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Mak DA, Dunn S, Coombes D, Carere CR, Allison JR, Nock V, Hudson AO, Dobson RCJ. Enzyme Kinetics Analysis: An online tool for analyzing enzyme initial rate data and teaching enzyme kinetics. Biochem Mol Biol Educ 2024; 52:348-358. [PMID: 38400827 DOI: 10.1002/bmb.21823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 01/29/2024] [Indexed: 02/26/2024]
Abstract
Enzymes are nature's catalysts, mediating chemical processes in living systems. The study of enzyme function and mechanism includes defining the maximum catalytic rate and affinity for substrate/s (among other factors), referred to as enzyme kinetics. Enzyme kinetics is a staple of biochemistry curricula and other disciplines, from molecular and cellular biology to pharmacology. However, because enzyme kinetics involves concepts rarely employed in other areas of biology, it can be challenging for students and researchers. Traditional graphical analysis was replaced by computational analysis, requiring another skill not core to many life sciences curricula. Computational analysis can be time-consuming and difficult in free software (e.g., R) or require costly software (e.g., GraphPad Prism). We present Enzyme Kinetics Analysis (EKA), a web-tool to augment teaching and learning and streamline EKA. EKA is an interactive and free tool for analyzing enzyme kinetic data and improving student learning through simulation, built using R and RStudio's ShinyApps. EKA provides kinetic models (Michaelis-Menten, Hill, simple reversible inhibition models, ternary-complex, and ping-pong) for users to fit experimental data, providing graphical results and statistics. Additionally, EKA enables users to input parameters and create data and graphs, to visualize changes to parameters (e.g.,K M or number of measurements). This function is designed for students learning kinetics but also for researchers to design experiments. EKA (enzyme-kinetics.shinyapps.io/enzkinet_webpage/) provides a simple, interactive interface for teachers, students, and researchers to explore enzyme kinetics. It gives researchers the ability to design experiments and analyze data without specific software requirements.
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Affiliation(s)
- Daniel A Mak
- Biomolecular Interaction Centre, Maurice Wilkins Centre for Molecular Biodiscovery, MacDiarmid Institute for Advanced Materials and Nanotechnology, and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- Department of Electrical and Computer Engineering, MacDiarmid Institute for Advanced Materials and Nanotechnology, Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
| | - Sebastian Dunn
- Digital Life Institute, Maurice Wilkins Centre for Molecular Biodiscovery, School of Biological Sciences, University of Auckland and The Graphics Group and School of Computer Science, University of Auckland, Auckland, New Zealand
| | - David Coombes
- Biomolecular Interaction Centre, Maurice Wilkins Centre for Molecular Biodiscovery, MacDiarmid Institute for Advanced Materials and Nanotechnology, and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Carlo R Carere
- Department of Chemical and Process Engineering, Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
| | - Jane R Allison
- Digital Life Institute, Maurice Wilkins Centre for Molecular Biodiscovery, Biomolecular Interaction Centre, and School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Volker Nock
- Department of Electrical and Computer Engineering, MacDiarmid Institute for Advanced Materials and Nanotechnology, Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
| | - André O Hudson
- The Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology (RIT), Rochester, New York, USA
| | - Renwick C J Dobson
- Biomolecular Interaction Centre, Maurice Wilkins Centre for Molecular Biodiscovery, MacDiarmid Institute for Advanced Materials and Nanotechnology, and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia
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2
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Shearer HL, Currie MJ, Agnew HN, Trappetti C, Stull F, Pace PE, Paton JC, Dobson RCJ, Dickerhof N. Hypothiocyanous acid reductase is critical for host colonization and infection by Streptococcus pneumoniae. J Biol Chem 2024; 300:107282. [PMID: 38604564 DOI: 10.1016/j.jbc.2024.107282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 03/26/2024] [Accepted: 04/01/2024] [Indexed: 04/13/2024] Open
Abstract
The major human pathogen Streptococcus pneumoniae encounters the immune-derived oxidant hypothiocyanous acid (HOSCN) at sites of colonization and infection. We recently identified the pneumococcal hypothiocyanous acid reductase (Har), a member of the flavoprotein disulfide reductase enzyme family, and showed that it contributes to the HOSCN tolerance of S. pneumoniae in vitro. Here, we demonstrate in mouse models of pneumococcal infection that Har is critical for colonization and invasion. In a colonization model, bacterial load was attenuated dramatically in the nasopharynx when har was deleted in S. pneumoniae. The Δhar strain was also less virulent compared to wild type in an invasion model as reflected by a significant reduction in bacteria in the lungs and no dissemination to the blood and brain. Kinetic measurements with recombinant Har demonstrated that this enzyme reduced HOSCN with near diffusion-limited catalytic efficiency, using either NADH (kcat/KM = 1.2 × 108 M-1s-1) or NADPH (kcat/KM = 2.5 × 107 M-1s-1) as electron donors. We determined the X-ray crystal structure of Har in complex with the FAD cofactor to 1.50 Å resolution, highlighting the active site architecture characteristic for this class of enzymes. Collectively, our results demonstrate that pneumococcal Har is a highly efficient HOSCN reductase, enabling survival against oxidative host immune defenses. In addition, we provide structural insights that may aid the design of Har inhibitors.
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Affiliation(s)
- Heather L Shearer
- Department of Pathology and Biomedical Science, Mātai Hāora - Centre for Redox Biology and Medicine, University of Otago Christchurch, Christchurch, New Zealand; Biomolecular Interaction Centre, MacDiarmid Institute for Advanced Materials and Nanotechnology and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, New Zealand
| | - Michael J Currie
- Biomolecular Interaction Centre, MacDiarmid Institute for Advanced Materials and Nanotechnology and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, New Zealand
| | - Hannah N Agnew
- Department of Molecular and Biomedical Science, Research Centre for Infectious Diseases, University of Adelaide, Adelaide, Australia
| | - Claudia Trappetti
- Department of Molecular and Biomedical Science, Research Centre for Infectious Diseases, University of Adelaide, Adelaide, Australia
| | - Frederick Stull
- Department of Chemistry, Western Michigan University, Kalamazoo, Michigan, USA
| | - Paul E Pace
- Department of Pathology and Biomedical Science, Mātai Hāora - Centre for Redox Biology and Medicine, University of Otago Christchurch, Christchurch, New Zealand
| | - James C Paton
- Department of Molecular and Biomedical Science, Research Centre for Infectious Diseases, University of Adelaide, Adelaide, Australia
| | - Renwick C J Dobson
- Biomolecular Interaction Centre, MacDiarmid Institute for Advanced Materials and Nanotechnology and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, New Zealand; Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Nina Dickerhof
- Department of Pathology and Biomedical Science, Mātai Hāora - Centre for Redox Biology and Medicine, University of Otago Christchurch, Christchurch, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, New Zealand.
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3
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Davies JS, Currie MJ, Dobson RCJ, Horne CR, North RA. TRAPs: the 'elevator-with-an-operator' mechanism. Trends Biochem Sci 2024; 49:134-144. [PMID: 38102017 DOI: 10.1016/j.tibs.2023.11.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 11/18/2023] [Accepted: 11/21/2023] [Indexed: 12/17/2023]
Abstract
Tripartite ATP-independent periplasmic (TRAP) transporters are nutrient-uptake systems found in bacteria and archaea. These evolutionary divergent transporter systems couple a substrate-binding protein (SBP) to an elevator-type secondary transporter, which is a first-of-its-kind mechanism of transport. Here, we highlight breakthrough TRAP transporter structures and recent functional data that probe the mechanism of transport. Furthermore, we discuss recent structural and biophysical studies of the ion transporter superfamily (ITS) members and highlight mechanistic principles that are relevant for further exploration of the TRAP transporter system.
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Affiliation(s)
- James S Davies
- Department of Biochemistry and Biophysics, Stockholm University, 106 91 Stockholm, Sweden
| | - Michael J Currie
- Biomolecular Interaction Centre, Maurice Wilkins Centre for Biodiscovery, MacDiarmid Institute for Advanced Materials and Nanotechnology, Christchurch 8140, New Zealand; School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
| | - Renwick C J Dobson
- Biomolecular Interaction Centre, Maurice Wilkins Centre for Biodiscovery, MacDiarmid Institute for Advanced Materials and Nanotechnology, Christchurch 8140, New Zealand; School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand; Bio21 Molecular Science and Biotechnology Institute, Department of Biochemistry and Pharmacology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Christopher R Horne
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia; Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Parkville, VIC 3052, Australia.
| | - Rachel A North
- Department of Biochemistry and Biophysics, Stockholm University, 106 91 Stockholm, Sweden; School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia.
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4
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Manners SH, Carere CR, Dhami MK, Dobson RCJ, Stott MB. Draft genome sequence of Thermococcus waiotapuensis WT1 T, a thermophilic sulfur-dependent archaeon from the order Thermococcales. Microbiol Resour Announc 2024; 13:e0081523. [PMID: 38095867 DOI: 10.1128/mra.00815-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Accepted: 11/21/2023] [Indexed: 12/23/2023] Open
Abstract
Thermococcus waiotapuensis WT1T is a thermophilic, peptide, and amino acid-fermenting archaeon from the order Thermococcales. It was isolated from Waiotapu, Aotearoa-New Zealand, and has a genome size of 1.80 Mbp. The genome contains 2,000 total genes, of which 1,913 encode proteins and 46 encode tRNA.
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Affiliation(s)
- Sarah H Manners
- Te Kura Pūtaiao Koiora School of Biological Sciences, Te Whare Wānanga o Waitaha University of Canterbury , Christchurch, New Zealand
- Biomolecular Interaction Centre, Te Whare Wānanga o Waitaha, University of Canterbury , Christchurch, New Zealand
| | - Carlo R Carere
- Biomolecular Interaction Centre, Te Whare Wānanga o Waitaha, University of Canterbury , Christchurch, New Zealand
- Department of Chemical and Process Engineering, Te Tari Pūhanga Tukanga Matū, Te Whare Wānanga o Waitaha, University of Canterbury , Christchurch, New Zealand
| | - Manpreet K Dhami
- Biocontrol and Molecular Ecology, Manaaki Whenua Landcare Research , Lincoln, New Zealand
| | - Renwick C J Dobson
- Te Kura Pūtaiao Koiora School of Biological Sciences, Te Whare Wānanga o Waitaha University of Canterbury , Christchurch, New Zealand
- Biomolecular Interaction Centre, Te Whare Wānanga o Waitaha, University of Canterbury , Christchurch, New Zealand
| | - Matthew B Stott
- Te Kura Pūtaiao Koiora School of Biological Sciences, Te Whare Wānanga o Waitaha University of Canterbury , Christchurch, New Zealand
- Biomolecular Interaction Centre, Te Whare Wānanga o Waitaha, University of Canterbury , Christchurch, New Zealand
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5
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Watkin SAJ, Bennie RZ, Gilkes JM, Nock VM, Pearce FG, Dobson RCJ. On the utility of microfluidic systems to study protein interactions: advantages, challenges, and applications. Eur Biophys J 2023; 52:459-471. [PMID: 36583735 PMCID: PMC9801160 DOI: 10.1007/s00249-022-01626-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 12/15/2022] [Accepted: 12/20/2022] [Indexed: 12/31/2022]
Abstract
Within the complex milieu of a cell, which comprises a large number of different biomolecules, interactions are critical for function. In this post-reductionist era of biochemical research, the 'holy grail' for studying biomolecular interactions is to be able to characterize them in native environments. While there are a limited number of in situ experimental techniques currently available, there is a continuing need to develop new methods for the analysis of biomolecular complexes that can cope with the additional complexities introduced by native-like solutions. We think approaches that use microfluidics allow researchers to access native-like environments for studying biological problems. This review begins with a brief overview of the importance of studying biomolecular interactions and currently available methods for doing so. Basic principles of diffusion and microfluidics are introduced and this is followed by a review of previous studies that have used microfluidics to measure molecular diffusion and a discussion of the advantages and challenges of this technique.
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Affiliation(s)
- Serena A J Watkin
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Rachel Z Bennie
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Jenna M Gilkes
- Protein Science and Engineering Team, Callaghan Innovation, Christchurch, New Zealand
| | - Volker M Nock
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand.
- Department of Electrical and Computer Engineering, University of Canterbury, Christchurch, New Zealand.
- The MacDiarmid Institute for Advanced Materials and Nanotechnology, Wellington, New Zealand.
| | - F Grant Pearce
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand.
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.
| | - Renwick C J Dobson
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand.
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.
- The MacDiarmid Institute for Advanced Materials and Nanotechnology, Wellington, New Zealand.
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, VIC, Australia.
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Mckerchar HJ, Lento C, Bennie RZ, Crowther JM, Dolamore F, Dyer JM, Clerens S, Mercadante D, Wilson DJ, Dobson RCJ. The protein dynamics of bovine and caprine β-lactoglobulin differ as a function of pH. Food Chem 2023; 408:135229. [PMID: 36563618 DOI: 10.1016/j.foodchem.2022.135229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 11/28/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022]
Abstract
The properties of milk proteins differ between mammalian species. β-Lactoglobulin (βlg) proteins from caprine and bovine milk are sequentially and structurally highly similar, yet their physicochemical properties differ, particularly in response to pH. To resolve this conundrum, we compared the dynamics of both the monomeric and dimeric states for each homologue at pH 6.9 and 7.5 using hydrogen/deuterium exchange experiments. At pH 7.5, the rate of exchange is similar across both homologues, but at pH 6.9 the dimeric states of the bovine βlg B variant homologue have significantly more conformational flexibility compared with caprine βlg. Molecular dynamics simulations provide a mechanistic rationale for the experimental observations, revealing that variant-specific substitutions encode different conformational ensembles with different dynamic properties consistent with the hydrogen/deuterium exchange experiments. Understanding the dynamic differences across βlg homologues is essential to understand the different responses of these milks to processing, human digestion, and differences in immunogenicity.
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Affiliation(s)
- Hannah J Mckerchar
- Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand; Riddet Institute, based at Massey University, Palmerston North 4442, New Zealand; Protein and Metabolites Team, AgResearch Lincoln Research Centre, Lincoln 7608, New Zealand
| | - Cristina Lento
- Department of Chemistry, York University, Toronto, Ontario M3J 1P3, Canada
| | - Rachel Z Bennie
- Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
| | - Jennifer M Crowther
- Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
| | - Fabian Dolamore
- Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
| | - Jolon M Dyer
- Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand; The New Zealand Institute for Plant and Food Research, Lincoln Research Centre, Lincoln 7608, New Zealand; Department of Wine, Food and Molecular Biosciences, Lincoln University, Lincoln 7647, New Zealand
| | - Stefan Clerens
- Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand; Riddet Institute, based at Massey University, Palmerston North 4442, New Zealand; Protein and Metabolites Team, AgResearch Lincoln Research Centre, Lincoln 7608, New Zealand
| | - Davide Mercadante
- School of Chemical Sciences, The University of Auckland, Auckland 1010, New Zealand
| | - Derek J Wilson
- Department of Chemistry, York University, Toronto, Ontario M3J 1P3, Canada; Centre for Research in Mass Spectrometry, Toronto, Ontario M3J 1P3, Canada
| | - Renwick C J Dobson
- Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand; Riddet Institute, based at Massey University, Palmerston North 4442, New Zealand; Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria 3010, Australia.
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7
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Davies JS, Currie MJ, North RA, Scalise M, Wright JD, Copping JM, Remus DM, Gulati A, Morado DR, Jamieson SA, Newton-Vesty MC, Abeysekera GS, Ramaswamy S, Friemann R, Wakatsuki S, Allison JR, Indiveri C, Drew D, Mace PD, Dobson RCJ. Structure and mechanism of a tripartite ATP-independent periplasmic TRAP transporter. Nat Commun 2023; 14:1120. [PMID: 36849793 PMCID: PMC9971032 DOI: 10.1038/s41467-023-36590-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 02/07/2023] [Indexed: 03/01/2023] Open
Abstract
In bacteria and archaea, tripartite ATP-independent periplasmic (TRAP) transporters uptake essential nutrients. TRAP transporters receive their substrates via a secreted soluble substrate-binding protein. How a sodium ion-driven secondary active transporter is strictly coupled to a substrate-binding protein is poorly understood. Here we report the cryo-EM structure of the sialic acid TRAP transporter SiaQM from Photobacterium profundum at 2.97 Å resolution. SiaM comprises a "transport" domain and a "scaffold" domain, with the transport domain consisting of helical hairpins as seen in the sodium ion-coupled elevator transporter VcINDY. The SiaQ protein forms intimate contacts with SiaM to extend the size of the scaffold domain, suggesting that TRAP transporters may operate as monomers, rather than the typically observed oligomers for elevator-type transporters. We identify the Na+ and sialic acid binding sites in SiaM and demonstrate a strict dependence on the substrate-binding protein SiaP for uptake. We report the SiaP crystal structure that, together with docking studies, suggest the molecular basis for how sialic acid is delivered to the SiaQM transporter complex. We thus propose a model for substrate transport by TRAP proteins, which we describe herein as an 'elevator-with-an-operator' mechanism.
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Affiliation(s)
- James S Davies
- Biomolecular Interaction Centre, Maurice Wilkins Centre for Biodiscovery, MacDiarmid Institute for Advanced Materials and Nanotechnology and School of Biological Sciences, University of Canterbury, PO Box 4800, Christchurch, 8140, New Zealand.,Department of Biochemistry and Biophysics, Stockholm University, 10691, Stockholm, Sweden
| | - Michael J Currie
- Biomolecular Interaction Centre, Maurice Wilkins Centre for Biodiscovery, MacDiarmid Institute for Advanced Materials and Nanotechnology and School of Biological Sciences, University of Canterbury, PO Box 4800, Christchurch, 8140, New Zealand
| | - Rachel A North
- Biomolecular Interaction Centre, Maurice Wilkins Centre for Biodiscovery, MacDiarmid Institute for Advanced Materials and Nanotechnology and School of Biological Sciences, University of Canterbury, PO Box 4800, Christchurch, 8140, New Zealand. .,Department of Biochemistry and Biophysics, Stockholm University, 10691, Stockholm, Sweden.
| | - Mariafrancesca Scalise
- Department DiBEST (Biologia, Ecologia, Scienze della Terra) Unit of Biochemistry and Molecular Biotechnology, University of Calabria, Via P. Bucci 4C, 87036, Arcavacata di Rende, Italy
| | - Joshua D Wright
- Biomolecular Interaction Centre, Maurice Wilkins Centre for Biodiscovery, MacDiarmid Institute for Advanced Materials and Nanotechnology and School of Biological Sciences, University of Canterbury, PO Box 4800, Christchurch, 8140, New Zealand
| | - Jack M Copping
- Biomolecular Interaction Centre, Digital Life Institute, Maurice Wilkins Centre for Molecular Biodiscovery, and School of Biological Sciences, University of Auckland, Auckland, 1010, New Zealand
| | - Daniela M Remus
- Biomolecular Interaction Centre, Maurice Wilkins Centre for Biodiscovery, MacDiarmid Institute for Advanced Materials and Nanotechnology and School of Biological Sciences, University of Canterbury, PO Box 4800, Christchurch, 8140, New Zealand
| | - Ashutosh Gulati
- Department of Biochemistry and Biophysics, Stockholm University, 10691, Stockholm, Sweden
| | - Dustin R Morado
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 17165, Solna, Sweden
| | - Sam A Jamieson
- Biochemistry Department, School of Biomedical Sciences, University of Otago, Dunedin, 9054, New Zealand
| | - Michael C Newton-Vesty
- Biomolecular Interaction Centre, Maurice Wilkins Centre for Biodiscovery, MacDiarmid Institute for Advanced Materials and Nanotechnology and School of Biological Sciences, University of Canterbury, PO Box 4800, Christchurch, 8140, New Zealand
| | - Gayan S Abeysekera
- Biomolecular Interaction Centre, Maurice Wilkins Centre for Biodiscovery, MacDiarmid Institute for Advanced Materials and Nanotechnology and School of Biological Sciences, University of Canterbury, PO Box 4800, Christchurch, 8140, New Zealand
| | - Subramanian Ramaswamy
- Biological Sciences and Biomedical Engineering, Bindley Bioscience Center, Purdue University, 1203 W State St, West Lafayette, IN 47906, USA
| | - Rosmarie Friemann
- Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Box 440, S-40530, Gothenburg, Sweden
| | - Soichi Wakatsuki
- Biological Sciences Division, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA.,Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Jane R Allison
- Biomolecular Interaction Centre, Digital Life Institute, Maurice Wilkins Centre for Molecular Biodiscovery, and School of Biological Sciences, University of Auckland, Auckland, 1010, New Zealand
| | - Cesare Indiveri
- Department DiBEST (Biologia, Ecologia, Scienze della Terra) Unit of Biochemistry and Molecular Biotechnology, University of Calabria, Via P. Bucci 4C, 87036, Arcavacata di Rende, Italy.,CNR Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), Via Amendola 122/O, 70126, Bari, Italy
| | - David Drew
- Department of Biochemistry and Biophysics, Stockholm University, 10691, Stockholm, Sweden
| | - Peter D Mace
- Biochemistry Department, School of Biomedical Sciences, University of Otago, Dunedin, 9054, New Zealand
| | - Renwick C J Dobson
- Biomolecular Interaction Centre, Maurice Wilkins Centre for Biodiscovery, MacDiarmid Institute for Advanced Materials and Nanotechnology and School of Biological Sciences, University of Canterbury, PO 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.
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Watkin SAJ, Hashemi A, Thomson DR, Pearce FG, Dobson RCJ, Nock VM. Laminar flow-based microfluidic systems for molecular interaction analysis-Part 1: Chip development, system operation and measurement setup. Methods Enzymol 2023; 682:53-100. [PMID: 36948712 DOI: 10.1016/bs.mie.2022.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The recent advent of laminar flow-based microfluidic systems for molecular interaction analysis has enabled transformative new profiling of proteins in regards to their structure, disordering, complex formation and interactions in general. Based on the diffusive transport of molecules perpendicular to the direction of laminar flow in a microfluidic channel, systems of this type promise continuous-flow, high-throughput screening of complex, multi-molecule interactions, while remaining tolerant to heterogeneous mixtures. Using common microfluidic device processing, the technology provides unique opportunities, as well as device design and experimental challenges, for integrative sample handling approaches that can investigate biomolecular interaction events in complex samples with readily available laboratory equipment. In this first chapter of a two-part series, we introduce system design and experimental setup requirements for a typical laminar flow-based microfluidic system for molecular interaction analysis in the form of what we call the 'LaMInA system' (Laminar flow-based Molecular Interaction Analysis system). We provide microfluidic device development advice on choice of device material, device design, including impact of channel geometry on the signal acquisition, and on design limitations and possible post-fabrication treatments to redress these. Finally. we cover aspects of fluidic actuation, such as selecting, measuring and controlling the flow rate appropriately, and provide a guide to possible fluorescent labels for proteins, as well as options for the fluorescence detection hardware, all in the context of assisting the reader in developing their own laminar flow-based experimental setup for biomolecular interaction analysis.
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Affiliation(s)
- Serena A J Watkin
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand; School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Azadeh Hashemi
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand; School of Biological Sciences, University of Canterbury, Christchurch, New Zealand; Department of Electrical & Computer Engineering, University of Canterbury, Christchurch, New Zealand; The MacDiarmid Institute for Advanced Materials and Nanotechnology, Wellington, New Zealand
| | - Dion R Thomson
- Protein Science & Engineering Team, Callaghan Innovation, Christchurch, New Zealand
| | - F Grant Pearce
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand; School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.
| | - Renwick C J Dobson
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand; School of Biological Sciences, University of Canterbury, Christchurch, New Zealand; The MacDiarmid Institute for Advanced Materials and Nanotechnology, Wellington, New Zealand; Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, Australia.
| | - Volker M Nock
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand; Department of Electrical & Computer Engineering, University of Canterbury, Christchurch, New Zealand; The MacDiarmid Institute for Advanced Materials and Nanotechnology, Wellington, New Zealand.
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9
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Watkin SAJ, Hashemi A, Thomson DR, Nock VM, Dobson RCJ, Pearce FG. Laminar flow-based microfluidic systems for molecular interaction analysis-Part 2: Data extraction, processing and analysis. Methods Enzymol 2023; 682:429-464. [PMID: 36948710 DOI: 10.1016/bs.mie.2022.12.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The rate at which fluorescently-labeled biomolecules, that are flowing at a constant speed in a microfluidic channel, diffuse into an adjacent buffer stream can be used to calculate the diffusion coefficient of the molecule, which then gives a measure of its size. Experimentally, determining the rate of diffusion involves capturing concentration gradients in fluorescence microscopy images at different distances along the length of the microfluidic channel, where distance corresponds to residence time, based on the flow velocity. The preceding chapter in this journal covered the development of the experimental setup, including information about the microscope camera detection systems used to acquire fluorescence microscopy data. In order to calculate diffusion coefficients from fluorescence microscopy images, intensity data are extracted from the images and then appropriate methods of processing and analyzing the data, including the mathematical models used for fitting, are applied to the extracted data. This chapter begins with a brief overview of digital imaging and analysis principles, before introducing custom software for extracting the intensity data from the fluorescence microscopy images. Subsequently, methods and explanations for performing the necessary corrections and appropriate scaling of the data are provided. Finally, the mathematics of one-dimensional molecular diffusion is described, and analytical approaches to obtaining the diffusion coefficient from the fluorescence intensity profiles are discussed and compared.
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Affiliation(s)
- Serena A J Watkin
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand; School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Azadeh Hashemi
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand; School of Biological Sciences, University of Canterbury, Christchurch, New Zealand; Department of Electrical & Computer Engineering, University of Canterbury, Christchurch, New Zealand; The MacDiarmid Institute for Advanced Materials and Nanotechnology, Wellington, New Zealand
| | - Dion R Thomson
- Protein Science & Engineering Team, Callaghan Innovation, Christchurch, New Zealand
| | - Volker M Nock
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand; Department of Electrical & Computer Engineering, University of Canterbury, Christchurch, New Zealand; The MacDiarmid Institute for Advanced Materials and Nanotechnology, Wellington, New Zealand.
| | - Renwick C J Dobson
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand; School of Biological Sciences, University of Canterbury, Christchurch, New Zealand; The MacDiarmid Institute for Advanced Materials and Nanotechnology, Wellington, New Zealand; Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, Australia.
| | - F Grant Pearce
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand; School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.
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10
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Abeysekera GS, Love MJ, Manners SH, Billington C, Dobson RCJ. Bacteriophage-encoded lethal membrane disruptors: Advances in understanding and potential applications. Front Microbiol 2022; 13:1044143. [PMID: 36345304 PMCID: PMC9636201 DOI: 10.3389/fmicb.2022.1044143] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Accepted: 10/10/2022] [Indexed: 09/09/2023] Open
Abstract
Holins and spanins are bacteriophage-encoded membrane proteins that control bacterial cell lysis in the final stage of the bacteriophage reproductive cycle. Due to their efficient mechanisms for lethal membrane disruption, these proteins are gaining interest in many fields, including the medical, food, biotechnological, and pharmaceutical fields. However, investigating these lethal proteins is challenging due to their toxicity in bacterial expression systems and the resultant low protein yields have hindered their analysis compared to other cell lytic proteins. Therefore, the structural and dynamic properties of holins and spanins in their native environment are not well-understood. In this article we describe recent advances in the classification, purification, and analysis of holin and spanin proteins, which are beginning to overcome the technical barriers to understanding these lethal membrane disrupting proteins, and through this, unlock many potential biotechnological applications.
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Affiliation(s)
- Gayan S. Abeysekera
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Michael J. Love
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- Health and Environment Group, Institute of Environmental Science and Research, Christchurch, New Zealand
| | - Sarah H. Manners
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Craig Billington
- Health and Environment Group, Institute of Environmental Science and Research, Christchurch, New Zealand
| | - Renwick C. J. Dobson
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- Department of Biochemistry and Molecular Biology, University of Melbourne, Melbourne, VIC, Australia
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11
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Bozzola T, Scalise M, Larsson CU, Newton-Vesty MC, Rovegno C, Mitra A, Cramer J, Wahlgren WY, Radhakrishnan Santhakumari P, Johnsson RE, Schwardt O, Ernst B, Friemann R, Dobson RCJ, Indiveri C, Schelin J, Nilsson UJ, Ellervik U. Sialic Acid Derivatives Inhibit SiaT Transporters and Delay Bacterial Growth. ACS Chem Biol 2022; 17:1890-1900. [PMID: 35675124 PMCID: PMC9295122 DOI: 10.1021/acschembio.2c00321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
![]()
Antibiotic resistance
is a major worldwide concern, and new drugs
with mechanistically novel modes of action are urgently needed. Here,
we report the structure-based drug design, synthesis, and evaluation
in vitro and in cellular systems of sialic acid derivatives able to
inhibit the bacterial sialic acid symporter SiaT. We designed and
synthesized 21 sialic acid derivatives and screened their affinity
for SiaT by a thermal shift assay and elucidated the inhibitory mechanism
through binding thermodynamics, computational methods, and inhibitory
kinetic studies. The most potent compounds, which have a 180-fold
higher affinity compared to the natural substrate, were tested in
bacterial growth assays and indicate bacterial growth delay in methicillin-resistant Staphylococcus aureus. This study represents the
first example and a promising lead in developing sialic acid uptake
inhibitors as novel antibacterial agents.
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Affiliation(s)
- Tiago Bozzola
- Centre for Analysis and Synthesis, Department of Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden.,Molecular Pharmacy Group, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
| | - Mariafrancesca Scalise
- Department DiBEST (Biologia, Ecologia, Scienze della Terra) Unit of Biochemistry and Molecular Biotechnology, University of Calabria, Via P. Bucci 4C, 87036 Arcavacata di Rende, Italy
| | - Christer U Larsson
- Division of Applied Microbiology, Department of Chemistry, Lund University, 22100 Lund, Sweden
| | - Michael C Newton-Vesty
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, 8140 Christchurch, New Zealand
| | - Caterina Rovegno
- Centre for Analysis and Synthesis, Department of Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Ankita Mitra
- Centre for Analysis and Synthesis, Department of Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Jonathan Cramer
- Molecular Pharmacy Group, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland.,Institute for Pharmaceutical and Medicinal Chemistry, Heinrich-Heine-University of Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Weixiao Yuan Wahlgren
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, S-40530 Gothenburg, Sweden
| | - Partha Radhakrishnan Santhakumari
- Institute for Stem Cell Science and Regenerative Medicine, Bengaluru, Karnataka 560065, India.,Manipal Academy of Higher Education, Tiger Circle Road, Manipal, Karnataka 576104, India
| | | | - Oliver Schwardt
- Molecular Pharmacy Group, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
| | - Beat Ernst
- Molecular Pharmacy Group, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
| | - Rosmarie Friemann
- Department of Clinical Microbiology, Sahlgrenska University Hospital, 41345 Gothenburg, Sweden.,Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, 40530 Gothenburg, Sweden
| | - Renwick C J Dobson
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, 8140 Christchurch, New Zealand.,Bio21 Molecular Science and Biotechnology Institute, Department of Biochemistry and Pharmacology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Cesare Indiveri
- Department DiBEST (Biologia, Ecologia, Scienze della Terra) Unit of Biochemistry and Molecular Biotechnology, University of Calabria, Via P. Bucci 4C, 87036 Arcavacata di Rende, Italy.,Institute of Biomembranes, Bioenergetics and Molecular Biotechnology (IBIOM), National Research Council-CNR, Via Amendola 122/O, 70126 Bari, Italy
| | - Jenny Schelin
- Division of Applied Microbiology, Department of Chemistry, Lund University, 22100 Lund, Sweden
| | - Ulf J Nilsson
- Centre for Analysis and Synthesis, Department of Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Ulf Ellervik
- Centre for Analysis and Synthesis, Department of Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
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12
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Harper AR, Dobson RCJ, Morris VK, Moggré GJ. Fermentation of plant-based dairy alternatives by lactic acid bacteria. Microb Biotechnol 2022; 15:1404-1421. [PMID: 35393728 PMCID: PMC9049613 DOI: 10.1111/1751-7915.14008] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 01/12/2022] [Accepted: 01/14/2022] [Indexed: 12/19/2022] Open
Abstract
Ethical, environmental and health concerns around dairy products are driving a fast‐growing industry for plant‐based dairy alternatives, but undesirable flavours and textures in available products are limiting their uptake into the mainstream. The molecular processes initiated during fermentation by lactic acid bacteria in dairy products is well understood, such as proteolysis of caseins into peptides and amino acids, and the utilisation of carbohydrates to form lactic acid and exopolysaccharides. These processes are fundamental to developing the flavour and texture of fermented dairy products like cheese and yoghurt, yet how these processes work in plant‐based alternatives is poorly understood. With this knowledge, bespoke fermentative processes could be engineered for specific food qualities in plant‐based foods. This review will provide an overview of recent research that reveals how fermentation occurs in plant‐based milk, with a focus on how differences in plant proteins and carbohydrate structure affect how they undergo the fermentation process. The practical aspects of how this knowledge has been used to develop plant‐based cheeses and yoghurts is also discussed.
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Affiliation(s)
- Aimee R Harper
- Biomolecular Interaction Centre, Food Transitions 2050 Joint Postgraduate School, and School of Biological Sciences, University of Canterbury, PO Box 4800, Christchurch, 8140, New Zealand.,The New Zealand Institute for Plant and Food Research Limited, 74 Gerald St, Lincoln, 7608, New Zealand.,The Riddet Institute, MacDiarmid Institute for Advanced Materials and Nanotechnology, University of Canterbury, PO Box 4800, Christchurch, 8140, New Zealand
| | - Renwick C J Dobson
- Biomolecular Interaction Centre, Food Transitions 2050 Joint Postgraduate School, and School of Biological Sciences, University of Canterbury, PO Box 4800, Christchurch, 8140, New Zealand.,The Riddet Institute, MacDiarmid Institute for Advanced Materials and Nanotechnology, University of Canterbury, PO Box 4800, Christchurch, 8140, New Zealand.,Bio21 Molecular Science and Biotechnology Institute, Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Vic., 3010, Australia
| | - Vanessa K Morris
- Biomolecular Interaction Centre, Food Transitions 2050 Joint Postgraduate School, and School of Biological Sciences, University of Canterbury, PO Box 4800, Christchurch, 8140, New Zealand
| | - Gert-Jan Moggré
- The New Zealand Institute for Plant and Food Research Limited, 74 Gerald St, Lincoln, 7608, New Zealand
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13
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Meffan C, Menges J, Dolamore F, Mak D, Fee C, Dobson RCJ, Nock V. Capillaric field effect transistors. Microsyst Nanoeng 2022; 8:33. [PMID: 35371537 PMCID: PMC8934874 DOI: 10.1038/s41378-022-00360-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 11/29/2021] [Accepted: 01/27/2022] [Indexed: 06/14/2023]
Abstract
Controlling fluid flow in capillaric circuits is a key requirement to increase their uptake for assay applications. Capillary action off-valves provide such functionality by pushing an occluding bubble into the channel using a difference in capillary pressure. Previously, we utilized the binary switching mode of this structure to develop a powerful set of fundamental fluidic valving operations. In this work, we study the transistor-like qualities of the off-valve and provide evidence that these structures are in fact functionally complementary to electronic junction field effect transistors. In view of this, we propose the new term capillaric field effect transistor to describe these types of valves. To support this conclusion, we present a theoretical description, experimental characterization, and practical application of analog flow resistance control. In addition, we demonstrate that the valves can also be reopened. We show modulation of the flow resistance from fully open to pinch-off, determine the flow rate-trigger channel volume relationship and demonstrate that the latter can be modeled using Shockley's equation for electronic transistors. Finally, we provide a first example of how the valves can be opened and closed repeatedly.
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Affiliation(s)
- Claude Meffan
- Department of Electrical and Computer Engineering, University of Canterbury, Christchurch, 8041 New Zealand
- Department of Microengineering, Kyoto University, 615-8540 Kyoto, Japan
| | - Julian Menges
- Department of Electrical and Computer Engineering, University of Canterbury, Christchurch, 8041 New Zealand
- School of Biological Sciences, University of Canterbury, Christchurch, 8041 New Zealand
- Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Christchurch, 8041 New Zealand
| | - Fabian Dolamore
- School of Biological Sciences, University of Canterbury, Christchurch, 8041 New Zealand
- Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Christchurch, 8041 New Zealand
| | - Daniel Mak
- Department of Electrical and Computer Engineering, University of Canterbury, Christchurch, 8041 New Zealand
- Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Christchurch, 8041 New Zealand
| | - Conan Fee
- Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Christchurch, 8041 New Zealand
- School of Product Design, University of Canterbury, Christchurch, 8041 New Zealand
| | - Renwick C. J. Dobson
- Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Christchurch, 8041 New Zealand
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC 3010 Australia
- The MacDiarmid Institute for Advanced Materials and Nanotechnology, Wellington, 6140 New Zealand
| | - Volker Nock
- Department of Electrical and Computer Engineering, University of Canterbury, Christchurch, 8041 New Zealand
- Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Christchurch, 8041 New Zealand
- The MacDiarmid Institute for Advanced Materials and Nanotechnology, Wellington, 6140 New Zealand
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14
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Lassé M, Stampfli AR, Orban T, Bothara RK, Gerrard JA, Fairbanks AJ, Pattinson NR, Dobson RCJ. Corrigendum to "Reaction dynamics and residue identification of haemoglobin modification by acrolein, a lipid-peroxidation by-product" [Biochimica et Biophysica Acta (BBA) - General Subjects Volume 1865, Issue 12, December 2021, 130013]. Biochim Biophys Acta Gen Subj 2022; 1866:130117. [PMID: 35249766 DOI: 10.1016/j.bbagen.2022.130117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
- Moritz Lassé
- Christchurch Heart Institute, Department of Medicine, University of Otago, Christchurch, New Zealand
| | - Anja R Stampfli
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Thomas Orban
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | | | - Juliet A Gerrard
- Faculty of Science, Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Antony J Fairbanks
- Biomolecular Interaction Centre, and School of Physical and Chemical Sciences, University of Canterbury, Christchurch, New Zealand
| | - Neil R Pattinson
- Canterbury Scientific Ltd, 71 Whiteleigh Ave, Christchurch, New Zealand
| | - Renwick C J Dobson
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand; Biol21 Molecular Science and Biotechnology Institute, Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria 3010, Australia.
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15
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Board AJ, Crowther JM, Acevedo-Fani A, Meisrimler CN, Jameson GB, Dobson RCJ. How plants solubilise seed fats: revisiting oleosin structure and function to inform commercial applications. Biophys Rev 2022; 14:257-266. [PMID: 35340610 PMCID: PMC8921422 DOI: 10.1007/s12551-021-00923-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 11/23/2021] [Indexed: 01/11/2023] Open
Abstract
Plants store triacylglycerides in organelles called oil bodies, which are important fuel sources for germination. Oil bodies consist of a lipid core surrounded by an interfacial single layer membrane of phospholipids and proteins. Oleosins are highly conserved plant proteins that are important for oil body formation, solubilising the triacylglycerides, stabilising oil bodies, and playing a role in mobilising the fuel during the germination process. The domain structure of oleosins is well established, with N- and C-terminal domains that are hydrophilic flanking a long hydrophobic domain that is proposed to protrude into the triacylglyceride core of the oil body. However, beyond this general understanding, little molecular level detail on the structure is available and what is known is disputed. This lack of knowledge limits our understanding of oleosin function and concomitantly our ability to engineer them. Here, we review the state of play in the literature regarding oleosin structure and function, and provide some examples of how oleosins can be used in commercial settings.
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Affiliation(s)
- Amanda J. Board
- Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Christchurch, 8041 New Zealand ,Riddet Institute, Massey University, Palmerston North, New Zealand
| | - Jennifer M. Crowther
- Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Christchurch, 8041 New Zealand ,Riddet Institute, Massey University, Palmerston North, New Zealand
| | | | - Claudia-Nicole Meisrimler
- Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Christchurch, 8041 New Zealand
| | - Geoffrey B. Jameson
- Riddet Institute, Massey University, Palmerston North, New Zealand ,School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Renwick C. J. Dobson
- Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Christchurch, 8041 New Zealand ,Riddet Institute, Massey University, Palmerston North, New Zealand ,Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC Australia
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16
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Arif T, Currie MJ, Dobson RCJ, Newson HL, Poonthiyil V, Fairbanks AJ, North RA, Rendle PM. Synthesis of N-acetylmannosamine-6-phosphate derivatives to investigate the mechanism of N-acetylmannosamine-6-phosphate 2-epimerase. Carbohydr Res 2021; 510:108445. [PMID: 34607125 DOI: 10.1016/j.carres.2021.108445] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 09/14/2021] [Accepted: 09/21/2021] [Indexed: 11/19/2022]
Abstract
The synthesis of analogues of natural enzyme substrates can be used to help deduce enzymatic mechanisms. N-Acetylmannosamine-6-phosphate 2-epimerase is an enzyme in the bacterial sialic acid catabolic pathway. To investigate whether the mechanism of this enzyme involves a re-protonation mechanism by the same neighbouring lysine that performed the deprotonation or a unique substrate-assisted proton displacement mechanism involving the substrate C5 hydroxyl, the syntheses of two analogues of the natural substrate, N-acetylmannosamine-6-phosphate, are described. In these novel analogues, the C5 hydroxyl has been replaced with a proton and a methyl ether respectively. As recently reported, Staphylococcus aureus N-acetylmannosamine-6-phosphate 2-epimerase was co-crystallized with these two compounds. The 5-deoxy variant bound to the enzyme active site in a different orientation to the natural substrate, while the 5-methoxy variant did not bind, adding to the evidence that this enzyme uses a substrate-assisted proton displacement mechanism. This mechanistic information may help in the design of potential antibacterial drug candidates.
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Affiliation(s)
- Tanzeel Arif
- Ferrier Research Institute, Victoria University of Wellington, PO Box 33-436, Lower Hutt, 5046, New Zealand
| | - Michael J Currie
- University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand
| | - Renwick C J Dobson
- University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand
| | - Harriet L Newson
- Ferrier Research Institute, Victoria University of Wellington, PO Box 33-436, Lower Hutt, 5046, New Zealand
| | - Vivek Poonthiyil
- University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand
| | - Antony J Fairbanks
- University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand
| | - Rachel A North
- University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand
| | - Phillip M Rendle
- Ferrier Research Institute, Victoria University of Wellington, PO Box 33-436, Lower Hutt, 5046, New Zealand.
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17
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Currie MJ, Manjunath L, Horne CR, Rendle PM, Subramanian R, Friemann R, Fairbanks AJ, Muscroft-Taylor AC, North RA, Dobson RCJ. N-acetylmannosamine-6-phosphate 2-epimerase uses a novel substrate-assisted mechanism to catalyze amino sugar epimerization. J Biol Chem 2021; 297:101113. [PMID: 34437902 PMCID: PMC8482478 DOI: 10.1016/j.jbc.2021.101113] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 08/18/2021] [Accepted: 08/20/2021] [Indexed: 11/14/2022] Open
Abstract
There are five known general catalytic mechanisms used by enzymes to catalyze carbohydrate epimerization. The amino sugar epimerase N-acetylmannosamine-6-phosphate 2-epimerase (NanE) has been proposed to use a deprotonation-reprotonation mechanism, with an essential catalytic lysine required for both steps. However, the structural determinants of this mechanism are not clearly established. We characterized NanE from Staphylococcus aureus using a new coupled assay to monitor NanE catalysis in real time and found that it has kinetic constants comparable with other species. The crystal structure of NanE from Staphylococcus aureus, which comprises a triosephosphate isomerase barrel fold with an unusual dimeric architecture, was solved with both natural and modified substrates. Using these substrate-bound structures, we identified the following active-site residues lining the cleft at the C-terminal end of the β-strands: Gln11, Arg40, Lys63, Asp124, Glu180, and Arg208, which were individually substituted and assessed in relation to the mechanism. From this, we re-evaluated the central role of Glu180 in this mechanism alongside the catalytic lysine. We observed that the substrate is bound in a conformation that ideally positions the C5 hydroxyl group to be activated by Glu180 and donate a proton to the C2 carbon. Taken together, we propose that NanE uses a novel substrate-assisted proton displacement mechanism to invert the C2 stereocenter of N-acetylmannosamine-6-phosphate. Our data and mechanistic interpretation may be useful in the development of inhibitors of this enzyme or in enzyme engineering to produce biocatalysts capable of changing the stereochemistry of molecules that are not amenable to synthetic methods.
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Affiliation(s)
- Michael J Currie
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Lavanyaa Manjunath
- Institute of Stem Cell Science and Regenerative Medicine, NCBS, Bangalore, Karnataka, India
| | - Christopher R Horne
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Phillip M Rendle
- Ferrier Research Institute, Victoria University of Wellington, Lower Hutt, New Zealand
| | - Ramaswamy Subramanian
- Institute of Stem Cell Science and Regenerative Medicine, NCBS, Bangalore, Karnataka, India
| | - Rosmarie Friemann
- Fujirebio Diagnostics, Gothenburg, Sweden; Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Antony J Fairbanks
- Biomolecular Interaction Centre and School of Physical and Chemical Sciences, University of Canterbury, Christchurch, New Zealand
| | - Andrew C Muscroft-Taylor
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Rachel A North
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand; Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
| | - Renwick C J Dobson
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand; Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia.
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18
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Lassé M, Stampfli AR, Orban T, Bothara RK, Gerrard JA, Fairbanks AJ, Pattinson NR, Dobson RCJ. Reaction dynamics and residue identification of haemoglobin modification by acrolein, a lipid-peroxidation by-product. Biochim Biophys Acta Gen Subj 2021; 1865:130013. [PMID: 34534644 DOI: 10.1016/j.bbagen.2021.130013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 09/06/2021] [Accepted: 09/10/2021] [Indexed: 11/15/2022]
Abstract
BACKGROUND Lipid hydroperoxides decompose to reactive aldehydes, such as acrolein. Measurement of oxidative stress markers in the clinic could improve risk stratification for patients. METHODS To aid the development of diagnostic oxidative stress markers, we defined the acrolein modifications of haemoglobin using mass spectrometry. RESULTS Acrolein modifications have little effect on the secondary structure of haemoglobin. They do not disrupt the quaternary structure, but instead promote crosslinked octamers. For acrolein modified haemoglobin the response to O2 binding is altered such that cooperativity is lost. Mass spectrometry experiments at a 1:1 acrolein:haemoglobin molar ratio demonstrate that the α-chain quickly forms an aza-Michael adduct (+56 Da), which then forms a more stable adduct, Nε-(3-methylpyridinium)lysine (MP-lysine, +76 Da) over 7 days. The β-chain remains relatively unchanged over the duration of the 7 days and the aza-Michael adduct is dominant. At 2:1 and 5:1 molar ratios the α-chain was consistently modified at K7, H20, H50, and the β-chain at C93 and H97 with the aza-Michael adduct. Beyond 5 h, an MP-adduct (+76 Da) was located predominantly at K7 of the α-chain, while an FDP-adduct (+94 Da) was observed at K95 of the β-chain. CONCLUSIONS We have generated qualitative evidence identifying the acrolein target sites on haemoglobin, a potential oxidative stress marker that is easily measured in circulation. GENERAL SIGNIFICANCE We provide data for the community to develop targeted mass spectrometric or immunometric assays for acrolein modified haemoglobin to further validate the potential of haemoglobin as an oxidative stress marker in patients .
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Affiliation(s)
- Moritz Lassé
- Christchurch Heart Institute, Department of Medicine, University of Otago, Christchurch, New Zealand
| | - Anja R Stampfli
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Thomas Orban
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | | | - Juliet A Gerrard
- Faculty of Science, Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Antony J Fairbanks
- Biomolecular Interaction Centre, and School of Physical and Chemical Sciences, University of Canterbury, Christchurch, New Zealand
| | - Neil R Pattinson
- Canterbury Scientific Ltd, 71 Whiteleigh Ave, Christchurch, New Zealand
| | - Renwick C J Dobson
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand; Biol21 Molecular Science and Biotechnology Institute, Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria 3010, Australia.
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19
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Davies JS, Currie MJ, Wright JD, Newton-Vesty MC, North RA, Mace PD, Allison JR, Dobson RCJ. Selective Nutrient Transport in Bacteria: Multicomponent Transporter Systems Reign Supreme. Front Mol Biosci 2021; 8:699222. [PMID: 34268334 PMCID: PMC8276074 DOI: 10.3389/fmolb.2021.699222] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 06/02/2021] [Indexed: 11/24/2022] Open
Abstract
Multicomponent transporters are used by bacteria to transport a wide range of nutrients. These systems use a substrate-binding protein to bind the nutrient with high affinity and then deliver it to a membrane-bound transporter for uptake. Nutrient uptake pathways are linked to the colonisation potential and pathogenicity of bacteria in humans and may be candidates for antimicrobial targeting. Here we review current research into bacterial multicomponent transport systems, with an emphasis on the interaction at the membrane, as well as new perspectives on the role of lipids and higher oligomers in these complex systems.
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Affiliation(s)
- James S Davies
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Michael J Currie
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Joshua D Wright
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Michael C Newton-Vesty
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Rachel A North
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Peter D Mace
- Biochemistry Department, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Jane R Allison
- Maurice Wilkins Centre for Molecular Biodiscovery and School of Biological Sciences, Digital Life Institute, University of Auckland, Auckland, New Zealand
| | - Renwick C J Dobson
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.,Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, Australia
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20
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Pilapitiya DH, Harris PWR, Hanson-Manful P, McGregor R, Kowalczyk R, Raynes JM, Carlton LH, Dobson RCJ, Baker MG, Brimble M, Lukomski S, Moreland NJ. Antibody responses to collagen peptides and streptococcal collagen-like 1 proteins in acute rheumatic fever patients. Pathog Dis 2021; 79:6311134. [PMID: 34185083 DOI: 10.1093/femspd/ftab033] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 06/26/2021] [Indexed: 11/13/2022] Open
Abstract
Acute rheumatic fever (ARF) is a serious post-infectious immune sequelae of Group A streptococcus (GAS). Pathogenesis remains poorly understood, including the events associated with collagen autoantibody generation. GAS express streptococcal collagen-like proteins (Scl) that contain a collagenous domain resembling human collagen. Here, the relationship between antibody reactivity to GAS Scl proteins and human collagen in ARF was investigated. Serum IgG specific for a representative Scl protein (Scl1.1) together with collagen-I and collagen-IV mimetic peptides were quantified in ARF patients (n = 36) and healthy matched controls (n = 36). Reactivity to Scl1.1 was significantly elevated in ARF compared to controls (P < 0.0001) and this was mapped to the collagen-like region of the protein, rather than the N-terminal non-collagenous region. Reactivity to collagen-1 and collagen-IV peptides was also significantly elevated in ARF cases (P < 0.001). However, there was no correlation between Scl1.1 and collagen peptide antibody binding, and hierarchical clustering of ARF cases by IgG reactivity showed two distinct clusters, with Scl1.1 antigens in one and collagen peptides in the other, demonstrating that collagen autoantibodies are not immunologically related to those targeting Scl1.1. Thus, anti-collagen antibodies in ARF appear to be generated as part of the autoreactivity process, independent of any mimicry with GAS collagen-like proteins.
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Affiliation(s)
- Devaki H Pilapitiya
- School of Medical Sciences, The University of Auckland, Auckland, New Zealand
| | - Paul W R Harris
- School of Chemical Sciences, The University of Auckland, Auckland, New Zealand.,Maurice Wilkins Centre for Biodiscovery, The University of Auckland, Auckland, New Zealand.,School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Paulina Hanson-Manful
- School of Medical Sciences, The University of Auckland, Auckland, New Zealand.,Maurice Wilkins Centre for Biodiscovery, The University of Auckland, Auckland, New Zealand
| | - Reuben McGregor
- School of Medical Sciences, The University of Auckland, Auckland, New Zealand.,Maurice Wilkins Centre for Biodiscovery, The University of Auckland, Auckland, New Zealand
| | - Renata Kowalczyk
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Jeremy M Raynes
- School of Medical Sciences, The University of Auckland, Auckland, New Zealand.,Maurice Wilkins Centre for Biodiscovery, The University of Auckland, Auckland, New Zealand
| | - Lauren H Carlton
- School of Medical Sciences, The University of Auckland, Auckland, New Zealand
| | - Renwick C J Dobson
- Maurice Wilkins Centre for Biodiscovery, The University of Auckland, Auckland, New Zealand.,Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.,Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Michael G Baker
- Maurice Wilkins Centre for Biodiscovery, The University of Auckland, Auckland, New Zealand.,Department of Public Health, University of Otago, Wellington, New Zealand
| | - Margaret Brimble
- School of Chemical Sciences, The University of Auckland, Auckland, New Zealand.,Maurice Wilkins Centre for Biodiscovery, The University of Auckland, Auckland, New Zealand
| | - Slawomir Lukomski
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University School of Medicine, Morgantown, WV, USA
| | - Nicole J Moreland
- School of Medical Sciences, The University of Auckland, Auckland, New Zealand.,Maurice Wilkins Centre for Biodiscovery, The University of Auckland, Auckland, New Zealand
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21
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Turk LS, Kuang X, Dal Pozzo V, Patel K, Chen M, Huynh K, Currie MJ, Mitchell D, Dobson RCJ, D'Arcangelo G, Dai W, Comoletti D. The structure-function relationship of a signaling-competent, dimeric Reelin fragment. Structure 2021; 29:1156-1170.e6. [PMID: 34089653 DOI: 10.1016/j.str.2021.05.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 04/26/2021] [Accepted: 05/14/2021] [Indexed: 01/21/2023]
Abstract
Reelin operates through canonical and non-canonical pathways that mediate several aspects of brain development and function. Reelin's dimeric central fragment (CF), generated through proteolytic cleavage, is required for the lipoprotein-receptor-dependent canonical pathway activation. Here, we analyze the signaling properties of a variety of Reelin fragments and measure the differential binding affinities of monomeric and dimeric CF fragments to lipoprotein receptors to investigate the mode of canonical signal activation. We also present the cryoelectron tomography-solved dimeric structure of Reelin CF and support it using several other biophysical techniques. Our findings suggest that Reelin CF forms a covalent parallel dimer with some degree of flexibility between the two protein chains. As a result of this conformation, Reelin binds to lipoprotein receptors in a manner inaccessible to its monomeric form and is capable of stimulating canonical pathway signaling.
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Affiliation(s)
- Liam S Turk
- Child Health Institute of New Jersey, New Brunswick, NJ 08901, USA; Department of Neuroscience and Cell Biology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA; School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Xuyuan Kuang
- Department of Cell Biology and Neuroscience, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Department of Hyperbaric Oxygen, Central South University, Changsha, Hunan Province, China
| | - Valentina Dal Pozzo
- Department of Cell Biology and Neuroscience, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Khush Patel
- Department of Cell Biology and Neuroscience, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Muyuan Chen
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kevin Huynh
- Department of Cell Biology and Neuroscience, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Michael J Currie
- Biomolecular Interactions Centre and School of Biological Sciences, University of Canterbury, Christchurch 8041, New Zealand
| | - Daniel Mitchell
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Renwick C J Dobson
- Biomolecular Interactions Centre and School of Biological Sciences, University of Canterbury, Christchurch 8041, New Zealand; Bio21 Molecular Science and Biotechnology Institute, Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Gabriella D'Arcangelo
- Department of Cell Biology and Neuroscience, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Wei Dai
- Department of Cell Biology and Neuroscience, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
| | - Davide Comoletti
- Child Health Institute of New Jersey, New Brunswick, NJ 08901, USA; Department of Neuroscience and Cell Biology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA; School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand.
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22
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Horne CR, Venugopal H, Panjikar S, Wood DM, Henrickson A, Brookes E, North RA, Murphy JM, Friemann R, Griffin MDW, Ramm G, Demeler B, Dobson RCJ. Mechanism of NanR gene repression and allosteric induction of bacterial sialic acid metabolism. Nat Commun 2021; 12:1988. [PMID: 33790291 PMCID: PMC8012715 DOI: 10.1038/s41467-021-22253-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 03/03/2021] [Indexed: 12/20/2022] Open
Abstract
Bacteria respond to environmental changes by inducing transcription of some genes and repressing others. Sialic acids, which coat human cell surfaces, are a nutrient source for pathogenic and commensal bacteria. The Escherichia coli GntR-type transcriptional repressor, NanR, regulates sialic acid metabolism, but the mechanism is unclear. Here, we demonstrate that three NanR dimers bind a (GGTATA)3-repeat operator cooperatively and with high affinity. Single-particle cryo-electron microscopy structures reveal the DNA-binding domain is reorganized to engage DNA, while three dimers assemble in close proximity across the (GGTATA)3-repeat operator. Such an interaction allows cooperative protein-protein interactions between NanR dimers via their N-terminal extensions. The effector, N-acetylneuraminate, binds NanR and attenuates the NanR-DNA interaction. The crystal structure of NanR in complex with N-acetylneuraminate reveals a domain rearrangement upon N-acetylneuraminate binding to lock NanR in a conformation that weakens DNA binding. Our data provide a molecular basis for the regulation of bacterial sialic acid metabolism. The GntR superfamily is one of the largest families of transcription factors in prokaryotes. Here the authors combine biophysical analysis and structural biology to dissect the mechanism by which NanR — a GntR-family regulator — binds to its promoter to repress the transcription of genes necessary for sialic acid metabolism.
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Affiliation(s)
- Christopher R Horne
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Hariprasad Venugopal
- Clive and Vera Ramaciotti Centre for Cryo-Electron Microscopy, Monash University, Clayton, VIC, Australia
| | - Santosh Panjikar
- Australian Synchrotron, ANSTO, Clayton, VIC, Australia.,Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
| | - David M Wood
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Amy Henrickson
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, Canada
| | - Emre Brookes
- Department of Chemistry, University of Montana, Missoula, MT, USA
| | - Rachel A North
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - James M Murphy
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Rosmarie Friemann
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden.,Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Michael D W Griffin
- Bio21 Molecular Science and Biotechnology Institute, Department of Biochemistry and Pharmacology, University of Melbourne, Parkville, VIC, Australia
| | - Georg Ramm
- Clive and Vera Ramaciotti Centre for Cryo-Electron Microscopy, Monash University, Clayton, VIC, Australia.,Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
| | - Borries Demeler
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, Canada.,Department of Chemistry, University of Montana, Missoula, MT, USA
| | - Renwick C J Dobson
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand. .,Bio21 Molecular Science and Biotechnology Institute, Department of Biochemistry and Pharmacology, University of Melbourne, Parkville, VIC, Australia.
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23
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Peskin AV, Meotti FC, Kean KM, Göbl C, Peixoto AS, Pace PE, Horne CR, Heath SG, Crowther JM, Dobson RCJ, Karplus PA, Winterbourn CC. Modifying the resolving cysteine affects the structure and hydrogen peroxide reactivity of peroxiredoxin 2. J Biol Chem 2021; 296:100494. [PMID: 33667550 PMCID: PMC8049995 DOI: 10.1016/j.jbc.2021.100494] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 02/23/2021] [Accepted: 02/26/2021] [Indexed: 01/05/2023] Open
Abstract
Peroxiredoxin 2 (Prdx2) is a thiol peroxidase with an active site Cys (C52) that reacts rapidly with H2O2 and other peroxides. The sulfenic acid product condenses with the resolving Cys (C172) to form a disulfide which is recycled by thioredoxin or GSH via mixed disulfide intermediates or undergoes hyperoxidation to the sulfinic acid. C172 lies near the C terminus, outside the active site. It is not established whether structural changes in this region, such as mixed disulfide formation, affect H2O2 reactivity. To investigate, we designed mutants to cause minimal (C172S) or substantial (C172D and C172W) structural disruption. Stopped flow kinetics and mass spectrometry showed that mutation to Ser had minimal effect on rates of oxidation and hyperoxidation, whereas Asp and Trp decreased both by ∼100-fold. To relate to structural changes, we solved the crystal structures of reduced WT and C172S Prdx2. The WT structure is highly similar to that of the published hyperoxidized form. C172S is closely related but more flexible and as demonstrated by size exclusion chromatography and analytical ultracentrifugation, a weaker decamer. Size exclusion chromatography and analytical ultracentrifugation showed that the C172D and C172W mutants are also weaker decamers than WT, and small-angle X-ray scattering analysis indicated greater flexibility with partially unstructured regions consistent with C-terminal unfolding. We propose that these structural changes around C172 negatively impact the active site geometry to decrease reactivity with H2O2. This is relevant for Prdx turnover as intermediate mixed disulfides with C172 would also be disruptive and could potentially react with peroxides before resolution is complete.
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Affiliation(s)
- Alexander V Peskin
- Department of Pathology and Biomedical Science, University of Otago Christchurch, Christchurch, New Zealand
| | - Flavia C Meotti
- Department of Biochemistry, Chemistry Institute, University of Sao Paulo, Sao Paulo, SP, Brazil
| | - Kelsey M Kean
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon, USA
| | - Christoph Göbl
- Department of Pathology and Biomedical Science, University of Otago Christchurch, Christchurch, New Zealand
| | - Albert Souza Peixoto
- Department of Biochemistry, Chemistry Institute, University of Sao Paulo, Sao Paulo, SP, Brazil
| | - Paul E Pace
- Department of Pathology and Biomedical Science, University of Otago Christchurch, Christchurch, New Zealand
| | - Christopher R Horne
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Sarah G Heath
- Department of Pathology and Biomedical Science, University of Otago Christchurch, Christchurch, New Zealand
| | - Jennifer M Crowther
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Renwick C J Dobson
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - P Andrew Karplus
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon, USA.
| | - Christine C Winterbourn
- Department of Pathology and Biomedical Science, University of Otago Christchurch, Christchurch, New Zealand.
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24
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Parthasarathy A, Borrego EJ, Savka MA, Dobson RCJ, Hudson AO. Amino acid-derived defense metabolites from plants: A potential source to facilitate novel antimicrobial development. J Biol Chem 2021; 296:100438. [PMID: 33610552 PMCID: PMC8024917 DOI: 10.1016/j.jbc.2021.100438] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 02/16/2021] [Accepted: 02/17/2021] [Indexed: 12/23/2022] Open
Abstract
For millennia, humanity has relied on plants for its medicines, and modern pharmacology continues to reexamine and mine plant metabolites for novel compounds and to guide improvements in biological activity, bioavailability, and chemical stability. The critical problem of antibiotic resistance and increasing exposure to viral and parasitic diseases has spurred renewed interest into drug treatments for infectious diseases. In this context, an urgent revival of natural product discovery is globally underway with special attention directed toward the numerous and chemically diverse plant defensive compounds such as phytoalexins and phytoanticipins that combat herbivores, microbial pathogens, or competing plants. Moreover, advancements in “omics,” chemistry, and heterologous expression systems have facilitated the purification and characterization of plant metabolites and the identification of possible therapeutic targets. In this review, we describe several important amino acid–derived classes of plant defensive compounds, including antimicrobial peptides (e.g., defensins, thionins, and knottins), alkaloids, nonproteogenic amino acids, and phenylpropanoids as potential drug leads, examining their mechanisms of action, therapeutic targets, and structure–function relationships. Given their potent antibacterial, antifungal, antiparasitic, and antiviral properties, which can be superior to existing drugs, phytoalexins and phytoanticipins are an excellent resource to facilitate the rational design and development of antimicrobial drugs.
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Affiliation(s)
- Anutthaman Parthasarathy
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, New York, USA
| | - Eli J Borrego
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, New York, USA
| | - Michael A Savka
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, New York, USA
| | - Renwick C J Dobson
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand; Bio21 Molecular Science and Biotechnology Institute, Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria, Australia
| | - André O Hudson
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, New York, USA.
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25
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Gangi Setty T, Sarkar A, Coombes D, Dobson RCJ, Subramanian R. Structure and Function of N-Acetylmannosamine Kinases from Pathogenic Bacteria. ACS Omega 2020; 5:30923-30936. [PMID: 33324800 PMCID: PMC7726757 DOI: 10.1021/acsomega.0c03699] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Accepted: 10/20/2020] [Indexed: 06/12/2023]
Abstract
Several pathogenic bacteria import and catabolize sialic acids as a source of carbon and nitrogen. Within the sialic acid catabolic pathway, the enzyme N-acetylmannosamine kinase (NanK) catalyzes the phosphorylation of N-acetylmannosamine to N-acetylmannosamine-6-phosphate. This kinase belongs to the ROK superfamily of enzymes, which generally contain a conserved zinc-finger (ZnF) motif that is important for their structure and function. Previous structural studies have shown that the ZnF motif is absent in NanK of Fusobacterium nucleatum (Fn-NanK), a Gram-negative bacterium that causes the gum disease gingivitis. However, the effect in loss of the ZnF motif on the kinase activity is unknown. Using kinetic and thermodynamic studies, we have studied the functional properties of Fn-NanK to its substrates ManNAc and ATP, compared its activity with other ZnF motif-containing NanK enzymes from closely related Gram-negative pathogenic bacteria Haemophilus influenzae (Hi-NanK), Pasteurella multocida (Pm-NanK), and Vibrio cholerae (Vc-NanK). Our studies show a 10-fold decrease in substrate binding affinity between Fn-NanK (apparent KM ≈ 700 μM) and ZnF motif-containing NanKs (apparent KM ≈ 60 μM). To understand the structural features that combat the loss of the ZnF motif in Fn-NanK, we solved the crystal structures of functionally homologous ZnF motif-containing NanKs from P. multocida and H. influenzae. Here, we report Pm-NanK:unliganded, Pm-NanK:AMPPNP, Pm-NanK:ManNAc, Hi-NanK:ManNAc, and Hi-NanK:ManNAc-6P:ADP crystal structures. Structural comparisons of Fn-NanK with Hi-NanK, Pm-NanK, and hMNK (human N-acetylmannosamine kinase domain of UDP-N-acetylglucosamine-2-epimerase/N-acetylmannosamine kinase, GNE) show that even though there is less sequence identity, they have high degree of structural similarity. Furthermore, our structural analyses highlight that the ZnF motif of Fn-NanK is substituted by a set of hydrophobic residues, which forms a hydrophobic cluster that helps the proper orientation of ManNac in the active site. In summary, ZnF-containing and ZnF-lacking NanK enzymes from different Gram-negative pathogenic bacteria are functionally very similar but differ in their metal requirement. Our structural studies unveil the structural modifications in Fn-NanK that compensate the loss of the ZnF motif in comparison to other NanK enzymes.
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Affiliation(s)
- Thanuja Gangi Setty
- Institute for Stem
Cell Science and Regenerative Medicine, GKVK Post, Bangalore, KA 560065, India
- The University of Trans-Disciplinary Health Sciences
& Technology (TDU), Bangalore, KA 560064, India
| | - Arunabha Sarkar
- National Centre for Biological Sciences − TIFR, Bangalore 560065, India
| | - David Coombes
- Biomolecular Interaction Centre and School
of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
| | - Renwick C. J. Dobson
- Biomolecular Interaction Centre and School
of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
- Bio21 Molecular Science and Biotechnology
Institute, Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Ramaswamy Subramanian
- Institute for Stem
Cell Science and Regenerative Medicine, GKVK Post, Bangalore, KA 560065, India
- Department of Biological
Sciences and Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana 47907, United States
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26
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Crowther JM, Broadhurst M, Laue TM, Jameson GB, Hodgkinson AJ, Dobson RCJ. On the utility of fluorescence-detection analytical ultracentrifugation in probing biomolecular interactions in complex solutions: a case study in milk. Eur Biophys J 2020; 49:677-685. [PMID: 33052462 DOI: 10.1007/s00249-020-01468-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 09/25/2020] [Accepted: 09/29/2020] [Indexed: 12/24/2022]
Abstract
β-Lactoglobulin is the most abundant protein in the whey fraction of ruminant milks, yet is absent in human milk. It has been studied intensively due to its impact on the processing and allergenic properties of ruminant milk products. However, the physiological function of β-lactoglobulin remains unclear. Using the fluorescence-detection system within the analytical ultracentrifuge, we observed an interaction involving fluorescently labelled β-lactoglobulin in its native environment, i.e. cow and goat milk, for the first time. Co-elution experiments support that these β-lactoglobulin interactions occur naturally in milk and provide evidence that the interacting partners are immunoglobulins, while further sedimentation velocity experiments confirm that an interaction occurs between these molecules. The identification of these interactions, made possible through the use of fluorescence-detected analytical ultracentrifugation, provides possible clues to the long debated physiological function of this abundant milk protein.
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Affiliation(s)
- Jennifer M Crowther
- Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.
- The Riddet Institute, Massey University, Palmerston North, New Zealand.
| | - Marita Broadhurst
- Food and Bio-Based Products, AgResearch Limited, Ruakura Research Centre, Hamilton, New Zealand
| | - Thomas M Laue
- Center To Advance Molecular Interaction Science, University of New Hampshire, Durham, NH, USA
| | - Geoffrey B Jameson
- Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- The Riddet Institute, Massey University, Palmerston North, New Zealand
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Alison J Hodgkinson
- Food and Bio-Based Products, AgResearch Limited, Ruakura Research Centre, Hamilton, New Zealand.
- On-Farm R&D, Farm Source, Fonterra Co-Operative Group, Hamilton, 3200, New Zealand.
| | - Renwick C J Dobson
- Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.
- The Riddet Institute, Massey University, Palmerston North, New Zealand.
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, VIC, Australia.
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27
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Sugrue E, Coombes D, Wood D, Zhu T, Donovan KA, Dobson RCJ. The lid domain is important, but not essential, for catalysis of Escherichia coli pyruvate kinase. Eur Biophys J 2020; 49:761-772. [PMID: 32978636 DOI: 10.1007/s00249-020-01466-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 08/24/2020] [Accepted: 09/14/2020] [Indexed: 11/28/2022]
Abstract
Pyruvate kinase catalyses the final step of the glycolytic pathway in central energy metabolism. The monomeric structure comprises three domains: a catalytic TIM-barrel, a regulatory domain involved in allosteric activation, and a lid domain that encloses the substrates. The lid domain is thought to close over the TIM-barrel domain forming contacts with the substrates to promote catalysis and may be involved in stabilising the activated state when the allosteric activator is bound. However, it remains unknown whether the lid domain is essential for pyruvate kinase catalytic or regulatory function. To address this, we removed the lid domain of Escherichia coli pyruvate kinase type 1 (PKTIM+Reg) using protein engineering. Biochemical analyses demonstrate that, despite the absence of key catalytic residues in the lid domain, PKTIM+Reg retains a low level of catalytic activity and has a reduced binding affinity for the substrate phosphoenolpyruvate. The enzyme retains allosteric activation, but the regulatory profile of the enzyme is changed relative to the wild-type enzyme. Analytical ultracentrifugation and small-angle X-ray scattering data show that, beyond the loss of the lid domain, the PKTIM+Reg structure is not significantly altered and is consistent with the wild-type tetramer that is assembled through interactions at the TIM and regulatory domains. Our results highlight the contribution of the lid domain for facilitating pyruvate kinase catalysis and regulation, which could aid in the development of small molecule inhibitors for pyruvate kinase and related lid-regulated enzymes.
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Affiliation(s)
- Elena Sugrue
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, PO Box 4800, Christchurch, 8140, New Zealand.,MRC-University of Glasgow Centre for Virus Research, Glasgow, G61 1QH, UK
| | - David Coombes
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, PO Box 4800, Christchurch, 8140, New Zealand
| | - David Wood
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, PO Box 4800, Christchurch, 8140, New Zealand
| | - Tong Zhu
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, PO Box 4800, Christchurch, 8140, New Zealand
| | - Katherine A Donovan
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, PO Box 4800, Christchurch, 8140, New Zealand.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Renwick C J Dobson
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, PO Box 4800, Christchurch, 8140, New Zealand. .,Biol21 Molecular Science and Biotechnology Institute, Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, VIC, 3010, Australia.
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28
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Manjunath L, Coombes D, Davies J, Dhurandhar M, Tiwari VR, Dobson RCJ, Sowdhamini R, Ramaswamy S, Bose S. Quaternary variations in the structural assembly of N-acetylglucosamine-6-phosphate deacetylase from Pasteurella multocida. Proteins 2020; 89:81-93. [PMID: 32865821 DOI: 10.1002/prot.25996] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 07/14/2020] [Accepted: 08/25/2020] [Indexed: 12/13/2022]
Abstract
N-acetylglucosamine 6-phosphate deacetylase (NagA) catalyzes the conversion of N-acetylglucosamine-6-phosphate to glucosamine-6-phosphate in amino sugar catabolism. This conversion is an essential step in the catabolism of sialic acid in several pathogenic bacteria, including Pasteurella multocida, and thus NagA is identified as a potential drug target. Here, we report the unique structural features of NagA from P. multocida (PmNagA) resolved to 1.95 Å. PmNagA displays an altered quaternary architecture with unique interface interactions compared to its close homolog, the Escherichia coli NagA (EcNagA). We confirmed that the altered quaternary structure is not a crystallographic artifact using single particle electron cryo-microscopy. Analysis of the determined crystal structure reveals a set of hot-spot residues involved in novel interactions at the dimer-dimer interface. PmNagA binds to one Zn2+ ion in the active site and demonstrates kinetic parameters comparable to other bacterial homologs. Kinetic studies reveal that at high substrate concentrations (~10-fold the KM ), the tetrameric PmNagA displays hysteresis similar to its distant neighbor, the dimeric Staphylococcus aureus NagA (SaNagA). Our findings provide key information on structural and functional properties of NagA in P. multocida that could be utilized to design novel antibacterials.
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Affiliation(s)
- Lavanyaa Manjunath
- Institute for Stem Cell Science and Regenerative Medicine, NCBS, GKVK Campus, Bangalore, Karnataka, India
- Manipal Academy of Higher Education, Tiger Circle, Manipal, Karnataka, India
| | - David Coombes
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - James Davies
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Mugdha Dhurandhar
- National Centre for Biological Sciences, GKVK Campus, Bangalore, Karnataka, India
| | - Vikas R Tiwari
- National Centre for Biological Sciences, GKVK Campus, Bangalore, Karnataka, India
| | - Renwick C J Dobson
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- Bio21 Molecular Science and Biotechnology Institute, Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria, Australia
| | - R Sowdhamini
- National Centre for Biological Sciences, GKVK Campus, Bangalore, Karnataka, India
| | - S Ramaswamy
- Institute for Stem Cell Science and Regenerative Medicine, NCBS, GKVK Campus, Bangalore, Karnataka, India
- Department of Biological Sciences and Department of Biomedical Engineering, Purdue University, West Lafayette, Indiana, USA
| | - Sucharita Bose
- Institute for Stem Cell Science and Regenerative Medicine, NCBS, GKVK Campus, Bangalore, Karnataka, India
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29
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Cree SL, Chua EW, Crowther J, Dobson RCJ, Kennedy MA. G-quadruplex structures bind to EZ-Tn5 transposase. Biochimie 2020; 177:190-197. [PMID: 32805304 DOI: 10.1016/j.biochi.2020.07.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 07/31/2020] [Accepted: 07/31/2020] [Indexed: 11/17/2022]
Abstract
Next generation DNA sequencing and analysis of amplicons spanning the pharmacogene CYP2D6 suggested that the Nextera transposase used for fragmenting and providing sequencing priming sites displayed a targeting bias. This manifested as dramatically lower sequencing coverage at sites in the amplicon that appeared likely to form G-quadruplex structures. Since secondary DNA structures such as G-quadruplexes are abundant in the human genome, and are known to interact with many other proteins, we further investigated these sites of low coverage. Our investigation revealed that G-quadruplex structures are formed in vitro within the CYP2D6 pharmacogene at these sites, and G-quadruplexes can interact with the hyperactive Tn5 transposase (EZ-Tn5) with high affinity. These findings indicate that secondary DNA structures such as G-quadruplexes may represent preferential transposon integration sites and provide additional evidence for the role of G-quadruplex structures in transposition or viral integration processes.
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Affiliation(s)
- Simone L Cree
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, 8140, New Zealand
| | - Eng Wee Chua
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, 8140, New Zealand
| | - Jennifer Crowther
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Renwick C J Dobson
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand; Bio21 Molecular Science and Biotechnology Institute, Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Martin A Kennedy
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, 8140, New Zealand.
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30
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Suzuki H, Mahapatra D, Board AJ, Steel PJ, Dyer JM, Gerrard JA, Dobson RCJ, Valéry C. Sub-Ångstrom structure of collagen model peptide (GPO) 10 shows a hydrated triple helix with pitch variation and two proline ring conformations. Food Chem 2020; 319:126598. [PMID: 32182540 DOI: 10.1016/j.foodchem.2020.126598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 02/18/2020] [Accepted: 03/10/2020] [Indexed: 11/17/2022]
Abstract
Collagens are large structural proteins that are prevalent in mammalian connective tissue. Peptides designed to include a glycine-proline-hydroxyproline (GPO) amino acid triad are biomimetic analogs of the collagen triple helix, a fold that is a hallmark of collagen-like sequences. To inform the rational engineering of collagen-like peptides and proteins for food systems, we report the crystal structure of the (GPO)10 peptide at 0.89-Å resolution, solved using direct methods. We determined that a single chain in the asymmetric unit forms a pseudo-hexagonal network of triple helices that have a pitch variation consistent with the model 7/2 helix (3.5 residues per turn). The proline rings occupied one of two states, while the helix was found to have a well-defined hydration shell involved in the stabilization of the inter-helix crystal network. This structure offers a new high-resolution basis for understanding the hierarchical assembly of native collagens, which will aid the food industry in engineering new sustainable food systems.
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Affiliation(s)
- Hironori Suzuki
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
| | - Deepti Mahapatra
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand; AgResearch Ltd, Lincoln, New Zealand
| | - Amanda J Board
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand; Riddet Institute, Massey University, Palmerston North, New Zealand
| | - Peter J Steel
- Chemistry Department, University of Canterbury, Christchurch, New Zealand
| | - Jolon M Dyer
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand; AgResearch Ltd, Lincoln, New Zealand; Riddet Institute, Massey University, Palmerston North, New Zealand
| | - Juliet A Gerrard
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand; School of Biological Sciences and School of Chemical Sciences, University of Auckland, Auckland, New Zealand; Riddet Institute, Massey University, Palmerston North, New Zealand; Callaghan Innovation Research Limited, Lower Hutt, New Zealand
| | - Renwick C J Dobson
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand; Riddet Institute, Massey University, Palmerston North, New Zealand; Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria, Australia.
| | - Céline Valéry
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand; School of Medical Sciences, RMIT University, Bundoora, Victoria, Australia.
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31
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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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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
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32
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Horne CR, Kind L, Davies JS, Dobson RCJ. Cover Image, Volume 88, Issue 5. Proteins 2020. [DOI: 10.1002/prot.25721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Christopher R. Horne
- Biomolecular Interaction Centre and School of Biological SciencesUniversity of Canterbury Christchurch New Zealand
| | - Laura Kind
- Department of BiomedicineUniversity of Bergen Bergen Norway
| | - James S. Davies
- Biomolecular Interaction Centre and School of Biological SciencesUniversity of Canterbury Christchurch New Zealand
| | - Renwick C. J. Dobson
- Biomolecular Interaction Centre and School of Biological SciencesUniversity of Canterbury Christchurch New Zealand
- Department of Biochemistry and Molecular BiologyBio21 Molecular Science and Biotechnology Institute Parkville Victoria Australia
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33
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Metcalfe RD, Aizel K, Zlatic CO, Nguyen PM, Morton CJ, Lio DSS, Cheng HC, Dobson RCJ, Parker MW, Gooley PR, Putoczki TL, Griffin MDW. The structure of the extracellular domains of human interleukin 11α receptor reveals mechanisms of cytokine engagement. J Biol Chem 2020; 295:8285-8301. [PMID: 32332100 DOI: 10.1074/jbc.ra119.012351] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 04/23/2020] [Indexed: 12/27/2022] Open
Abstract
Interleukin (IL) 11 activates multiple intracellular signaling pathways by forming a complex with its cell surface α-receptor, IL-11Rα, and the β-subunit receptor, gp130. Dysregulated IL-11 signaling has been implicated in several diseases, including some cancers and fibrosis. Mutations in IL-11Rα that reduce signaling are also associated with hereditary cranial malformations. Here we present the first crystal structure of the extracellular domains of human IL-11Rα and a structure of human IL-11 that reveals previously unresolved detail. Disease-associated mutations in IL-11Rα are generally distal to putative ligand-binding sites. Molecular dynamics simulations showed that specific mutations destabilize IL-11Rα and may have indirect effects on the cytokine-binding region. We show that IL-11 and IL-11Rα form a 1:1 complex with nanomolar affinity and present a model of the complex. Our results suggest that the thermodynamic and structural mechanisms of complex formation between IL-11 and IL-11Rα differ substantially from those previously reported for similar cytokines. This work reveals key determinants of the engagement of IL-11 by IL-11Rα that may be exploited in the development of strategies to modulate formation of the IL-11-IL-11Rα complex.
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Affiliation(s)
- Riley D Metcalfe
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute
| | - Kaheina Aizel
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute.,Inflammation Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Courtney O Zlatic
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute
| | - Paul M Nguyen
- Inflammation Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Personalised Oncology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Craig J Morton
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute
| | - Daisy Sio-Seng Lio
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute.,Structural Biology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Heung-Chin Cheng
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute
| | - Renwick C J Dobson
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute.,Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Michael W Parker
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute.,Australian Cancer Research Foundation Rational Drug Discovery Centre, St. Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia
| | - Paul R Gooley
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute
| | - Tracy L Putoczki
- Inflammation Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Personalised Oncology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology and Department of Surgery, University of Melbourne, Parkville, Victoria, Australia
| | - Michael D W Griffin
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute
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34
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Adams LE, Rynkiewicz P, Babbitt GA, Mortensen JS, North RA, Dobson RCJ, Hudson AO. Comparative Molecular Dynamics Simulations Provide Insight Into Antibiotic Interactions: A Case Study Using the Enzyme L,L-Diaminopimelate Aminotransferase (DapL). Front Mol Biosci 2020; 7:46. [PMID: 32274387 PMCID: PMC7113581 DOI: 10.3389/fmolb.2020.00046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 03/04/2020] [Indexed: 12/03/2022] Open
Abstract
The L,L-diaminopimelate aminotransferase (DapL) pathway, a recently discovered variant of the lysine biosynthetic pathway, is an attractive pipeline to identify targets for the development of novel antibiotic compounds. DapL is a homodimer that catalyzes the conversion of tetrahydrodipicolinate to L,L-diaminopimelate in a single transamination reaction. The penultimate and ultimate products of the lysine biosynthesis pathway, meso-diaminopimelate and lysine, are key components of the Gram-negative and Gram-positive bacterial peptidoglycan cell wall. Humans are not able to synthesize lysine, and DapL has been identified in 13% of bacteria whose genomes have been sequenced and annotated to date, thus it is an attractive target for the development of narrow spectrum antibiotics through the prevention of both lysine biosynthesis and peptidoglycan crosslinking. To address the common lack of structural information when conducting compound screening experiments and provide support for the use of modeled structures, our analyses utilized inferred structures from related homologous enzymes. Using a comprehensive and comparative molecular dynamics (MD) software package-DROIDS (Detecting Relative Outlier Impacts in Dynamic Simulations) 2.0, we investigated the binding dynamics of four previously identified antagonistic ligands of DapL from Verrucomicrobium spinosum, a non-pathogenic relative of Chlamydia trachomatis. Here, we present putative docking positions of the four ligands and provide confirmatory comparative molecular dynamics simulations supporting the conformations. The simulations performed in this study can be applied to evaluate putative targets to predict compound effectiveness prior to in vivo and in vitro experimentation. Moreover, this approach has the potential to streamline the process of antibiotic development.
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Affiliation(s)
- Lily E. Adams
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, United States
| | - Patrick Rynkiewicz
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, United States
| | - Gregory A. Babbitt
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, United States
| | - Jamie S. Mortensen
- Department of Biomedical Engineering, Rochester Institute of Technology, Rochester, NY, United States
| | - Rachel A. North
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Renwick C. J. Dobson
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, VIC, Australia
| | - André O. Hudson
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, United States
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35
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Trevelyan SJ, Brewster JL, Burgess AE, Crowther JM, Cadell AL, Parker BL, Croucher DR, Dobson RCJ, Murphy JM, Mace PD. Structure-based mechanism of preferential complex formation by apoptosis signal–regulating kinases. Sci Signal 2020; 13:13/622/eaay6318. [DOI: 10.1126/scisignal.aay6318] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Apoptosis signal–regulating kinases (ASK1, ASK2, and ASK3) are activators of the p38 and c-Jun N-terminal kinase (JNK) mitogen-activated protein kinase (MAPK) pathways. ASK1–3 form oligomeric complexes known as ASK signalosomes that initiate signaling cascades in response to diverse stress stimuli. Here, we demonstrated that oligomerization of ASK proteins is driven by previously uncharacterized sterile-alpha motif (SAM) domains that reside at the carboxy-terminus of each ASK protein. SAM domains from ASK1–3 exhibited distinct behaviors, with the SAM domain of ASK1 forming unstable oligomers, that of ASK2 remaining predominantly monomeric, and that of ASK3 forming a stable oligomer even at a low concentration. In contrast to their behavior in isolation, the ASK1 and ASK2 SAM domains preferentially formed a stable heterocomplex. The crystal structure of the ASK3 SAM domain, small-angle x-ray scattering, and mutagenesis suggested that ASK3 oligomers and ASK1-ASK2 complexes formed discrete, quasi-helical rings through interactions between the mid-loop of one molecule and the end helix of another molecule. Preferential ASK1-ASK2 binding was consistent with mass spectrometry showing that full-length ASK1 formed hetero-oligomeric complexes incorporating large amounts of ASK2. Accordingly, disrupting the association between SAM domains impaired ASK activity in the context of electrophilic stress induced by 4-hydroxy-2-nonenal (HNE). These findings provide a structural template for how ASK proteins assemble foci that drive inflammatory signaling and reinforce the notion that strategies to target ASK proteins should consider the concerted actions of multiple ASK family members.
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Affiliation(s)
- Sarah J. Trevelyan
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, P.O. Box 56, 710 Cumberland St., Dunedin 9054, New Zealand
| | - Jodi L. Brewster
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, P.O. Box 56, 710 Cumberland St., Dunedin 9054, New Zealand
| | - Abigail E. Burgess
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, P.O. Box 56, 710 Cumberland St., Dunedin 9054, New Zealand
| | - Jennifer M. Crowther
- Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Antonia L. Cadell
- Kinghorn Cancer Centre, Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia
| | - Benjamin L. Parker
- Department of Physiology, School of Biomedical Sciences, University of Melbourne, Parkville, Victoria 3010, Australia
| | - David R. Croucher
- Kinghorn Cancer Centre, Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia
- St Vincent’s Hospital Clinical School, University of New South Wales, Sydney, New South Wales, 2052, Australia
- School of Medicine and Medical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Renwick C. J. Dobson
- Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - James M. Murphy
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Peter D. Mace
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, P.O. Box 56, 710 Cumberland St., Dunedin 9054, New Zealand
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36
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Meng Y, Sheen CR, Magon NJ, Hampton MB, Dobson RCJ. Structure-function analyses of alkylhydroperoxidase D from Streptococcus pneumoniae reveal an unusual three-cysteine active site architecture. J Biol Chem 2020; 295:2984-2999. [PMID: 31974167 DOI: 10.1074/jbc.ra119.012226] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 01/19/2020] [Indexed: 12/12/2022] Open
Abstract
During aerobic growth, the Gram-positive facultative anaerobe and opportunistic human pathogen Streptococcus pneumoniae generates large amounts of hydrogen peroxide that can accumulate to millimolar concentrations. The mechanism by which this catalase-negative bacterium can withstand endogenous hydrogen peroxide is incompletely understood. The enzyme alkylhydroperoxidase D (AhpD) has been shown to contribute to pneumococcal virulence and oxidative stress responses in vivo We demonstrate here that SpAhpD exhibits weak thiol-dependent peroxidase activity and, unlike the previously reported Mycobacterium tuberculosis AhpC/D system, SpAhpD does not mediate electron transfer to SpAhpC. A 2.3-Å resolution crystal structure revealed several unusual structural features, including a three-cysteine active site architecture that is buried in a deep pocket, in contrast to the two-cysteine active site found in other AhpD enzymes. All single-cysteine SpAhpD variants remained partially active, and LC-MS/MS analyses revealed that the third cysteine, Cys-163, formed disulfide bonds with either of two cysteines in the canonical Cys-78-X-X-Cys-81 motif. We observed that SpAhpD formed a dimeric quaternary structure both in the crystal and in solution, and that the highly conserved Asn-76 of the AhpD core motif is important for SpAhpD folding. In summary, SpAhpD is a weak peroxidase and does not transfer electrons to AhpC, and therefore does not fit existing models of bacterial AhpD antioxidant defense mechanisms. We propose that it is unlikely that SpAhpD removes peroxides either directly or via AhpC, and that SpAhpD cysteine oxidation may act as a redox switch or mediate electron transfer with other thiol proteins.
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Affiliation(s)
- Yanxiang Meng
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch 8041, New Zealand
| | - Campbell R Sheen
- Callaghan Innovation, University of Canterbury, Christchurch 8041, New Zealand
| | - Nicholas J Magon
- Centre for Free Radical Research, Department of Pathology and Biomedical Science, University of Otago, Christchurch 8011, New Zealand
| | - Mark B Hampton
- Centre for Free Radical Research, Department of Pathology and Biomedical Science, University of Otago, Christchurch 8011, New Zealand.
| | - Renwick C J Dobson
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch 8041, New Zealand; Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria 3010, Australia.
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Coombes D, Davies JS, Newton-Vesty MC, Horne CR, Setty TG, Subramanian R, Moir JWB, Friemann R, Panjikar S, Griffin MDW, North RA, Dobson RCJ. The basis for non-canonical ROK family function in the N-acetylmannosamine kinase from the pathogen Staphylococcus aureus. J Biol Chem 2020; 295:3301-3315. [PMID: 31949045 DOI: 10.1074/jbc.ra119.010526] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 12/31/2019] [Indexed: 12/31/2022] Open
Abstract
In environments where glucose is limited, some pathogenic bacteria metabolize host-derived sialic acid as a nutrient source. N-Acetylmannosamine kinase (NanK) is the second enzyme of the bacterial sialic acid import and degradation pathway and adds phosphate to N-acetylmannosamine using ATP to prime the molecule for future pathway reactions. Sequence alignments reveal that Gram-positive NanK enzymes belong to the Repressor, ORF, Kinase (ROK) family, but many lack the canonical Zn-binding motif expected for this function, and the sugar-binding EXGH motif is altered to EXGY. As a result, it is unclear how they perform this important reaction. Here, we study the Staphylococcus aureus NanK (SaNanK), which is the first characterization of a Gram-positive NanK. We report the kinetic activity of SaNanK along with the ligand-free, N-acetylmannosamine-bound and substrate analog GlcNAc-bound crystal structures (2.33, 2.20, and 2.20 Å resolution, respectively). These demonstrate, in combination with small-angle X-ray scattering, that SaNanK is a dimer that adopts a closed conformation upon substrate binding. Analysis of the EXGY motif reveals that the tyrosine binds to the N-acetyl group to select for the "boat" conformation of N-acetylmannosamine. Moreover, SaNanK has a stacked arginine pair coordinated by negative residues critical for thermal stability and catalysis. These combined elements serve to constrain the active site and orient the substrate in lieu of Zn binding, representing a significant departure from canonical NanK binding. This characterization provides insight into differences in the ROK family and highlights a novel area for antimicrobial discovery to fight Gram-positive and S. aureus infections.
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Affiliation(s)
- David Coombes
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
| | - James S Davies
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
| | - Michael C Newton-Vesty
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
| | - Christopher R Horne
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
| | - Thanuja G Setty
- Institute for Stem Cell Biology and Regenerative Medicine, NCBS, GKVK Campus, Bellary Road, Bangalore, Karnataka 560 065, India; The University of Trans-Disciplinary Health Sciences and Technology (TDU), Bangalore, KA 560064, India
| | - Ramaswamy Subramanian
- Institute for Stem Cell Biology and Regenerative Medicine, NCBS, GKVK Campus, Bellary Road, Bangalore, Karnataka 560 065, India
| | - James W B Moir
- Department of Biology, University of York, Helsington, York YO10 5DD, United Kingdom
| | - Rosmarie Friemann
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Guldhedsgatan 10A, 413 46 Gothenburg, Sweden; Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, 40530 Gothenburg, Sweden
| | - Santosh Panjikar
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia; Australian Synchrotron, ANSTO, Victoria 3168, Australia
| | - Michael D W Griffin
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Rachel A North
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand.
| | - Renwick C J Dobson
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand; Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia.
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Horne CR, Kind L, Davies JS, Dobson RCJ. On the structure and function of Escherichia coli YjhC: An oxidoreductase involved in bacterial sialic acid metabolism. Proteins 2019; 88:654-668. [PMID: 31697432 DOI: 10.1002/prot.25846] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 10/11/2019] [Accepted: 11/03/2019] [Indexed: 11/06/2022]
Abstract
Human pathogenic and commensal bacteria have evolved the ability to scavenge host-derived sialic acids and subsequently degrade them as a source of nutrition. Expression of the Escherichia coli yjhBC operon is controlled by the repressor protein nanR, which regulates the core machinery responsible for the import and catabolic processing of sialic acid. The role of the yjhBC encoded proteins is not known-here, we demonstrate that the enzyme YjhC is an oxidoreductase/dehydrogenase involved in bacterial sialic acid degradation. First, we demonstrate in vivo using knockout experiments that YjhC is broadly involved in carbohydrate metabolism, including that of N-acetyl-d-glucosamine, N-acetyl-d-galactosamine and N-acetylneuraminic acid. Differential scanning fluorimetry demonstrates that YjhC binds N-acetylneuraminic acid and its lactone variant, along with NAD(H), which is consistent with its role as an oxidoreductase. Next, we solved the crystal structure of YjhC in complex with the NAD(H) cofactor to 1.35 Å resolution. The protein fold belongs to the Gfo/Idh/MocA protein family. The dimeric assembly observed in the crystal form is confirmed through solution studies. Ensemble refinement reveals a flexible loop region that may play a key role during catalysis, providing essential contacts to stabilize the substrate-a unique feature to YjhC among closely related structures. Guided by the structure, in silico docking experiments support the binding of sialic acid and several common derivatives in the binding pocket, which has an overall positive charge distribution. Taken together, our results verify the role of YjhC as a bona fide oxidoreductase/dehydrogenase and provide the first evidence to support its involvement in sialic acid metabolism.
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Affiliation(s)
- Christopher R Horne
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Laura Kind
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - James S Davies
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Renwick C J Dobson
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.,Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, Parkville, Victoria, Australia
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Gilkes JM, Sheen CR, Frampton RA, Smith GR, Dobson RCJ. The First Purification of Functional Proteins from the Unculturable, Genome-Reduced, Bottlenecked α-Proteobacterium ' Candidatus Liberibacter solanacearum'. Phytopathology 2019; 109:1141-1148. [PMID: 30887888 DOI: 10.1094/phyto-12-18-0486-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
'Candidatus Liberibacter solanacearum' is an unculturable α-proteobacterium that is the causal agent of zebra chip disease of potato-a major problem in potato-growing areas, because it affects growth and yield. Developing effective treatments for 'Ca. L. solanacearum' has been hampered by the difficulty in functionally characterizing the proteins of this organism, largely because they are not easily expressed and purified in standard expression systems. 'Ca. L. solanacearum' has a reduced genome and its proteins are predicted to be prone to instability and aggregation. Among intracellular-dwelling bacteria, chaperone proteins are conserved and overexpressed to buffer against problems in protein folding. We mimicked this approach for expressing and purifying 'Ca. L. solanacearum' proteins in Escherichia coli by coexpressing them with chaperones. Neither of the representative 'Ca. L. solanacearum' enzymes, dihydrodipicolinate synthase (key in lysine biosynthesis) and pyruvate kinase (involved in glycolysis), were overexpressed in standard E. coli expression plasmids or strains. However, soluble dihydrodipicolinate synthase was successfully coexpressed with GroEL/GroES, while soluble pyruvate kinase was successfully coexpressed with either GroEL/GroES, dnaK/dnaJ/grpE, or a trigger factor. Both enzymes, believed to be key proteins for the organism, were purified by a combination of affinity chromatography and size-exclusion chromatography. Additionally, both 'Ca. L. solanacearum' enzymes are active and have the canonical tetrameric oligomeric structure in solution, consistent with other bacterial orthologs. This is the first study to successfully isolate and functionally characterize proteins from 'Ca. L. solanacearum'. Thus, we provide a general strategy for characterizing its proteins, enabling new research and drug discovery programs to study and manage the pathogenicity of the organism.
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Affiliation(s)
- Jenna M Gilkes
- 1 Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Christchurch 8041, New Zealand
- 2 The New Zealand Institute for Plant & Food Research Limited, Lincoln 7608, New Zealand
| | - Campbell R Sheen
- 3 Callaghan Innovation, University of Canterbury, Christchurch 8041, New Zealand; and
| | - Rebekah A Frampton
- 2 The New Zealand Institute for Plant & Food Research Limited, Lincoln 7608, New Zealand
| | - Grant R Smith
- 2 The New Zealand Institute for Plant & Food Research Limited, Lincoln 7608, New Zealand
| | - Renwick C J Dobson
- 1 Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Christchurch 8041, New Zealand
- 4 Bio21 Molecular Science and Biotechnology Institute, Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria 3010, Australia
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40
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Hoskin TS, Crowther JM, Cheung J, Epton MJ, Sly PD, Elder PA, Dobson RCJ, Kettle AJ, Dickerhof N. Oxidative cross-linking of calprotectin occurs in vivo, altering its structure and susceptibility to proteolysis. Redox Biol 2019; 24:101202. [PMID: 31015146 PMCID: PMC6477633 DOI: 10.1016/j.redox.2019.101202] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 04/09/2019] [Accepted: 04/11/2019] [Indexed: 01/27/2023] Open
Abstract
Calprotectin, the major neutrophil protein, is a critical alarmin that modulates inflammation and plays a role in host immunity by strongly binding trace metals essential for bacterial growth. It has two cysteine residues favourably positioned to act as a redox switch. Whether their oxidation occurs in vivo and affects the function of calprotectin has received little attention. Here we show that in saliva from healthy adults, and in lavage fluid from the lungs of patients with respiratory diseases, a substantial proportion of calprotectin was cross-linked via disulfide bonds between the cysteine residues on its S100A8 and S100A9 subunits. Stimulated human neutrophils released calprotectin and subsequently cross-linked it by myeloperoxidase-dependent production of hypochlorous acid. The myeloperoxidase-derived oxidants hypochlorous acid, taurine chloramine, hypobromous acid, and hypothiocyanous acid, all at 10 μM, cross-linked calprotectin (5 μM) via reversible disulfide bonds. Hypochlorous acid generated A9-A9 and A8-A9 cross links. Hydrogen peroxide (10 μM) did not cross-link the protein. Purified neutrophil calprotectin existed as a non-covalent heterodimer of A8/A9 which was converted to a heterotetramer - (A8/A9)2 - with excess calcium ions. Low level oxidation of calprotectin with hypochlorous acid produced substantial proportions of high order oligomers, whether oxidation occurred before or after addition of calcium ions. At high levels of oxidation the heterodimer could not form tetramers with calcium ions, but prior addition of calcium ions afforded some protection for the heterotetramer. Oxidation and formation of the A8-A9 disulfide cross link enhanced calprotectin's susceptibility to proteolysis by neutrophil proteases. We propose that reversible disulfide cross-linking of calprotectin occurs during inflammation and affects its structure and function. Its increased susceptibility to proteolysis will ultimately result in a loss of function.
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Affiliation(s)
- Teagan S Hoskin
- Centre for Free Radical Research, Department of Pathology and Biomedical Science, University of Otago Christchurch, Christchurch, New Zealand.
| | - Jennifer M Crowther
- Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Jeanette Cheung
- Canterbury Respiratory Research Group, Respiratory Services, Christchurch Hospital, Canterbury District Health Board, New Zealand
| | - Michael J Epton
- Canterbury Respiratory Research Group, Respiratory Services, Christchurch Hospital, Canterbury District Health Board, New Zealand
| | - Peter D Sly
- Child Health Research Centre, University of Queensland, Brisbane, Australia
| | - Peter A Elder
- Endocrinology and Steroid Laboratory, Canterbury Health Laboratories, New Zealand
| | - Renwick C J Dobson
- Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Christchurch, New Zealand; Bio21 Molecular Science and Biotechnology Institute, Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Anthony J Kettle
- Centre for Free Radical Research, Department of Pathology and Biomedical Science, University of Otago Christchurch, Christchurch, New Zealand
| | - Nina Dickerhof
- Centre for Free Radical Research, Department of Pathology and Biomedical Science, University of Otago Christchurch, Christchurch, New Zealand
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Crowther JM, Cross PJ, Oliver MR, Leeman MM, Bartl AJ, Weatherhead AW, North RA, Donovan KA, Griffin MDW, Suzuki H, Hudson AO, Kasanmascheff M, Dobson RCJ. Structure-function analyses of two plant meso-diaminopimelate decarboxylase isoforms reveal that active-site gating provides stereochemical control. J Biol Chem 2019; 294:8505-8515. [PMID: 30962284 DOI: 10.1074/jbc.ra118.006825] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 03/26/2019] [Indexed: 11/06/2022] Open
Abstract
meso-Diaminopimelate decarboxylase catalyzes the decarboxylation of meso-diaminopimelate, the final reaction in the diaminopimelate l-lysine biosynthetic pathway. It is the only known pyridoxal-5-phosphate-dependent decarboxylase that catalyzes the removal of a carboxyl group from a d-stereocenter. Currently, only prokaryotic orthologs have been kinetically and structurally characterized. Here, using complementation and kinetic analyses of enzymes recombinantly expressed in Escherichia coli, we have functionally tested two putative eukaryotic meso-diaminopimelate decarboxylase isoforms from the plant species Arabidopsis thaliana We confirm they are both functional meso-diaminopimelate decarboxylases, although with lower activities than those previously reported for bacterial orthologs. We also report in-depth X-ray crystallographic structural analyses of each isoform at 1.9 and 2.4 Å resolution. We have captured the enzyme structure of one isoform in an asymmetric configuration, with one ligand-bound monomer and the other in an apo-form. Analytical ultracentrifugation and small-angle X-ray scattering solution studies reveal that A. thaliana meso-diaminopimelate decarboxylase adopts a homodimeric assembly. On the basis of our structural analyses, we suggest a mechanism whereby molecular interactions within the active site transduce conformational changes to the active-site loop. These conformational differences are likely to influence catalytic activity in a way that could allow for d-stereocenter selectivity of the substrate meso-diaminopimelate to facilitate the synthesis of l-lysine. In summary, the A. thaliana gene loci At3g14390 and At5g11880 encode functional. meso-diaminopimelate decarboxylase enzymes whose structures provide clues to the stereochemical control of the decarboxylation reaction catalyzed by these eukaryotic proteins.
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Affiliation(s)
- Jennifer M Crowther
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand; School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JG, Scotland, United Kingdom
| | - Penelope J Cross
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
| | - Michael R Oliver
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JG, Scotland, United Kingdom
| | - Mary M Leeman
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology (RIT), Rochester, New York 14623
| | - Austin J Bartl
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology (RIT), Rochester, New York 14623
| | - Anthony W Weatherhead
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
| | - Rachel A North
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
| | - Katherine A Donovan
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215
| | - Michael D W Griffin
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Hironori Suzuki
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
| | - André O Hudson
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology (RIT), Rochester, New York 14623.
| | - Müge Kasanmascheff
- Department of Chemistry and Chemical Biology, Technical University of Dortmund, D-44227 Dortmund, Germany.
| | - Renwick C J Dobson
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand; Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia.
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Peng F, Widmann S, Wünsche A, Duan K, Donovan KA, Dobson RCJ, Lenski RE, Cooper TF. Effects of Beneficial Mutations in pykF Gene Vary over Time and across Replicate Populations in a Long-Term Experiment with Bacteria. Mol Biol Evol 2019; 35:202-210. [PMID: 29069429 PMCID: PMC5850340 DOI: 10.1093/molbev/msx279] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The fitness effects of mutations can depend on the genetic backgrounds in which they occur and thereby influence future opportunities for evolving populations. In particular, mutations that fix in a population might change the selective benefit of subsequent mutations, giving rise to historical contingency. We examine these effects by focusing on mutations in a key metabolic gene, pykF, that arose independently early in the history of 12 Escherichia coli populations during a long-term evolution experiment. Eight different evolved nonsynonymous mutations conferred similar fitness benefits of ∼10% when transferred into the ancestor, and these benefits were greater than the one conferred by a deletion mutation. In contrast, the same mutations had highly variable fitness effects, ranging from ∼0% to 25%, in evolved clones isolated from the populations at 20,000 generations. Two mutations that were moved into these evolved clones conferred similar fitness effects in a given clone, but different effects between the clones, indicating epistatic interactions between the evolved pykF alleles and the other mutations that had accumulated in each evolved clone. We also measured the fitness effects of six evolved pykF alleles in the same populations in which they had fixed, but at seven time points between 0 and 50,000 generations. Variation in fitness effects was high at intermediate time points, and declined to a low level at 50,000 generations, when the mean fitness effect was lowest. Our results demonstrate the importance of genetic context in determining the fitness effects of different beneficial mutations even within the same gene.
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Affiliation(s)
- Fen Peng
- Department of Biology and Biochemistry, University of Houston, Houston, TX
| | - Scott Widmann
- Department of Biology and Biochemistry, University of Houston, Houston, TX
| | - Andrea Wünsche
- Department of Biology and Biochemistry, University of Houston, Houston, TX
| | - Kristina Duan
- Department of Biology and Biochemistry, University of Houston, Houston, TX
| | - Katherine A Donovan
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Renwick C J Dobson
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.,Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Australia
| | - Richard E Lenski
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI
| | - Tim F Cooper
- Department of Biology and Biochemistry, University of Houston, Houston, TX
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Mantravadi PK, Kalesh KA, Dobson RCJ, Hudson AO, Parthasarathy A. The Quest for Novel Antimicrobial Compounds: Emerging Trends in Research, Development, and Technologies. Antibiotics (Basel) 2019; 8:E8. [PMID: 30682820 PMCID: PMC6466574 DOI: 10.3390/antibiotics8010008] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 01/17/2019] [Accepted: 01/20/2019] [Indexed: 12/11/2022] Open
Abstract
Pathogenic antibiotic resistant bacteria pose one of the most important health challenges of the 21st century. The overuse and abuse of antibiotics coupled with the natural evolutionary processes of bacteria has led to this crisis. Only incremental advances in antibiotic development have occurred over the last 30 years. Novel classes of molecules, such as engineered antibodies, antibiotic enhancers, siderophore conjugates, engineered phages, photo-switchable antibiotics, and genome editing facilitated by the CRISPR/Cas system, are providing new avenues to facilitate the development of antimicrobial therapies. The informatics revolution is transforming research and development efforts to discover novel antibiotics. The explosion of nanotechnology and micro-engineering is driving the invention of antimicrobial materials, enabling the cultivation of "uncultivable" microbes and creating specific and rapid diagnostic technologies. Finally, a revival in the ecological aspects of microbial disease management, the growth of prebiotics, and integrated management based on the "One Health" model, provide additional avenues to manage this health crisis. These, and future scientific and technological developments, must be coupled and aligned with sound policy and public awareness to address the risks posed by rising antibiotic resistance.
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Affiliation(s)
| | | | - Renwick C J Dobson
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Private Bag 4800 Christchurch, New Zealand.
| | - André O Hudson
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, 85 Lomb Memorial Dr, Rochester, NY 14623, USA.
| | - Anutthaman Parthasarathy
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, 85 Lomb Memorial Dr, Rochester, NY 14623, USA.
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Schlechter RO, Jun H, Bernach M, Oso S, Boyd E, Muñoz-Lintz DA, Dobson RCJ, Remus DM, Remus-Emsermann MNP. Chromatic Bacteria - A Broad Host-Range Plasmid and Chromosomal Insertion Toolbox for Fluorescent Protein Expression in Bacteria. Front Microbiol 2018; 9:3052. [PMID: 30631309 PMCID: PMC6315172 DOI: 10.3389/fmicb.2018.03052] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 11/27/2018] [Indexed: 12/26/2022] Open
Abstract
Differential fluorescent labeling of bacteria has become instrumental for many aspects of microbiological research, such as the study of biofilm formation, bacterial individuality, evolution, and bacterial behavior in complex environments. We designed a variety of plasmids, each bearing one of eight unique, constitutively expressed fluorescent protein genes in conjunction with one of four different antibiotic resistance combinations. The fluorophores mTagBFP2, mTurquoise2, sGFP2, mClover3, sYFP2, mOrange2, mScarlet-I, and mCardinal, encoding for blue, cyan, green, green-yellow, yellow, orange, red, and far-red fluorescent proteins, respectively, were combined with selectable markers conferring tetracycline, gentamicin, kanamycin, and/or chloramphenicol resistance. These constructs were cloned into three different plasmid backbones: a broad host-range plasmid, a Tn5 transposon delivery plasmid, and a Tn7 transposon delivery plasmid. The utility of the plasmids and transposons was tested in bacteria from the phyla Actinobacteria, Proteobacteria, and Bacteroidetes. We were able to tag representatives from the phylum Proteobacteria at least via our Tn5 transposon delivery system. The present study enables labeling bacteria with a set of plasmids available to the community. One potential application of fluorescently-tagged bacterial species is the study of bacteria-bacteria, bacteria-host, and bacteria-environment interactions.
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Affiliation(s)
- Rudolf O. Schlechter
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
| | - Hyunwoo Jun
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Michał Bernach
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
| | - Simisola Oso
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Erica Boyd
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Dian A. Muñoz-Lintz
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Renwick C. J. Dobson
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
- Bio21 Molecular Science and Biotechnology Institute, Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Daniela M. Remus
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
- Protein Science & Engineering, Callaghan Innovation, School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Mitja N. P. Remus-Emsermann
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
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45
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Davies JS, Coombes D, Horne CR, Pearce FG, Friemann R, North RA, Dobson RCJ. Functional and solution structure studies of amino sugar deacetylase and deaminase enzymes from Staphylococcus aureus. FEBS Lett 2018; 593:52-66. [PMID: 30411345 DOI: 10.1002/1873-3468.13289] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 10/25/2018] [Accepted: 10/26/2018] [Indexed: 12/13/2022]
Abstract
N-Acetylglucosamine-6-phosphate deacetylase (NagA) and glucosamine-6-phosphate deaminase (NagB) are branch point enzymes that direct amino sugars into different pathways. For Staphylococcus aureus NagA, analytical ultracentrifugation and small-angle X-ray scattering data demonstrate that it is an asymmetric dimer in solution. Initial rate experiments show hysteresis, which may be related to pathway regulation, and kinetic parameters similar to other bacterial isozymes. The enzyme binds two Zn2+ ions and is not substrate inhibited, unlike the Escherichia coli isozyme. S. aureus NagB adopts a novel dimeric structure in solution and shows kinetic parameters comparable to other Gram-positive isozymes. In summary, these functional data and solution structures are of use for understanding amino sugar metabolism in S. aureus, and will inform the design of inhibitory molecules.
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Affiliation(s)
- James S Davies
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - David Coombes
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Christopher R Horne
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - F Grant Pearce
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Rosmarie Friemann
- Department of Chemistry and Molecular Biology, University of Gothenburg, Sweden.,Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Sweden
| | - Rachel A North
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.,Department of Chemistry and Molecular Biology, University of Gothenburg, Sweden
| | - Renwick C J Dobson
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.,Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Vic., Australia
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46
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North RA, Wahlgren WY, Remus DM, Scalise M, Kessans SA, Dunevall E, Claesson E, Soares da Costa TP, Perugini MA, Ramaswamy S, Allison JR, Indiveri C, Friemann R, Dobson RCJ. The Sodium Sialic Acid Symporter From Staphylococcus aureus Has Altered Substrate Specificity. Front Chem 2018; 6:233. [PMID: 30023356 PMCID: PMC6039549 DOI: 10.3389/fchem.2018.00233] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 06/01/2018] [Indexed: 11/13/2022] Open
Abstract
Mammalian cell surfaces are decorated with complex glycoconjugates that terminate with negatively charged sialic acids. Commensal and pathogenic bacteria can use host-derived sialic acids for a competitive advantage, but require a functional sialic acid transporter to import the sugar into the cell. This work investigates the sodium sialic acid symporter (SiaT) from Staphylococcus aureus (SaSiaT). We demonstrate that SaSiaT rescues an Escherichia coli strain lacking its endogenous sialic acid transporter when grown on the sialic acids N-acetylneuraminic acid (Neu5Ac) or N-glycolylneuraminic acid (Neu5Gc). We then develop an expression, purification and detergent solubilization system for SaSiaT and demonstrate that the protein is largely monodisperse in solution with a stable monomeric oligomeric state. Binding studies reveal that SaSiaT has a higher affinity for Neu5Gc over Neu5Ac, which was unexpected and is not seen in another SiaT homolog. We develop a homology model and use comparative sequence analyses to identify substitutions in the substrate-binding site of SaSiaT that may explain the altered specificity. SaSiaT is shown to be electrogenic, and transport is dependent upon more than one Na+ ion for every sialic acid molecule. A functional sialic acid transporter is essential for the uptake and utilization of sialic acid in a range of pathogenic bacteria, and developing new inhibitors that target these transporters is a valid mechanism for inhibiting bacterial growth. By demonstrating a route to functional recombinant SaSiaT, and developing the in vivo and in vitro assay systems, our work underpins the design of inhibitors to this transporter.
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Affiliation(s)
- Rachel A North
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.,Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand.,Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Weixiao Y Wahlgren
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden.,Centre for Antibiotic Resistance Research, University of Gothenburg, Gothenburg, Sweden
| | - Daniela M Remus
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.,Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
| | - Mariafrancesca Scalise
- Unit of Biochemistry and Molecular Biotechnology, Department DiBEST (Biologia, Ecologia, Scienze della Terra), University of Calabria, Arcavacata di Rende, Italy
| | - Sarah A Kessans
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.,Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
| | - Elin Dunevall
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Elin Claesson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Tatiana P Soares da Costa
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - Matthew A Perugini
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - S Ramaswamy
- The Institute for Stem Cell Biology and Regenerative Medicine, Bangalore, India
| | - Jane R Allison
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand.,Centre for Theoretical Chemistry and Physics, Institute of Natural and Mathematical Sciences, Massey University, Auckland, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand
| | - Cesare Indiveri
- Unit of Biochemistry and Molecular Biotechnology, Department DiBEST (Biologia, Ecologia, Scienze della Terra), University of Calabria, Arcavacata di Rende, Italy
| | - Rosmarie Friemann
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden.,Centre for Antibiotic Resistance Research, University of Gothenburg, Gothenburg, Sweden
| | - Renwick C J Dobson
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.,Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, Australia
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47
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Atkinson SC, Dogovski C, Wood K, Griffin MDW, Gorman MA, Hor L, Reboul CF, Buckle AM, Wuttke J, Parker MW, Dobson RCJ, Perugini MA. Substrate Locking Promotes Dimer-Dimer Docking of an Enzyme Antibiotic Target. Structure 2018; 26:948-959.e5. [PMID: 29804823 DOI: 10.1016/j.str.2018.04.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 02/27/2018] [Accepted: 04/19/2018] [Indexed: 11/19/2022]
Abstract
Protein dynamics manifested through structural flexibility play a central role in the function of biological molecules. Here we explore the substrate-mediated change in protein flexibility of an antibiotic target enzyme, Clostridium botulinum dihydrodipicolinate synthase. We demonstrate that the substrate, pyruvate, stabilizes the more active dimer-of-dimers or tetrameric form. Surprisingly, there is little difference between the crystal structures of apo and substrate-bound enzyme, suggesting protein dynamics may be important. Neutron and small-angle X-ray scattering experiments were used to probe substrate-induced dynamics on the sub-second timescale, but no significant changes were observed. We therefore developed a simple technique, coined protein dynamics-mass spectrometry (ProD-MS), which enables measurement of time-dependent alkylation of cysteine residues. ProD-MS together with X-ray crystallography and analytical ultracentrifugation analyses indicates that pyruvate locks the conformation of the dimer that promotes docking to the more active tetrameric form, offering insight into ligand-mediated stabilization of multimeric enzymes.
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Affiliation(s)
- Sarah C Atkinson
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, 30 Flemington Road, University of Melbourne, Parkville, VIC 3010, Australia
| | - Con Dogovski
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, 30 Flemington Road, University of Melbourne, Parkville, VIC 3010, Australia
| | - Kathleen Wood
- Australian Nuclear Science and Technology Organisation, Lucas Heights, NSW 2234, Australia
| | - Michael D W Griffin
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, 30 Flemington Road, University of Melbourne, Parkville, VIC 3010, Australia
| | - Michael A Gorman
- ACRF Rational Drug Discovery Centre, St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | - Lilian Hor
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, 30 Flemington Road, University of Melbourne, Parkville, VIC 3010, Australia; Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia; ARC Centre of Excellence in Advanced Molecular Imaging, La Trobe University, Melbourne, VIC 3086, Australia
| | - Cyril F Reboul
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Ashley M Buckle
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Joachim Wuttke
- Juelich Centre for Neutron Science (JCNS), at Heinz Maier-Leibnitz Zentrum (MLZ), Forschungszentrum Juelich GmbH, Lichtenstrasse 1, Garching 85 747, Germany
| | - Michael W Parker
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, 30 Flemington Road, University of Melbourne, Parkville, VIC 3010, Australia; ACRF Rational Drug Discovery Centre, St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | - Renwick C J Dobson
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, 30 Flemington Road, University of Melbourne, Parkville, VIC 3010, Australia; Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Private Bag, Christchurch 4800, New Zealand
| | - Matthew A Perugini
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, 30 Flemington Road, University of Melbourne, Parkville, VIC 3010, Australia; Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia.
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48
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Manjunath L, Guntupalli SR, Currie MJ, North RA, Dobson RCJ, Nayak V, Subramanian R. Crystal structures and kinetic analyses of N-acetylmannosamine-6-phosphate 2-epimerases from Fusobacterium nucleatum and Vibrio cholerae. Acta Crystallogr F Struct Biol Commun 2018; 74:431-440. [PMID: 29969107 PMCID: PMC6038449 DOI: 10.1107/s2053230x18008543] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Accepted: 06/10/2018] [Indexed: 03/03/2023] Open
Abstract
Sialic acids are nine-carbon sugars that are found abundantly on the cell surfaces of mammals as glycoprotein or glycolipid complexes. Several Gram-negative and Gram-positive bacteria have the ability to scavenge and catabolize sialic acids to use as a carbon source. This gives them an advantage in colonizing sialic acid-rich environments. The genes of the sialic acid catabolic pathway are generally present as the operon nanAKE. The third gene in the operon encodes the enzyme N-acetylmannosamine-6-phosphate 2-epimerase (NanE), which catalyzes the conversion of N-acetylmannosamine 6-phosphate to N-acetylglucosamine 6-phosphate, thus committing it to enter glycolysis. The NanE enzyme belongs to the isomerase class of enzymes possessing the triose phosphate isomerase (TIM) barrel fold. Here, comparative structural and functional characterizations of the NanE epimerases from two pathogenic Gram-negative bacteria, Fusobacterium nucleatum (Fn) and Vibrio cholerae (Vc), have been carried out. Structures of NanE from Vc (VcNanE) with and without ligand bound have been determined to 1.7 and 2.7 Å resolution, respectively. The structure of NanE from Fn (FnNanE) has been determined to 2.2 Å resolution. The enzymes show kinetic parameters that are consistent with those of Clostridium perfringens NanE. These studies allowed an evaluation of whether NanE may be a good drug target against these pathogenic bacteria.
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Affiliation(s)
- Lavanyaa Manjunath
- Institute for Stem Cell Biology and Regenerative Medicine, NCBS, GKVK Campus, Bellary Road, Bangalore, Karnataka 560 065, India
- Manipal Academy of Higher Education, Tiger Circle Road, Manipal, Karnataka 576 104, India
| | - Sai Rohit Guntupalli
- Institute for Stem Cell Biology and Regenerative Medicine, NCBS, GKVK Campus, Bellary Road, Bangalore, Karnataka 560 065, India
- Manipal Academy of Higher Education, Tiger Circle Road, Manipal, Karnataka 576 104, India
| | - Michael J. Currie
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, New Zealand
| | - Rachel A. North
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, New Zealand
| | - Renwick C. J. Dobson
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, New Zealand
- Bio21 Molecular Science and Biotechnology Institute, Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Vinod Nayak
- Institute for Stem Cell Biology and Regenerative Medicine, NCBS, GKVK Campus, Bellary Road, Bangalore, Karnataka 560 065, India
| | - Ramaswamy Subramanian
- Institute for Stem Cell Biology and Regenerative Medicine, NCBS, GKVK Campus, Bellary Road, Bangalore, Karnataka 560 065, India
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49
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Crowther JM, Allison JR, Smolenski GA, Hodgkinson AJ, Jameson GB, Dobson RCJ. The self-association and thermal denaturation of caprine and bovine β-lactoglobulin. Eur Biophys J 2018; 47:739-750. [PMID: 29663020 DOI: 10.1007/s00249-018-1300-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 02/27/2018] [Accepted: 04/10/2018] [Indexed: 11/29/2022]
Abstract
Milk components, such as proteins and lipids, have different physicochemical properties depending upon the mammalian species from which they come. Understanding the different responses of these milks to digestion, processing, and differences in their immunogenicity requires detailed knowledge of these physicochemical properties. Here we report on the oligomeric state of β-lactoglobulin from caprine milk, the most abundant protein present in the whey fraction. At pH 2.5 caprine β-lactoglobulin is predominantly monomeric, whereas bovine β-lactoglobulin exists in a monomer-dimer equilibrium at the same protein concentrations. This behaviour was also observed in molecular dynamics simulations and can be rationalised in terms of the amino acid substitutions present between caprine and bovine β-lactoglobulin that result in a greater positive charge on each subunit of caprine β-lactoglobulin at low pH. The denaturation of β-lactoglobulin when milk is heat-treated contributes to the fouling of heat-exchange surfaces, reducing yields and increasing cleaning costs. The bovine and caprine orthologues of β-lactoglobulin display different responses to thermal treatment, with caprine β-lactoglobulin precipitating at higher pH values than bovine β-lactoglobulin (pH 7.1 compared to pH 5.6) that are closer to the natural pH of these milks (pH 6.7). This property of caprine β-lactoglobulin likely contributes to the reduced heat stability of caprine milk compared to bovine milk at its natural pH.
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Affiliation(s)
- Jennifer M Crowther
- School of Biological Sciences, University of Canterbury, PO Box 4800, Christchurch, 8140, New Zealand
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
| | - Jane R Allison
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
- Centre for Theoretical Chemistry and Physics, Institute of Natural and Mathematical Sciences, Massey University, Auckland, New Zealand
| | - Grant A Smolenski
- Food and Bio-Based Products, AgResearch Limited, Ruakura Research Centre, Hamilton, New Zealand
- MS3 Solutions Ltd, Ruakura Research Centre, Hamilton, 3240, New Zealand
| | - Alison J Hodgkinson
- Food and Bio-Based Products, AgResearch Limited, Ruakura Research Centre, Hamilton, New Zealand
| | - Geoffrey B Jameson
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
- The Riddet Institute, Massey University, Palmerston North, New Zealand
| | - Renwick C J Dobson
- School of Biological Sciences, University of Canterbury, PO Box 4800, Christchurch, 8140, New Zealand.
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand.
- The Riddet Institute, Massey University, Palmerston North, New Zealand.
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, Australia.
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50
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Parthasarathy A, Cross PJ, Dobson RCJ, Adams LE, Savka MA, Hudson AO. A Three-Ring Circus: Metabolism of the Three Proteogenic Aromatic Amino Acids and Their Role in the Health of Plants and Animals. Front Mol Biosci 2018; 5:29. [PMID: 29682508 PMCID: PMC5897657 DOI: 10.3389/fmolb.2018.00029] [Citation(s) in RCA: 154] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Accepted: 03/21/2018] [Indexed: 12/19/2022] Open
Abstract
Tyrosine, phenylalanine and tryptophan are the three aromatic amino acids (AAA) involved in protein synthesis. These amino acids and their metabolism are linked to the synthesis of a variety of secondary metabolites, a subset of which are involved in numerous anabolic pathways responsible for the synthesis of pigment compounds, plant hormones and biological polymers, to name a few. In addition, these metabolites derived from the AAA pathways mediate the transmission of nervous signals, quench reactive oxygen species in the brain, and are involved in the vast palette of animal coloration among others pathways. The AAA and metabolites derived from them also have integral roles in the health of both plants and animals. This review delineates the de novo biosynthesis of the AAA by microbes and plants, and the branching out of AAA metabolism into major secondary metabolic pathways in plants such as the phenylpropanoid pathway. Organisms that do not possess the enzymatic machinery for the de novo synthesis of AAA must obtain these primary metabolites from their diet. Therefore, the metabolism of AAA by the host animal and the resident microflora are important for the health of all animals. In addition, the AAA metabolite-mediated host-pathogen interactions in general, as well as potential beneficial and harmful AAA-derived compounds produced by gut bacteria are discussed. Apart from the AAA biosynthetic pathways in plants and microbes such as the shikimate pathway and the tryptophan pathway, this review also deals with AAA catabolism in plants, AAA degradation via the monoamine and kynurenine pathways in animals, and AAA catabolism via the 3-aryllactate and kynurenine pathways in animal-associated microbes. Emphasis will be placed on structural and functional aspects of several key AAA-related enzymes, such as shikimate synthase, chorismate mutase, anthranilate synthase, tryptophan synthase, tyrosine aminotransferase, dopachrome tautomerase, radical dehydratase, and type III CoA-transferase. The past development and current potential for interventions including the development of herbicides and antibiotics that target key enzymes in AAA-related pathways, as well as AAA-linked secondary metabolism leading to antimicrobials are also discussed.
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Affiliation(s)
- Anutthaman Parthasarathy
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, United States
| | - Penelope J. Cross
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Renwick C. J. Dobson
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, Australia
| | - Lily E. Adams
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, United States
| | - Michael A. Savka
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, United States
| | - André O. Hudson
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, United States
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