![]() ![]() ![]() ![]() These REP functions are also exhibited to some degree in other extragenic prokaryotic DNA elements, such as the Correia elements in Neisseria gonorrhoeae, or RUP elements in Streptococcus pneumoniae ( 11–14 ). REPs also increase mRNA stability and can cause transcription termination ( 9, 10 ). REPs are known to interact with several partners, by providing binding sites for proteins such as Integration Host Factor and DNA polymerase I, and providing the necessary cleavage sites for DNA gyrase to unwind DNA ( 6–8 ). Repetitive extragenic palindromic sequences (REPs) are a distinct class of abundant repeats important in regulation of certain bacterial functions. This paradigm changed considerably over the last two decades, as it has become apparent that these sequences often encode unexpected functions as evidenced by the discovery of microRNAs and their role in gene regulation ( 1, 2 ), and by the identification of a new class of short palindromic repeats, known as Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR), which are critical in prokaryotic immunity ( 3–5 ). These features suggest that, relative to IS 200 /IS 605 transposases, it has evolved a different mechanism for the movement of discrete segments of DNA and has been severely down-regulated, perhaps to prevent REPs from sweeping through genomes.įor many years, a large part of the extragenic sequence in genomes was thought to be essentially silent and devoid of function, hence the popular term ‘junk DNA’. Sequence analysis showed that TnpA REP is highly related to the IS 200 /IS 605 family, but in contrast to IS 200 /IS 605 transposases, TnpA REP is a monomer, is auto-inhibited and is active only in manganese. We report here the structure to 2.6 Å of TnpA REP from Escherichia coli MG1655 bound to a REP. Although a new clade of putative transposases (RAYTs or TnpA REP ) is often associated with an increase in these repeats, it is not clear how these proteins might have directed amplification of REPs. REPs are found in many bacterial species at a high copy number and are important in regulation of certain bacterial functions, such as Integration Host Factor recruitment and mRNA turnover. Repetitive extragenic palindromic sequences (REPs) are a class of extragenic sequences, which form nucleotide stem-loop structures. Extragenic sequences in genomes, such as microRNA and CRISPR, are vital players in the cell. ![]()
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