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Isolation of Translating Ribosomes Containing Peptidyl-tRNAs for Functional and Structural Analyses
Published on: February 25, 2011
Variations on the tmRNA gene
Chunhong Mao1, Kanchan Bhardwaj, Stephen M Sharkady
1Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, USA.
Abstract:
tmRNA employs both tRNA-like and mRNA-like properties as it rescues stalled bacterial ribosomes, while targeting the defective mRNA and incomplete nascent protein for degradation. We describe variation of the tmRNA gene (ssrA) and how it informs tmRNA structure and function. Endosymbiont tmRNAs tend to lose secondary structure and length in the mRNA-like region as nucleotide composition drifts with that of the whole genome. A dramatic gene structure variation is circular permutation, which produces two-piece tmRNAs in three bacterial lineages; new sequences blur these lineages. We present evidence that Sinorhizobium two-piece tmRNA retains the 5'-triphosphate of transcriptional initiation and predict a new structure at the 5' end of cyanobacterial two-piece tmRNA precursor. ssrA is a target for some mobile DNAs and a passenger on others. It has been found interrupted (but not functionally disrupted) by mobile elements such as group I introns, genomic islands and palindromic elements. The alphaproteobacterial permuted genes are significantly less frequently interrupted by genomic islands than are their standard counterparts, yet are a hotspot for insertion or swapping of rickettsial palindromic elements, in contrast to other rickettsial loci that show steady decay of a single ancestral element. Bacteriophages, plasmids and genomic islands can carry tmRNA genes; we describe a native bacterial ssrA disrupted by insertion of a genomic island that carries its own ssrA, a genome encoding both one- and two-piece tmRNA, and a phage encoding a tmRNA variant lacking the mRNA-like function, which may counteract host tmRNA during infection.
Insights
Bacterial tmRNA (ssrA) genes show significant structural variation, including circular permutation, impacting their function and interaction with mobile genetic elements. These variations influence how tmRNA rescues stalled ribosomes and interacts with bacterial genomes.
Area of Science:
- Bacterial genetics
- Molecular biology
- Genomics
Background:
- tmRNA (ssrA) possesses both tRNA-like and mRNA-like functions, crucial for rescuing stalled bacterial ribosomes and degrading aberrant proteins.
- Variations in tmRNA structure and gene organization can significantly alter its biological roles.
Purpose of the Study:
- To investigate the structural diversity of the tmRNA gene (ssrA) across different bacterial lineages.
- To understand how tmRNA gene variations influence its structure, function, and interactions with mobile genetic elements.
- To explore the evolutionary implications of tmRNA gene structure and its association with endosymbionts and mobile DNA.
Main Methods:
- Comparative genomic analysis of ssrA sequences from diverse bacterial species.
- Phylogenetic analysis to trace the evolutionary history of tmRNA gene variations.
- Bioinformatic prediction of secondary structures for novel tmRNA variants.
- Examination of mobile element insertions within ssrA loci.
Main Results:
- Endosymbiont tmRNAs often exhibit reduced secondary structure and length in their mRNA-like regions.
- Circularly permuted tmRNA genes, forming two-piece tmRNAs, were identified in distinct bacterial lineages, with new sequences blurring these distinctions.
- Sinorhizobium two-piece tmRNA retains a 5'-triphosphate, suggesting a unique transcriptional initiation.
- ssrA genes are frequently targets for mobile elements like introns and genomic islands, with variations in insertion patterns observed between standard and permuted genes.
- Examples of ssrA acquisition via genomic islands, co-existence of one- and two-piece tmRNAs, and phage-encoded tmRNA variants were documented.
Conclusions:
- Bacterial tmRNA (ssrA) exhibits remarkable structural and evolutionary plasticity.
- Gene structure variations, such as circular permutation, are linked to specific bacterial lineages and influence ssrA's interaction with mobile genetic elements.
- The study highlights the dynamic nature of tmRNA evolution and its role in bacterial adaptation and genome dynamics.
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