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.

Computational studies on photolyase (Phr) proteins of cyanobacteria

“…Hence, it can be predicted that presence of various types of Phrs in cyanobacteria might enable them to survive and sustain even in higher intensities of harmful UVR in their natural habits. Cryptochrome/Phr has aroused great research interests, and numerous works on the photoreaction have been reported recently (Kavakli et al 2017;Rajneesh et al 2017;Ramírez et al 2021).…”

“…Photoreactivation is one of the unique repair process found in cyanobacteria (Rajneesh et al 2017(Rajneesh et al , 2018 which incorporates photolyase (Phr) enzyme utilizing blue light for reverting back cyclobutane pyrimidine dimers (CPD) generated by ultraviolet radiation (UVR) into the normal state. Phrs are very critical enzymes for the survival of photoautotrophic organisms, including cyanobacteria.…”

“…The main lesions induced by UV-B radiation are CPD and (6-4) photoproducts, causes mutagenesis, which if not repaired in organisms lead to cell death/programmed cell death (PCD) (Batista et al 2009;Rastogi et al 2011;Kavakli et al 2017;Rajneesh et al 2018;Pathak et al 2019). Phrs are monomeric proteins which are encoded by GC rich codons (Rajneesh et al 2017), their size ranges from 50-61 kDa depending upon the species.…”

“…Phrs are present in all three domains of life and are generally accepted as homologous of the cryptochrome/Phr family (CPF) (Rajneesh et al 2017). Contrary to this, it was believed that (6-4) Phrs are only found in eukaryotes but recently, they have also been traced in prokaryotes but with a different chromophore (Muller and Carell 2009;Kavakli et al 2017).…”