TY - JOUR
T1 - On the Organizational Dynamics of the Genetic Code
AU - Zhang, Zhang
AU - Yu, Jun
N1 - KAUST Repository Item: Exported on 2020-10-01
PY - 2011/6/24
Y1 - 2011/6/24
N2 - The organization of the canonical genetic code needs to be thoroughly illuminated. Here we reorder the four nucleotides—adenine, thymine, guanine and cytosine—according to their emergence in evolution, and apply the organizational rules to devising an algebraic representation for the canonical genetic code. Under a framework of the devised code, we quantify codon and amino acid usages from a large collection of 917 prokaryotic genome sequences, and associate the usages with its intrinsic structure and classification schemes as well as amino acid physicochemical properties. Our results show that the algebraic representation of the code is structurally equivalent to a content-centric organization of the code and that codon and amino acid usages under different classification schemes were correlated closely with GC content, implying a set of rules governing composition dynamics across a wide variety of prokaryotic genome sequences. These results also indicate that codons and amino acids are not randomly allocated in the code, where the six-fold degenerate codons and their amino acids have important balancing roles for error minimization. Therefore, the content-centric code is of great usefulness in deciphering its hitherto unknown regularities as well as the dynamics of nucleotide, codon, and amino acid compositions.
AB - The organization of the canonical genetic code needs to be thoroughly illuminated. Here we reorder the four nucleotides—adenine, thymine, guanine and cytosine—according to their emergence in evolution, and apply the organizational rules to devising an algebraic representation for the canonical genetic code. Under a framework of the devised code, we quantify codon and amino acid usages from a large collection of 917 prokaryotic genome sequences, and associate the usages with its intrinsic structure and classification schemes as well as amino acid physicochemical properties. Our results show that the algebraic representation of the code is structurally equivalent to a content-centric organization of the code and that codon and amino acid usages under different classification schemes were correlated closely with GC content, implying a set of rules governing composition dynamics across a wide variety of prokaryotic genome sequences. These results also indicate that codons and amino acids are not randomly allocated in the code, where the six-fold degenerate codons and their amino acids have important balancing roles for error minimization. Therefore, the content-centric code is of great usefulness in deciphering its hitherto unknown regularities as well as the dynamics of nucleotide, codon, and amino acid compositions.
UR - http://hdl.handle.net/10754/552438
UR - http://linkinghub.elsevier.com/retrieve/pii/S1672022911600041
UR - http://www.scopus.com/inward/record.url?scp=79957916493&partnerID=8YFLogxK
U2 - 10.1016/S1672-0229(11)60004-1
DO - 10.1016/S1672-0229(11)60004-1
M3 - Article
C2 - 21641559
SN - 1672-0229
VL - 9
SP - 21
EP - 29
JO - Genomics, Proteomics & Bioinformatics
JF - Genomics, Proteomics & Bioinformatics
IS - 1-2
ER -