Single-Frame, Multiple-Frame and Framing Motifs in Genes

• Main Author: Christian J. Michel
• Format: Article
• Language: English
• Published: MDPI AG 2019-02-01
• Series: Life
• Subjects: single-frame motifs; multiple-frame motifs; framing motifs; gene coding; antiparallel and parallel sequences; early life genes
• Online Access: https://www.mdpi.com/2075-1729/9/1/18

We study the distribution of new classes of motifs in genes, a research field that has not been investigated to date. A single-frame motif <i>SF</i> has no trinucleotide in reading frame (frame 0) that occurs in a shifted frame (frame 1 or 2), e.g., the dicodon <i>AAACAA</i> is <inline-formula> <math display="inline"> <semantics> <mrow> <mi>S</mi> <mi>F</mi> </mrow> </semantics> </math> </inline-formula> as the trinucleotides <i>AAA</i> and <i>CAA</i> do not occur in a shifted frame. A motif which is not single-frame <inline-formula> <math display="inline"> <semantics> <mrow> <mi>S</mi> <mi>F</mi> </mrow> </semantics> </math> </inline-formula> is multiple-frame <inline-formula> <math display="inline"> <semantics> <mrow> <mi>M</mi> <mi>F</mi> </mrow> </semantics> </math> </inline-formula>. Several classes of <inline-formula> <math display="inline"> <semantics> <mrow> <mi>M</mi> <mi>F</mi> </mrow> </semantics> </math> </inline-formula> motifs are defined and analysed. The distributions of single-frame <inline-formula> <math display="inline"> <semantics> <mrow> <mi>S</mi> <mi>F</mi> </mrow> </semantics> </math> </inline-formula> motifs (associated with an unambiguous trinucleotide decoding in the two <inline-formula> <math display="inline"> <semantics> <mrow> <msup> <mn>5</mn> <mo>&#8242;</mo> </msup> <mo>&#8315;</mo> <msup> <mn>3</mn> <mo>&#8242;</mo> </msup> </mrow> </semantics> </math> </inline-formula> and <inline-formula> <math display="inline"> <semantics> <mrow> <msup> <mn>3</mn> <mo>&#8242;</mo> </msup> <mo>&#8315;</mo> <msup> <mn>5</mn> <mo>&#8242;</mo> </msup> </mrow> </semantics> </math> </inline-formula> directions) and 5&#8242; unambiguous motifs <inline-formula> <math display="inline"> <semantics> <mrow> <msup> <mn>5</mn> <mo>&#8242;</mo> </msup> <mi>U</mi> </mrow> </semantics> </math> </inline-formula> (associated with an unambiguous trinucleotide decoding in the <inline-formula> <math display="inline"> <semantics> <mrow> <msup> <mn>5</mn> <mo>&#8242;</mo> </msup> <mo>&#8315;</mo> <msup> <mn>3</mn> <mo>&#8242;</mo> </msup> </mrow> </semantics> </math> </inline-formula> direction only) are analysed without and with constraints. The constraints studied are: initiation and stop codons, periodic codons <inline-formula> <math display="inline"> <semantics> <mrow> <mrow> <mo>{</mo> <mrow> <mi>A</mi> <mi>A</mi> <mi>A</mi> <mo>,</mo> <mi>C</mi> <mi>C</mi> <mi>C</mi> <mo>,</mo> <mi>G</mi> <mi>G</mi> <mi>G</mi> <mo>,</mo> <mi>T</mi> <mi>T</mi> <mi>T</mi> </mrow> <mo>}</mo> </mrow> </mrow> </semantics> </math> </inline-formula>, antiparallel complementarity and parallel complementarity. Taken together, these results suggest that the complementarity property involved in the antiparallel (DNA double helix, RNA stem) and parallel sequences could also be fundamental for coding genes with an unambiguous trinucleotide decoding in the two <inline-formula> <math display="inline"> <semantics> <mrow> <msup> <mn>5</mn> <mo>&#8242;</mo> </msup> <mo>&#8315;</mo> <msup> <mn>3</mn> <mo>&#8242;</mo> </msup> </mrow> </semantics> </math> </inline-formula> and <inline-formula> <math display="inline"> <semantics> <mrow> <msup> <mn>3</mn> <mo>&#8242;</mo> </msup> <mo>&#8315;</mo> <msup> <mn>5</mn> <mo>&#8242;</mo> </msup> </mrow> </semantics> </math> </inline-formula> directions or the <inline-formula> <math display="inline"> <semantics> <mrow> <msup> <mn>5</mn> <mo>&#8242;</mo> </msup> <mo>&#8315;</mo> <msup> <mn>3</mn> <mo>&#8242;</mo> </msup> </mrow> </semantics> </math> </inline-formula> direction only. Furthermore, the single-frame motifs <inline-formula> <math display="inline"> <semantics> <mrow> <mi>S</mi> <mi>F</mi> </mrow> </semantics> </math> </inline-formula> with a property of trinucleotide decoding and the framing motifs <inline-formula> <math display="inline"> <semantics> <mi>F</mi> </semantics> </math> </inline-formula> (also called circular code motifs; first introduced by Michel (2012)) with a property of reading frame decoding may have been involved in the early life genes to build the modern genetic code and the extant genes. They could have been involved in the stage without anticodon-amino acid interactions or in the Implicated Site Nucleotides (ISN) of RNA interacting with the amino acids. Finally, the <inline-formula> <math display="inline"> <semantics> <mrow> <mi>S</mi> <mi>F</mi> </mrow> </semantics> </math> </inline-formula> and <inline-formula> <math display="inline"> <semantics> <mrow> <mi>M</mi> <mi>F</mi> </mrow> </semantics> </math> </inline-formula> dipeptides associated with the <inline-formula> <math display="inline"> <semantics> <mrow> <mi>S</mi> <mi>F</mi> </mrow> </semantics> </math> </inline-formula> and <inline-formula> <math display="inline"> <semantics> <mrow> <mi>M</mi> <mi>F</mi> </mrow> </semantics> </math> </inline-formula> dicodons, respectively, are studied and their importance for biology and the origin of life discussed.