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Site-specific Bacterial Chromosome Engineering: ΦC31 Integrase Mediated Cassette Exchange (IMCE)
Published on: March 16, 2012
ISAfe1, an ISL3 family insertion sequence from Acidithiobacillus ferrooxidans ATCC 19859
D S Holmes1, H L Zhao, G Levican
1Department of Biological Sciences, Faculty of Chemistry and Biology, University of Santiago, Santiago, Chile. dsholmes@hotmail.com
Journal of Bacteriology
|June 22, 2001
Summary
A novel insertion sequence, ISAfe1, was identified in Acidithiobacillus ferrooxidans. This bacterial insertion sequence exhibits transposition and may promote plasmid cointegrate formation and resolution.
Area of Science:
- Microbiology
- Genetics
- Molecular Biology
Background:
- Insertion sequences (IS) are mobile genetic elements found in bacteria.
- Understanding IS elements is crucial for comprehending genome dynamics and evolution.
- Acidithiobacillus ferrooxidans is an important bacterium in bioleaching and environmental remediation.
Purpose of the Study:
- To characterize a newly identified insertion sequence, ISAfe1, from Acidithiobacillus ferrooxidans.
- To investigate the potential functions and genomic behavior of ISAfe1.
- To explore the evolutionary implications of ISAfe1 in its host genome.
Main Methods:
- Sequence analysis of ISAfe1, including identification of open reading frames (ORFs) and regulatory sites.
- Experimental detection of transcriptional start sites.
- Southern blot analysis to assess the distribution and copy number of ISAfe1-like elements.
- Codon adaptation index (CAI) analysis to evaluate host adaptation.
- Analysis of target insertion sites.
Main Results:
- ISAfe1 is a 1.3-kb insertion sequence with terminal inverted repeats and an ORF encoding a putative transposase (TPase) similar to the ISL3 family.
- Potential promoter and ribosome-binding sites were identified for the TPase ORF.
- ISAfe1-like elements are present in multiple copies in various A. ferrooxidans strains and exhibit transposition.
- The TPase shows a high CAI, suggesting ISAfe1 is well-adapted and potentially ancient.
- Insertion site analysis revealed a preference for 8-bp pseudopalindromic sequences.
- Evidence suggests ISAfe1 can mediate plasmid cointegrate formation and resolution in E. coli.
Conclusions:
- ISAfe1 is a functional bacterial insertion sequence with characteristics of the ISL3 family.
- Its presence in multiple copies and transpositional activity indicate its mobility within A. ferrooxidans genomes.
- The high codon adaptation index suggests ISAfe1 is an ancient element in A. ferrooxidans.
- ISAfe1 has the potential to influence genome evolution through its insertion preferences and ability to mediate plasmid recombination.
