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Multiple, non-allelic, intein-coding sequences in eukaryotic RNA polymerase genes.

Timothy J D Goodwin¹, Margaret I Butler, Russell T M Poulter

¹Department of Biochemistry, University of Otago, Dunedin, New Zealand. timg@sanger.otago.ac.nz

|October 31, 2006

Summary

New intein coding sequences were discovered in diverse eukaryotes, expanding their known host range. These findings suggest inteins are ancient elements that occupied conserved sites in proteins across early eukaryotic evolution.

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Area of Science:

Molecular Biology
Evolutionary Biology
Genomics

Background:

Inteins are self-splicing protein segments found across life, encoded within host genes.
Their distribution is sporadic, with few identified in eukaryotic nuclear genes, primarily from fungi.
Inteins excise themselves and ligate flanking extein sequences via a peptide bond.

Purpose of the Study:

To identify novel intein coding sequences in eukaryotic nuclear genes.
To investigate the evolutionary origins and distribution of inteins in diverse eukaryotes.
To understand the preferred insertion sites of inteins within host proteins.

Main Methods:

Bioinformatic analysis of nuclear genes encoding RNA polymerase subunits.
Comparative sequence analysis of identified intein coding sequences.
Phylogenetic analysis to infer evolutionary relationships.

Main Results:

Seven intein coding sequences were identified in RNA polymerase subunits (RPA2, RPC2, RPB2) from diverse eukaryotes, including algae and fungi.
The first nuclear-encoded inteins outside of fungi were found in Chlamydomonas reinhardtii and Dictyostelium discoideum.
Inteins were located in homologous proteins, inserted at multiple conserved regions of RNA polymerase.

Conclusions:

The discovery expands the known eukaryotic host range for inteins.
Inteins are suggested to be ancient elements widely distributed in early microbial eukaryotes.
Inteins persist sporadically, preferentially occupying highly conserved protein regions.