Crystal structures of a putative periplasmic cystine‐binding protein from <i>Candidatus</i> Liberibacter asiaticus: insights into an adapted mechanism of ligand binding

Kumar, Pranav; Kesari, Pooja; Kokane, Sunil; Ghosh, Dilip K.; Kumar, Pravindra; Sharma, Ashwani

doi:10.1111/febs.14921

Cited by 9 publications

(6 citation statements)

References 42 publications

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“…As yet, there are no molecular structures for Ca. L. solanacearum proteins reported and structures from Liberibacter species in general are limited (Jiang et al 2014;Saini et al 2018;Kumar, Kesari, et al 2019;Kumar, Dalal, et al 2019;Nan et al 2020), which hinders our understanding of the biology of this genus. This investigation to express, purify and characterise the 'Candidatus Liberibacter solanacearum' lysine biosynthetic enzyme dihydrodipicolinate synthase, which is well studied in other bacterial systems, provides a unique opportunity to assess how evolution shapes enzymes in context of a reduced genome and a bottlenecked lifestyle.…”

Section: Discussionmentioning

confidence: 99%

Genetic drift and genome reduction in the plant pathogenCandidatusLiberibacter solanacearum shapes a new enzyme in lysine biosynthesis

Gilkes

Frampton

Board

et al. 2023

Preprint

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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 effects of genome reduction and genetic drift on the function of Ca. L. solanacearum dihydrodipicolinate synthase (CLsoDHDPS), which catalyses 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 increased aggregation propensity, implying mutations have destabilised the enzyme but are compensated for through elevated chaperone expression and a stabilised oligomeric state. CLsoDHDPS uses a ternary-complex kinetic mechanism, which is 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 reveals the effects of genome reduction and genetic drift on the function of essential enzymes and provides insights on bacteria-host co-evolutionary association. We suggest 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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Section: Discussionmentioning

confidence: 99%

Genetic drift and genome reduction in the plant pathogenCandidatusLiberibacter solanacearum shapes a new enzyme in lysine biosynthesis

Gilkes

Frampton

Board

et al. 2023

Preprint

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“…These facts could explain why TcyABC might be able to accommodate both CSSC and Cys in its substrate-binding site. Further studies will provide insight into the flexible substrate-binding site of TcyABC, but TcyA has been crystalized and the structure has been determined with either CSSC or Cys bound to the binding site, revealing that it has affinity for both derivatives (54).…”

Section: Discussionmentioning

confidence: 99%

The Staphylococcus aureus Cystine Transporters TcyABC and TcyP Facilitate Nutrient Sulfur Acquisition during Infection

et al. 2020

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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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“…Crystal structure and binding studies of CLasTcyA by SPR and microscale thermophoresis (MST) showed a maximum affinity with cystine ligand. Detailed crystal structure analysis of CLasTcyA showed some unique features, like a relatively larger binding pocket, presence of an extended c-terminal loop stabilized by a disulfide bond, and involvement of residue from the hinge region in the stabilization of the ligand [ 145 ]. Biophysical characterization of mutant CLasTcyA confirmed this unique feature.…”

Section: Triangular Management Strategiesmentioning

confidence: 99%

“…In C Las, only two specific periplasmic amino-acid-binding proteins are present: one is cationic amino acid, and another is CLasTcyA. Based on the unique feature of CLasTcyA and the presence of permease, it was hypothesized that CLasTcyA might be involved in the transport of cystine and other branched-chain amino acids [ 145 ]. Insilico structure-based inhibitor screening against CLasTcyA showed five compounds in the zinc database (ZINC000000211883, ZINC000004707227, ZINC000013843286, ZINC000018063863, and ZINC000100640093) that exhibit higher binding energy than the ligand molecule [ 146 ].…”

Section: Triangular Management Strategiesmentioning

confidence: 99%

Huanglongbing Pandemic: Current Challenges and Emerging Management Strategies

Ghosh

Kokane

Savita

et al. 2022

Plants

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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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Crystal structures of a putative periplasmic cystine‐binding protein from Candidatus Liberibacter asiaticus: insights into an adapted mechanism of ligand binding

Cited by 9 publications

References 42 publications

Genetic drift and genome reduction in the plant pathogenCandidatusLiberibacter solanacearum shapes a new enzyme in lysine biosynthesis

Genetic drift and genome reduction in the plant pathogenCandidatusLiberibacter solanacearum shapes a new enzyme in lysine biosynthesis

The Staphylococcus aureus Cystine Transporters TcyABC and TcyP Facilitate Nutrient Sulfur Acquisition during Infection

Huanglongbing Pandemic: Current Challenges and Emerging Management Strategies

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