Sunita Gupta Vibha Gupta


World Health Organization (WHO) reports that one-third of the world’s population is infected with a persistent form of Mycobacterium tuberculosis (M.tb), the causative bacterium responsible for causing the dreaded tuberculosis disease. Targeting mycobacterial persisters is important for achieving WHO’s End TB target. The de-novo cysteine biosynthetic pathway is a novel target for addressing M.tb persistence.  The two-step pathway comprises of serine acetyltransferase/CysE and O-acetyl-serine-sulfhydrylase/OASS/CysK. The present study is an attempt to understand the structural features of mycobacterial CysE by investigating the divergence amongst orthologous through phylogenetic analysis. Mapping of mycobacterial CysE sequences on the whole orthologous (COG1045) tree segregated the species into four clusters and several isoforms leading to their descendants identification. Interestingly the analysis revealed that the extended C-terminal α-helix believed unique to M.tb is also present in other organisms such as: Campylobacter ureolyticus, Bacillus cereus, Geminocystis herdmanii and Paenibacillus borealis. Further, the Hidden Markov model search against the whole Uniprot database suggests a plausible role of C-terminal α-helix of CysE in strengthening the substrate and/or co-factor binding. In addition, phylogenetic analysis of CysE sequences from the Mycobacteriaceae family facilitates grouping them under ten well-formed and six monophyletic clades, each based on characteristic features with respect to domain architecture, oligomeric assembly, C-terminal tetra-peptide tail, regulatory and feedback mechanism etc. Employing molecular phylogeny in conjunction with structural analysis has provided detailed insights for mycobacterial CysEs as drug target.


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Serine acetyltransferase, Mycobacterium tuberculosis, Phylogenetic analysis, HMM profile, 3D-structure

Altenhoff, A. M., Studer, R. A., Robinson-Rechavi, M. & Dessimoz, C. (2012). Resolving the ortholog conjecture: Orthologs tend to be weakly, but significantly, more similar in function than paralogs. PLoS Computational Biology, 8(5), 1-10 https://doi.org/10.1371/journal.pcbi.1002514
Bateman, A., Martin, M. J., O’Donovan, C., Magrane, M., Apweiler, R., Alpi, E., …& Zhang, J. (2015). UniProt: A hub for protein information. Nucleic Acids Research, 43(D1), D204–D212. https://doi.org/10.1093/nar/gku989
Berglund, A. C., Sjölund, E., Östlund, G. & Sonnhammer, E. L. L. (2008). InParanoid 6: Eukaryotic ortholog clusters with inparalogs. Nucleic Acids Research, 36(SUPPL. 1). https://doi.org/10.1093/nar/gkm1020
Colovos, C. & Yeates, T. O. (1993). Verification of protein structures: Patterns of nonbonded atomic interactions. Protein Science, 2(9), 1511–1519. https://doi.org/10.1002/PRO.5560020916
Devayani P. Bhave, Wilson B. Muse III. & Kate S. Carroll. (2008). Drug targets in mycobacterial sulfur metabolism. Infectious Disorders - Drug Targets, 7(2), 140–158. https://doi.org/10.2174/187152607781001772
Eddy, S. R. (2009). A new generation of homology search tools based on probabilistic inference. Genome Informatics. International Conference on Genome Informatics, 23(1), 205–211. https://doi.org/10.1142/978184816563 2_0019
Gao, B. & Gupta, R. S. (2012). Phylogenetic Framework and Molecular Signatures for the Main Clades of the Phylum Actinobacteria. Microbiology and Molecular Biology Reviews, 76(1), 66–112. https://doi.org/10.1128/mmbr.0 5011-11
Global Tuberculosis Report (2021). Geneva: World Health Organization. Licence: CC BY-NC-SA 3.0 IGO. Retrieved from https://www.who.int/publications/i/item/9789240 037021
Gorman, J. & Shapiro, L. (2004). Structure of serine acetyltransferase from Haemophilus influenzae Rd. Acta Crystallographica Section D: Biological Crystallography, 60(9), 1600–1605. https://doi.org/10.1107/S090744490 4015240
Gupta, S. & Gupta, V. (2020). Homology modeling, structural insights and in-silico screening for selective inhibitors of mycobacterial CysE. Journal of Biomolecular Structure and Dynamics, 39(5), 1547–1560. https://doi.org/10.10 80/07391102.2020.1734089
Hampshire, T., Soneji, S., Bacon, J., James, B. W., Hinds, J., Laing, K., …& Butcher, P. D. (2004). Stationary phase gene expression of Mycobacterium tuberculosis following a progressive nutrient depletion: A model for persistent organisms? Tuberculosis, 84(3–4), 228–238. https://doi.org/10.1016/j.tube.2003.12.010
Han, M. V. & Zmasek, C. M. (2009). PhyloXML: XML for evolutionary biology and comparative genomics. BMC Bioinformatics, 10(1), 1–6. https://doi.org/10.1186/1471-2105-10-356
Handwerger, S. & Tomasz, A. (1985). Antibiotic Tolerance Among Clinical Isolates of Bacteria. Reviews of Infectious Diseases, 7(3), 368–386. https://doi.org/10.1093/CLINIDS/7.3.368
Huang, B., Vetting, M. W. & Roderick, S. L. (2005). The active site of O-acetylserine sulfhydrylase is the anchor point for bienzyme complex formation with serine acetyltransferase. Journal of Bacteriology, 187(9), 3201–3205. https://doi.org/10.1128/JB.187.9.3201-3205.2005
Hubbard, T. J. P., Aken, B. L., Beal, K., Ballester, B., Caccamo, M., Chen, Y., …& Birney, E. (2007). Ensembl 2007. Nucleic Acids Research, 35(SUPPL. 1). https://doi.org/10.1093/nar/gkl996
Huerta-Cepas, J., Szklarczyk, D., Heller, D., Hernández-Plaza, A., Forslund, S. K., Cook, H., …& Bork, P. (2019). EggNOG 5.0: A hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Research, 47(D1), D309–D314. https://doi.org/10.1093/nar/gky1085
Jean Kumar, V. U., Poyraz, Ö., Saxena, S., Schnell, R., Yogeeswari, P., Schneider, G. & Sriram, D. (2013). Discovery of novel inhibitors targeting the Mycobacterium tuberculosis O-acetylserine sulfhydrylase (CysK1) using virtual high-throughput screening. Bioorganic and Medicinal Chemistry Letters, 23(5), 1182–1186. https://doi.org/10.1016/j.bmcl.2013.01.031
Jensen, L. J., Julien, P., Kuhn, M., von Mering, C., Muller, J., Doerks, T. & Bork, P. (2008). eggNOG: Automated construction and annotation of orthologous groups of genes. Nucleic Acids Research, 36(SUPPL. 1). https://doi.org/10.1093/nar/gkm796
Johnson, C. M., Huang, B., Roderick, S. L. & Cook, P. F. (2004). Kinetic mechanism of the serine acetyltransferase from Haemophilus influenzae. Archives of Biochemistry and Biophysics, 429(2), 115–122. https://doi.org/10.1016/j.abb.2004.06.006
Joshi, P., Gupta, A. & Gupta, V. (2019). Insights into multifaceted activities of CysK for therapeutic interventions. 3 Biotech, 9(2), 0. https://doi.org/10.1007/s13205-019-1572-4
Katoh, K., Misawa, K., Kuma, K. I. & Miyata, T. (2002). MAFFT: A novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Research, 30(14), 3059–3066. https://doi.org/10.1093/nar/gkf436
Katoh, K. & Standley, D. M. (2013). MAFFT multiple sequence alignment software version 7: Improvements in performance and usability. Molecular Biology and Evolution, 30(4), 772–780. https://doi.org/10.1093/molbev/mst 010
Keikha, M. (2018). Importance of the identification of Segniliparus species from pulmonary infection. New Microbes and New Infections. Elsevier Ltd. https://doi.org/10.1016/j.nmni.2018.05.002
Kriventseva, E. V., Tegenfeldt, F., Petty, T. J., Waterhouse, R. M., Simão, F. A., Pozdnyakov, I. A., …& Zdobnov, E. M. (2015). OrthoDB v8: Update of the hierarchical catalog of orthologs and the underlying free software. Nucleic Acids Research, 43(D1), D250–D256. https://doi.org/10.1093/nar/gku1220
Kumar, S., Kumar, N., Alam, N. & Gourinath, S. (2014). Crystal structure of serine acetyl transferase from Brucella abortus and its complex with coenzyme A. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, 1844(10), 1741–1748. https://doi.org/10.1016/j.bbapap.201 4.07.009
Kumar, S., Mazumder, M., Dharavath, S. & Gourinath, S. (2013). Single Residue Mutation in Active Site of Serine Acetyltransferase Isoform 3 from Entamoeba histolytica Assists in Partial Regaining of Feedback Inhibition by Cysteine. PLoS ONE, 8(2). https://doi.org/10.1371/journal.pone.0055932
Kumar, S., Raj, I., Nagpal, I., Subbarao, N. & Gourinath, S. (2011). Structural and biochemical studies of serine acetyltransferase reveal why the parasite Entamoeba histolytica cannot form a cysteine synthase complex. Journal of Biological Chemistry, 286(14), 12533–12541. https://doi.org/10.1074/jbc.M110.197376
Li, L., Stoeckert, C. J. & Roos, D. S. (2003). OrthoMCL: Identification of ortholog groups for eukaryotic genomes. Genome Research, 13(9), 2178–2189. https://doi.org/1 0.1101/gr.1224503
Nakamori, S., Kobayashi, S. I., Kobayashi, C. & Takagi, H. (1998). Overproduction of L-cysteine and L-cystine by Escherichia coli strains with a genetically altered serine acetyltransferase. Applied and Environmental Microbiology, 64(5), 1607–1611. https://doi.org/10.1128/aem.64.5.16 07-1611.1998
Nguyen, L., Kozlov, G. & Gehring, K. (2008). Structure of Escherichia coli tetrahydrodipicolinate N-succinyl transferase reveals the role of a conserved C-terminal helix in cooperative substrate binding. FEBS Letters, 582(5), 623–626. https://doi.org/10.1016/j.febslet.200 8.01.032
Olsen, L. R., Huang, B., Vetting, M. W. & Roderick, S. L. (2004). Structure of serine acetyltransferase in complexes with CoA and its cysteine feedback inhibitor. Biochemistry, 43(20), 6013–6019. https://doi.org/10.1021/bi0358521
Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C. & Ferrin, T. E. (2004). UCSF Chimera - A visualization system for exploratory research and analysis. Journal of Computational Chemistry, 25(13), 1605–1612. https://doi.org/10.1002/jcc.20084
Poyraz, Ö., Jeankumar, V. U., Saxena, S., Schnell, R., Haraldsson, M., Yogeeswari, P., …& Schneider, G. (2013). Structure-guided design of novel thiazolidine inhibitors of O -Acetyl serine sulfhydrylase from mycobacterium tuberculosis. Journal of Medicinal Chemistry, 56(16), 6457–6466. https://doi.org/10.1021/jm400710k
Price, M. N., Dehal, P. S. & Arkin, A. P. (2010). FastTree 2 - Approximately maximum-likelihood trees for large alignments. PLoS ONE, 5(3), e9490. https://doi.org/10.1371/journal.pone.0009490
Pye, V. E., Tingey, A. P., Robson, R. L. & Moody, P. C. E. (2004). The structure and mechanism of serine acetyltransferase from Escherichia coli. The Journal of Biological Chemistry, 279(39), 40729–40736. https://doi.org/10.1074/jbc.M403751200
Rengarajan, J., Bloom, B. R. & Rubin, E. J. (2005). Genome-wide requirements for Mycobacterium tuberculosis adaptation and survival in macrophages. Proceedings of the National Academy of Sciences of the United States of America, 102(23), 8327–8332. https://doi.org/10.1073/pnas.0503272102
Roth, A. C. J., Gonnet, G. H. & Dessimoz, C. (2008). Algorithm of OMA for large-scale orthology inference. BMC Bioinformatics, 9. https://doi.org/10.1186/1471-2105-9-518
Sassetti, C. M. & Rubin, E. J. (2003). Genetic requirements for mycobacterial survival during infection. Proceedings of the National Academy of Sciences of the United States of America, 100(22), 12989–12994. https://doi.org/10.1073/PNAS.2134250100/SUPPL_FILE/4250 TABLE3.XLS
Schnell, R., Oehlmann, W., Singh, M. & Schneider, G. (2007). Structural insights into catalysis and inhibition of O-acetylserine sulfhydrylase from Mycobacterium tuberculosis. Crystal structures of the enzyme alpha-aminoacrylate intermediate and an enzyme-inhibitor complex. The Journal of Biological Chemistry, 282(32), 23473–23481. https://doi.org/10.1074/JBC.M703518200
Sievers, F. & Higgins, D. G. (2014). Clustal Omega. Current Protocols in Bioinformatics, 2014, 3.13.1-3.13.16. https://doi.org/10.1002/0471250953.bi0313s48
Smith, I. K. & Thompson, J. F. (1969). The synthesis of O-acetylserine by extracts prepared from higher plants. Biochemical and Biophysical Research Communications, 35(6), 939–945. https://doi.org/10.1016/0006-291X(69)9071 5-3
Tatusov, R. L., Natale, D. A., Garkavtsev, I. V., Tatusova, T. A., Shankavaram, U. T., Rao, B. S., …& Koonin, E. V. (2001). The COG database: New developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Research, 29(1), 22–28. https://doi.org/10.1093/nar/29.1.22
Trachana., K., Forslund., K., Larsson, T., Powell, S., Doerks, T., Von Mering, C. & Bork, P. (2014). A Phylogeny-Based benchmarking test for orthology inference reveals the limitations of Function-Based validation. PLoS ONE, 9(11). https://doi.org/10.1371/journal.pone.0111122
Ullas, V., Poyraz, Ö., Saxena, S., Schnell, R., Yogeeswari, P., Schneider, G. & Sriram, D. (2013). Discovery of novel inhibitors targeting the Mycobacterium tuberculosis O -acetylserine sulfhydrylase ( CysK1 ) using virtual high-throughput screening. Bioorganic & Medicinal Chemistry Letters, 23(5), 1182–1186. https://doi.org/10.1016/j.bmcl.2013.01.031
Vasudevan, S., YI, W., JJ, Y., DA, N., RL, T., ND, F., …& AV, S. (2003). The COG database: an updated version includes eukaryotes.. BMC Bioinformatics. Retrieved from http://www.biomedcentral.com/1471-2105/4/41
Verma, D., Gupta, S., Saxena, R., Kaur, P., Rachana, R. R., Srivastava, S. & Gupta, V. (2020). Allosteric inhibition and kinetic characterization of Klebsiella pneumoniae CysE: An emerging drug target. International Journal of Biological Macromolecules, 151, 1240–1249. https://doi.org/10.1016/j.ijbiomac.2019.10.170
Waterhouse, A. M., Procter, J. B., Martin, D. M. A., Clamp, M. & Barton, G. J. (2009). Jalview Version 2--a multiple sequence alignment editor and analysis workbench. Bioinformatics, 25(9), 1189–1191. https://doi.org/10.1093/bioinformatics/btp033
Wiederstein, M. & Sippl, M. J. (2007). ProSA-web: Interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Research, 35(SUPPL.2), W407–W410. https://doi.org/10.10 93/nar/gkm290
Zhang, Y. (2009). I-TASSER: fully automated protein structure prediction in CASP8. Proteins, 77 Suppl 9(Suppl 9), 100–113. https://doi.org/10.1002/PROT.22588
Yang, J., Yan, R., Roy, A., Xu, D., Poisson, J. & Zhang, Y. (2014). The I-TASSER suite: Protein structure and function prediction. Nature Methods. https://doi.org/10.10 38/nmeth.3213
Yelamanchi, S. D. & Surolia, A. (2021). Targeting amino acid metabolism of Mycobacterium tuberculosis for developing inhibitors to curtail its survival. IUBMB Life, 73(4), 643–658. https://doi.org/10.1002/IUB.2455
Yi, H., Dey, S., Kumaran, S., Lee, S. G., Krishnan, H. B. & Jez, J. M. (2013). Structure of soybean serine acetyltransferase and formation of the cysteine regulatory complex as a molecular chaperone. Journal of Biological Chemistry, 288(51), 36463–36472. https://doi.org/10.107 4/jbc.M113.527143
Zhang, Z., Esther, M. M., Bunker, R. D., Baker, E. N. & Squire, C. J. (2009). research papers Structure and function of GlmU from Mycobacterium tuberculosis research papers, 275–283. https://doi.org/10.1107/S09074449090 01036
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Gupta, S., & Gupta, V. (2022). Unveiling the structural features of CysE: a novel target for therapeutic interventions against persistent mycobacteria. Journal of Applied and Natural Science, 14(2), 531–542. https://doi.org/10.31018/jans.v14i2.3461
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