Codon usage analysis of photolyase encoding genes of cyanobacteria inhabiting diverse habitats

Abstract

Nucleotide and amino acid compositions were studied to determine the genomic and structural relationship of photolyase gene in freshwater, marine and hot spring cyanobacteria. Among three habitats, photolyase encoding genes from hot spring cyanobacteria were found to have highest GC content. The genomic GC content was found to influence the codon usage and amino acid variability in photolyases. The third position of codon was found to have more effect on amino acid variability in photolyases than the first and second positions of codon. The variation of amino acids Ala, Asp, Glu, Gly, His, Leu, Pro, Gln, Arg and Val in photolyases of three different habitats was found to be controlled by first position of codon (G1C1). However, second position (G2C2) of codon regulates variation of Ala, Cys, Gly, Pro, Arg, Ser, Thr and Tyr contents in photolyases. Third position (G3C3) of codon controls incorporation of amino acids such as Ala, Phe, Gly, Leu, Gln, Pro, Arg, Ser, Thr and Tyr in photolyases from three habitats. Photolyase encoding genes of hot spring cyanobacteria have 85% codons with G or C at third position, whereas marine and freshwater cyanobacteria showed 82 and 60% codons, respectively, with G or C at third position. Principal component analysis (PCA) showed that GC content has a profound effect in separating the genes along the first major axis according to their RSCU (relative synonymous codon usage) values, and neutrality analysis indicated that mutational pressure has resulted in codon bias in photolyase genes of cyanobacteria.

Keywords: Codon usage bias; Cyanobacteria; Mutational pressure; Photolyase; Photoreactivation.

Fig. 1

Average percentage composition of each amino acid in photolyase of cyanobacteria from diverse habitats. a Fresh water, b marine and c hot spring. Error bars represent standard deviation of the mean (mean ± SD). Significance of data was evaluated by Duncan’s multiple range test in the range of p < 0.05

Fig. 2

Variation in average percentage of GC composition of photolyases in cyanobacteria from diverse habitats. a Fresh water, b marine and c hot spring

Fig. 3

Correlation and regression analysis of scatter plot of the Gi + Ci levels (‘i’ denotes first, second and third position of the codon) between total genomic GC constituents and the relative variability at the first, second and third nucleotide positions of photolyase encoding genes. a Fresh water, b marine and c hot spring

Fig. 4

Neutrality plot of individual photolyase encoding genes plotted as the average of GC content in the first and second codon position versus the GC content of the third codon position (G3C3). a Fresh water, b marine and c hot spring

Fig. 5

G1 + C1 associated codon variation with respect of their frequency per unit for 10 amino acids (abbreviated as A, D, E, G, H, L, P, Q, R and V) in photolyase of cyanobacteria

Fig. 6

G2 + C2 associated codon variation with respect to their frequency per unit for 8 amino acids (abbreviated as A, C, G, P, R, S, T, W) in photolyase of cyanobacteria

Fig. 7

G3 + C3 associated codon variation with respect to their frequency per unit for 20 amino acids (abbreviated as A, C, D, E, F, G, H, I, L, K, M, N, P, Q, R, S, V, T, Y and W) in photolyase of cyanobacteria

Fig. 8

Principal component analysis depicting the variation among the RSCU values of codons in the photolyase gene. a Fresh water, b marine and c hot spring

Fig. 8

Principal component analysis depicting the variation among the RSCU values of codons in the photolyase gene. a Fresh water, b marine and c hot spring