Simple sequence repeats in Helicobacter canadensis and their role in phase variable expression and C-terminal
Lori A S Snyder1, Nicholas J Loman, James D Linton
1Centre for Systems Biology, School of Biosciences, University of Birmingham, Edgbaston, Birmingham B152TT, UK. l.snyder@kingston.ac.uk
BMC Genomics
|January 29, 2010
Summary
Helicobacter canadensis exhibits phase variation in 29 coding regions due to changes in homopolymeric tract length. This variation impacts gene expression and protein sequence, affecting the pathogen
Area of Science:
- Microbiology
- Genomics
- Bacterial Pathogenesis
Background:
- Helicobacter canadensis is an emerging pathogen with zoonotic potential.
- Previous genome sequencing identified 29 coding regions associated with homopolymeric tracts in H. canadensis.
Purpose of the Study:
- To investigate the role and mechanisms of homopolymeric tract variations in Helicobacter canadensis.
- To determine the potential for transcriptional and translational phase variation in H. canadensis coding regions.
Main Methods:
- Bioinformatic analysis of the Helicobacter canadensis genome sequence.
- Identification and characterization of homopolymeric tracts within coding and promoter regions.
- Assessment of tract location relative to coding sequences to infer phase variation mechanisms.
Main Results:
- Twenty-nine coding regions in H. canadensis display homopolymeric tract length variability.
- Twenty-one regions are potentially transcriptionally or translationally phase variable based on tract location.
- Eight coding sequences have repeats at the 3' end, suggesting C-terminal protein sequence variation.
Conclusions:
- Homopolymeric tract variations in H. canadensis are indicative of widespread phase variation.
- Mechanisms include transcriptional (5 regions), translational (16 regions), and C-terminal (8 regions) phase variation.
- C-terminal phase variation offers a novel mechanism for altering protein sequences in response to environmental cues.
More Related Videos
09:40Quantitation and Analysis of the Formation of HO-Endonuclease Stimulated Chromosomal Translocations by Single-Strand Annealing in Saccharomyces cerevisiae
Published on: September 23, 2011
08:34MS2-Affinity Purification Coupled with RNA Sequencing in Gram-Positive Bacteria
Published on: February 23, 2021
Related Concept Videos
02:53Conservative Site-specific Recombination and Phase Variation
Because the DNA segments are cut and reorganized in a direction-specific manner, site-specific recombination has emerged as an efficient genetic engineering technique. Flippase and Cyclization recombinases or Flp and Cre, respectively, are two members of the tyrosine recombinase family derived from bacteriophages, that are used to mediate site-specific DNA insertions, deletions, and targeted expression of proteins in mammalian cell lines.
The recognition sites for Cre recombinase called LoxP...
The recognition sites for Cre recombinase called LoxP...
02:02Cis-regulatory Sequences
Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
02:02Cis-regulatory Sequences
Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
01:29Coordination of Gene Expression Processes in Bacteria
The DNA replication, transcription, and translation processes are intricately coupled in bacteria, allowing efficient gene expression and rapid protein synthesis. While this physical and functional coordination is advantageous, it introduces challenges that bacteria overcome through specific regulatory mechanisms.Coupling of Replication, Transcription, and TranslationThe coupling of replication, transcription, and translation is a hallmark of bacterial gene expression. As the replisome unwinds...
02:51Multi-species Conserved Sequences
Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved DNA...
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved DNA...
00:43Bacterial RNA Polymerase
Unlike eukaryotes, bacteria use a single RNA Polymerase (RNAP) to transcribe all genes. The different subunits of bacterial RNAPhave distinct functions. The multisubunit structure of the bacterial RNAP helps the enzyme to maintain catalytic function, facilitate assembly, interact with DNA and RNA, and self-regulate its activity.
In most genes, the transcription site is a single base present upstream of the coding sequence. Though RNAP is a catalytically efficient enzyme, it does not recognize...
In most genes, the transcription site is a single base present upstream of the coding sequence. Though RNAP is a catalytically efficient enzyme, it does not recognize...