1
|
Muduli S, Karmakar S, Mishra S. The coordinated action of the enzymes in the L-lysine biosynthetic pathway and how to inhibit it for antibiotic targets. Biochim Biophys Acta Gen Subj 2023; 1867:130320. [PMID: 36813209 DOI: 10.1016/j.bbagen.2023.130320] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 01/19/2023] [Accepted: 02/02/2023] [Indexed: 02/22/2023]
Abstract
BACKGROUND Antimicrobial resistance is a global health issue that requires immediate attention in terms of new antibiotics and new antibiotic targets. The l-lysine biosynthesis pathway (LBP) is a promising avenue for drug discovery as it is essential for bacterial growth and survival and is not required by human beings. SCOPE OF REVIEW The LBP involves a coordinated action of fourteen different enzymes distributed over four distinct sub-pathways. The enzymes involved in this pathway belong to different classes, such as aspartokinase, dehydrogenase, aminotransferase, epimerase, etc. This review provides a comprehensive account of the secondary and tertiary structure, conformational dynamics, active site architecture, mechanism of catalytic action, and inhibitors of all enzymes involved in LBP of different bacterial species. MAJOR CONCLUSIONS LBP offers a wide scope for novel antibiotic targets. The enzymology of a majority of the LBP enzymes is well understood, although these enzymes are less widely studied in the critical pathogens (according to the 2017 WHO report) that require immediate attention. In particular, the enzymes in the acetylase pathway, DapAT, DapDH, and Aspartokinase in critical pathogens have received little attention. High throughput screening for inhibitor design against the enzymes of lysine biosynthetic pathway is rather limited, both in number and in the extent of success. GENERAL SIGNIFICANCE This review can serve as a guide for the enzymology of LBP and help in identifying new drug targets and designing potential inhibitors.
Collapse
Affiliation(s)
- Sunita Muduli
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Soumyajit Karmakar
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Sabyashachi Mishra
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, India.
| |
Collapse
|
2
|
Weatherhead AW, Crowther JM, Horne CR, Meng Y, Coombes D, Currie MJ, Watkin SAJ, Adams LE, Parthasarathy A, Dobson RCJ, Hudson AO. Structure-Function Studies of the Antibiotic Target l,l-Diaminopimelate Aminotransferase from Verrucomicrobium spinosum Reveal an Unusual Oligomeric Structure. Biochemistry 2020; 59:2274-2288. [PMID: 32478518 DOI: 10.1021/acs.biochem.0c00185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
While humans lack the biosynthetic pathways for meso-diaminopimelate and l-lysine, they are essential for bacterial survival and are therefore attractive targets for antibiotics. It was recently discovered that members of the Chlamydia family utilize a rare aminotransferase route of the l-lysine biosynthetic pathway, thus offering a new enzymatic drug target. Here we characterize diaminopimelate aminotransferase from Verrucomicrobium spinosum (VsDapL), a nonpathogenic model bacterium for Chlamydia trachomatis. Complementation experiments verify that the V. spinosum dapL gene encodes a bona fide diaminopimelate aminotransferase, because the gene rescues an Escherichia coli strain that is auxotrophic for meso-diaminopimelate. Kinetic studies show that VsDapL follows a Michaelis-Menten mechanism, with a KMapp of 4.0 mM toward its substrate l,l-diaminopimelate. The kcat (0.46 s-1) and the kcat/KM (115 s-1 M-1) are somewhat lower than values for other diaminopimelate aminotransferases. Moreover, whereas other studied DapL orthologs are dimeric, sedimentation velocity experiments demonstrate that VsDapL exists in a monomer-dimer self-association, with a KD2-1 of 7.4 μM. The 2.25 Å resolution crystal structure presents the canonical dimer of chalice-shaped monomers, and small-angle X-ray scattering experiments confirm the dimer in solution. Sequence and structural alignments reveal that active site residues important for activity are conserved in VsDapL, despite the lower activity compared to those of other DapL homologues. Although the dimer interface buries 18% of the total surface area, several loops that contribute to the interface and active site, notably the L1, L2, and L5 loops, are highly mobile, perhaps explaining the unstable dimer and lower catalytic activity. Our kinetic, biophysical, and structural characterization can be used to inform the development of antibiotics.
Collapse
Affiliation(s)
- Anthony W Weatherhead
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, P.O. Box 4800, Christchurch 8140, New Zealand
| | - Jennifer M Crowther
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, P.O. Box 4800, Christchurch 8140, New Zealand
| | - Christopher R Horne
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, P.O. Box 4800, Christchurch 8140, New Zealand
| | - Yanxiang Meng
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, P.O. Box 4800, Christchurch 8140, New Zealand
| | - David Coombes
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, P.O. Box 4800, Christchurch 8140, New Zealand
| | - Michael J Currie
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, P.O. Box 4800, Christchurch 8140, New Zealand
| | - Serena A J Watkin
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, P.O. Box 4800, Christchurch 8140, New Zealand
| | - Lily E Adams
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, New York 14623-5603, United States
| | - Anutthaman Parthasarathy
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, New York 14623-5603, United States
| | - Renwick C J Dobson
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, P.O. Box 4800, Christchurch 8140, New Zealand.,Bio21 Molecular Science and Biotechnology Institute, Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - André O Hudson
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, New York 14623-5603, United States
| |
Collapse
|
3
|
Hudson AO, Harkness TCM, Savka MA. Functional Complementation Analysis (FCA): A Laboratory Exercise Designed and Implemented to Supplement the Teaching of Biochemical Pathways. J Vis Exp 2016:53850. [PMID: 27403640 PMCID: PMC4993271 DOI: 10.3791/53850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023] Open
Abstract
Functional complementation assay (FCA) is an in vivo assay that is widely used to elucidate the function/role of genes/enzymes. This technique is very common in biochemistry, genetics and many other disciplines. A comprehensive overview of the technique to supplement the teaching of biochemical pathways pertaining to amino acids, peptidoglycan and the bacterial stringent response is reported in this manuscript. Two cDNAs from the model plant organism Arabidopsis thaliana that are involved in the metabolism of lysine (L,L-diaminopimelate aminotransferase (dapL) and tyrosine aminotransferase (tyrB) involved in the metabolism of tyrosine and phenylalanine are highlighted. In addition, the bacterial peptidoglycan anabolic pathway is highlighted through the analysis of the UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-meso-2,6-diaminopimelate ligase (murE) gene from the bacterium Verrucomicrobium spinosum involved in the cross-linking of peptidoglycan. The bacterial stringent response is also reported through the analysis of the rsh (relA/spoT homolog) bifunctional gene responsible for a hyper-mucoid phenotype in the bacterium Novosphingobium sp. Four examples of FCA are presented. The video will focus on three of them, namely lysine, peptidoglycan and the stringent response.
Collapse
Affiliation(s)
- André O Hudson
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology;
| | - Taylor C M Harkness
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology
| | - Michael A Savka
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology
| |
Collapse
|
4
|
Nachar VR, Savka FC, McGroty SE, Donovan KA, North RA, Dobson RCJ, Buckley LJ, Hudson AO. Genomic and Biochemical Analysis of the Diaminopimelate and Lysine Biosynthesis Pathway in Verrucomicrobium spinosum: Identification and Partial Characterization of L,L-Diaminopimelate Aminotransferase and UDP-N-Acetylmuramoylalanyl-D-glutamyl-2,6-meso-Diaminopimelate Ligase. Front Microbiol 2012; 3:183. [PMID: 22783236 PMCID: PMC3390587 DOI: 10.3389/fmicb.2012.00183] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2012] [Accepted: 05/02/2012] [Indexed: 11/20/2022] Open
Abstract
The Gram-negative bacterium Verrucomicrobium spinosum has attracted interest in recent years following the sequencing and annotation of its genome. Comparative genomic analysis of V. spinosum using diaminopimelate/lysine metabolic genes from Chlamydia trachomatis suggests that V. spinosum employs the L,L-diaminopimelate aminotransferase (DapL) pathway for diaminopimelate/lysine biosynthesis. The open reading frame corresponding to the putative dapL ortholog was cloned and the recombinant enzyme was shown to possess L,L-diaminopimelate aminotransferase activity in vitro. In vivo analysis using functional complementation confirmed that the dapL ortholog was able to functionally complement an E. coli mutant that confers auxotrophy for diaminopimelate and lysine. In addition to its role in lysine biosynthesis, the intermediate diaminopimelate has an integral role in peptidoglycan biosynthesis. To this end, the UDP-N-acetylmuramoylalanyl-d-glutamyl-2,6-meso-diaminopimelate ligase ortholog was also identified, cloned, and was shown to possess meso-diaminopimelate ligase activity in vivo. The L,L-diaminopimelate aminotransferase pathway has been experimentally confirmed in several bacteria, some of which are deemed pathogenic to animals. Since animals, and particularly humans, lack the genetic machinery for the synthesis of diaminopimelate/lysine de novo, the enzymes involved in this pathway are attractive targets for development of antibiotics. Whether dapL is an essential gene in any bacteria is currently not known. V. spinosum is an excellent candidate to investigate the essentiality of dapL, since the bacterium employs the DapL pathway for lysine and cell wall biosynthesis, is non-pathogenic to humans, facile to grow, and can be genetically manipulated.
Collapse
Affiliation(s)
- Victoria R Nachar
- The Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology Rochester, NY, USA
| | | | | | | | | | | | | | | |
Collapse
|
5
|
Dobson RCJ, Girón I, Hudson AO. L,L-diaminopimelate aminotransferase from Chlamydomonas reinhardtii: a target for algaecide development. PLoS One 2011; 6:e20439. [PMID: 21633707 PMCID: PMC3102117 DOI: 10.1371/journal.pone.0020439] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2011] [Accepted: 04/29/2011] [Indexed: 11/21/2022] Open
Abstract
In some bacterial species and photosynthetic cohorts, including algae, the enzyme
l,l-diaminopimelate aminotransferase
(DapL) (E.C. 2.6.1.83) is involved in the anabolism of the essential amino acid
L-lysine. DapL catalyzes the conversion of
tetrahydrodipicolinate (THDPA) to
l,l-diaminopimelate
(l,l-DAP), in one step bypassing the
DapD, DapC and DapE enzymatic reactions present in the acyl DAP pathways. Here
we present an in vivo and in vitro
characterization of the DapL ortholog from the alga Chlamydomonas
reinhardtii (Cr-DapL). The in
vivo analysis illustrated that the enzyme is able to functionally
complement the E. coli dap auxotrophs and was essential for
plant development in Arabidopsis. In vitro, the enzyme was able
to inter-convert THDPA and l,l-DAP, showing
strong substrate specificity. Cr-DapL was dimeric in both
solution and when crystallized. The structure of Cr-DapL was
solved in its apo form, showing an overall architecture of a
α/β protein with each monomer in the dimer adopting a pyridoxal
phosphate-dependent transferase-like fold in a V-shaped conformation. The active
site comprises residues from both monomers in the dimer and shows some
rearrangement when compared to the apo-DapL structure from
Arabidopsis. Since animals do not possess the enzymatic machinery necessary for
the de novo synthesis of the amino acid
l-lysine, enzymes involved in this pathway are
attractive targets for the development of antibiotics, herbicides and
algaecides.
Collapse
Affiliation(s)
- Renwick C. J. Dobson
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science
and Biotechnology Institute, The University of Melbourne, Parkville, Victoria,
Australia
- Biomolecular Interaction Centre, School of Biological Sciences,
University of Canterbury, Christchurch, New Zealand
- * E-mail: (RCJD); (AOH)
| | - Irma Girón
- School of Biological Sciences, Rochester Institute of Technology,
Rochester, New York, United States of America
| | - André O. Hudson
- School of Biological Sciences, Rochester Institute of Technology,
Rochester, New York, United States of America
- * E-mail: (RCJD); (AOH)
| |
Collapse
|