Research On Mitochondrial And Cell Nuclear Nonstandard Genetic Codes And The Evolutionary Relationship Among Codes

The deviant phenomena of the genetic code have been discovered in many mitochondrial codes and some nuclear genomes. The theoretical study of these deviant codes is comparatively scarce. The thesis devotes to giving a unified explanation of the deviant phenomena and deducing the evolutionary relationship among the standard genetic code and all deviant genetic codes, including mitochondrial and cell nuclear. Further, it shows all nonstandard codes can occur due to evolutionary change of the standard genetic code and the order of appearance of deviant codes is basically consistent with the chronological order of species.The thesis is divided into three chapters. In the first chapter the essential characteristics of the genetic code are reviewed generally to lay a foundation for a unified understanding of the evolution of genetic code. Following the concept and formulation of minimal mutational deterioration, in the second chapter we deduce minimization of the global mutational deterioration (GMD) of the mitochondrial and the cell nuclear nonstandard genetic codes. It is demonstrated that each nonstandardgenetic code is a minimal code under some constraints, which gives a unified point of view to deviant codes—both the evolutionary stability principle and the 'frozen accident' playing a key role in the evolution. The result also shows the evolutionary traces of the deviant codes from the standard genetic code. Finally in the chapter 3, we set up a universal theoretical model for both mitochondrial and cell nuclear systems, propose the Distance Amplitude Definition Rule (DADR), and reconstruct evolutionary relationship between the standard code and the mitochondrial nonstandard codes and between the standard code and the nuclear nonstandard codes respectively. The deduced evolutionary relationship is basically consistent with the chronological order of species. Meanwhile it is found that the nonsense mutation and its reverse are the key factors for the tree reconstruction. The research shows that in spite of the large physiochemical distance between amino acids and terminators, the mutation between them can still happen frequently and there exists the interference of mutation for different codons. The evolution of the genetic code tends toward decreasing the number of stop codons and the direction can be expressed by the symbol of distance amplitude. Further, the evolutionary relationship of the genetic codes is closely related to the change of terminators. Set the stop codon, UAA UAG and/or UGA, coding for amino acid ? in a deviant code. The symbol of corresponding distance amplitude is determined by which kind of single base mutation has happened, namely the mutation between the stop codon and amino acid ?, occurring in 1st 2nd or 3rd codon position in the standard code.At the end of the third chapter, we briefly discuss the possibility of reconstruction of the evolutionary relationship without use of DADR (based on non-DADR).