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De Vitto H, Belfon KKJ, Sharma N, Toay S, Abendroth J, Dranow DM, Lukacs CM, Choi R, Udell HS, Willis S, Barrera G, Beyer O, Li TD, Hicks KA, Torelli AT, French JB. Characterization of an Acinetobacter baumannii Monofunctional Phosphomethylpyrimidine Kinase That Is Inhibited by Pyridoxal Phosphate. Biochemistry 2024. [PMID: 38306231 DOI: 10.1021/acs.biochem.3c00640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2024]
Abstract
Thiamin and its phosphate derivatives are ubiquitous molecules involved as essential cofactors in many cellular processes. The de novo biosynthesis of thiamin employs the parallel synthesis of 4-methyl-5-(2-hydroxyethyl)thiazole (THZ-P) and 4-amino-2-methyl-5(diphosphooxymethyl) pyrimidine (HMP) pyrophosphate (HMP-PP), which are coupled to generate thiamin phosphate. Most organisms that can biosynthesize thiamin employ a kinase (HMPK or ThiD) to generate HMP-PP. In nearly all cases, this enzyme is bifunctional and can also salvage free HMP, producing HMP-P, the monophosphate precursor of HMP-PP. Here we present high-resolution crystal structures of an HMPK from Acinetobacter baumannii (AbHMPK), both unliganded and with pyridoxal 5-phosphate (PLP) noncovalently bound. Despite the similarity between HMPK and pyridoxal kinase enzymes, our kinetics analysis indicates that AbHMPK accepts HMP exclusively as a substrate and cannot turn over pyridoxal, pyridoxamine, or pyridoxine nor does it display phosphatase activity. PLP does, however, act as a weak inhibitor of AbHMPK with an IC50 of 768 μM. Surprisingly, unlike other HMPKs, AbHMPK catalyzes only the phosphorylation of HMP and does not generate the diphosphate HMP-PP. This suggests that an additional kinase is present in A. baumannii, or an alternative mechanism is in operation to complete the biosynthesis of thiamin.
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Affiliation(s)
- Humberto De Vitto
- The Hormel Institute, University of Minnesota, Austin, Minnesota 55912, United States
| | - Kafi K J Belfon
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York 11790, United States
| | - Nandini Sharma
- The Hormel Institute, University of Minnesota, Austin, Minnesota 55912, United States
| | - Sarah Toay
- Department of Biological Chemistry, Grinnell College, Grinnell, Iowa 50112, United States
| | - Jan Abendroth
- UCB BioSciences, Bainbridge Island, Washington 98110, United States
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98104, United States
| | - David M Dranow
- UCB BioSciences, Bainbridge Island, Washington 98110, United States
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98104, United States
| | - Christine M Lukacs
- UCB BioSciences, Bainbridge Island, Washington 98110, United States
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98104, United States
| | - Ryan Choi
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98104, United States
| | - Hannah S Udell
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98104, United States
| | - Sydney Willis
- Department of Chemistry, Rollins College, Winter Park, Florida 32789, United States
| | - George Barrera
- Department of Chemistry and Biochemistry, Weber State University, Ogden, Utah 84408, United States
| | - Olive Beyer
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland 21250, United States
| | - Teng Da Li
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York 11790, United States
| | - Katherine A Hicks
- Chemistry Department, State University of New York at Cortland, Cortland, New York 13045, United States
| | - Andrew T Torelli
- Department of Chemistry, Ithaca College, Ithaca, New York 14850, United States
| | - Jarrod B French
- The Hormel Institute, University of Minnesota, Austin, Minnesota 55912, United States
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Paxhia MD, Swanson MS, Downs DM. Functional characterization of the HMP-P synthase of Legionella pneumophila (Lpg1565). Mol Microbiol 2020; 115:539-553. [PMID: 33034117 DOI: 10.1111/mmi.14622] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 09/29/2020] [Accepted: 10/04/2020] [Indexed: 11/30/2022]
Abstract
The production of the pyrimidine moiety in thiamine synthesis, 2-methyl-4-amino-5-hydroxymethylpyrimidine phosphate (HMP-P), has been described to proceed through the Thi5-dependent pathway in Saccharomyces cerevisiae and other yeast. Previous work found that ScThi5 functioned poorly in a heterologous context. Here we report a bacterial ortholog to the yeast HMP-P synthase (Thi5) was necessary for HMP synthesis in Legionella pneumophila. Unlike ScThi5, LpThi5 functioned in vivo in Salmonella enterica under multiple growth conditions. The protein LpThi5 is a dimer that binds pyridoxal-5'-phosphate (PLP), apparently without a solvent-exposed Schiff base. A small percentage of LpThi5 protein co-purifies with a bound molecule that can be converted to HMP. Analysis of variant proteins both in vivo and in vitro confirmed that residues in sequence motifs conserved across bacterial and eukaryotic orthologs modulate the function of LpThi5. IMPORTANCE: Thiamine is an essential vitamin for the vast majority of organisms. There are multiple strategies to synthesize and salvage this vitamin. The predominant pathway for synthesis of the pyrimidine moiety of thiamine involves the Fe-S cluster protein ThiC. An alternative pathway utilizes Thi5, a novel enzyme that uses PLP as a substrate. The Thi5-dependent pathway is poorly characterized in yeast and has not been characterized in Bacteria. Here we demonstrate that a Thi5-dependent pathway is necessary for thiamine biosynthesis in Legionella pneumophila and provide biochemical data to extend knowledge of the Thi5 enzyme, the corresponding biosynthetic pathway, and the role of metabolic network architecture in optimizing its function.
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Affiliation(s)
- Michael D Paxhia
- Department of Microbiology, University of Georgia, Athens, GA, USA
| | - Michele S Swanson
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Diana M Downs
- Department of Microbiology, University of Georgia, Athens, GA, USA
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Chen Y, Wang L, Shang F, Liu W, Lan J, Chen J, Ha NC, Quan C, Nam KH, Xu Y. Structural insight of the 5-(Hydroxyethyl)-methylthiazole kinase ThiM involving vitamin B1 biosynthetic pathway from the Klebsiella pneumoniae. Biochem Biophys Res Commun 2019; 518:513-518. [PMID: 31439375 DOI: 10.1016/j.bbrc.2019.08.086] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 08/14/2019] [Indexed: 01/08/2023]
Abstract
Thiamin pyrophosphate (TPP) is an essential co-factor in amino acid and carbohydrate metabolic pathways. The TPP-related vitamin B1 biosynthetic pathway is found in most bacterial, plant and lower eukaryotic processes; however, it is not present in humans. In bacterial thiamin synthesis and salvage pathways, the 5-(hydroxyethyl)-methylthiazole kinase (ThiM) is essential in the pathway forming TPP. Thus, ThiM is considered to be an attractive antibacterial drug target. Here, we determined the crystal structures of ThiM from pathogenic Klebsiella pneumoniae (KpThiM) and KpThiM in complex with its substrate 5-(hydroxyethyl)-4-methylthiazole (TZE). KpThiM, consisting of an α-β-α domain, shows a pseudosymmetric trimeric formation. TZE molecules are located in the interface between the KpThiM subunits in the trimer and interact with Met49 and Cys200. Superimposition of the apo and TZE-complexed structures of KpThiM show that the side chains of the amino acids interacting with TZE and Mg2+ have a rigid configuration. Comparison of the ThiM structures shows that KpThiM could, in terms of sequence and configuration, be different from other ThiM proteins, which possess different amino acids that recognize TZE and Mg2+. The structures will provide new insight into the ThiM subfamily proteins for antibacterial drug development.
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Affiliation(s)
- Yuanyuan Chen
- Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian, 116600, Liaoning, China; Key Laboratory of Biotechnology and Bioresources Utilization (Dalian Minzu University), Ministry of Education, China
| | - Lulu Wang
- Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian, 116600, Liaoning, China; Key Laboratory of Biotechnology and Bioresources Utilization (Dalian Minzu University), Ministry of Education, China; School of Life Science and Biotechnology, Dalian University of Technology, No 2 Linggong Road, Dalian, 116024, Liaoning, China
| | - Fei Shang
- Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian, 116600, Liaoning, China; Key Laboratory of Biotechnology and Bioresources Utilization (Dalian Minzu University), Ministry of Education, China
| | - Wei Liu
- Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian, 116600, Liaoning, China; Key Laboratory of Biotechnology and Bioresources Utilization (Dalian Minzu University), Ministry of Education, China
| | - Jing Lan
- Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian, 116600, Liaoning, China; Key Laboratory of Biotechnology and Bioresources Utilization (Dalian Minzu University), Ministry of Education, China
| | - Jinli Chen
- Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian, 116600, Liaoning, China; Key Laboratory of Biotechnology and Bioresources Utilization (Dalian Minzu University), Ministry of Education, China
| | - Nam-Chul Ha
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Chunshan Quan
- Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian, 116600, Liaoning, China; Key Laboratory of Biotechnology and Bioresources Utilization (Dalian Minzu University), Ministry of Education, China.
| | - Ki Hyun Nam
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Republic of Korea; Institute of Life Science and Natural Resources, Korea University, Seoul, 02841, Republic of Korea.
| | - Yongbin Xu
- Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian, 116600, Liaoning, China; Key Laboratory of Biotechnology and Bioresources Utilization (Dalian Minzu University), Ministry of Education, China.
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The PLUTO plastidial nucleobase transporter also transports the thiamin precursor hydroxymethylpyrimidine. Biosci Rep 2018; 38:BSR20180048. [PMID: 29507060 PMCID: PMC5874261 DOI: 10.1042/bsr20180048] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 03/03/2018] [Accepted: 03/05/2018] [Indexed: 12/31/2022] Open
Abstract
In plants, the hydroxymethylpyrimidine (HMP) and thiazole precursors of thiamin are synthesized and coupled together to form thiamin in plastids. Mutants unable to form HMP can be rescued by exogenous HMP, implying the presence of HMP transporters in the plasma membrane and plastids. Analysis of bacterial genomes revealed a transporter gene that is chromosomally clustered with thiamin biosynthesis and salvage genes. Its closest Arabidopsis homolog, the plastidic nucleobase transporter (PLUTO), is co-expressed with several thiamin biosynthetic enzymes. Heterologous expression of PLUTO in Escherichia coli or Saccharomyces cerevisiae increased sensitivity to a toxic HMP analog, and disrupting PLUTO in an HMP-requiring Arabidopsis line reduced root growth at low HMP concentrations. These data implicate PLUTO in plastidial transport and salvage of HMP.
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Wang L, Maranas CD. MinGenome: An In Silico Top-Down Approach for the Synthesis of Minimized Genomes. ACS Synth Biol 2018; 7:462-473. [PMID: 29254336 DOI: 10.1021/acssynbio.7b00296] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Genome minimized strains offer advantages as production chassis by reducing transcriptional cost, eliminating competing functions and limiting unwanted regulatory interactions. Existing approaches for identifying stretches of DNA to remove are largely ad hoc based on information on presumably dispensable regions through experimentally determined nonessential genes and comparative genomics. Here we introduce a versatile genome reduction algorithm MinGenome that implements a mixed-integer linear programming (MILP) algorithm to identify in size descending order all dispensable contiguous sequences without affecting the organism's growth or other desirable traits. Known essential genes or genes that cause significant fitness or performance loss can be flagged and their deletion can be prohibited. MinGenome also preserves needed transcription factors and promoter regions ensuring that retained genes will be properly transcribed while also avoiding the simultaneous deletion of synthetic lethal pairs. The potential benefit of removing even larger contiguous stretches of DNA if only one or two essential genes (to be reinserted elsewhere) are within the deleted sequence is explored. We applied the algorithm to design a minimized E. coli strain and found that we were able to recapitulate the long deletions identified in previous experimental studies and discover alternative combinations of deletions that have not yet been explored in vivo.
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Affiliation(s)
- Lin Wang
- Department of Chemical
Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Costas D. Maranas
- Department of Chemical
Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
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