Unveiling the structural features of CysE: a novel target for therapeutic interventions against persistent mycobacteria
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Abstract
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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Keywords
Serine acetyltransferase, Mycobacterium tuberculosis, Phylogenetic analysis, HMM profile, 3D-structure
References
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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
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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
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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
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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
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Unveiling the structural features of CysE: a novel target for therapeutic interventions against persistent mycobacteria. (2022). Journal of Applied and Natural Science, 14(2), 531-542. https://doi.org/10.31018/jans.v14i2.3461
