1
|
Chen H, Shi Y, Huang M, Lu T, Zhang H, Zhou C, Hou T, Feng Y. Recognition and acquisition of FakB2-loaded exogenous fatty acid (eFA) by a streptococcal FakA kinase. Sci Bull (Beijing) 2024:S2095-9273(24)00349-9. [PMID: 38806393 DOI: 10.1016/j.scib.2024.05.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 04/12/2024] [Accepted: 05/07/2024] [Indexed: 05/30/2024]
Affiliation(s)
- Haiyi Chen
- Key Laboratory of Multiple Organ Failure, Ministry of Education, Departments of Microbiology and General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China; College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yu Shi
- Key Laboratory of Multiple Organ Failure, Ministry of Education, Departments of Microbiology and General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Man Huang
- Key Laboratory of Multiple Organ Failure, Ministry of Education, Departments of Microbiology and General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Ting Lu
- Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana 61801, USA
| | - Huimin Zhang
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana 61801, USA
| | - Chun Zhou
- School of Public Health, Zhejiang University School of Medicine, Hangzhou 310058, China.
| | - Tingjun Hou
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Youjun Feng
- Key Laboratory of Multiple Organ Failure, Ministry of Education, Departments of Microbiology and General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China; Department of Clinical Laboratory, Shenzhen Third People's Hospital, National Clinical Research Center for Infectious Diseases, The Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen 518444, China.
| |
Collapse
|
2
|
Myers MJ, Xu Z, Ryan BJ, DeMars ZR, Ridder MJ, Johnson DK, Krute CN, Flynn TS, Kashipathy MM, Battaile KP, Schnicker N, Lovell S, Freudenthal BD, Bose JL. Molecular basis for the activation of the Fatty Acid Kinase complex of Staphylococcus aureus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.19.585040. [PMID: 38562735 PMCID: PMC10983944 DOI: 10.1101/2024.03.19.585040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Gram-positive bacteria utilize a Fatty Acid Kinase (FAK) complex to harvest fatty acids from the environment. The complex, consisting of the fatty acid kinase, FakA, and an acyl carrier protein, FakB, is known to impact virulence and disease outcomes. However, FAK's structure and enzymatic mechanism remain poorly understood. Here, we used a combination of modeling, biochemical, and cell-based approaches to establish critical details of FAK activity. Solved structures of the apo and ligand-bound FakA kinase domain captured the protein state through ATP hydrolysis. Additionally, targeted mutagenesis of an understudied FakA Middle domain identified critical residues within a metal-binding pocket that contribute to FakA dimer stability and protein function. Regarding the complex, we demonstrated nanomolar affinity between FakA and FakB and generated computational models of the complex's quaternary structure. Together, these data provide critical insight into the structure and function of the FAK complex which is essential for understanding its mechanism.
Collapse
|
3
|
Radka CD. Interfacial Enzymes Enable Gram-Positive Microbes to Eat Fatty Acids. MEMBRANES 2023; 13:423. [PMID: 37103850 PMCID: PMC10146087 DOI: 10.3390/membranes13040423] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 04/08/2023] [Accepted: 04/09/2023] [Indexed: 06/19/2023]
Abstract
Exogenous fatty acid (eFA) activation and utilization play key roles in bacterial physiology and confer growth advantages by bypassing the need to make fatty acids for lipid synthesis. In Gram-positive bacteria, eFA activation and utilization is generally carried out by the fatty acid kinase (FakAB) two-component system that converts eFA to acyl phosphate, and the acyl-ACP:phosphate transacylase (PlsX) that catalyzes the reversible conversion of acyl phosphate to acyl-acyl carrier protein. Acyl-acyl carrier protein is a soluble format of the fatty acid that is compatible with cellular metabolic enzymes and can feed multiple processes including the fatty acid biosynthesis pathway. The combination of FakAB and PlsX enables the bacteria to channel eFA nutrients. These key enzymes are peripheral membrane interfacial proteins that associate with the membrane through amphipathic helices and hydrophobic loops. In this review, we discuss the biochemical and biophysical advances that have established the structural features that drive FakB or PlsX association with the membrane, and how these protein-lipid interactions contribute to enzyme catalysis.
Collapse
Affiliation(s)
- Christopher D Radka
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| |
Collapse
|
4
|
Whaley SG, Frank MW, Rock CO. A short-chain acyl-CoA synthetase that supports branched-chain fatty acid synthesis in Staphylococcus aureus. J Biol Chem 2023; 299:103036. [PMID: 36806679 PMCID: PMC10026030 DOI: 10.1016/j.jbc.2023.103036] [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: 12/19/2022] [Revised: 01/24/2023] [Accepted: 02/09/2023] [Indexed: 02/18/2023] Open
Abstract
Staphylococcus aureus controls its membrane biophysical properties using branched-chain fatty acids (BCFAs). The branched-chain acyl-CoA precursors, utilized to initiate fatty acid synthesis, are derived from branched-chain ketoacid dehydrogenase (Bkd), a multiprotein complex that converts α-keto acids to their corresponding acyl-CoAs; however, Bkd KO strains still contain BCFAs. Here, we show that commonly used rich medias contain substantial concentrations of short-chain acids, like 2-methylbutyric and isobutyric acids, that are incorporated into membrane BCFAs. Bkd-deficient strains cannot grow in defined medium unless it is supplemented with either 2-methylbutyric or isobutyric acid. We performed a screen of candidate KO strains and identified the methylbutyryl-CoA synthetase (mbcS gene; SAUSA300_2542) as required for the incorporation of 2-methylbutyric and isobutyric acids into phosphatidylglycerol. Our mass tracing experiments show that isobutyric acid is converted to isobutyryl-CoA that flows into the even-chain acyl-acyl carrier protein intermediates in the type II fatty acid biosynthesis elongation cycle. Furthermore, purified MbcS is an ATP-dependent acyl-CoA synthetase that selectively catalyzes the activation of 2-methylbutyrate and isobutyrate. We found that butyrate and isovalerate are poor MbcS substrates and activity was not detected with acetate or short-chain dicarboxylic acids. Thus, MbcS functions to convert extracellular 2-methylbutyric and isobutyric acids to their respective acyl-CoAs that are used by 3-ketoacyl-ACP synthase III (FabH) to initiate BCFA biosynthesis.
Collapse
Affiliation(s)
- Sarah G Whaley
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Matthew W Frank
- Department of Infectious Diseases, 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.
| |
Collapse
|
5
|
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.
Collapse
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.
| |
Collapse
|
6
|
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.
Collapse
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
| |
Collapse
|