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Use of Alu Element Containing Minigenes to Analyze Circular RNAs

Use of Alu Element Containing Minigenes to Analyze Circular RNAs

Published on: March 10, 2020

Structural clones of UAG decoding RNA.

Smarajit Das¹, Ritwik Mukherjee, Satyabrata Sahoo

¹Computational Biology Group, Indian Association for the Cultivation of Science, Calcutta, India.

Journal of Biomolecular Structure & Dynamics

|October 3, 2009

Summary

This summary is machine-generated.

Researchers explored the unique secondary structures of non-coding RNAs (ncRNAs) involved in pyrrolysine (pyl) decoding. They discovered split pyl-tRNA (pylT) genes in archaeal methanogens, with ligated pairs mimicking the functional pylT structure.

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Area of Science:

Molecular Biology
Bioinformatics
Genomics

Background:

The function of non-coding RNAs (ncRNAs) is intrinsically linked to their secondary structures.
Pyrrolysine (pyl) is an unusual amino acid decoded by specific ncRNAs, including the pyrrolysyl-tRNA (pylT).

Purpose of the Study:

To investigate the uniqueness of the secondary structure of the ncRNA responsible for decoding UAG to pyrrolysine (pyl).
To identify and analyze split pyrrolysyl-tRNA (pylT) genes in archaeal methanogens.

Main Methods:

Utilized a custom perl-script, tRNA-pyl-tracker (TPYLT), to search nineteen archaeal methanogen genomes.
Performed in silico ligation of identified conjugate halves of the pylT gene.
Analyzed the secondary structures of ligated gene pairs and compared them to known pylT structures.

Main Results:

Discovered numerous split pylT gene halves in Methanosarcinaceae, which upon ligation, formed structures similar to the pylT clover-leaf of M. barkeri.
Identified four methanogens (M. stadtmanae, M. kandleri, M. hungatei, and M. thermautotrophicus) with split pylT pairs at levels comparable to or exceeding pyl-carrying strains.
Ligated pairs from these four methanogens showed homology to the M. barkeri pylT gene, with intervening sequences resembling exon-intron boundaries.

Conclusions:

The secondary structures of split pylT gene halves can reconstitute functional pylT molecules in archaeal methanogens.
The findings suggest a potential mechanism for the evolution and maintenance of pylT genes through gene fragmentation and recombination.
The study highlights the structural diversity and evolutionary adaptability of ncRNAs involved in non-canonical amino acid incorporation.