Abstract
The biosynthesis of cysteine is crucial and critically regulated by two enzymes. i.e., serine acetyl transferase (SAT) and O-acetyl serine (thiol) lyase (OAS-TL). A descriptive account on the activity and regulatory mechanism of the enzyme is available in bacteria and plants. But no such studies yet performed in cyanobacteria, to understand the evolutionary aspect of cysteine biosynthesis and its regulation. Therefore, in our study a detailed bioinformatic analysis has been performed to understand all the possible features of cyanobacterial SATs and OAS-TLs. The analysis of SAT and OAS-TL sequences from cyanobacteria depicted that the large genome and morphological complexities favoured acquisition of these genes. Besides, conserved function of these enzymes was presumed by their sequence similarity. Further, the phylogenetic tree consisted of distinct clusters for unicellular, filamentous, and heterocytous strains. Nevertheless, the specificity pocket, SVKDR for OAS-TL having K as catalytic residue was also identified. Additionally, in silico protein modelling of SAT (SrpG) and OAS-TL (SrpH) of Synechococcus elongatus PCC 7942 was performed to gain insight into the structural attributes of the proteins. Finally, here we showed the possibility of hetero-oligomeric bi-enzyme cysteine synthase complex formation upon interaction of SAT and OAS-TL through protein–protein docking analysis thus provides a way to understand the regulation of cysteine biosynthesis in cyanobacteria.
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Acknowledgements
Surbhi Kharwar wants to thank University Grants Commission (UGC), New Delhi, India, for financial grant and also grateful to Dr. Vinay Kumar Singh, Information Officer, School of Biotechnology, Banaras Hindu University, Varanasi, India for providing molecular docking facility by Biovia Discovery Studio 2019. Samujjal Bhattacharjee is thankful to Council of Scientific and Industrial Research (CSIR), New Delhi, for awarding Junior Research Fellowship. The authors would also like to take this opportunity to thank Head, Department of Botany, Banaras Hindu University for providing the necessary facilities and encouragement to carry out this work.
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SK and AKM conceived the idea and designed the experiments. SK conducted the experiments and wrote the manuscript. SK, SB, and AKM critically review the manuscript. The manuscript was approved by all the authors.
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Supplementary file3 Fig. S1. Hidden Markov Model (HMM) logos of cyanobacterial SAT (a) and OAS-TL (b) proteins. Logos were built with Skylign based on the alignment of protein sequences. The height of each amino acid code for each position reflects the weighted probability of occurrence at that position. The first amino acids Val, Leu, or Ile, followed often by Gly in the hexapeptide repeats with a consensus sequence of {V/L/I}-G-X-X-X-X, are marked with red boxes in the classical SAT proteins sequences. The blue box indicates the PLP-binding residues in the protein sequences. The SAT binding sites were indicated by pink represent OAS binding sites. Fig. S2. Structural verification by VADAR analysis of SAT (a) and OAS-TL (b) proteins showing functional accessible surface area, functional residues volume, stero/packing quality index, and 3D profile quality index. Fig. S3. Interacting sites of the SAT and OAS-TL proteins. (PDF 3189 kb)
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Kharwar, S., Bhattacharjee, S. & Mishra, A.K. Bioinformatics analysis of enzymes involved in cysteine biosynthesis: first evidence for the formation of cysteine synthase complex in cyanobacteria. 3 Biotech 11, 354 (2021). https://doi.org/10.1007/s13205-021-02899-1
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DOI: https://doi.org/10.1007/s13205-021-02899-1