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Conserved intergenic sequences revealed by CTAG-profiling in Salmonella: thermodynamic modeling for function
Le Tang1,2,3, Songling Zhu1,2, Emilio Mastriani1,2
1Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, Harbin, China.
Scientific Reports
|March 7, 2017
Summary
Highly conserved CTAG sequences in Salmonella genomes suggest biological importance, forming stable structures in intergenic regions. Their degeneration patterns reveal insights into Salmonella evolution and genomic divergence.
Area of Science:
- Genomics
- Molecular Biology
- Evolutionary Biology
Background:
- Highly conserved short sequences are crucial for identifying functional genomic regions and aiding genomic annotation.
- The tetranucleotide sequence CTAG was selected for investigation due to its potential functional significance.
Purpose of the Study:
- To identify and characterize evolutionarily conserved regions in the Salmonella genome.
- To investigate the biological importance and structural properties of the CTAG sequence in Salmonella.
Main Methods:
- Genomic analysis of Salmonella to identify conserved regions, focusing on the CTAG tetranucleotide.
- Computer modeling to assess the structural stability of CTAG-containing sequences.
- Comparative analysis of CTAG distribution in vertically and horizontally transmitted genomic segments.
Main Results:
- CTAG is highly conserved across Salmonella lineages, with numerous occurrences in intergenic regions, indicating biological importance.
- Computer modeling revealed that CTAG sequences can form stable stem-loop structures in intergenic regions, sensitive to nucleotide substitution.
- Distinct patterns of CTAG degeneration were observed among Salmonella lineages, providing insights into genomic divergence.
- Horizontally acquired genomic segments showed different CTAG distribution compared to vertically transmitted segments, with evidence of CTAG removal during genome amelioration.
Conclusions:
- The CTAG sequence plays a significant role in Salmonella genome function and evolution.
- The structural stability and lineage-specific degeneration patterns of CTAG offer novel insights into bacterial pathogen evolution.
- Genome amelioration processes actively shape the distribution of CTAG in horizontally acquired DNA.
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