Single nucleotide variation catalog from clinical isolates mapped on tertiary and quaternary structures of ESX-1-related proteins reveals critical regions as putative Mtb therapeutic targets

Oren Tzfadia; Abril Gijsbers; Alexandra Vujkovic; Jihad Snobre; Roger Vargas; Klaas Dewaele; Conor J Meehan; Maha Farhat; Sneha Hakke; Peter J Peters; Bouke C de Jong; Axel Siroy; Raimond B G Ravelli

doi:10.1128/spectrum.03816-23

Single nucleotide variation catalog from clinical isolates mapped on tertiary and quaternary structures of ESX-1-related proteins reveals critical regions as putative Mtb therapeutic targets

Oren Tzfadia, Abril Gijsbers, Alexandra Vujkovic, Jihad Snobre, Roger Vargas, Klaas Dewaele, Conor J Meehan, Maha Farhat, Sneha Hakke, Peter J Peters, Bouke C de Jong, Axel Siroy, Raimond B G Ravelli

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Abstract

Proteins encoded by the ESX-1 genes of interest are essential for full virulence in all Mycobacterium tuberculosis complex (Mtbc) lineages, the pathogens causing the highest mortality worldwide. Identifying critical regions in these ESX-1-related proteins could provide preventive or therapeutic targets for Mtb infection, the game changer needed for tuberculosis control. We analyzed a compendium of whole genome sequences of clinical Mtb isolates from all lineages from >32,000 patients and identified single nucleotide polymorphisms. When mutations corresponding to all non-synonymous single nucleotide polymorphisms were mapped on structural models of the ESX-1 proteins, fully conserved regions emerged. Some could be assigned to known quaternary structures, whereas others could be predicted to be involved in yet-to-be-discovered interactions. Some mutants had clonally expanded (found in >1% of the isolates); these mutants were mostly located at the surface of globular domains, remote from known intra- and inter-molecular protein-protein interactions. Fully conserved intrinsically disordered regions of proteins were found, suggesting that these regions are crucial for the pathogenicity of the Mtbc. Altogether, our findings highlight fully conserved regions of proteins as attractive vaccine antigens and drug targets to control Mtb virulence. Extending this approach to the whole Mtb genome as well as other microorganisms will enhance vaccine development for various pathogens.

IMPORTANCE: We mapped all non-synonymous single nucleotide polymorphisms onto each of the experimental and predicted ESX-1 proteins' structural models and inspected their placement. Varying sizes of conserved regions were found. Next, we analyzed predicted intrinsically disordered regions within our set of proteins, finding two putative long stretches that are fully conserved, and discussed their potential essential role in immunological recognition. Combined, our findings highlight new targets for interfering with Mycobacterium tuberculosis complex virulence.

Original language	English
Article number	e0381623
Pages (from-to)	1-19
Number of pages	19
Journal	Microbiology spectrum
Volume	12
Issue number	8
DOIs	https://doi.org/10.1128/spectrum.03816-23
Publication status	Published - 6 Aug 2024

Bibliographical note

Funding Information:
We thank the patients for consenting to participate in the study. The authors want to thank Jens Vereecken for helping with Sanger sequencing of EspI, Wim Mulders for technical support, and Hang Nguyen for the critical reading of the manuscript. This study was supported by the Research Foundation-Flanders (FWO IntegrOmics G0B0222N to B.C.D.J. and O.T.). O.T., C.J.M., and B.C.D.J. conceived the study and study design. O.T., A.S., A.G., A.V., J.S., R.V., and K.D. contributed to the bioinformatic and results analysis. S.H. performed the cloning and antibody binding assays and mass spectrometry sample preparation. M.F. supervised R.V. analyses. O.T., R.B.G.R., A.S., A.G., B.C.D.J., and P.J.P. evaluated and interpreted the data and drafted the paper. All authors edited and approved the finalmanuscript Fonds Wetenschappelijk Onderzoek (FWO) G0B0222N Oren Tzfadia Jihad Snobre Bouke C. de Jong

Publisher Copyright:
© 2024 Tzfadia et al.

Keywords

Polymorphism, Single Nucleotide
Bacterial Proteins/genetics
Mycobacterium tuberculosis/genetics
Tuberculosis/microbiology
Antigens, Bacterial/genetics
Virulence/genetics
Mutation
Genome, Bacterial/genetics
Models, Molecular

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Tzfadia, O., Gijsbers, A., Vujkovic, A., Snobre, J., Vargas, R., Dewaele, K., Meehan, C. J., Farhat, M., Hakke, S., Peters, P. J., de Jong, B. C., Siroy, A., & Ravelli, R. B. G. (2024). Single nucleotide variation catalog from clinical isolates mapped on tertiary and quaternary structures of ESX-1-related proteins reveals critical regions as putative Mtb therapeutic targets. Microbiology spectrum, 12(8), 1-19. Article e0381623. https://doi.org/10.1128/spectrum.03816-23

@article{00cf696bbea2430391268aa50ed5cf05,

title = "Single nucleotide variation catalog from clinical isolates mapped on tertiary and quaternary structures of ESX-1-related proteins reveals critical regions as putative Mtb therapeutic targets",

abstract = "Proteins encoded by the ESX-1 genes of interest are essential for full virulence in all Mycobacterium tuberculosis complex (Mtbc) lineages, the pathogens causing the highest mortality worldwide. Identifying critical regions in these ESX-1-related proteins could provide preventive or therapeutic targets for Mtb infection, the game changer needed for tuberculosis control. We analyzed a compendium of whole genome sequences of clinical Mtb isolates from all lineages from >32,000 patients and identified single nucleotide polymorphisms. When mutations corresponding to all non-synonymous single nucleotide polymorphisms were mapped on structural models of the ESX-1 proteins, fully conserved regions emerged. Some could be assigned to known quaternary structures, whereas others could be predicted to be involved in yet-to-be-discovered interactions. Some mutants had clonally expanded (found in >1% of the isolates); these mutants were mostly located at the surface of globular domains, remote from known intra- and inter-molecular protein-protein interactions. Fully conserved intrinsically disordered regions of proteins were found, suggesting that these regions are crucial for the pathogenicity of the Mtbc. Altogether, our findings highlight fully conserved regions of proteins as attractive vaccine antigens and drug targets to control Mtb virulence. Extending this approach to the whole Mtb genome as well as other microorganisms will enhance vaccine development for various pathogens.IMPORTANCE: We mapped all non-synonymous single nucleotide polymorphisms onto each of the experimental and predicted ESX-1 proteins' structural models and inspected their placement. Varying sizes of conserved regions were found. Next, we analyzed predicted intrinsically disordered regions within our set of proteins, finding two putative long stretches that are fully conserved, and discussed their potential essential role in immunological recognition. Combined, our findings highlight new targets for interfering with Mycobacterium tuberculosis complex virulence.",

keywords = "Polymorphism, Single Nucleotide, Bacterial Proteins/genetics, Mycobacterium tuberculosis/genetics, Tuberculosis/microbiology, Antigens, Bacterial/genetics, Virulence/genetics, Mutation, Genome, Bacterial/genetics, Models, Molecular",

author = "Oren Tzfadia and Abril Gijsbers and Alexandra Vujkovic and Jihad Snobre and Roger Vargas and Klaas Dewaele and Meehan, {Conor J} and Maha Farhat and Sneha Hakke and Peters, {Peter J} and {de Jong}, {Bouke C} and Axel Siroy and Ravelli, {Raimond B G}",

note = "Funding Information: We thank the patients for consenting to participate in the study. The authors want to thank Jens Vereecken for helping with Sanger sequencing of EspI, Wim Mulders for technical support, and Hang Nguyen for the critical reading of the manuscript. This study was supported by the Research Foundation-Flanders (FWO IntegrOmics G0B0222N to B.C.D.J. and O.T.). O.T., C.J.M., and B.C.D.J. conceived the study and study design. O.T., A.S., A.G., A.V., J.S., R.V., and K.D. contributed to the bioinformatic and results analysis. S.H. performed the cloning and antibody binding assays and mass spectrometry sample preparation. M.F. supervised R.V. analyses. O.T., R.B.G.R., A.S., A.G., B.C.D.J., and P.J.P. evaluated and interpreted the data and drafted the paper. All authors edited and approved the finalmanuscript Fonds Wetenschappelijk Onderzoek (FWO) G0B0222N Oren Tzfadia Jihad Snobre Bouke C. de Jong Publisher Copyright: {\textcopyright} 2024 Tzfadia et al.",

year = "2024",

month = aug,

day = "6",

doi = "10.1128/spectrum.03816-23",

language = "English",

volume = "12",

pages = "1--19",

journal = "Microbiology spectrum",

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Tzfadia, O, Gijsbers, A, Vujkovic, A, Snobre, J, Vargas, R, Dewaele, K, Meehan, CJ, Farhat, M, Hakke, S, Peters, PJ, de Jong, BC, Siroy, A & Ravelli, RBG 2024, 'Single nucleotide variation catalog from clinical isolates mapped on tertiary and quaternary structures of ESX-1-related proteins reveals critical regions as putative Mtb therapeutic targets', Microbiology spectrum, vol. 12, no. 8, e0381623, pp. 1-19. https://doi.org/10.1128/spectrum.03816-23

Single nucleotide variation catalog from clinical isolates mapped on tertiary and quaternary structures of ESX-1-related proteins reveals critical regions as putative Mtb therapeutic targets. / Tzfadia, Oren; Gijsbers, Abril; Vujkovic, Alexandra et al.
In: Microbiology spectrum, Vol. 12, No. 8, e0381623, 06.08.2024, p. 1-19.

Research output: Contribution to journal › Article › peer-review

TY - JOUR

T1 - Single nucleotide variation catalog from clinical isolates mapped on tertiary and quaternary structures of ESX-1-related proteins reveals critical regions as putative Mtb therapeutic targets

AU - Tzfadia, Oren

AU - Gijsbers, Abril

AU - Vujkovic, Alexandra

AU - Snobre, Jihad

AU - Vargas, Roger

AU - Dewaele, Klaas

AU - Meehan, Conor J

AU - Farhat, Maha

AU - Hakke, Sneha

AU - Peters, Peter J

AU - de Jong, Bouke C

AU - Siroy, Axel

AU - Ravelli, Raimond B G

N1 - Funding Information: We thank the patients for consenting to participate in the study. The authors want to thank Jens Vereecken for helping with Sanger sequencing of EspI, Wim Mulders for technical support, and Hang Nguyen for the critical reading of the manuscript. This study was supported by the Research Foundation-Flanders (FWO IntegrOmics G0B0222N to B.C.D.J. and O.T.). O.T., C.J.M., and B.C.D.J. conceived the study and study design. O.T., A.S., A.G., A.V., J.S., R.V., and K.D. contributed to the bioinformatic and results analysis. S.H. performed the cloning and antibody binding assays and mass spectrometry sample preparation. M.F. supervised R.V. analyses. O.T., R.B.G.R., A.S., A.G., B.C.D.J., and P.J.P. evaluated and interpreted the data and drafted the paper. All authors edited and approved the finalmanuscript Fonds Wetenschappelijk Onderzoek (FWO) G0B0222N Oren Tzfadia Jihad Snobre Bouke C. de Jong Publisher Copyright: © 2024 Tzfadia et al.

PY - 2024/8/6

Y1 - 2024/8/6

N2 - Proteins encoded by the ESX-1 genes of interest are essential for full virulence in all Mycobacterium tuberculosis complex (Mtbc) lineages, the pathogens causing the highest mortality worldwide. Identifying critical regions in these ESX-1-related proteins could provide preventive or therapeutic targets for Mtb infection, the game changer needed for tuberculosis control. We analyzed a compendium of whole genome sequences of clinical Mtb isolates from all lineages from >32,000 patients and identified single nucleotide polymorphisms. When mutations corresponding to all non-synonymous single nucleotide polymorphisms were mapped on structural models of the ESX-1 proteins, fully conserved regions emerged. Some could be assigned to known quaternary structures, whereas others could be predicted to be involved in yet-to-be-discovered interactions. Some mutants had clonally expanded (found in >1% of the isolates); these mutants were mostly located at the surface of globular domains, remote from known intra- and inter-molecular protein-protein interactions. Fully conserved intrinsically disordered regions of proteins were found, suggesting that these regions are crucial for the pathogenicity of the Mtbc. Altogether, our findings highlight fully conserved regions of proteins as attractive vaccine antigens and drug targets to control Mtb virulence. Extending this approach to the whole Mtb genome as well as other microorganisms will enhance vaccine development for various pathogens.IMPORTANCE: We mapped all non-synonymous single nucleotide polymorphisms onto each of the experimental and predicted ESX-1 proteins' structural models and inspected their placement. Varying sizes of conserved regions were found. Next, we analyzed predicted intrinsically disordered regions within our set of proteins, finding two putative long stretches that are fully conserved, and discussed their potential essential role in immunological recognition. Combined, our findings highlight new targets for interfering with Mycobacterium tuberculosis complex virulence.

AB - Proteins encoded by the ESX-1 genes of interest are essential for full virulence in all Mycobacterium tuberculosis complex (Mtbc) lineages, the pathogens causing the highest mortality worldwide. Identifying critical regions in these ESX-1-related proteins could provide preventive or therapeutic targets for Mtb infection, the game changer needed for tuberculosis control. We analyzed a compendium of whole genome sequences of clinical Mtb isolates from all lineages from >32,000 patients and identified single nucleotide polymorphisms. When mutations corresponding to all non-synonymous single nucleotide polymorphisms were mapped on structural models of the ESX-1 proteins, fully conserved regions emerged. Some could be assigned to known quaternary structures, whereas others could be predicted to be involved in yet-to-be-discovered interactions. Some mutants had clonally expanded (found in >1% of the isolates); these mutants were mostly located at the surface of globular domains, remote from known intra- and inter-molecular protein-protein interactions. Fully conserved intrinsically disordered regions of proteins were found, suggesting that these regions are crucial for the pathogenicity of the Mtbc. Altogether, our findings highlight fully conserved regions of proteins as attractive vaccine antigens and drug targets to control Mtb virulence. Extending this approach to the whole Mtb genome as well as other microorganisms will enhance vaccine development for various pathogens.IMPORTANCE: We mapped all non-synonymous single nucleotide polymorphisms onto each of the experimental and predicted ESX-1 proteins' structural models and inspected their placement. Varying sizes of conserved regions were found. Next, we analyzed predicted intrinsically disordered regions within our set of proteins, finding two putative long stretches that are fully conserved, and discussed their potential essential role in immunological recognition. Combined, our findings highlight new targets for interfering with Mycobacterium tuberculosis complex virulence.

KW - Polymorphism, Single Nucleotide

KW - Bacterial Proteins/genetics

KW - Mycobacterium tuberculosis/genetics

KW - Tuberculosis/microbiology

KW - Antigens, Bacterial/genetics

KW - Virulence/genetics

KW - Mutation

KW - Genome, Bacterial/genetics

KW - Models, Molecular

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U2 - 10.1128/spectrum.03816-23

DO - 10.1128/spectrum.03816-23

M3 - Article

C2 - 38874407

SN - 2165-0497

VL - 12

SP - 1

EP - 19

JO - Microbiology spectrum

JF - Microbiology spectrum

IS - 8

M1 - e0381623

ER -

Single nucleotide variation catalog from clinical isolates mapped on tertiary and quaternary structures of ESX-1-related proteins reveals critical regions as putative Mtb therapeutic targets

Abstract

Bibliographical note

Keywords

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