Second codon positions of genes and the secondary structures of proteins. Relationships and implications for the origin of the genetic code

Chiusano, Maria Luisa; Álvarez-Valín, Fernando; Giulio, Massimo Di; D’Onofrio, Giuseppe; Ammirato, Gaetano; Colonna, Giovanni; Bernardi, Giorgio

doi:10.1016/s0378-1119(00)00521-7

Cited by 81 publications

(56 citation statements)

References 29 publications

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“…The physical properties of the amino acids are linked with the nucleotide bases of codons. If the second nucleotide position of a codon is A (adenine), it signifies the encoded residue is hydrophilic that tend to sit outside the protein, similarly U (uracil) indicates the hydrophobic residues that tend to embed itself within the protein core (Chiusano et al, 2000). In addition to U bases in the second position of the codon, hydrophobic amino acids have a high U base content (>45%) as shown in Fig.…”

Section: Uracil Richness In Hydrophobic Codons Among Transmembrane Hementioning

confidence: 99%

Insight into pattern of codon biasness and nucleotide base usage in serotonin receptor gene family from different mammalian species

Dass

Sudandiradoss

2012

Gene

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Section: Uracil Richness In Hydrophobic Codons Among Transmembrane Hementioning

confidence: 99%

Insight into pattern of codon biasness and nucleotide base usage in serotonin receptor gene family from different mammalian species

Dass

Sudandiradoss

2012

Gene

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“…It is now widely accepted that a protein is composed of many and various second structures. Previous study (Chiusano et al 2000) proposed that the physicochemical properties of those most frequently used amino acids are reflected in their secondary structures, and found that Ala, Glu, Lys, and Val prefer alpha-helix and b-sheet structures, whilst Asp, Pro, Gly, Ser prefer aperiodic structures in prokaryotic and human proteins. We have shown in this study that almost all amino acids preferred by secondary structures are also significantly biased among essential and nonessential genes, the only exception being Pro (P).…”

Section: Comparison On Amino Acid Usagementioning

confidence: 99%

Comparative analysis of essential genes and nonessential genes in Escherichia coli K12

et al. 2007

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Genes can be classified as essential or nonessential based on their indispensability for a living organism. Previous researches have suggested that essential genes evolve more slowly than nonessential genes and the impact of gene dispensability on a gene's evolutionary rate is not as strong as expected. However, findings have not been consistent and evidence is controversial regarding the relationship between the gene indispensability and the rate of gene evolution. Understanding how different classes of genes evolve is essential for a full understanding of evolutionary biology, and may have medical relevance in the design of new antibacterial agents. We therefore performed an investigation into the properties of essential and nonessential genes. Analysis of evolutionary conservation, protein length distribution and amino acid usage between essential and nonessential genes in Escherichia coli K12 demonstrated that essential genes are relatively preserved throughout the bacterial kingdom when compared to nonessential genes. Furthermore, results show that essential genes, compared to nonessential genes, have a significantly higher proportion of large (>534 amino acids) and small proteins (<139 amino acids) relative to medium-sized proteins. The pattern of amino acids usage shows a similar trend for essential and nonessential genes, although some notable exceptions are observed. These findings help to clarify our understanding of the evolutionary mechanisms of essential and nonessential genes, relevant to the study of mutagenesis and possibly allowing prediction of gene properties in other poorly understood organisms.

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“…We found a significant negative correlation between FFE of the 2nd codon residue and the helix content of protein structures, which was not expected even though this possibility is mentioned in the literature [9]. Our previous work on a Common Periodic Table of Codons and Nucleic Acids [22] indicated that the second codon residue is intimately coupled with the known physico-chemical properties of the amino acids.…”

Section: Resultsmentioning

confidence: 50%

“…Studies on the relationships between synonymous codon usage and protein secondary structural units are especially popular [8][9][10]. The genetic code is redundant (61 codons code 20 amino acids) and as many as 6 synonymous codons can code the same amino acid (Arg, Leu, Ser).…”

Section: Introductionmentioning

confidence: 99%

The Meaning of a Redundant Codon: There is Protein Folding Information in Nucleic Acids in Addition to the Genetic Code

Biro¹,

Biro²

2006

American J. of Biochemistry and Biotechnology

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All the information necessary for protein folding is supposed to be present in the amino acid sequence. It is still not possible to provide specific ab initio structure predictions by bioinformatical methods. It is suspected that additional folding information is present in protein coding nucleic acid sequences, which is not represented by the known genetic code. Nucleic acid subsequences comprising the 1st and/or 3rd codon residues in mRNAs express significantly higher free folding energy (FFE) than the subsequence containing only the 2nd residues (p<0.0001, n=81). This periodic FFE difference is not present in introns and therefore it is a specific physico-chemical characteristic of coding sequences and it might contribute to unambiguous definition of codon boundaries during translation. The FFE in the 1st and 3rd residues is additive, which suggests that these residues contain a significant number of complementary bases and contribute to selection for local RNA secondary structures in coding regions. This periodic, codon-related structure-forming of mRNAs indicates a connection between the structure of exons and the corresponding (translated) proteins. The folding energy dot plots of RNAs and the residue contact maps of the coded proteins are indeed similar. Residue contact statistics using 81 different protein structures confirmed that amino acids that are coded by partially reverse and complementary codons (Watson-Crick (WC) base pairs at the 1st and 3rd codon positions and translated in reverse orientation) are preferentially co-located in protein structures. Exons are distinguished from introns and codon boundaries are physico-chemically defined by periodically distributed FFE differences between codon positions. There is a selection for local RNA secondary structures in coding regions and this nucleic acid structure resembles the folding profiles of the coded proteins. The preferentially (specifically) interacting amino acids are coded by partially complementary codons, which strongly supports the connection between mRNA and the corresponding protein structures and indicates that there is protein folding information in nucleic acids that is not present in the genetic code. This might give some additional explanation of codon redundancy.

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Second codon positions of genes and the secondary structures of proteins. Relationships and implications for the origin of the genetic code

Cited by 81 publications

References 29 publications

Insight into pattern of codon biasness and nucleotide base usage in serotonin receptor gene family from different mammalian species

Insight into pattern of codon biasness and nucleotide base usage in serotonin receptor gene family from different mammalian species

Comparative analysis of essential genes and nonessential genes in Escherichia coli K12

The Meaning of a Redundant Codon: There is Protein Folding Information in Nucleic Acids in Addition to the Genetic Code

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