrane-integral diacylglycerol kinase. Science 2009; 324:1726-9. [PMID: 19556511 PMCID: PMC2764269 DOI: 10.1126/science.1171716] [Citation(s) in RCA: 186] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Escherichia coli diacylglycerol kinase (DAGK) represents a family of integral membrane enzymes that is unrelated to all other phosphotransferases. We have determined the three-dimensional structure of the DAGK homotrimer with the use of solution nuclear magnetic resonance. The third transmembrane helix from each subunit is domain-swapped with the first and second transmembrane segments from an adjacent subunit. Each of DAGK's three active sites resembles a portico. The cornice of the portico appears to be the determinant of DAGK's lipid substrate specificity and overhangs the site of phosphoryl transfer near the water-membrane interface. Mutations to cysteine that caused severe misfolding were located in or near the active site, indicating a high degree of overlap between sites responsible for folding and for catalysis.
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Affiliation(s)
- Wade D. Van Horn
- Dept. of Biochemistry and Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Hak-Jun Kim
- Dept. of Biochemistry and Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
- Korea Polar Research Institute, Incheon, 406-840, Korea
| | - Charles D. Ellis
- Dept. of Biochemistry and Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Arina Hadziselimovic
- Dept. of Biochemistry and Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Endah S. Sulistijo
- Dept. of Biochemistry and Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Murthy D. Karra
- Dept. of Biochemistry and Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Changlin Tian
- Dept. of Biochemistry and Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
- School of Life Science, University of Science and Technology of China, Hefei, Anhui, 230026, P. R. China
| | - Frank D. Sönnichsen
- Otto Diels Institute for Organic Chemistry, Christian Albrechts University of Kiel, Germany
| | - Charles R. Sanders
- Dept. of Biochemistry and Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
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Jerga A, Miller DJ, White SW, Rock CO. Molecular determinants for interfacial binding and conformational change in a soluble diacylglycerol kinase. J Biol Chem 2008; 284:7246-54. [PMID: 19112175 DOI: 10.1074/jbc.m805962200] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
DgkB is a soluble diacylglycerol (DAG) kinase that is essential for membrane lipid homeostasis in many Gram-positive pathogens. Anionic phospholipids, like phosphatidylglycerol (PtdGro), were required for DgkB to recognize diacylglycerol embedded in a phospholipid bilayer. An activity-independent vesicle binding assay was used to determine the role of specific residues in DgkB-PtdGro interactions. Lys15 and Lys165 were required for DgkB to dock with PtdGro vesicles and flank the entrance to the DgkB active site. Mg2+ was required for vesicle binding. The compromised vesicle binding by mutants in the key asparate residues forming the structural Mg2+-aspartate-water network within the substrate binding domain revealed that interfacial binding of DgkB required a Mg2+-dependent conformational change. DgkB interaction with phospholipid vesicles was not influenced by the presence of ATP, but anionic vesicles decreased the Km of the enzyme for ATP. Arg100 and Lys15 are two surface residues in the ATP binding domain that were necessary for high affinity ATP binding. The key residues responsible for the structural Mg2+ binding site, the conformational changes that increase ATP affinity, and interfacial recognition of anionic phospholipids were identical in DgkB and the mammalian diacylglycerol kinase catalytic cores. This sequence conservation suggests that the mammalian enzymes also require a structural divalent cation and surface positively charged residues to bind phospholipid bilayers and trigger conformational changes that accelerate catalysis.
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Affiliation(s)
- Agoston Jerga
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
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46
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Raben DM, Wattenberg BW. Signaling at the membrane interface by the DGK/SK enzyme family. J Lipid Res 2008; 50 Suppl:S35-9. [PMID: 19066401 DOI: 10.1194/jlr.r800071-jlr200] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The sphingosine (SK) and diacylglycerol (DGK) kinases have become the subject of considerable focus recently due to their involvement as signaling enzymes in a variety of important biological processes. These lipid signaling kinases are closely related by sequence as well as functional properties. These enzymes are soluble, yet their substrates are hydrophobic. Therefore, they must act at the membrane interface. Second, for both of these enzyme families, their substrates (diacylglycerol for DGKs, sphingosine for SKs) as well as their products (phosphatidic acid for DGK, sphingosine-1-phosphate for SK) have signaling function. To understand how the signaling processes emanating from these kinases are regulated it is critical to understand the fundamental mechanisms that control their enzymatic activity. This is particularly true for the rational design of small molecules that would be useful as therapeutic compounds. Here we summarize enzymological properties of the diacylglycerol and SKs. Further, because the three-dimensional structure of the eukaryotic members of this family has yet to be determined, we discuss what can be gleaned from the recently reported structures of related prokaryotic members of this enzyme family.
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Affiliation(s)
- Daniel M Raben
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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