Identification and characterization of repetitive extragenic palindromes (REP)-associated tyrosine transposases: implications for REP evolution and dynamics in bacterial genomes
<p>Abstract</p> <p>Background</p> <p>Bacterial repetitive extragenic palindromes (REPs) compose a distinct group of genomic repeats. They usually occur in high abundance (>100 copies/genome) and are often arranged in composite repetitive structures - bacterial inters...
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| Format: | Article |
| Language: | English |
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BMC
2010-01-01
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| Series: | BMC Genomics |
| Online Access: | http://www.biomedcentral.com/1471-2164/11/44 |
| _version_ | 1818833022963679232 |
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| author | Licha Irena Huckova Tereza Nunvar Jaroslav |
| author_facet | Licha Irena Huckova Tereza Nunvar Jaroslav |
| author_sort | Licha Irena |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>Bacterial repetitive extragenic palindromes (REPs) compose a distinct group of genomic repeats. They usually occur in high abundance (>100 copies/genome) and are often arranged in composite repetitive structures - bacterial interspersed mosaic elements (BIMEs). In BIMEs, regularly spaced REPs are present in alternating orientations. BIMEs and REPs have been shown to serve as binding sites for several proteins and suggested to play role in chromosome organization and transcription termination. Their origins are, at present, unknown.</p> <p>Results</p> <p>In this report, we describe a novel class of putative transposases related to IS<it>200</it>/IS<it>605 </it>transposase family and we demonstrate that they are obligately associated with bacterial REPs. Open reading frames coding for these REP-associated tyrosine transposases (RAYTs) are always flanked by two REPs in inverted orientation and thus constitute a unit reminiscent of typical transposable elements. Besides conserved residues involved in catalysis of DNA cleavage, RAYTs carry characteristic structural motifs that are absent in typical IS<it>200</it>/IS<it>605 </it>transposases. DNA sequences flanking <it>rayt </it>genes are in one third of examined cases arranged in modular BIMEs. RAYTs and their flanking REPs apparently coevolve with each other. The <it>rayt </it>genes themselves are subject to rapid evolution, substantially exceeding the substitution rate of neighboring genes. Strong correlation was found between the presence of a particular <it>rayt </it>in a genome and the abundance of its cognate REPs.</p> <p>Conclusions</p> <p>In light of our findings, we propose that RAYTs are responsible for establishment of REPs and BIMEs in bacterial genomes, as well as for their exceptional dynamics and species-specifity. Conversely, we suggest that BIMEs are in fact a special type of nonautonomous transposable elements, mobilizable by RAYTs.</p> |
| first_indexed | 2024-12-19T02:12:19Z |
| format | Article |
| id | doaj.art-e0677012abc440d39ac9c8583a74277d |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-19T02:12:19Z |
| publishDate | 2010-01-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-e0677012abc440d39ac9c8583a74277d2022-12-21T20:40:40ZengBMCBMC Genomics1471-21642010-01-011114410.1186/1471-2164-11-44Identification and characterization of repetitive extragenic palindromes (REP)-associated tyrosine transposases: implications for REP evolution and dynamics in bacterial genomesLicha IrenaHuckova TerezaNunvar Jaroslav<p>Abstract</p> <p>Background</p> <p>Bacterial repetitive extragenic palindromes (REPs) compose a distinct group of genomic repeats. They usually occur in high abundance (>100 copies/genome) and are often arranged in composite repetitive structures - bacterial interspersed mosaic elements (BIMEs). In BIMEs, regularly spaced REPs are present in alternating orientations. BIMEs and REPs have been shown to serve as binding sites for several proteins and suggested to play role in chromosome organization and transcription termination. Their origins are, at present, unknown.</p> <p>Results</p> <p>In this report, we describe a novel class of putative transposases related to IS<it>200</it>/IS<it>605 </it>transposase family and we demonstrate that they are obligately associated with bacterial REPs. Open reading frames coding for these REP-associated tyrosine transposases (RAYTs) are always flanked by two REPs in inverted orientation and thus constitute a unit reminiscent of typical transposable elements. Besides conserved residues involved in catalysis of DNA cleavage, RAYTs carry characteristic structural motifs that are absent in typical IS<it>200</it>/IS<it>605 </it>transposases. DNA sequences flanking <it>rayt </it>genes are in one third of examined cases arranged in modular BIMEs. RAYTs and their flanking REPs apparently coevolve with each other. The <it>rayt </it>genes themselves are subject to rapid evolution, substantially exceeding the substitution rate of neighboring genes. Strong correlation was found between the presence of a particular <it>rayt </it>in a genome and the abundance of its cognate REPs.</p> <p>Conclusions</p> <p>In light of our findings, we propose that RAYTs are responsible for establishment of REPs and BIMEs in bacterial genomes, as well as for their exceptional dynamics and species-specifity. Conversely, we suggest that BIMEs are in fact a special type of nonautonomous transposable elements, mobilizable by RAYTs.</p>http://www.biomedcentral.com/1471-2164/11/44 |
| spellingShingle | Licha Irena Huckova Tereza Nunvar Jaroslav Identification and characterization of repetitive extragenic palindromes (REP)-associated tyrosine transposases: implications for REP evolution and dynamics in bacterial genomes BMC Genomics |
| title | Identification and characterization of repetitive extragenic palindromes (REP)-associated tyrosine transposases: implications for REP evolution and dynamics in bacterial genomes |
| title_full | Identification and characterization of repetitive extragenic palindromes (REP)-associated tyrosine transposases: implications for REP evolution and dynamics in bacterial genomes |
| title_fullStr | Identification and characterization of repetitive extragenic palindromes (REP)-associated tyrosine transposases: implications for REP evolution and dynamics in bacterial genomes |
| title_full_unstemmed | Identification and characterization of repetitive extragenic palindromes (REP)-associated tyrosine transposases: implications for REP evolution and dynamics in bacterial genomes |
| title_short | Identification and characterization of repetitive extragenic palindromes (REP)-associated tyrosine transposases: implications for REP evolution and dynamics in bacterial genomes |
| title_sort | identification and characterization of repetitive extragenic palindromes rep associated tyrosine transposases implications for rep evolution and dynamics in bacterial genomes |
| url | http://www.biomedcentral.com/1471-2164/11/44 |
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