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Next-generation Sequencing of 16S Ribosomal RNA Gene Amplicons

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Published on: August 29, 2014

A versatile palindromic amphipathic repeat coding sequence horizontally distributed among diverse bacterial and

Kerstin Röske¹, Mark F Foecking, Shibu Yooseph

¹Saxony Academy of Sciences Leipzig, D-04107 Leipzig, Germany. kerstin.roeske@mailbox.tu-dresden.de

|July 15, 2010

Summary

Novel repeat protein domains, termed PARCELs, are found across diverse microbes. These elements likely spread via horizontal gene transfer (HGT) and intra-genomic shuffling, contributing to microbial adaptation and diversity.

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Bacterial Artificial Chromosomes: A Functional Genomics Tool for the Study of Positive-strand RNA Viruses

Bacterial Artificial Chromosomes: A Functional Genomics Tool for the Study of Positive-strand RNA Viruses

Published on: December 29, 2015

Area of Science:

Microbial genomics
Molecular evolution
Protein structure and function

Background:

Intragenic tandem repeats are widespread, influencing protein variability.
Repeat proteins affect surface phenotypes in unicellular organisms, including Mollicutes.
A specific repeat pattern suggests horizontal gene transfer (HGT) and is found across bacteria and eukaryotes.

Purpose of the Study:

To investigate the genomic distribution and structural features of a novel repeat motif.
To determine the association of these repeats with membrane-targeted proteins.
To understand the evolutionary dynamics and dissemination of these repeat elements.

Main Methods:

Utilized a refined hidden Markov model to identify repeat motifs.
Analyzed genomic distribution across diverse bacterial and eukaryotic clades.
Predicted protein structure, membrane-targeting sequences, and phylogenetic distribution.

Main Results:

Identified a 25-residue protein motif in variable-number tandem repeats (VNTRs) in ORFs without assigned functions.
The motif is found sporadically in diverse microbes from various environments, exhibiting malleable configurations and amphipathic secondary structures.
Many ORFs containing these domains possess membrane-targeting sequences, and some are associated with mobile elements, suggesting HGT and intra-genomic shuffling.

Conclusions:

Introduced PARCELs (Palindromic Amphipathic Repeat Coding ELements) as widely distributed repeat protein domains.
PARCELs were likely acquired via HGT, mobilized and diversified within genomes, and integrated into the membrane proteome.
These elements contribute to accessory gene pools and the mobilome, connecting diverse microbial clades.