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Gilkes JM, Frampton RA, Board AJ, Hudson AO, Price TG, Morris VK, Crittenden DL, Muscroft‐Taylor AC, Sheen CR, Smith GR, Dobson RCJ. A new lysine biosynthetic enzyme from a bacterial endosymbiont shaped by genetic drift and genome reduction. Protein Sci 2024; 33:e5083. [PMID: 38924211 PMCID: PMC11201819 DOI: 10.1002/pro.5083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 05/16/2024] [Accepted: 06/03/2024] [Indexed: 06/28/2024]
Abstract
The effect of population bottlenecks and genome reduction on enzyme function is poorly understood. Candidatus Liberibacter solanacearum is a bacterium with a reduced genome that is transmitted vertically to the egg of an infected psyllid-a population bottleneck that imposes genetic drift and is predicted to affect protein structure and function. Here, we define the function of Ca. L. solanacearum dihydrodipicolinate synthase (CLsoDHDPS), which catalyzes the committed branchpoint reaction in diaminopimelate and lysine biosynthesis. We demonstrate that CLsoDHDPS is expressed in Ca. L. solanacearum and expression is increased ~2-fold in the insect host compared to in planta. CLsoDHDPS has decreased thermal stability and increased aggregation propensity, implying mutations have destabilized the enzyme but are compensated for through elevated chaperone expression and a stabilized oligomeric state. CLsoDHDPS uses a ternary-complex kinetic mechanism, which is to date unique among DHDPS enzymes, has unusually low catalytic ability, but an unusually high substrate affinity. Structural studies demonstrate that the active site is more open, and the structure of CLsoDHDPS with both pyruvate and the substrate analogue succinic-semialdehyde reveals that the product is both structurally and energetically different and therefore evolution has in this case fashioned a new enzyme. Our study suggests the effects of genome reduction and genetic drift on the function of essential enzymes and provides insights on bacteria-host co-evolutionary associations. We propose that bacteria with endosymbiotic lifestyles present a rich vein of interesting enzymes useful for understanding enzyme function and/or informing protein engineering efforts.
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Affiliation(s)
- Jenna M. Gilkes
- Biomolecular Interaction CentreSchool of Biological Sciences, University of CanterburyChristchurchNew Zealand
- The New Zealand Institute for Plant and Food Research LimitedLincolnNew Zealand
- Callaghan Innovation, University of CanterburyChristchurchNew Zealand
| | - Rebekah A. Frampton
- The New Zealand Institute for Plant and Food Research LimitedLincolnNew Zealand
| | - Amanda J. Board
- Biomolecular Interaction CentreSchool of Biological Sciences, University of CanterburyChristchurchNew Zealand
| | - André O. Hudson
- Rochester Institute of Technology, Thomas H. Gosnell School of Life SciencesRochesterNew YorkUSA
| | - Thomas G. Price
- Biomolecular Interaction CentreSchool of Chemical and Physical Sciences, University of CanterburyChristchurchNew Zealand
| | - Vanessa K. Morris
- Biomolecular Interaction CentreSchool of Biological Sciences, University of CanterburyChristchurchNew Zealand
| | - Deborah L. Crittenden
- Biomolecular Interaction CentreSchool of Chemical and Physical Sciences, University of CanterburyChristchurchNew Zealand
| | | | - Campbell R. Sheen
- Callaghan Innovation, University of CanterburyChristchurchNew Zealand
| | - Grant R. Smith
- The New Zealand Institute for Plant and Food Research LimitedLincolnNew Zealand
| | - Renwick C. J. Dobson
- Biomolecular Interaction CentreSchool of Biological Sciences, University of CanterburyChristchurchNew Zealand
- Bio21 Molecular Science and Biotechnology Institute, Department of Biochemistry and Molecular BiologyUniversity of MelbourneParkvilleVictoriaAustralia
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Gupta DN, Lonare S, Rani R, Singh A, Ghosh DK, Tomar S, Sharma AK. Comparative Analysis of Inhibitor Binding to Peroxiredoxins from Candidatus Liberibacter asiaticus and Its Host Citrus sinensis. Appl Biochem Biotechnol 2023:10.1007/s12010-023-04798-y. [PMID: 38157153 DOI: 10.1007/s12010-023-04798-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/09/2023] [Indexed: 01/03/2024]
Abstract
The peroxiredoxins (Prxs), potential drug targets, constitute an important class of antioxidant enzymes present in both pathogen and their host. The comparative binding potential of inhibitors to Prxs from pathogen and host could be an important step in drug development against pathogens. Huanglongbing (HLB) is a most devastating disease of citrus caused by Candidatus Liberibacter asiaticus (CLa). In this study, the binding of conoidin-A (conoidin) and celastrol inhibitor molecules to peroxiredoxin of bacterioferritin comigratory protein family from CLa (CLaBCP) and its host plant peroxiredoxin from Citrus sinensis (CsPrx) was assessed. The CLaBCP has a lower specific activity than CsPrx and is efficiently inhibited by conoidin and celastrol molecules. The biophysical studies showed conformational changes and significant thermal stability of CLaBCP in the presence of inhibitor molecules as compared to CsPrx. The surface plasmon resonance (SPR) studies revealed that the conoidin and celastrol inhibitor molecules have a strong binding affinity (KD) with CLaBCP at 33.0 µM, and 18.5 µM as compared to CsPrx at 52.0 µM and 61.6 µM, respectively. The docked complexes of inhibitor molecules showed more structural stability of CLaBCP as compared to CsPrx during the run of molecular dynamics-based simulations for 100 ns. The present study suggests that the conoidin and celastrol molecules can be exploited as potential inhibitor molecules against the CLa to manage the HLB disease.
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Affiliation(s)
- Deena Nath Gupta
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, 247667, India
| | - Sapna Lonare
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, 247667, India
| | - Ruchi Rani
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, 247667, India
| | - Ankur Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, 247667, India
| | - Dilip Kumar Ghosh
- Plant Virology Laboratory, ICAR Central Citrus Research Institute, Nagpur, India
| | - Shailly Tomar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, 247667, India
| | - Ashwani Kumar Sharma
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, 247667, India.
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Lonare S, Sharma M, Dalal V, Gubyad M, Kumar P, Nath Gupta D, Pareek A, Tomar S, Kumar Ghosh D, Kumar P, Kumar Sharma A. Identification and evaluation of potential inhibitor molecules against TcyA from Candidatus Liberibacter asiaticus. J Struct Biol 2023; 215:107992. [PMID: 37394197 DOI: 10.1016/j.jsb.2023.107992] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 06/19/2023] [Accepted: 06/29/2023] [Indexed: 07/04/2023]
Abstract
Of the two putative amino acid binding periplasmic receptors of ABC transporter family in Candidatus Liberibacter asiaticus (CLas), cystine binding receptor (CLasTcyA) has been shown to mainly express in phloem of citrus plant and is a target for inhibitor development. The crystal structure of CLasTcyA in complex with substrates has been reported earlier. The present work reports the identification and evaluation of potential candidates for their inhibitory potential against CLasTcyA. Among many compounds, selected through virtual screening, and MD simulation, pimozide, clidinium, sulfasalazine and folic acid showed significantly higher affinities and stability in complex with CLasTcyA. The SPR studies with CLasTcyA revealed significantly higher binding affinities for pimozide and clidinium (Kd, 2.73 nM and 70 nM, respectively) as compared to cystine (Kd, 1.26 µM). The higher binding affinities could be attributed to significantly increased number of interactions in the binding pocket as evident from the crystal structures of CLasTcyA in complex with pimozide and clidinium as compared to cystine. The CLasTcyA possess relatively large binding pocket where bulkier inhibitors fit quite well. In planta studies, carried out to assess the effect of inhibitors on HLB infected Mosambi plants, showed significant reduction in CLas titre in plants treated with inhibitors as compared to control plants. The results showed that pimozide exhibited higher efficiency as compared to clidinium in reducing CLas titre in treated plants. Our results showed that the inhibitor development against critical proteins like CLasTcyA can be an important strategy in management of HLB.
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Affiliation(s)
- Sapna Lonare
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee-247667, India
| | - Monica Sharma
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee-247667, India
| | - Vikram Dalal
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee-247667, India
| | - Mrugendra Gubyad
- Plant Virology Laboratory, ICAR Central Citrus Research Institute, Nagpur, India
| | - Pranav Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee-247667, India
| | - Deena Nath Gupta
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee-247667, India
| | - Akshay Pareek
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee-247667, India
| | - Shailly Tomar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee-247667, India
| | - Dilip Kumar Ghosh
- Plant Virology Laboratory, ICAR Central Citrus Research Institute, Nagpur, India
| | - Pravindra Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee-247667, India
| | - Ashwani Kumar Sharma
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee-247667, India.
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Ghosh D, Kokane S, Savita BK, Kumar P, Sharma AK, Ozcan A, Kokane A, Santra S. Huanglongbing Pandemic: Current Challenges and Emerging Management Strategies. PLANTS (BASEL, SWITZERLAND) 2022; 12:plants12010160. [PMID: 36616289 PMCID: PMC9824665 DOI: 10.3390/plants12010160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 12/06/2022] [Accepted: 12/07/2022] [Indexed: 05/09/2023]
Abstract
Huanglongbing (HLB, aka citrus greening), one of the most devastating diseases of citrus, has wreaked havoc on the global citrus industry in recent decades. The culprit behind such a gloomy scenario is the phloem-limited bacteria "Candidatus Liberibacter asiaticus" (CLas), which are transmitted via psyllid. To date, there are no effective long-termcommercialized control measures for HLB, making it increasingly difficult to prevent the disease spread. To combat HLB effectively, introduction of multipronged management strategies towards controlling CLas population within the phloem system is deemed necessary. This article presents a comprehensive review of up-to-date scientific information about HLB, including currently available management practices and unprecedented challenges associated with the disease control. Additionally, a triangular disease management approach has been introduced targeting pathogen, host, and vector. Pathogen-targeting approaches include (i) inhibition of important proteins of CLas, (ii) use of the most efficient antimicrobial or immunity-inducing compounds to suppress the growth of CLas, and (iii) use of tools to suppress or kill the CLas. Approaches for targeting the host include (i) improvement of the host immune system, (ii) effective use of transgenic variety to build the host's resistance against CLas, and (iii) induction of systemic acquired resistance. Strategies for targeting the vector include (i) chemical and biological control and (ii) eradication of HLB-affected trees. Finally, a hypothetical model for integrated disease management has been discussed to mitigate the HLB pandemic.
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Affiliation(s)
- Dilip Ghosh
- Plant Virology Laboratory, ICAR-Central Citrus Research Institute, Nagpur 440033, India
- Correspondence: (D.G.); (A.K.S.); (S.S.)
| | - Sunil Kokane
- Plant Virology Laboratory, ICAR-Central Citrus Research Institute, Nagpur 440033, India
| | - Brajesh Kumar Savita
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, India
| | - Pranav Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, India
| | - Ashwani Kumar Sharma
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, India
- Correspondence: (D.G.); (A.K.S.); (S.S.)
| | - Ali Ozcan
- Vocational School of Technical Sciences, Karamanoglu Mehmetbey University, 70200 Karaman, Turkey
- Scientific and Technological Studies Application and Research Center, Karamanoglu Mehmetbey University, 70200 Karaman, Turkey
| | - Amol Kokane
- Plant Virology Laboratory, ICAR-Central Citrus Research Institute, Nagpur 440033, India
| | - Swadeshmukul Santra
- Departments of Chemistry, Nano Science Technology Center, and Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL 32816, USA
- Correspondence: (D.G.); (A.K.S.); (S.S.)
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Kumar P, Dalal V, Kokane A, Singh S, Lonare S, Kaur H, Ghosh DK, Kumar P, Sharma AK. Mutation studies and structure-based identification of potential inhibitor molecules against periplasmic amino acid binding protein of Candidatus Liberibacter asiaticus (CLasTcyA). Int J Biol Macromol 2020; 147:1228-1238. [DOI: 10.1016/j.ijbiomac.2019.09.250] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 09/26/2019] [Accepted: 09/27/2019] [Indexed: 11/16/2022]
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The Staphylococcus aureus Cystine Transporters TcyABC and TcyP Facilitate Nutrient Sulfur Acquisition during Infection. Infect Immun 2020; 88:IAI.00690-19. [PMID: 31843961 DOI: 10.1128/iai.00690-19] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Accepted: 12/06/2019] [Indexed: 12/21/2022] Open
Abstract
Staphylococcus aureus is a significant human pathogen due to its capacity to cause a multitude of diseases. As such, S. aureus efficiently pillages vital nutrients from the host; however, the molecular mechanisms that support sulfur acquisition during infection have not been established. One of the most abundant extracellular sulfur-containing metabolites within the host is cysteine, which acts as the major redox buffer in the blood by transitioning between reduced and oxidized (cystine) forms. We therefore hypothesized that S. aureus acquires host-derived cysteine and cystine as sources of nutrient sulfur during systemic infection. To test this hypothesis, we used the toxic cystine analogue selenocystine to initially characterize S. aureus homologues of the Bacillus subtilis cystine transporters TcyABC and TcyP. We found that genetic inactivation of both TcyA and TcyP induced selenocystine resistance. The double mutant also failed to proliferate in medium supplemented with cystine, cysteine, or N-acetyl cysteine as the sole sulfur source. However, only TcyABC was necessary for proliferation in defined medium containing homocystine as the sulfur source. Using a murine model of systemic infection, we observed tcyP-dependent competitive defects in the liver and heart, indicating that this sulfur acquisition strategy supports proliferation of S. aureus in these organs. Phylogenetic analyses identified TcyP homologues in many pathogenic species, implying that this sulfur procurement strategy is conserved. In total, this study is the first to experimentally validate sulfur acquisition systems in S. aureus and establish their importance during pathogenesis.
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