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Kuźniewska A, Thiel M, Kowalska D, Felberg-Miętka A, Szynkowski P, Ołdziej S, Arjona E, Jongerius I, Rodriguez de Córdoba S, Okrój M, Urban A. Substitutions at position 263 within the von Willebrand factor type A domain determine the functionality of complement C2 protein. Front Immunol 2022; 13:1061696. [PMID: 36591303 PMCID: PMC9797810 DOI: 10.3389/fimmu.2022.1061696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 11/28/2022] [Indexed: 12/23/2022] Open
Abstract
The complement system is one of the first defense lines protecting from invading pathogens. However, it may turn offensive to the body's own cells and tissues when deregulated by the presence of rare genetic variants that impair physiological regulation and/or provoke abnormal activity of key enzymatic components. Factor B and complement C2 are examples of paralogs engaged in the alternative and classical/lectin complement pathway, respectively. Pathogenic mutations in the von Willebrand factor A domain (vWA) of FB have been known for years. Despite substantial homology between two proteins and the demonstration that certain substitutions in FB translated to C2 result in analogous phenotype, there was a limited number of reports on pathogenic C2 variants in patients. Recently, we studied a cohort of patients suffering from rare kidney diseases and confirmed the existence of two gain-of-function and three loss-of-function mutations within the C2 gene sequences coding for the vWA domain (amino acids 254-452) or nearly located unstructured region (243-253) of C2 protein. Herein, we report the functional consequences of amino acid substitution of glutamine at position 263. The p.Q263G variant resulted in the gain-of-function phenotype, similarly to a homologous mutation p.D279G in FB. Conversely, the p.Q263P variant found in a patient with C3 glomerulopathy resulted in the loss of C2 function. Our results confirm that the N-terminal part of the vWA domain is a hot spot crucial for the complement C2 function.
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Affiliation(s)
- Alicja Kuźniewska
- Department of Cell Biology and Immunology, Intercollegiate Faculty of Biotechnology of University of Gdańsk and Medical University of Gdańsk, Gdańsk, Poland
| | - Marcel Thiel
- Department of Cell Biology and Immunology, Intercollegiate Faculty of Biotechnology of University of Gdańsk and Medical University of Gdańsk, Gdańsk, Poland
| | - Daria Kowalska
- Department of Cell Biology and Immunology, Intercollegiate Faculty of Biotechnology of University of Gdańsk and Medical University of Gdańsk, Gdańsk, Poland
| | - Anna Felberg-Miętka
- Department of Cell Biology and Immunology, Intercollegiate Faculty of Biotechnology of University of Gdańsk and Medical University of Gdańsk, Gdańsk, Poland
| | - Patryk Szynkowski
- Department of Cell Biology and Immunology, Intercollegiate Faculty of Biotechnology of University of Gdańsk and Medical University of Gdańsk, Gdańsk, Poland
| | - Stanisław Ołdziej
- Department of Cell Biology and Immunology, Intercollegiate Faculty of Biotechnology of University of Gdańsk and Medical University of Gdańsk, Gdańsk, Poland
| | - Emilia Arjona
- Department of Molecular Biomedicine, Centro de Investigaciones Biológicas and Centro de Investigación Biomédica en Enfermedades Raras, Madrid, Spain
| | - Ilse Jongerius
- Department of Pediatric Immunology, Rheumatology, and Infectious Diseases, Emma Children’s Hospital, Amsterdam University Medical Centre, Amsterdam, Netherlands,Department of Immunopathology, Sanquin Research, Landsteiner Laboratory, Amsterdam University Medical Centers (UMC), University of Amsterdam, Amsterdam, Netherlands
| | - Santiago Rodriguez de Córdoba
- Department of Molecular Biomedicine, Centro de Investigaciones Biológicas and Centro de Investigación Biomédica en Enfermedades Raras, Madrid, Spain
| | - Marcin Okrój
- Department of Cell Biology and Immunology, Intercollegiate Faculty of Biotechnology of University of Gdańsk and Medical University of Gdańsk, Gdańsk, Poland,*Correspondence: Marcin Okrój,
| | - Aleksandra Urban
- Department of Cell Biology and Immunology, Intercollegiate Faculty of Biotechnology of University of Gdańsk and Medical University of Gdańsk, Gdańsk, Poland,Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
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Nakatani M, Nakahara SY, Fukui K, Urano M, Fujii Y, Murakawa T, Baba S, Kumasaka T, Okanishi H, Kanai Y, Yano T, Masui R. Crystal structure of a nucleotide-binding domain of fatty acid kinase FakA from Thermus thermophilus HB8. J Struct Biol 2022; 214:107904. [PMID: 36228973 DOI: 10.1016/j.jsb.2022.107904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/26/2022] [Accepted: 10/04/2022] [Indexed: 12/04/2022]
Abstract
Fatty acid kinase is necessary for the incorporation of exogenous fatty acids into membrane phospholipids. Fatty acid kinase consists of two components: a kinase component, FakA, that phosphorylates a fatty acid bound to a fatty acid-binding component, FakB. However, the molecular details underlying the phosphotransfer reaction remain to be resolved. We determined the crystal structure of the N-terminal domain of FakA bound to ADP from Thermus thermophilus HB8. The overall structure of this domain showed that the helical barrel fold is similar to the nucleotide-binding component of dihydroxyacetone kinase. The structure of the nucleotide-binding site revealed the roles of the conserved residues in recognition of ADP and Mg2+, but the N-terminal domain of FakA lacked the ADP-capping loop found in the dihydroxyacetone kinase component. Based on the structural similarity to the two subunits of dihydroxyacetone kinase complex, we constructed a model of the complex of T. thermophilus FakB and the N-terminal domain of FakA. In this model, the invariant Arg residue of FakB occupied a position that was spatially similar to that of the catalytically important Arg residue of dihydroxyacetone kinase, which predicted a composite active site in the Fatty acid kinase complex.
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Affiliation(s)
- Maya Nakatani
- Graduate School of Science, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka 558-8585, Japan
| | - Shun-Ya Nakahara
- Graduate School of Science, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka 558-8585, Japan
| | - Kenji Fukui
- Department of Biochemistry, Faculty of Medicine, Osaka Medical and Pharmaceutical University, 2-7 Daigakumachi, Takatsuki, Osaka 569-8686, Japan
| | - Momoka Urano
- Graduate School of Science, Osaka Metropolitan University, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka 558-8585, Japan
| | - Yuki Fujii
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Takeshi Murakawa
- Department of Biochemistry, Faculty of Medicine, Osaka Medical and Pharmaceutical University, 2-7 Daigakumachi, Takatsuki, Osaka 569-8686, Japan
| | - Seiki Baba
- The Japan Synchrotron Radiation Research Institute (JASRI), Sayo-gun, Hyogo 679-5198, Japan
| | - Takashi Kumasaka
- The Japan Synchrotron Radiation Research Institute (JASRI), Sayo-gun, Hyogo 679-5198, Japan
| | - Hiroki Okanishi
- Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita 565-0871, Japan
| | - Yoshikatsu Kanai
- Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita 565-0871, Japan; Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiative, Osaka University, Suita, Osaka 565-0871, Japan
| | - Takato Yano
- Department of Biochemistry, Faculty of Medicine, Osaka Medical and Pharmaceutical University, 2-7 Daigakumachi, Takatsuki, Osaka 569-8686, Japan
| | - Ryoji Masui
- Graduate School of Science, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka 558-8585, Japan; Graduate School of Science, Osaka Metropolitan University, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka 558-8585, Japan.
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3
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Shi Y, Zang N, Lou N, Xu Y, Sun J, Huang M, Zhang H, Lu H, Zhou C, Feng Y. Structure and mechanism for streptococcal fatty acid kinase (Fak) system dedicated to host fatty acid scavenging. SCIENCE ADVANCES 2022; 8:eabq3944. [PMID: 36054360 PMCID: PMC10848957 DOI: 10.1126/sciadv.abq3944] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 07/13/2022] [Indexed: 06/15/2023]
Abstract
Staphylococcus and Streptococcus, two groups of major human pathogens, are equipped with a fatty acid kinase (Fak) machinery to scavenge host fatty acids. The Fak complex is contains an ATP-binding subunit FakA, which interacts with varied FakB isoforms, and synthesizes acyl-phosphate from extracellular fatty acids. However, how FakA recognizes its FakB partners and then activates different fatty acids is poorly understood. Here, we systematically describe the Fak system from the zoonotic pathogen, Streptococcus suis. The crystal structure of SsFakA complexed with SsFakB2 was determined at 2.6 Å resolution. An in vitro system of Fak-PlsX (phosphate: acyl-ACP transacylase) was developed to track acyl-phosphate intermediate and its final product acyl-ACP. Structure-guided mutagenesis enabled us to characterize a mechanism for streptococcal FakA working with FakB partners engaged in host fatty acid scavenging. These findings offer a comprehensive description of the Fak kinase machinery, thus advancing the discovery of attractive targets against deadly infections with Streptococcus.
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Affiliation(s)
- Yu Shi
- Departments of Microbiology and General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Ning Zang
- Department of Toxicology, School of Public Health, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Ningjie Lou
- Departments of Microbiology and General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Yongchang Xu
- Departments of Microbiology and General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Jingdu Sun
- Departments of Microbiology and General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Man Huang
- Departments of Microbiology and General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Huimin Zhang
- Departments of Microbiology and General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
- Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Huijie Lu
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Chun Zhou
- Department of Toxicology, School of Public Health, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
- Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Youjun Feng
- Departments of Microbiology and General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
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Monterrey DT, Ayuso-Fernández I, Oroz-Guinea I, García-Junceda E. Design and biocatalytic applications of genetically fused multifunctional enzymes. Biotechnol Adv 2022; 60:108016. [PMID: 35781046 DOI: 10.1016/j.biotechadv.2022.108016] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 06/27/2022] [Accepted: 06/27/2022] [Indexed: 01/01/2023]
Abstract
Fusion proteins, understood as those created by joining two or more genes that originally encoded independent proteins, have numerous applications in biotechnology, from analytical methods to metabolic engineering. The use of fusion enzymes in biocatalysis may be even more interesting due to the physical connection of enzymes catalyzing successive reactions into covalently linked complexes. The proximity of the active sites of two enzymes in multi-enzyme complexes can make a significant contribution to the catalytic efficiency of the reaction. However, the physical proximity of the active sites does not guarantee this result. Other aspects, such as the nature and length of the linker used for the fusion or the order in which the enzymes are fused, must be considered and optimized to achieve the expected increase in catalytic efficiency. In this review, we will relate the new advances in the design, creation, and use of fused enzymes with those achieved in biocatalysis over the past 20 years. Thus, we will discuss some examples of genetically fused enzymes and their application in carbon‑carbon bond formation and oxidative reactions, generation of chiral amines, synthesis of carbohydrates, biodegradation of plant biomass and plastics, and in the preparation of other high-value products.
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Affiliation(s)
- Dianelis T Monterrey
- Departamento de Química Bioorgánica, Instituto de Química Orgánica General (IQOG), CSIC, Juan de la Cierva 3, 28006 Madrid, Spain.
| | - Iván Ayuso-Fernández
- Departamento de Química Bioorgánica, Instituto de Química Orgánica General (IQOG), CSIC, Juan de la Cierva 3, 28006 Madrid, Spain.
| | - Isabel Oroz-Guinea
- Departamento de Química Bioorgánica, Instituto de Química Orgánica General (IQOG), CSIC, Juan de la Cierva 3, 28006 Madrid, Spain.
| | - Eduardo García-Junceda
- Departamento de Química Bioorgánica, Instituto de Química Orgánica General (IQOG), CSIC, Juan de la Cierva 3, 28006 Madrid, Spain.
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5
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Subramanian C, Cuypers MG, Radka CD, White SW, Rock CO. Domain architecture and catalysis of the Staphylococcus aureus fatty acid kinase. J Biol Chem 2022; 298:101993. [PMID: 35490779 PMCID: PMC9136124 DOI: 10.1016/j.jbc.2022.101993] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/25/2022] [Accepted: 04/26/2022] [Indexed: 12/02/2022] Open
Abstract
Fatty acid kinase (Fak) is a two-component enzyme that generates acyl-phosphate for phospholipid synthesis. Fak consists of a kinase domain protein (FakA) that phosphorylates a fatty acid enveloped by a fatty acid binding protein (FakB). The structural basis for FakB function has been established, but little is known about FakA. Here, we used limited proteolysis to define three separate FakA domains: the amino terminal FakA_N, the central FakA_L, and the carboxy terminal FakA_C. The isolated domains lack kinase activity, but activity is restored when FakA_N and FakA_L are present individually or connected as FakA_NL. The X-ray structure of the monomeric FakA_N captures the product complex with ADP and two Mg2+ ions bound at the nucleotide site. The FakA_L domain encodes the dimerization interface along with conserved catalytic residues Cys240, His282, and His284. AlphaFold analysis of FakA_L predicts the catalytic residues are spatially clustered and pointing away from the dimerization surface. Furthermore, the X-ray structure of FakA_C shows that it consists of two subdomains that are structurally related to FakB. Analytical ultracentrifugation demonstrates that FakA_C binds FakB, and site-directed mutagenesis confirms that a positively charged wedge on FakB meshes with a negatively charged groove on FakA_C. Finally, small angle X-ray scattering analysis is consistent with freely rotating FakA_N and FakA_C domains tethered by flexible linkers to FakA_L. These data reveal specific roles for the three independently folded FakA protein domains in substrate binding and catalysis.
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Affiliation(s)
- Chitra Subramanian
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Maxime G Cuypers
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Christopher D Radka
- 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
| | - Charles O Rock
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.
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6
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Viecenz JM, Garavaglia PA, Tasso LM, Maidana CG, Bautista Cannata JJ, García GA. Identification and biochemical characterization of an ATP-dependent dihydroxyacetone kinase from Trypanosoma cruzi. Exp Parasitol 2021; 231:108178. [PMID: 34767777 DOI: 10.1016/j.exppara.2021.108178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 10/12/2021] [Accepted: 11/05/2021] [Indexed: 11/16/2022]
Abstract
Dihydroxyacetone (DHA) can be used as an energy source by many cell types; however, it is toxic at high concentrations. The enzyme dihydroxyacetone kinase (DAK) has shown to be involved in DHA detoxification and osmoregulation. Among protozoa of the genus Trypanosoma, T. brucei, which causes sleeping sickness, is highly sensitive to DHA and does not have orthologous genes to DAK. Conversely, T. cruzi, the etiological agent of Chagas Disease, has two putative ATP-dependent DAK (TcDAKs) sequences in its genome. Here we show that T. cruzi epimastigote lysates present a DAK specific activity of 27.1 nmol/min/mg of protein and that this form of the parasite is able to grow in the presence of 2 mM DHA. TcDAK gene was cloned and the recombinant enzyme (recTcDAK) was expressed in Escherichia coli. An anti-recTcDAK serum reacted with a protein of the expected molecular mass of 61 kDa in epimastigotes. recTcDAK presented maximal activity using Mg+2, showing a Km of 6.5 μM for DHA and a K0.5 of 124.7 μM for ATP. As it was reported for other DAKs, recTcDAK activity was inhibited by FAD with an IC50 value of 0.33 mM. In conclusion, TcDAK is the first DAK described in trypanosomatids confirming another divergent metabolism between T. brucei and T. cruzi.
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Affiliation(s)
- Juan Matías Viecenz
- Instituto Nacional de Parasitología "Dr. Mario Fatala Chaben"-ANLIS "Dr. Carlos G. Malbrán". Paseo Colón 568, Buenos Aires, (1063), Argentina
| | - Patricia Andrea Garavaglia
- Instituto Nacional de Parasitología "Dr. Mario Fatala Chaben"-ANLIS "Dr. Carlos G. Malbrán". Paseo Colón 568, Buenos Aires, (1063), Argentina
| | - Laura Mónica Tasso
- Instituto Nacional de Parasitología "Dr. Mario Fatala Chaben"-ANLIS "Dr. Carlos G. Malbrán". Paseo Colón 568, Buenos Aires, (1063), Argentina
| | - Cristina Graciela Maidana
- Instituto Nacional de Parasitología "Dr. Mario Fatala Chaben"-ANLIS "Dr. Carlos G. Malbrán". Paseo Colón 568, Buenos Aires, (1063), Argentina
| | - Joaquín Juan Bautista Cannata
- Instituto de Investigaciones Biotecnológicas (IIB-INTECH) "Dr. Rodolfo A. Ugalde", Universidad Nacional de General San Martín-CONICET, San Martín, (1650), Prov. Buenos Aires, Argentina
| | - Gabriela Andrea García
- Instituto Nacional de Parasitología "Dr. Mario Fatala Chaben"-ANLIS "Dr. Carlos G. Malbrán". Paseo Colón 568, Buenos Aires, (1063), Argentina.
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7
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Kataoka N, Hirata K, Matsutani M, Ano Y, Nguyen TM, Adachi O, Matsushita K, Yakushi T. Three ATP-dependent phosphorylating enzymes in the first committed step of dihydroxyacetone metabolism in Gluconobacter thailandicus NBRC3255. Appl Microbiol Biotechnol 2021; 105:1227-1236. [PMID: 33475798 DOI: 10.1007/s00253-021-11092-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 12/14/2020] [Accepted: 01/03/2021] [Indexed: 11/29/2022]
Abstract
Dihydroxyacetone (DHA), a chemical suntan agent, is produced by the regiospecific oxidation of glycerol with Gluconobacter thailandicus NBRC3255. However, this microorganism consumes DHA produced in the culture medium. Here, we attempted to understand the pathway for DHA metabolism in NBRC3255 to minimize DHA degradation. The two gene products, NBRC3255_2003 (DhaK) and NBRC3255_3084 (DerK), have been annotated as DHA kinases in the NBRC 3255 draft genome. Because the double deletion derivative for dhaK and derK showed ATP-dependent DHA kinase activity similar to that of the wild type, we attempted to purify DHA kinase from ∆dhaK ∆derK cells to identify the gene for DHA kinase. The identified gene was NBRC3255_0651, of which the product was annotated as glycerol kinase (GlpK). Mutant strains with several combinations of deletions for the dhaK, derK, and glpK genes were constructed. The single deletion strain ∆glpK showed approximately 10% of wild-type activity and grew slower on glycerol than the wild type. The double deletion strain ∆derK ∆glpK and the triple deletion strain ∆dhaK ∆derK ∆glpK showed DHA kinase activity less than a detection limit and did not grow on glycerol. In addition, although ΔderK ΔglpK consumed a small amount of DHA in the late phase of growth, ∆dhaK ΔderK ΔglpK did not show DHA consumption on glucose-glycerol medium. The transformants of the ∆dhaK ΔderK ΔglpK strain that expresses one of the genes from plasmids showed DHA kinase activity. We concluded that all three DHA kinases, DhaK, DerK, and GlpK, are involved in DHA metabolism of G. thailandicus. KEY POINTS: • Dihydroxyacetone (DHA) is produced but degraded by Gluconobacter thailandicus. • Phosphorylation rather than reduction is the first committed step in DHA metabolism. • Three kinases are involved in DHA metabolism with the different properties.
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Affiliation(s)
- Naoya Kataoka
- Faculty of Agriculture, Yamaguchi University, Yamaguchi, 753-8515, Japan.,Graduate School of Science and Technology for Innovation, Yamaguchi University, Yamaguchi, 753-8515, Japan.,Research Center for Thermotolerant Microbial Resources, Yamaguchi University, Yamaguchi, 753-8515, Japan
| | - Kaori Hirata
- Faculty of Agriculture, Yamaguchi University, Yamaguchi, 753-8515, Japan
| | - Minenosuke Matsutani
- Graduate School of Science and Technology for Innovation, Yamaguchi University, Yamaguchi, 753-8515, Japan.,NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo, 156-8502, Japan
| | - Yoshitaka Ano
- Graduate School of Agriculture, Ehime University, Matsuyama, 796-8566, Japan
| | - Thuy Minh Nguyen
- Graduate School of Science and Technology for Innovation, Yamaguchi University, Yamaguchi, 753-8515, Japan
| | - Osao Adachi
- Graduate School of Science and Technology for Innovation, Yamaguchi University, Yamaguchi, 753-8515, Japan
| | - Kazunobu Matsushita
- Faculty of Agriculture, Yamaguchi University, Yamaguchi, 753-8515, Japan.,Graduate School of Science and Technology for Innovation, Yamaguchi University, Yamaguchi, 753-8515, Japan.,Research Center for Thermotolerant Microbial Resources, Yamaguchi University, Yamaguchi, 753-8515, Japan
| | - Toshiharu Yakushi
- Faculty of Agriculture, Yamaguchi University, Yamaguchi, 753-8515, Japan. .,Graduate School of Science and Technology for Innovation, Yamaguchi University, Yamaguchi, 753-8515, Japan. .,Research Center for Thermotolerant Microbial Resources, Yamaguchi University, Yamaguchi, 753-8515, Japan.
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Bi-allelic Variants in TKFC Encoding Triokinase/FMN Cyclase Are Associated with Cataracts and Multisystem Disease. Am J Hum Genet 2020; 106:256-263. [PMID: 32004446 DOI: 10.1016/j.ajhg.2020.01.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Accepted: 01/07/2020] [Indexed: 12/19/2022] Open
Abstract
We report an inborn error of metabolism caused by TKFC deficiency in two unrelated families. Rapid trio genome sequencing in family 1 and exome sequencing in family 2 excluded known genetic etiologies, and further variant analysis identified rare homozygous variants in TKFC. TKFC encodes a bifunctional enzyme involved in fructose metabolism through its glyceraldehyde kinase activity and in the generation of riboflavin cyclic 4',5'-phosphate (cyclic FMN) through an FMN lyase domain. The TKFC homozygous variants reported here are located within the FMN lyase domain. Functional assays in yeast support the deleterious effect of these variants on protein function. Shared phenotypes between affected individuals with TKFC deficiency include cataracts and developmental delay, associated with cerebellar hypoplasia in one case. Further complications observed in two affected individuals included liver dysfunction and microcytic anemia, while one had fatal cardiomyopathy with lactic acidosis following a febrile illness. We postulate that deficiency of TKFC causes disruption of endogenous fructose metabolism leading to generation of by-products that can cause cataract. In line with this, an affected individual had mildly elevated urinary galactitol, which has been linked to cataract development in the galactosemias. Further, in light of a previously reported role of TKFC in regulating innate antiviral immunity through suppression of MDA5, we speculate that deficiency of TKFC leads to impaired innate immunity in response to viral illness, which may explain the fatal illness observed in the most severely affected individual.
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9
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Westbrook AW, Miscevic D, Kilpatrick S, Bruder MR, Moo-Young M, Chou CP. Strain engineering for microbial production of value-added chemicals and fuels from glycerol. Biotechnol Adv 2019; 37:538-568. [DOI: 10.1016/j.biotechadv.2018.10.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2017] [Revised: 10/03/2018] [Accepted: 10/10/2018] [Indexed: 12/22/2022]
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10
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Rodrigues JR, Cameselle JC, Cabezas A, Ribeiro JM. Closure of the Human TKFC Active Site: Comparison of the Apoenzyme and the Complexes Formed with Either Triokinase or FMN Cyclase Substrates. Int J Mol Sci 2019; 20:E1099. [PMID: 30836629 PMCID: PMC6429413 DOI: 10.3390/ijms20051099] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 02/20/2019] [Accepted: 02/27/2019] [Indexed: 11/17/2022] Open
Abstract
Human triokinase/flavin mononucleotide (FMN) cyclase (hTKFC) catalyzes the adenosine triphosphate (ATP)-dependent phosphorylation of D-glyceraldehyde and dihydroxyacetone (DHA), and the cyclizing splitting of flavin adenine dinucleotide (FAD). hTKFC structural models are dimers of identical subunits, each with two domains, K and L, with an L2-K1-K2-L1 arrangement. Two active sites lie between L2-K1 and K2-L1, where triose binds K and ATP binds L, although the resulting ATP-to-triose distance is too large (≈14 Å) for phosphoryl transfer. A 75-ns trajectory of molecular dynamics shows considerable, but transient, ATP-to-DHA approximations in the L2-K1 site (4.83 Å or 4.16 Å). To confirm the trend towards site closure, and its relationship to kinase activity, apo-hTKFC, hTKFC:2DHA:2ATP and hTKFC:2FAD models were submitted to normal mode analysis. The trajectory of hTKFC:2DHA:2ATP was extended up to 160 ns, and 120-ns trajectories of apo-hTKFC and hTKFC:2FAD were simulated. The three systems were comparatively analyzed for equal lengths (120 ns) following the principles of essential dynamics, and by estimating site closure by distance measurements. The full trajectory of hTKFC:2DHA:2ATP was searched for in-line orientations and short distances of DHA hydroxymethyl oxygens to ATP γ-phosphorus. Full site closure was reached only in hTKFC:2DHA:2ATP, where conformations compatible with an associative phosphoryl transfer occurred in L2-K1 for significant trajectory time fractions.
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Affiliation(s)
- Joaquim Rui Rodrigues
- Laboratório Associado LSRE-LCM, Escola Superior de Tecnologia e Gestão, Instituto Politécnico de Leiria, P-2411-901 Leiria, Portugal.
| | - José Carlos Cameselle
- Grupo de Enzimología, Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Medicina, Universidad de Extremadura, E-06006 Badajoz, Spain.
| | - Alicia Cabezas
- Grupo de Enzimología, Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Medicina, Universidad de Extremadura, E-06006 Badajoz, Spain.
| | - João Meireles Ribeiro
- Grupo de Enzimología, Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Medicina, Universidad de Extremadura, E-06006 Badajoz, Spain.
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11
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Miller WR, Tran TT, Diaz L, Rios R, Khan A, Reyes J, Prater AG, Panesso D, Shamoo Y, Arias CA. LiaR-independent pathways to daptomycin resistance in Enterococcus faecalis reveal a multilayer defense against cell envelope antibiotics. Mol Microbiol 2019; 111:811-824. [PMID: 30582877 PMCID: PMC6417935 DOI: 10.1111/mmi.14193] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/19/2018] [Indexed: 12/17/2022]
Abstract
The lipopeptide antibiotic daptomycin (DAP) is a key drug against serious enterococcal infections, but the emergence of resistance in the clinical setting is a major concern. The LiaFSR system plays a prominent role in the development of DAP resistance (DAP-R) in enterococci, and blocking this stress response system has been proposed as a novel therapeutic strategy. In this work, we identify LiaR-independent pathways in Enterococcus faecalis that regulate cell membrane adaptation in response to antibiotics. We adapted E. faecalis OG1RF (a laboratory strain) and S613TM (a clinical strain) lacking liaR to increasing concentrations of DAP, leading to the development of DAP-R and elevated MICs to bacitracin and ceftriaxone. Whole genome sequencing identified changes in the YxdJK two-component regulatory system and a putative fatty acid kinase (dak) in both DAP-R strains. Deletion of the gene encoding the YxdJ response regulator in both the DAP-R mutant and wild-type OG1RF decreased MICs to DAP, even when a functional LiaFSR system was present. Mutations in dak were associated with slower growth, decreased membrane fluidity and alterations of cell morphology. These findings suggest that overlapping stress response pathways can provide protection against antimicrobial peptides in E. faecalis at a significant cost in bacterial fitness.
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Affiliation(s)
- William R. Miller
- Center for Antimicrobial Resistance and Microbial Genomics, University of Texas Health Science Center, McGovern School of Medicine, Houston, TX, USA
- Division of Infectious Diseases, University of Texas Health Science Center, McGovern School of Medicine, Houston, TX, USA
| | - Truc T. Tran
- Center for Antimicrobial Resistance and Microbial Genomics, University of Texas Health Science Center, McGovern School of Medicine, Houston, TX, USA
- Division of Infectious Diseases, University of Texas Health Science Center, McGovern School of Medicine, Houston, TX, USA
| | - Lorena Diaz
- Center for Antimicrobial Resistance and Microbial Genomics, University of Texas Health Science Center, McGovern School of Medicine, Houston, TX, USA
- Molecular Genetics and Antimicrobial Resistance Unit, International Center for Microbial Genomics, Universidad El Bosque, Bogotá, Colombia
| | - Rafael Rios
- Molecular Genetics and Antimicrobial Resistance Unit, International Center for Microbial Genomics, Universidad El Bosque, Bogotá, Colombia
| | - Ayesha Khan
- Center for Antimicrobial Resistance and Microbial Genomics, University of Texas Health Science Center, McGovern School of Medicine, Houston, TX, USA
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, McGovern School of Medicine, Houston, TX, USA
| | - Jinnethe Reyes
- Center for Antimicrobial Resistance and Microbial Genomics, University of Texas Health Science Center, McGovern School of Medicine, Houston, TX, USA
- Molecular Genetics and Antimicrobial Resistance Unit, International Center for Microbial Genomics, Universidad El Bosque, Bogotá, Colombia
| | - Amy G. Prater
- Department of BioSciences, Rice University, Houston, TX, USA
| | - Diana Panesso
- Center for Antimicrobial Resistance and Microbial Genomics, University of Texas Health Science Center, McGovern School of Medicine, Houston, TX, USA
- Division of Infectious Diseases, University of Texas Health Science Center, McGovern School of Medicine, Houston, TX, USA
- Molecular Genetics and Antimicrobial Resistance Unit, International Center for Microbial Genomics, Universidad El Bosque, Bogotá, Colombia
| | - Yousif Shamoo
- Department of BioSciences, Rice University, Houston, TX, USA
| | - Cesar A. Arias
- Center for Antimicrobial Resistance and Microbial Genomics, University of Texas Health Science Center, McGovern School of Medicine, Houston, TX, USA
- Division of Infectious Diseases, University of Texas Health Science Center, McGovern School of Medicine, Houston, TX, USA
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, McGovern School of Medicine, Houston, TX, USA
- Center for Infectious Diseases, University of Texas Health Science Center, School of Public Health, Houston, TX, USA
- Molecular Genetics and Antimicrobial Resistance Unit, International Center for Microbial Genomics, Universidad El Bosque, Bogotá, Colombia
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12
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Zhou F, Jiang X, Wang T, Zhang B, Zhao H. Lyciumbarbarum Polysaccharide (LBP): A Novel Prebiotics Candidate for Bifidobacterium and Lactobacillus. Front Microbiol 2018; 9:1034. [PMID: 29867910 PMCID: PMC5968096 DOI: 10.3389/fmicb.2018.01034] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 05/01/2018] [Indexed: 11/13/2022] Open
Abstract
Lycium barbarum is a boxthorn that produces the goji berries. The aim of the current study was to evaluate the proliferative effect of L. barbarum polysaccharides (LBP) on probiotics. LBP was extracted from goji berries and its monosaccharide composition characterized by gas chromatography (GC). The LBP extract contained arabinose, rhamnose, xylose, mannose, galactose, and glucose. LBP obviously promoted the proliferation of lactic acid bacteria (LAB) strains, especially Bifidobacterium longum subsp. infantis Bi-26 and Lactobacillus acidophilus NCFM. In the presence of LBP in the growth medium, the β-galactosidase (β-GAL) and lactate dehydrogenase (LDH) activities of strain Bi-26 significantly increased. The activities of β-GAL, LDH, hexokinase (HK), 6-phosphofructokinase (PFK), and pyruvate kinase (PK) of strain NCFM significantly increased under those conditions. LAB transcriptome sequencing analysis was performed to elucidate the mechanism responsible for the proliferative effect of LBP. The data revealed that LBP promoted the bacterial biosynthetic and metabolic processes, gene expression, transcription, and transmembrane transport. Pyruvate metabolism, carbon metabolism, phosphotransferase system (PTS), and glycolysis/gluconeogenesis genes were overexpressed. Furthermore, LBP improved cell vitality during freeze-drying and tolerance of the gastrointestinal environment. In summary, LBP can be used as a potential prebiotic for Bifidobacterium and Lactobacillus.
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Affiliation(s)
- Fang Zhou
- Department of Food Science, College of Biological Science and Biotechnology, Beijing Forestry University, Beijing, China
| | - Xiaoying Jiang
- Department of Food Science, College of Biological Science and Biotechnology, Beijing Forestry University, Beijing, China
| | - Tao Wang
- Department of Food Science, College of Biological Science and Biotechnology, Beijing Forestry University, Beijing, China
- Beijing Key Laboratory of Forest Food Processing and Safety, Beijing Forestry University, Beijing, China
| | - Bolin Zhang
- Department of Food Science, College of Biological Science and Biotechnology, Beijing Forestry University, Beijing, China
- Beijing Key Laboratory of Forest Food Processing and Safety, Beijing Forestry University, Beijing, China
| | - Hongfei Zhao
- Department of Food Science, College of Biological Science and Biotechnology, Beijing Forestry University, Beijing, China
- Beijing Key Laboratory of Forest Food Processing and Safety, Beijing Forestry University, Beijing, China
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13
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Gauss D, Sánchez-Moreno I, Oroz-Guinea I, García-Junceda E, Wohlgemuth R. Phosphorylation Catalyzed by Dihydroxyacetone Kinase. European J Org Chem 2018. [DOI: 10.1002/ejoc.201800350] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Dominik Gauss
- Member of Merck Group; Sigma-Aldrich; Industriestrasse 25, CH -9470 Buchs Switzerland
| | - Israel Sánchez-Moreno
- Departamento de Química Bioorgánica; Instituto de Química Orgánica General; CSIC (IQOG-CSIC); Instituto de Química Orgánica General; 28006 Madrid Spain
| | - Isabel Oroz-Guinea
- Departamento de Química Bioorgánica; Instituto de Química Orgánica General; CSIC (IQOG-CSIC); Instituto de Química Orgánica General; 28006 Madrid Spain
| | - Eduardo García-Junceda
- Departamento de Química Bioorgánica; Instituto de Química Orgánica General; CSIC (IQOG-CSIC); Instituto de Química Orgánica General; 28006 Madrid Spain
| | - Roland Wohlgemuth
- Member of Merck Group; Sigma-Aldrich; Industriestrasse 25, CH -9470 Buchs Switzerland
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14
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VfrB Is a Key Activator of the Staphylococcus aureus SaeRS Two-Component System. J Bacteriol 2017; 199:JB.00828-16. [PMID: 28031278 DOI: 10.1128/jb.00828-16] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 12/14/2016] [Indexed: 12/22/2022] Open
Abstract
In previous studies, we identified the fatty acid kinase virulence factor regulator B (VfrB) as a potent regulator of α-hemolysin and other virulence factors in Staphylococcus aureus In this study, we demonstrated that VfrB is a positive activator of the SaeRS two-component regulatory system. Analysis of vfrB, saeR, and saeS mutant strains revealed that VfrB functions in the same pathway as SaeRS. At the transcriptional level, the promoter activities of SaeRS class I (coa) and class II (hla) target genes were downregulated during the exponential growth phase in the vfrB mutant, compared to the wild-type strain. In addition, saePQRS expression was decreased in the vfrB mutant strain, demonstrating a need for this protein in the autoregulation of SaeRS. The requirement for VfrB-mediated activation was circumvented when SaeS was constitutively active due to an SaeS (L18P) substitution. Furthermore, activation of SaeS via human neutrophil peptide 1 (HNP-1) overcame the dependence on VfrB for transcription from class I Sae promoters. Consistent with the role of VfrB in fatty acid metabolism, hla expression was decreased in the vfrB mutant with the addition of exogenous myristic acid. Lastly, we determined that aspartic acid residues D38 and D40, which are predicted to be key to VfrB enzymatic activity, were required for VfrB-mediated α-hemolysin production. Collectively, this study implicates VfrB as a novel accessory protein needed for the activation of SaeRS in S. aureusIMPORTANCE The SaeRS two-component system is a key regulator of virulence determinant production in Staphylococcus aureus Although the regulon of this two-component system is well characterized, the activation mechanisms, including the specific signaling molecules, remain elusive. Elucidating the complex regulatory circuit of SaeRS regulation is important for understanding how the system contributes to disease causation by this pathogen. To this end, we have identified the fatty acid kinase VfrB as a positive regulatory modulator of SaeRS-mediated transcription of virulence factors in S. aureus In addition to describing a new regulatory aspect of SaeRS, this study establishes a link between fatty acid kinase activity and virulence factor regulation.
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15
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Broussard TC, Miller DJ, Jackson P, Nourse A, White SW, Rock CO. Biochemical Roles for Conserved Residues in the Bacterial Fatty Acid-binding Protein Family. J Biol Chem 2016; 291:6292-303. [PMID: 26774272 PMCID: PMC4813577 DOI: 10.1074/jbc.m115.706820] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 01/11/2016] [Indexed: 12/11/2022] Open
Abstract
Fatty acid kinase (Fak) is a ubiquitous Gram-positive bacterial enzyme consisting of an ATP-binding protein (FakA) that phosphorylates the fatty acid bound to FakB. In Staphylococcus aureus, Fak is a global regulator of virulence factor transcription and is essential for the activation of exogenous fatty acids for incorporation into phospholipids. The 1.2-Å x-ray structure of S. aureus FakB2, activity assays, solution studies, site-directed mutagenesis, and in vivo complementation were used to define the functions of the five conserved residues that define the FakB protein family (Pfam02645). The fatty acid tail is buried within the protein, and the exposed carboxyl group is bound by a Ser-93-fatty acid carboxyl-Thr-61-His-266 hydrogen bond network. The guanidinium of the invariant Arg-170 is positioned to potentially interact with a bound acylphosphate. The reduced thermal denaturation temperatures of the T61A, S93A, and H266A FakB2 mutants illustrate the importance of the hydrogen bond network in protein stability. The FakB2 T61A, S93A, and H266A mutants are 1000-fold less active in the Fak assay, and the R170A mutant is completely inactive. All FakB2 mutants form FakA(FakB2)2 complexes except FakB2(R202A), which is deficient in FakA binding. Allelic replacement shows that strains expressing FakB2 mutants are defective in fatty acid incorporation into phospholipids and virulence gene transcription. These conserved residues are likely to perform the same critical functions in all bacterial fatty acid-binding proteins.
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Affiliation(s)
| | - Darcie J Miller
- Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105
| | | | - Amanda Nourse
- Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105
| | - Stephen W White
- Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105
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16
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Sánchez-Moreno I, Bordes I, Castillo R, Ruiz-Pernía JJ, Moliner V, García-Junceda E. Tuning the Phosphoryl Donor Specificity of Dihydroxyacetone Kinase from ATP to Inorganic Polyphosphate. An Insight from Computational Studies. Int J Mol Sci 2015; 16:27835-49. [PMID: 26610480 PMCID: PMC4661931 DOI: 10.3390/ijms161126073] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Revised: 11/05/2015] [Accepted: 11/09/2015] [Indexed: 11/23/2022] Open
Abstract
Dihydroxyacetone (DHA) kinase from Citrobacter freundii provides an easy entry for the preparation of DHA phosphate; a very important C3 building block in nature. To modify the phosphoryl donor specificity of this enzyme from ATP to inorganic polyphosphate (poly-P); a directed evolution program has been initiated. In the first cycle of evolution, the native enzyme was subjected to one round of error-prone PCR (EP-PCR) followed directly (without selection) by a round of DNA shuffling. Although the wild-type DHAK did not show activity with poly-P, after screening, sixteen mutant clones showed an activity with poly-phosphate as phosphoryl donor statistically significant. The most active mutant presented a single mutation (Glu526Lys) located in a flexible loop near of the active center. Interestingly, our theoretical studies, based on molecular dynamics simulations and hybrid Quantum Mechanics/Molecular Mechanics (QM/MM) optimizations, suggest that this mutation has an effect on the binding of the poly-P favoring a more adequate position in the active center for the reaction to take place.
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Affiliation(s)
- Israel Sánchez-Moreno
- Departamento de Química Bioorgánica, Instituto de Química Orgánica General, CSIC. Juan de la Cierva 3, Madrid 28006, Spain.
| | - Isabel Bordes
- Departament de Química Física i Analítica, Universitat Jaume I. Castellón 12071, Spain.
| | - Raquel Castillo
- Departament de Química Física i Analítica, Universitat Jaume I. Castellón 12071, Spain.
| | | | - Vicent Moliner
- Departament de Química Física i Analítica, Universitat Jaume I. Castellón 12071, Spain.
| | - Eduardo García-Junceda
- Departamento de Química Bioorgánica, Instituto de Química Orgánica General, CSIC. Juan de la Cierva 3, Madrid 28006, Spain.
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17
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Identification of a two-component fatty acid kinase responsible for host fatty acid incorporation by Staphylococcus aureus. Proc Natl Acad Sci U S A 2014; 111:10532-7. [PMID: 25002480 DOI: 10.1073/pnas.1408797111] [Citation(s) in RCA: 106] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Extracellular fatty acid incorporation into the phospholipids of Staphylococcus aureus occurs via fatty acid phosphorylation. We show that fatty acid kinase (Fak) is composed of two dissociable protein subunits encoded by separate genes. FakA provides the ATP binding domain and interacts with two distinct FakB proteins to produce acyl-phosphate. The FakBs are fatty acid binding proteins that exchange bound fatty acid/acyl-phosphate with fatty acid/acyl-phosphate presented in detergent micelles or liposomes. The ΔfakA and ΔfakB1 ΔfakB2 strains were unable to incorporate extracellular fatty acids into phospholipid. FakB1 selectively bound saturated fatty acids whereas FakB2 preferred unsaturated fatty acids. Affymetrix array showed a global perturbation in the expression of virulence genes in the ΔfakA strain. The severe deficiency in α-hemolysin protein secretion in ΔfakA and ΔfakB1 ΔfakB2 mutants coupled with quantitative mRNA measurements showed that fatty acid kinase activity was required to support virulence factor transcription. These data reveal the function of two conserved gene families, their essential role in the incorporation of host fatty acids by Gram-positive pathogens, and connects fatty acid kinase to the regulation of virulence factor transcription in S. aureus.
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18
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Rodrigues JR, Couto A, Cabezas A, Pinto RM, Ribeiro JM, Canales J, Costas MJ, Cameselle JC. Bifunctional homodimeric triokinase/FMN cyclase: contribution of protein domains to the activities of the human enzyme and molecular dynamics simulation of domain movements. J Biol Chem 2014; 289:10620-10636. [PMID: 24569995 DOI: 10.1074/jbc.m113.525626] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Mammalian triokinase, which phosphorylates exogenous dihydroxyacetone and fructose-derived glyceraldehyde, is neither molecularly identified nor firmly associated to an encoding gene. Human FMN cyclase, which splits FAD and other ribonucleoside diphosphate-X compounds to ribonucleoside monophosphate and cyclic X-phosphodiester, is identical to a DAK-encoded dihydroxyacetone kinase. This bifunctional protein was identified as triokinase. It was modeled as a homodimer of two-domain (K and L) subunits. Active centers lie between K1 and L2 or K2 and L1: dihydroxyacetone binds K and ATP binds L in different subunits too distant (≈ 14 Å) for phosphoryl transfer. FAD docked to the ATP site with ribityl 4'-OH in a possible near-attack conformation for cyclase activity. Reciprocal inhibition between kinase and cyclase reactants confirmed substrate site locations. The differential roles of protein domains were supported by their individual expression: K was inactive, and L displayed cyclase but not kinase activity. The importance of domain mobility for the kinase activity of dimeric triokinase was highlighted by molecular dynamics simulations: ATP approached dihydroxyacetone at distances below 5 Å in near-attack conformation. Based upon structure, docking, and molecular dynamics simulations, relevant residues were mutated to alanine, and kcat and Km were assayed whenever kinase and/or cyclase activity was conserved. The results supported the roles of Thr(112) (hydrogen bonding of ATP adenine to K in the closed active center), His(221) (covalent anchoring of dihydroxyacetone to K), Asp(401) and Asp(403) (metal coordination to L), and Asp(556) (hydrogen bonding of ATP or FAD ribose to L domain). Interestingly, the His(221) point mutant acted specifically as a cyclase without kinase activity.
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Affiliation(s)
- Joaquim Rui Rodrigues
- Grupo de Enzimología, Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Medicina, Universidad de Extremadura, E-06006 Badajoz, Spain; Escola Superior de Tecnologia e Gestão, Instituto Politécnico de Leiria, P-2411-901 Leiria, Portugal
| | - Ana Couto
- Grupo de Enzimología, Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Medicina, Universidad de Extremadura, E-06006 Badajoz, Spain
| | - Alicia Cabezas
- Grupo de Enzimología, Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Medicina, Universidad de Extremadura, E-06006 Badajoz, Spain
| | - Rosa María Pinto
- Grupo de Enzimología, Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Medicina, Universidad de Extremadura, E-06006 Badajoz, Spain
| | - João Meireles Ribeiro
- Grupo de Enzimología, Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Medicina, Universidad de Extremadura, E-06006 Badajoz, Spain
| | - José Canales
- Grupo de Enzimología, Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Medicina, Universidad de Extremadura, E-06006 Badajoz, Spain
| | - María Jesús Costas
- Grupo de Enzimología, Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Medicina, Universidad de Extremadura, E-06006 Badajoz, Spain
| | - José Carlos Cameselle
- Grupo de Enzimología, Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Medicina, Universidad de Extremadura, E-06006 Badajoz, Spain.
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19
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Ouellette M, Makkay AM, Papke RT. Dihydroxyacetone metabolism in Haloferax volcanii. Front Microbiol 2013; 4:376. [PMID: 24379808 PMCID: PMC3863723 DOI: 10.3389/fmicb.2013.00376] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Accepted: 11/21/2013] [Indexed: 12/03/2022] Open
Abstract
Dihydroxyacetone (DHA) is a ketose sugar that can be produced by oxidizing glycerol. DHA in the environment is taken up and phosphorylated to DHA-phosphate by glycerol kinase or DHA kinase. In hypersaline environments, it is hypothesized that DHA is produced as an overflow product from glycerol utilization by organisms such as Salinibacter ruber. Previous research has demonstrated that the halobacterial species Haloquadratum walsbyi can use DHA as a carbon source, and putative DHA kinase genes were hypothesized to be involved in this process. However, DHA metabolism has not been demonstrated in other halobacterial species, and the role of the DHA kinase genes was not confirmed. In this study, we examined the metabolism of DHA in Haloferax volcanii because putative DHA kinase genes were annotated in its genome, and it has an established genetic system to assay growth of mutant knockouts. Experiments in which Hfx. volcanii was grown on DHA as the sole carbon source demonstrated growth, and that it is concentration dependent. Three annotated DHA kinase genes (HVO_1544, HVO_1545, and HVO_1546), which are homologous to the putative DHA kinase genes present in Hqm. walsbyi, as well as the glycerol kinase gene (HVO_1541), were deleted to examine the effect of these genes on the growth of Hfx. volcanii on DHA. Experiments demonstrated that the DHA kinase deletion mutant exhibited diminished, but not absence of growth on DHA compared to the parent strain. Deletion of the glycerol kinase gene also reduced growth on DHA, and did so more than deletion of the DHA kinase. The results indicate that Hfx. volcanii can metabolize DHA and that DHA kinase plays a role in this metabolism. However, the glycerol kinase appears to be the primary enzyme involved in this process. BLASTp analyses demonstrate that the DHA kinase genes are patchily distributed among the Halobacteria, whereas the glycerol kinase gene is widely distributed, suggesting a widespread capability for DHA metabolism.
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Affiliation(s)
- Matthew Ouellette
- Department of Molecular and Cell Biology, University of Connecticut Storrs, CT, USA
| | - Andrea M Makkay
- Department of Molecular and Cell Biology, University of Connecticut Storrs, CT, USA
| | - R Thane Papke
- Department of Molecular and Cell Biology, University of Connecticut Storrs, CT, USA
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20
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Hypothetical Proteins Present During Recovery Phase of Radiation Resistant Bacterium Deinococcus radiodurans are Under Purifying Selection. J Mol Evol 2013; 77:31-42. [DOI: 10.1007/s00239-013-9577-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Accepted: 07/26/2013] [Indexed: 01/15/2023]
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21
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Erni B. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS): an interface between energy and signal transduction. JOURNAL OF THE IRANIAN CHEMICAL SOCIETY 2012. [DOI: 10.1007/s13738-012-0185-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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22
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Summerton JC, Evanseck JD, Chapman MS. Hyperconjugation-mediated solvent effects in phosphoanhydride bonds. J Phys Chem A 2012; 116:10209-17. [PMID: 23009395 DOI: 10.1021/jp306607k] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Density functional theory and natural bond orbital analysis are used to explore the impact of solvent on hyperconjugation in methyl triphosphate, a model for "energy rich" phosphoanhydride bonds, such as found in ATP. As expected, dihedral rotation of a hydroxyl group vicinal to the phosphoanhydride bond reveals that the conformational dependence of the anomeric effect involves modulation of the orbital overlap between the donor and acceptor orbitals. However, a conformational independence was observed in the rotation of a solvent hydrogen bond. As one lone pair orbital rotates away from an optimal antiperiplanar orientation, the overall magnitude of the anomeric effect is compensated approximately by the other lone pair as it becomes more antiperiplanar. Furthermore, solvent modulation of the anomeric effect is not restricted to the antiperiplanar lone pair; hydrogen bonds involving gauche lone pairs also affect the anomeric interaction and the strength of the phosphoanhydride bond. Both gauche and anti solvent hydrogen bonds lengthen nonbridging O-P bonds, increasing the distance between donor and acceptor orbitals and decreasing orbital overlap, which leads to a reduction of the anomeric effect. Solvent effects are additive with greater reduction in the anomeric effect upon increasing water coordination. By controlling the coordination environment of substrates in an active site, kinases, phosphatases, and other enzymes important in metabolism and signaling may have the potential to modulate the stability of individual phosphoanhydride bonds through stereoelectronic effects.
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Affiliation(s)
- Jean C Summerton
- Department of Biochemistry & Molecular Biology, School of Medicine, Oregon Health & Science University, Mail Code L224, 3181 SW Sam Jackson Park Road, Portland, Oregon 97239-3098, USA
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23
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Novel listerial glycerol dehydrogenase- and phosphoenolpyruvate-dependent dihydroxyacetone kinase system connected to the pentose phosphate pathway. J Bacteriol 2012; 194:4972-82. [PMID: 22773791 DOI: 10.1128/jb.00801-12] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Several bacteria use glycerol dehydrogenase to transform glycerol into dihydroxyacetone (Dha). Dha is subsequently converted into Dha phosphate (Dha-P) by an ATP- or phosphoenolpyruvate (PEP)-dependent Dha kinase. Listeria innocua possesses two potential PEP-dependent Dha kinases. One is encoded by 3 of the 11 genes forming the glycerol (gol) operon. This operon also contains golD (lin0362), which codes for a new type of Dha-forming NAD(+)-dependent glycerol dehydrogenase. The subsequent metabolism of Dha requires its phosphorylation via the PEP:sugar phosphotransferase system components enzyme I, HPr, and EIIA(Dha)-2 (Lin0369). P∼EIIA(Dha)-2 transfers its phosphoryl group to DhaL-2, which phosphorylates Dha bound to DhaK-2. The resulting Dha-P is probably metabolized mainly via the pentose phosphate pathway, because two genes of the gol operon encode proteins resembling transketolases and transaldolases. In addition, purified Lin0363 and Lin0364 exhibit ribose-5-P isomerase (RipB) and triosephosphate isomerase activities, respectively. The latter enzyme converts part of the Dha-P into glyceraldehyde-3-P, which, together with Dha-P, is metabolized via gluconeogenesis to form fructose-6-P. Together with another glyceraldehyde-3-P molecule, the transketolase transforms fructose-6-P into intermediates of the pentose phosphate pathway. The gol operon is preceded by golR, transcribed in the opposite orientation and encoding a DeoR-type repressor. Its inactivation causes the constitutive but glucose-repressible expression of the entire gol operon, including the last gene, encoding a pediocin immunity-like (PedB-like) protein. Its elevated level of synthesis in the golR mutant causes slightly increased immunity against pediocin PA-1 compared to the wild-type strain or a pedB-like deletion mutant.
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Molecular characterization of the glycerol-oxidative pathway of Clostridium butyricum VPI 1718. J Bacteriol 2011; 193:3127-34. [PMID: 21478343 DOI: 10.1128/jb.00112-11] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The glycerol oxidative pathway of Clostridium butyricum VPI 1718 plays an important role in glycerol dissimilation. We isolated, sequenced, and characterized the region coding for the glycerol oxidation pathway. Five open reading frames (ORFs) were identified: dhaR, encoding a putative transcriptional regulator; dhaD (1,142 bp), encoding a glycerol dehydrogenase; and dhaK (995 bp), dhaL (629 bp), and dhaM (386 bp), encoding a phosphoenolpyruvate (PEP)-dependent dihydroxyacetone (DHA) kinase enzyme complex. Northern blot analysis demonstrated that the last four genes are transcribed as a 3.2-kb polycistronic operon only in glycerol-metabolizing cultures, indicating that the expression of this operon is regulated at the transcriptional level. The transcriptional start site of the operon was determined by primer extension, and the promoter region was deduced. The glycerol dehydrogenase activity of DhaD and the PEP-dependent DHA kinase activity of DhaKLM were demonstrated by heterologous expression in different Escherichia coli mutants. Based on our complementation experiments, we proposed that the HPr phosphoryl carrier protein and His9 residue of the DhaM subunit are involved in the phosphoryl transfer to dihydroxyacetone-phosphate. DhaR, a potential regulator of this operon, was found to contain conserved transmitter and receiver domains that are characteristic of two-component systems present in the AraC family. To the best of our knowledge, this is the first molecular characterization of a glycerol oxidation pathway in a Gram-positive bacterium.
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Structural and mechanistic insight into covalent substrate binding by Escherichia coli dihydroxyacetone kinase. Proc Natl Acad Sci U S A 2011; 108:1302-7. [PMID: 21209328 DOI: 10.1073/pnas.1012596108] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Escherichia coli dihydroxyacetone (Dha) kinase is an unusual kinase because (i) it uses the phosphoenolpyruvate carbohydrate: phosphotransferase system (PTS) as the source of high-energy phosphate, (ii) the active site is formed by two subunits, and (iii) the substrate is covalently bound to His218(K)* of the DhaK subunit. The PTS transfers phosphate to DhaM, which in turn phosphorylates the permanently bound ADP coenzyme of DhaL. This phosphoryl group is subsequently transferred to the Dha substrate bound to DhaK. Here we report the crystal structure of the E. coli Dha kinase complex, DhaK-DhaL. The structure of the complex reveals that DhaK undergoes significant conformational changes to accommodate binding of DhaL. Combined mutagenesis and enzymatic activity studies of kinase mutants allow us to propose a catalytic mechanism for covalent Dha binding, phosphorylation, and release of the Dha-phosphate product. Our results show that His56(K) is involved in formation of the covalent hemiaminal bond with Dha. The structure of H56N(K) with noncovalently bound substrate reveals a somewhat different positioning of Dha in the binding pocket as compared to covalently bound Dha, showing that the covalent attachment to His218(K) orients the substrate optimally for phosphoryl transfer. Asp109(K) is critical for activity, likely acting as a general base activating the γ-OH of Dha. Our results provide a comprehensive picture of the roles of the highly conserved active site residues of dihydroxyacetone kinases.
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Iturrate L, Sánchez-Moreno I, Oroz-Guinea I, Pérez-Gil J, García-Junceda E. Preparation and Characterization of a Bifunctional Aldolase/Kinase Enzyme: A More Efficient Biocatalyst for CC Bond Formation. Chemistry 2010; 16:4018-30. [DOI: 10.1002/chem.200903096] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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The first peptides: The evolutionary transition between prebiotic amino acids and early proteins. J Theor Biol 2009; 261:531-9. [DOI: 10.1016/j.jtbi.2009.09.004] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2008] [Revised: 06/19/2009] [Accepted: 09/06/2009] [Indexed: 11/22/2022]
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Sánchez-Moreno I, Iturrate L, Martín-Hoyos R, Jimeno ML, Mena M, Bastida A, García-Junceda E. From kinase to cyclase: an unusual example of catalytic promiscuity modulated by metal switching. Chembiochem 2009; 10:225-9. [PMID: 19058275 DOI: 10.1002/cbic.200800573] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Israel Sánchez-Moreno
- Departamento de Química Orgánica Biológica, Instituto de Química Orgánica General, CSIC, Juan de la Cierva 3, 28006 Madrid, Spain
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Iturrate L, Sánchez-Moreno I, Doyagüez EG, García-Junceda E. Substrate channelling in an engineered bifunctional aldolase/kinase enzyme confers catalytic advantage for C-C bond formation. Chem Commun (Camb) 2009:1721-3. [PMID: 19294274 DOI: 10.1039/b822345a] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new bifunctional enzyme that displays both aldolase and kinase activities has been designed and successfully used in the synthesis of aldol adducts, employing DHA as initial donor, with an increase in the reaction rate of 20-fold over the parent enzymes, which can be interpreted in terms of substrate channelling.
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Affiliation(s)
- Laura Iturrate
- Departamento de Química Orgánica Biológica, Instituto de Química Orgánica General, CSIC, Madrid 28006, Spain
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Zurbriggen A, Jeckelmann JM, Christen S, Bieniossek C, Baumann U, Erni B. X-ray structures of the three Lactococcus lactis dihydroxyacetone kinase subunits and of a transient intersubunit complex. J Biol Chem 2008; 283:35789-96. [PMID: 18957416 DOI: 10.1074/jbc.m804893200] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Bacterial dihydroxyacetone (Dha) kinases do not exchange the ADP for ATP but utilize a subunit of the phosphoenolpyruvate carbohydrate phosphotransferase system for in situ rephosphorylation of a permanently bound ADP-cofactor. Here we report the 2.1-angstroms crystal structure of the transient complex between the phosphotransferase subunit DhaM of the phosphotransferase system and the nucleotide binding subunit DhaL of the Dha kinase of Lactococcus lactis, the 1.1-angstroms structure of the free DhaM dimer, and the 2.5-angstroms structure of the Dha-binding DhaK subunit. Conserved salt bridges and an edge-to-plane stacking contact between two tyrosines serve to orient DhaL relative to the DhaM dimer. The distance between the imidazole Nepsilon2 of the DhaM His-10 and the beta-phosphate oxygen of ADP, between which the gamma-phosphate is transferred, is 4.9 angstroms. An invariant arginine, which is essential for activity, is appropriately positioned to stabilize the gamma-phosphate in the transition state. The (betaalpha)4alpha fold of DhaM occurs a second time as a subfold in the DhaK subunit. By docking DhaL-ADP to this subfold, the nucleotide bound to DhaL and the C1-hydroxyl of Dha bound to DhaK are positioned for in-line transfer of phosphate.
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Affiliation(s)
- Andreas Zurbriggen
- Departement für Chemie und Biochemie, Universität Bern, Freiestrasse 3, Bern CH-3012, Switzerland
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Deutscher J, Francke C, Postma PW. How phosphotransferase system-related protein phosphorylation regulates carbohydrate metabolism in bacteria. Microbiol Mol Biol Rev 2007; 70:939-1031. [PMID: 17158705 PMCID: PMC1698508 DOI: 10.1128/mmbr.00024-06] [Citation(s) in RCA: 985] [Impact Index Per Article: 57.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The phosphoenolpyruvate(PEP):carbohydrate phosphotransferase system (PTS) is found only in bacteria, where it catalyzes the transport and phosphorylation of numerous monosaccharides, disaccharides, amino sugars, polyols, and other sugar derivatives. To carry out its catalytic function in sugar transport and phosphorylation, the PTS uses PEP as an energy source and phosphoryl donor. The phosphoryl group of PEP is usually transferred via four distinct proteins (domains) to the transported sugar bound to the respective membrane component(s) (EIIC and EIID) of the PTS. The organization of the PTS as a four-step phosphoryl transfer system, in which all P derivatives exhibit similar energy (phosphorylation occurs at histidyl or cysteyl residues), is surprising, as a single protein (or domain) coupling energy transfer and sugar phosphorylation would be sufficient for PTS function. A possible explanation for the complexity of the PTS was provided by the discovery that the PTS also carries out numerous regulatory functions. Depending on their phosphorylation state, the four proteins (domains) forming the PTS phosphorylation cascade (EI, HPr, EIIA, and EIIB) can phosphorylate or interact with numerous non-PTS proteins and thereby regulate their activity. In addition, in certain bacteria, one of the PTS components (HPr) is phosphorylated by ATP at a seryl residue, which increases the complexity of PTS-mediated regulation. In this review, we try to summarize the known protein phosphorylation-related regulatory functions of the PTS. As we shall see, the PTS regulation network not only controls carbohydrate uptake and metabolism but also interferes with the utilization of nitrogen and phosphorus and the virulence of certain pathogens.
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Affiliation(s)
- Josef Deutscher
- Microbiologie et Génétique Moléculaire, INRA-CNRS-INA PG UMR 2585, Thiverval-Grignon, France.
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Christen S, Srinivas A, Bähler P, Zeller A, Pridmore D, Bieniossek C, Baumann U, Erni B. Regulation of the Dha Operon of Lactococcus lactis. J Biol Chem 2006; 281:23129-37. [PMID: 16760471 DOI: 10.1074/jbc.m603486200] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Dihydroxyacetone (Dha) kinases are a novel family of kinases with signaling and metabolic functions. Here we report the x-ray structures of the transcriptional activator DhaS and the coactivator DhaQ and characterize their function. DhaQ is a paralog of the Dha binding Dha kinase subunit; DhaS belongs to the family of TetR repressors although, unlike all known members of this family, it is a transcriptional activator. DhaQ and DhaS form a stable complex that in the presence of Dha activates transcription of the Lactococcus lactis dha operon. Dha covalently binds to DhaQ through a hemiaminal bond with a histidine and thereby induces a conformational change, which is propagated to the surface via a cantilever-like structure. DhaS binding protects an inverted repeat whose sequence is GGACACATN6ATTTGTCC and renders two GC base pairs of the operator DNA hypersensitive to DNase I cleavage. The proximal half-site of the inverted repeat partially overlaps with the predicted -35 consensus sequence of the dha promoter.
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Affiliation(s)
- Sandra Christen
- Departement für Chemie und Biochemie, Universität Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
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Molin M, Blomberg A. Dihydroxyacetone detoxification in Saccharomyces cerevisiae involves formaldehyde dissimilation. Mol Microbiol 2006; 60:925-38. [PMID: 16677304 DOI: 10.1111/j.1365-2958.2006.05154.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
To investigate Saccharomyces cerevisiae physiology during growth on the conditionally toxic triose dihydroxyacetone (DHA), protein expression was studied in strains overexpressing either of the two dihydroxyacetone kinase isogenes, DAK1 or DAK2, that grow well utilizing DHA as a carbon and energy source. DHA metabolism was found mostly similar to ethanol utilization, involving a strong component of glucose derepression, but also involved DHA-specific regulatory changes. A specific and strong (10- to 30-fold induction of formaldehyde dehydrogenase, Fdhlp, indicated activation of the formaldehyde dissimilation pathway in DHA medium. The importance of this pathway was further supported by impaired adaptation to DHA growth and DHA survival in a glutathione-dependent formaldehyde dehydrogenase (SFA1) deletion mutant. Glutathione synthase (GSH1) deletion led to decreased DHA survival in agreement with the glutathione cofactor requirement for the SFA1-encoded activity. DHA toxicity did, however, not solely appear related to formaldehyde accumulation, because SFA1 overexpression only enhanced formaldehyde but not DHA tolerance. In further agreement with a low DHA-to-formaldehyde flux, GSH supplements in the low microM range also fully suppressed the DHA sensitivity of a gsh1Delta strain. Under growth reduction on high (100 mM) DHA medium we report increased levels of advanced glycation end-product (AGE) formation on total protein. Under these high-DHA conditions expression of several stress-related proteins, e.g. a heat-shock protein (Hsp104p) and the oxidative stress indicator, alkyl hydroperoxide reductase (Ahp1p) was also found induced. However, hallmark determinants of oxidative stress tolerance (e.g. YAP1, SKN7, HYR1/GPX3 and SOD2) were redundant for DHA tolerance, thus indicating mechanisms of DHA toxicity largely independent of central oxidative stress defence mechanisms. We conclude that mechanisms for DHA growth and detoxification appear complex and that the evolutionary strive to minimize detrimental effects of this intracellular metabolite links to both formaldehyde and glutathione metabolism.
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Affiliation(s)
- Mikael Molin
- Department of Cell and Molecular Biology, Microbiology, Göteborg University, Lundberg laboratory, Medicinaregatan 9c, S-413 90 Göteborg, Sweden
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Oberholzer AE, Schneider P, Baumann U, Erni B. Crystal structure of the nucleotide-binding subunit DhaL of the Escherichia coli dihydroxyacetone kinase. J Mol Biol 2006; 359:539-45. [PMID: 16647083 DOI: 10.1016/j.jmb.2006.03.057] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2006] [Revised: 03/21/2006] [Accepted: 03/29/2006] [Indexed: 11/16/2022]
Abstract
Dihydroxyacetone (Dha) kinases are a family of sequence-related enzymes that utilize either ATP or phosphoenolpyruvate (PEP) as source of high energy phosphate. The PEP-dependent Dha kinase of Escherichia coli consists of three subunits. DhaK and DhaL are homologous to the Dha and nucleotide-binding domains of the ATP-dependent kinase of Citrobacter freundii. The DhaM subunit is a multiphosphorylprotein of the PEP:sugar phosphotransferase system (PTS). DhaL contains a tightly bound ADP as coenzyme that gets transiently phosphorylated in the double displacement of phosphate between DhaM and Dha. Here we report the 2.6A crystal structure of the E.coli DhaL subunit. DhaL folds into an eight-helix barrel of regular up-down topology with a hydrophobic core made up of eight interlocked aromatic residues and a molecule of ADP bound at the narrower end of the barrel. The alpha and beta phosphates of ADP are complexed by two Mg2+ and by a hydrogen bond to the imidazole ring of an invariant histidine. The Mg ions in turn are coordinated by three gamma-carboxyl groups of invariant aspartate residues. Water molecules complete the octahedral coordination sphere. The nucleotide is capped by an alpha-helical segment connecting helices 7 and 8 of the barrel. DhaL and the nucleotide-binding domain of the C.freundii kinase assume the same fold but display strongly different surface potentials. The latter observation and biochemical data indicate that the domains of the C.freundii Dha kinase constitute one cooperative unit and are not randomly interacting and independent like the subunits of the E.coli enzyme.
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Affiliation(s)
- Anselm Erich Oberholzer
- Departement of Chemistry und Biochemistry, University of Berne, Freiestrasse 3, CH-3012 Bern, Switzerland
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Barabote RD, Saier MH. Comparative genomic analyses of the bacterial phosphotransferase system. Microbiol Mol Biol Rev 2005; 69:608-34. [PMID: 16339738 PMCID: PMC1306802 DOI: 10.1128/mmbr.69.4.608-634.2005] [Citation(s) in RCA: 223] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We report analyses of 202 fully sequenced genomes for homologues of known protein constituents of the bacterial phosphoenolpyruvate-dependent phosphotransferase system (PTS). These included 174 bacterial, 19 archaeal, and 9 eukaryotic genomes. Homologues of PTS proteins were not identified in archaea or eukaryotes, showing that the horizontal transfer of genes encoding PTS proteins has not occurred between the three domains of life. Of the 174 bacterial genomes (136 bacterial species) analyzed, 30 diverse species have no PTS homologues, and 29 species have cytoplasmic PTS phosphoryl transfer protein homologues but lack recognizable PTS permeases. These soluble homologues presumably function in regulation. The remaining 77 species possess all PTS proteins required for the transport and phosphorylation of at least one sugar via the PTS. Up to 3.2% of the genes in a bacterium encode PTS proteins. These homologues were analyzed for family association, range of protein types, domain organization, and organismal distribution. Different strains of a single bacterial species often possess strikingly different complements of PTS proteins. Types of PTS protein domain fusions were analyzed, showing that certain types of domain fusions are common, while others are rare or prohibited. Select PTS proteins were analyzed from different phylogenetic standpoints, showing that PTS protein phylogeny often differs from organismal phylogeny. The results document the frequent gain and loss of PTS protein-encoding genes and suggest that the lateral transfer of these genes within the bacterial domain has played an important role in bacterial evolution. Our studies provide insight into the development of complex multicomponent enzyme systems and lead to predictions regarding the types of protein-protein interactions that promote efficient PTS-mediated phosphoryl transfer.
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Affiliation(s)
- Ravi D Barabote
- Division of Biological Sciences, University of California at San Diego, La Jolla, California 92093-0116, USA
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Cabezas A, Costas MJ, Pinto RM, Couto A, Cameselle JC. Identification of human and rat FAD-AMP lyase (cyclic FMN forming) as ATP-dependent dihydroxyacetone kinases. Biochem Biophys Res Commun 2005; 338:1682-9. [PMID: 16289032 DOI: 10.1016/j.bbrc.2005.10.142] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2005] [Accepted: 10/24/2005] [Indexed: 10/25/2022]
Abstract
Rat liver FAD-AMP lyase or FMN cyclase is the only known enzymatic source of the unusual flavin nucleotide riboflavin 4',5'-cyclic phosphate. To determine its molecular identity, a peptide-mass fingerprint of the purified rat enzyme was obtained. It pointed to highly related, mammalian hypothetical proteins putatively classified as dihydroxyacetone (Dha) kinases due to weaker homologies to biochemically proven Dha kinases of plants, yeasts, and bacteria. The human protein LOC26007 cDNA was used to design PCR primers. The product amplified from human brain cDNA was cloned, sequenced (GenBank Accession No. ), and found to differ from protein LOC26007 cDNA by three SNPs. Its heterologous expression yielded a protein active both as FMN cyclase and ATP-dependent Dha kinase, each activity being inhibited by the substrate(s) of the other. Cyclase and kinase activities copurified from rat liver extracts. Evidence supports that a single protein sustains both activities, probably in a single active center. Putative Dha kinases from other mammals are likely to be FMN cyclases too. Future work will profit from the availability of the structure of Citrobacter freundii Dha kinase, which contains substrate-interacting residues conserved in human Dha kinase/FMN cyclase.
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Affiliation(s)
- Alicia Cabezas
- Unidad de Bioquímica y Biología Molecular, Facultad de Medicina, Universidad de Extremadura, 06080 Badajoz, Spain
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Saier MH, Hvorup RN, Barabote RD. Evolution of the bacterial phosphotransferase system: from carriers and enzymes to group translocators. Biochem Soc Trans 2005; 33:220-4. [PMID: 15667312 DOI: 10.1042/bst0330220] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The bacterial phosphotransferase system (PTS) is a structurally and functionally complex system with a surprising evolutionary history. The substrate-recognizing protein constituents of the PTS (Enzymes II) derive from at least four independent sources. Some of the non-PTS precursor constituents have been identified, and evolutionary pathways taken have been proposed. Our analyses suggest that two of these independently evolving systems are still in transition, not yet having acquired the full-fledged characteristics of PTS Enzyme II complexes. The work described provides detailed insight into the process of catalytic protein evolution.
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Affiliation(s)
- M H Saier
- Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0116, USA.
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Cheek S, Ginalski K, Zhang H, Grishin NV. A comprehensive update of the sequence and structure classification of kinases. BMC STRUCTURAL BIOLOGY 2005; 5:6. [PMID: 15771780 PMCID: PMC1079889 DOI: 10.1186/1472-6807-5-6] [Citation(s) in RCA: 94] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2005] [Accepted: 03/16/2005] [Indexed: 12/02/2022]
Abstract
Background A comprehensive update of the classification of all available kinases was carried out. This survey presents a complete global picture of this large functional class of proteins and confirms the soundness of our initial kinase classification scheme. Results The new survey found the total number of kinase sequences in the protein database has increased more than three-fold (from 17,310 to 59,402), and the number of determined kinase structures increased two-fold (from 359 to 702) in the past three years. However, the framework of the original two-tier classification scheme (in families and fold groups) remains sufficient to describe all available kinases. Overall, the kinase sequences were classified into 25 families of homologous proteins, wherein 22 families (~98.8% of all sequences) for which three-dimensional structures are known fall into 10 fold groups. These fold groups not only include some of the most widely spread proteins folds, such as the Rossmann-like fold, ferredoxin-like fold, TIM-barrel fold, and antiparallel β-barrel fold, but also all major classes (all α, all β, α+β, α/β) of protein structures. Fold predictions are made for remaining kinase families without a close homolog with solved structure. We also highlight two novel kinase structural folds, riboflavin kinase and dihydroxyacetone kinase, which have recently been characterized. Two protein families previously annotated as kinases are removed from the classification based on new experimental data. Conclusion Structural annotations of all kinase families are now revealed, including fold descriptions for all globular kinases, making this the first large functional class of proteins with a comprehensive structural annotation. Potential uses for this classification include deduction of protein function, structural fold, or enzymatic mechanism of poorly studied or newly discovered kinases based on proteins in the same family.
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Affiliation(s)
- Sara Cheek
- Department of Biochemistry, University of Texas Southwestern Medical Center 5323 Harry Hines Blvd., Dallas, Texas 75390, USA
| | - Krzysztof Ginalski
- Department of Biochemistry, University of Texas Southwestern Medical Center 5323 Harry Hines Blvd., Dallas, Texas 75390, USA
- Bioinformatics Laboratory, Interdisciplinary Centre for Mathematical and Computational Modelling Warsaw University, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Hong Zhang
- Department of Biochemistry, University of Texas Southwestern Medical Center 5323 Harry Hines Blvd., Dallas, Texas 75390, USA
| | - Nick V Grishin
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center 5323 Harry Hines Blvd., Dallas, Texas 75390, USA
- Department of Biochemistry, University of Texas Southwestern Medical Center 5323 Harry Hines Blvd., Dallas, Texas 75390, USA
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Bächler C, Flükiger-Brühwiler K, Schneider P, Bähler P, Erni B. From ATP as substrate to ADP as coenzyme: functional evolution of the nucleotide binding subunit of dihydroxyacetone kinases. J Biol Chem 2005; 280:18321-5. [PMID: 15753087 DOI: 10.1074/jbc.m500279200] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Dihydroxyacetone kinases are a family of sequence-related enzymes that utilize either ATP or a protein of the phosphoenolpyruvate:sugar phosphotransferase system (PTS) as a source of high energy phosphate. The PTS is a multicomponent system involved in carbohydrate uptake and control of carbon metabolism in bacteria. Phylogenetic analysis suggests that the PTS-dependent dihydroxyacetone kinases evolved from an ATP-dependent ancestor. Their nucleotide binding subunit, an eight-helix barrel of regular up-down topology, retains ADP as phosphorylation site for the double displacement of phosphate from a phospho-histidine of the PTS protein to dihydroxyacetone. ADP is bound essentially irreversibly with a t((1/2)) of 100 min. Complexation with ADP increases the thermal unfolding temperature of dihydroxyacetone L from 40 (apo-form) to 65 degrees C (holoenzyme). ADP assumes the same role as histidines, cysteines, and aspartic acids in histidine kinases and PTS proteins. This conversion of a substrate binding site into a cofactor binding site reflects a remarkable instance of parsimonious evolution.
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Affiliation(s)
- Christoph Bächler
- Departement für Chemie und Biochemie, Universität Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
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40
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Kinch LN, Cheek S, Grishin NV. EDD, a novel phosphotransferase domain common to mannose transporter EIIA, dihydroxyacetone kinase, and DegV. Protein Sci 2005; 14:360-7. [PMID: 15632288 PMCID: PMC2253402 DOI: 10.1110/ps.041114805] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Using a recently developed program (SCOPmap) designed to automatically assign new protein structures to existing evolutionary-based classification schemes, we identify a evolutionarily conserved domain (EDD) common to three different folds: mannose transporter EIIA domain (EIIA-man), dihydroxyacetone kinase (Dak), and DegV. Several lines of evidence support unification of these three folds into a single superfamily: statistically significant sequence similarity detected by PSI-BLAST; "closed structural grouping" using DALI Z-scores (each protein inside a group finds all other group members with scores higher than those to proteins outside the group) that includes only these proteins sharing a unique alpha-helical hairpin at the C-terminus and excludes all other proteins with similar topology; similar domain fusions connect Dak and DegV, and genomic neighborhood organizations connect Dak and EIIA-man. Finally, both Dak and EIIA-man perform similar phosphotransfer reactions, suggesting a phosphotransferase activity for the DegV-like family of proteins, whose function other than lipid binding revealed in the crystal structure remains unknown.
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Affiliation(s)
- Lisa N Kinch
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390-9050, USA
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Garcia-Alles LF, Siebold C, Nyffeler TL, Flükiger-Brühwiler K, Schneider P, Bürgi HB, Baumann U, Erni B. Phosphoenolpyruvate- and ATP-dependent dihydroxyacetone kinases: covalent substrate-binding and kinetic mechanism. Biochemistry 2004; 43:13037-45. [PMID: 15476397 DOI: 10.1021/bi048575m] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Dihydroxyacetone (Dha) kinases are a sequence-conserved family of enzymes, which utilize two different phosphoryldonors, ATP in animals, plants, and some bacteria, and a multiphosphoprotein of the phosphoenolpyruvate carbohydrate phosphotransferase system (PTS) in most bacteria. Here, we compare the PTS-dependent kinase of Escherichia coli and the ATP-dependent kinase of Citrobacter freundii. They display 30% sequence identity. The binding constants of the E. coli kinase for eleven short-chain carbonyl compounds were determined by acetone precipitation of the enzyme-substrate complexes. They are 3.4 microM for Dha, 780 microM for Dha-phosphate (DhaP), 50 microM for D,L-glyceraldehyde (GA), and 90 microM for D,L-glyceraldehyde-3-phosphate. The k(cat) for Dha of the PTS-dependent kinase is 290 min(-1), and that of the ATP-dependent kinase is 1050 min(-1). The Km for Dha of both kinases is <6 microM. The X-ray structures of the enzyme-GA and the enzyme-DhaP complex show that substrates as well as products are bound in hemiaminal linkage to an active-site histidine. Quantum-mechanical calculations offer no indication for activation of the reacting hydroxyl group by the formation of the hemiaminal. However, the formation of the hemiaminal bond allows selection for short-chain carbonyl compounds and discrimination against structurally similar polyols. The Dha kinase remains fully active in the presence of 2 M glycerol, and phosphorylates trace impurities of carbonyl compounds present in glycerol.
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Affiliation(s)
- Luis F Garcia-Alles
- Department of Chemistry and Biochemistry and Laboratory for Chemical and Mineralogical Crystallography, University of Berne, CH-3012 Berne, Switzerland
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Sánchez-Moreno I, García-García JF, Bastida A, García-Junceda E. Multienzyme system for dihydroxyacetone phosphate-dependent aldolase catalyzed C-C bond formation from dihydroxyacetone. Chem Commun (Camb) 2004:1634-5. [PMID: 15263954 DOI: 10.1039/b405220j] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A multienzyme system composed by recombinant dihydroxyacetone kinase from Citrobacter freundii, fuculose-1-phosphate aldolase and acetate kinase, allows a practical one-pot C-C bond formation catalysed by dihydroxyacetone phosphate-dependent aldolases from dihydroxyacetone and an aldehyde.
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Affiliation(s)
- Israel Sánchez-Moreno
- Departamento de Química Orgánica Biológica, Instituto de Química Orgánica General, CSIC, Madrid 28006, Spain
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