Identification of Widespread Adenosine Nucleotide Binding in Mycobacterium Tuberculosis

Overview

Journal Chem Biol

Publisher Elsevier

Specialties Biochemistry
Biology
Chemistry

Date 2013 Jan 29

PMID 23352146

Citations 29

Authors

Charles Ansong

Corrie Ortega

Samuel H Payne

Daniel H Haft

Lacie M Chauvigne-Hines

Michael P Lewis

Anja R Ollodart

Samuel O Purvine

Anil K Shukla

Suereta Fortuin

Richard D Smith

Joshua N Adkins

Christoph Grundner

Aaron T Wright

Affiliations

Soon will be listed here.

Abstract

Computational prediction of protein function is frequently error-prone and incomplete. In Mycobacterium tuberculosis (Mtb), ~25% of all genes have no predicted function and are annotated as hypothetical proteins, severely limiting our understanding of Mtb pathogenicity. Here, we utilize a high-throughput quantitative activity-based protein profiling (ABPP) platform to probe, annotate, and validate ATP-binding proteins in Mtb. We experimentally validate prior in silico predictions of >240 proteins and identify 72 hypothetical proteins as ATP binders. ATP interacts with proteins with diverse and unrelated sequences, providing an expanded view of adenosine nucleotide binding in Mtb. Several hypothetical ATP binders are essential or taxonomically limited, suggesting specialized functions in mycobacterial physiology and pathogenicity.

Citing Articles

Chemical Probes Review: Choosing the Right Path Towards Pharmacological Targets in Drug Discovery, Challenges and Future Perspectives.

Ahuja A, Singh S, Murti Y Comb Chem High Throughput Screen. 2023; 27(17):2544-2564.

PMID: 38083882 DOI: 10.2174/0113862073283304231118155730.

Chemoproteomic Approaches for Unraveling Prokaryotic Biology.

Malarney K, Chang P Isr J Chem. 2023; 63(3-4).

PMID: 37842282 PMC: 10575470. DOI: 10.1002/ijch.202200076.

Septum site placement in - identification and characterisation of mycobacterial homologues of MinD.

Kishore V, Gaiwala Sharma S, Raghunand T Microbiology (Reading). 2023; 169(8).

PMID: 37526955 PMC: 10482377. DOI: 10.1099/mic.0.001359.

Chemical approaches to unraveling the biology of mycobacteria.

Finin P, Khan R, Oh S, Boshoff H, Barry 3rd C Cell Chem Biol. 2023; 30(5):420-435.

PMID: 37207631 PMC: 10201459. DOI: 10.1016/j.chembiol.2023.04.014.

Genome-Wide Study of Drug Resistant and Its Intra-Host Evolution during Treatment.

Lagutkin D, Panova A, Vinokurov A, Gracheva A, Samoilova A, Vasilyeva I Microorganisms. 2022; 10(7).

PMID: 35889159 PMC: 9318467. DOI: 10.3390/microorganisms10071440.

References

Kelley L, Sternberg M . Protein structure prediction on the Web: a case study using the Phyre server. Nat Protoc. 2009; 4(3):363-71. DOI: 10.1038/nprot.2009.2. View

Doerks T, van Noort V, Minguez P, Bork P . Annotation of the M. tuberculosis hypothetical orfeome: adding functional information to more than half of the uncharacterized proteins. PLoS One. 2012; 7(4):e34302. PMC: 3317503. DOI: 10.1371/journal.pone.0034302. View

Sadler N, Angel T, Lewis M, Pederson L, Chauvigne-Hines L, Wiedner S . Activity-based protein profiling reveals mitochondrial oxidative enzyme impairment and restoration in diet-induced obese mice. PLoS One. 2012; 7(10):e47996. PMC: 3480472. DOI: 10.1371/journal.pone.0047996. View

Galperin M, Koonin E . From complete genome sequence to 'complete' understanding?. Trends Biotechnol. 2010; 28(8):398-406. PMC: 3065831. DOI: 10.1016/j.tibtech.2010.05.006. View

Qiu H, Wang Y . Probing adenosine nucleotide-binding proteins with an affinity-labeled nucleotide probe and mass spectrometry. Anal Chem. 2007; 79(15):5547-56. PMC: 2637870. DOI: 10.1021/ac0622375. View

Keseler I, Collado-Vides J, Santos-Zavaleta A, Peralta-Gil M, Gama-Castro S, Muniz-Rascado L . EcoCyc: a comprehensive database of Escherichia coli biology. Nucleic Acids Res. 2010; 39(Database issue):D583-90. PMC: 3013716. DOI: 10.1093/nar/gkq1143. View

Venter E, Smith R, Payne S . Proteogenomic analysis of bacteria and archaea: a 46 organism case study. PLoS One. 2011; 6(11):e27587. PMC: 3219674. DOI: 10.1371/journal.pone.0027587. View

Bork P . Powers and pitfalls in sequence analysis: the 70% hurdle. Genome Res. 2000; 10(4):398-400. DOI: 10.1101/gr.10.4.398. View

Bork P, Koonin E . Predicting functions from protein sequences--where are the bottlenecks?. Nat Genet. 1998; 18(4):313-8. DOI: 10.1038/ng0498-313. View

10.

Patricelli M, Szardenings A, Liyanage M, Nomanbhoy T, Wu M, Weissig H . Functional interrogation of the kinome using nucleotide acyl phosphates. Biochemistry. 2007; 46(2):350-8. DOI: 10.1021/bi062142x. View

11.

Cravatt B, Wright A, Kozarich J . Activity-based protein profiling: from enzyme chemistry to proteomic chemistry. Annu Rev Biochem. 2008; 77:383-414. DOI: 10.1146/annurev.biochem.75.101304.124125. View

12.

Sassetti C, Boyd D, Rubin E . Genes required for mycobacterial growth defined by high density mutagenesis. Mol Microbiol. 2003; 48(1):77-84. DOI: 10.1046/j.1365-2958.2003.03425.x. View

13.

MacGurn J, Raghavan S, Stanley S, Cox J . A non-RD1 gene cluster is required for Snm secretion in Mycobacterium tuberculosis. Mol Microbiol. 2005; 57(6):1653-63. DOI: 10.1111/j.1365-2958.2005.04800.x. View

14.

Kelkar D, Kumar D, Kumar P, Balakrishnan L, Muthusamy B, Yadav A . Proteogenomic analysis of Mycobacterium tuberculosis by high resolution mass spectrometry. Mol Cell Proteomics. 2011; 10(12):M111.011627. PMC: 3275902. DOI: 10.1074/mcp.M111.011445. View

15.

Rost B . Enzyme function less conserved than anticipated. J Mol Biol. 2002; 318(2):595-608. DOI: 10.1016/S0022-2836(02)00016-5. View

16.

Gomez J, Clatworthy A, Hung D . Probing bacterial pathogenesis with genetics, genomics, and chemical biology: past, present, and future approaches. Crit Rev Biochem Mol Biol. 2011; 46(1):41-66. DOI: 10.3109/10409238.2010.538663. View

17.

Speers A, Cravatt B . A tandem orthogonal proteolysis strategy for high-content chemical proteomics. J Am Chem Soc. 2005; 127(28):10018-9. PMC: 1538546. DOI: 10.1021/ja0532842. View

18.

Mawuenyega K, Forst C, Dobos K, Belisle J, Chen J, Bradbury E . Mycobacterium tuberculosis functional network analysis by global subcellular protein profiling. Mol Biol Cell. 2004; 16(1):396-404. PMC: 539182. DOI: 10.1091/mbc.e04-04-0329. View

19.

Sassetti C, Rubin E . Genetic requirements for mycobacterial survival during infection. Proc Natl Acad Sci U S A. 2003; 100(22):12989-94. PMC: 240732. DOI: 10.1073/pnas.2134250100. View

20.

Reddy T, Riley R, Wymore F, Montgomery P, DeCaprio D, Engels R . TB database: an integrated platform for tuberculosis research. Nucleic Acids Res. 2008; 37(Database issue):D499-508. PMC: 2686437. DOI: 10.1093/nar/gkn652. View