Pathak Jainendra, Kannaujiya Vinod K, Singh Shailendra P, Sinha Rajeshwar P
Laboratory of Photobiology and Molecular Microbiology, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005, India.
3 Biotech. 2017 Jul;7(3):192. doi: 10.1007/s13205-017-0826-2. Epub 2017 Jun 29.
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.
研究核苷酸和氨基酸组成以确定淡水、海洋和温泉蓝藻中光裂合酶基因的基因组和结构关系。在这三种生境中，发现温泉蓝藻的光裂合酶编码基因具有最高的GC含量。发现基因组GC含量会影响光裂合酶中的密码子使用和氨基酸变异性。发现密码子的第三位对光裂合酶中氨基酸变异性的影响大于密码子的第一位和第二位。发现三种不同生境的光裂合酶中氨基酸丙氨酸（Ala）、天冬氨酸（Asp）、谷氨酸（Glu）、甘氨酸（Gly）、组氨酸（His）、亮氨酸（Leu）、脯氨酸（Pro）、谷氨酰胺（Gln）、精氨酸（Arg）和缬氨酸（Val）的变异受密码子第一位（G1C1）控制。然而，密码子的第二位（G2C2）调节光裂合酶中丙氨酸、半胱氨酸（Cys）、甘氨酸、脯氨酸、精氨酸、丝氨酸（Ser）、苏氨酸（Thr）和酪氨酸（Tyr）含量的变异。密码子的第三位（G3C3）控制来自三种生境的光裂合酶中氨基酸如丙氨酸、苯丙氨酸（Phe）、甘氨酸、亮氨酸、谷氨酰胺、脯氨酸、精氨酸、丝氨酸、苏氨酸和酪氨酸的掺入。温泉蓝藻的光裂合酶编码基因在第三位有85%的密码子带有G或C，而海洋和淡水蓝藻在第三位分别有82%和60%的密码子带有G或C。主成分分析（PCA）表明，GC含量根据其相对同义密码子使用（RSCU）值在第一主成分轴上对基因分离有深远影响，中性分析表明突变压力导致了蓝藻光裂合酶基因的密码子偏好。
