Bioinformatics analysis of enzymes involved in cysteine biosynthesis: first evidence for the formation of cysteine synthase complex in cyanobacteria

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.

Supplementary information: The online version contains supplementary material available at 10.1007/s13205-021-02899-1.

Keywords: Cysteine; Cysteine synthase complex; In silico; O-acetyl serine (thiol) lyase; Serine acetyl transferase; Sulphur.

Fig. 1

a Percentage (%) contribution. Blue and red colour indicates SAT and OAS-TL, respectively; b and c habitat distribution of SAT and OAS-TL proteins in the different cyanobacterial strain, respectively

Fig. 2

Phylogenetic distribution of SAT (a) and OAS-TL (b) proteins among cyanobacterial strain. Amino acid sequences of SAT and OAS-TL were obtained from the NCBI database and subjected to unrooted phylogenetic tree construction using the neighbour-joining (NJ) method built in the MEGA software. The evolutionary distances were computed using the Poisson correction method and are in the units of the number of amino acid substitutions per site. Bootstrap values are hidden for clarity of the image and all positions containing gaps and missing data were eliminated

Fig. 3

Representation of 3-D models of SAT (a) and OAS-TL (b). Ramachandran plot analysis of SAT (c) and OAS-TL (d) proteins; the plot calculations were computed by PROCHECK server. The red regions in the graph indicate the most allowed regions [A, B, L];, additional allowed regions [a, b, l, p] are indicated as brown, and generously allowed regions[~ a, ~ b, ~ l, ~ p] are indicated as green and yellow shades; results of ProSA analysis of SAT (e) and OAS-TL (f) proteins; topology of SAT (g) and OAS-TL (h) proteins

Fig. 4

Protein–protein interaction analysis: STRING analysis of SAT (a) and OAS-TL (b) proteins with their interaction proteins; Ribbon diagram (c); Surface view of the docked model indicating interacting sites (d); COFACTOR analysis depicting binding of OAS-TL with PLP (e). This figure was produced using UCSF Chimera 1.13.1 Visualizer tool

Fig. 5

Schematic diagram deciphers equilibrium of CSC depending on cellular sulfate availability and its effect on downstream regulatory mechanisms