Naslov
Palindromes in prokaryotic genomes

Autori
Lisnić, Berislav ; Svetec, Ivan-Krešimir ; Štafa, Anamarija ; Zgaga, Zoran

Vrsta, podvrsta i kategorija rada
Sažeci sa skupova, sažetak, znanstveni

Izvornik
Book of abstracts / Kovarik, Z. - Zagreb, 2006, 60-60

Skup
Congress of the Croatian Society of Biochemistry and Molecular Biology on the occasion of the 30th Anniversary

Mjesto i datum
Vodice, Hrvatska, 03.10.2006. - 07.10.2006

Vrsta sudjelovanja
Pozvano predavanje

Vrsta recenzije
Međunarodna recenzija

Ključne riječi
Palindrome; Inverted repeat; Sequence analysis; Prokaryotic genomes

Sažetak
Closely spaced inverted repeats (IRs), palindromes and quasipalindromes can be found in the DNA of natural plasmids, viral and bacterial genomes and eukaryotic chromosomes and organelles. In prokaryotes, they may serve as binding sites for regulatory proteins, while short perfect palindromes are known as recognition sites for type II restriction-modification systems that play significant role in bacterial ecology and evolution. They are also contained in genes encoding functional RNA molecules and in different cis-acting genetic elements, like terminators, attenuators, plasmid and viral origins of replication. However, in spite of their importance and functional versatility, longer palindromes and IRs were shown to be very unstable in different organisms, from bacteria to mammalian cells. Given the importance of palindromic sequences in regulation of different cellular processes on one side and their influence on genetic stability on the other side, an analysis of the incidence of perfect palindromes at the genomic level seems particularly interesting. In our previous work we developed a computer program that may identify, locate and count palindromes in a given sequence in a strictly defined way and we used this program to analyze the palindrome content of the entire genome of the yeast Saccharomyces cerevisiae (Lisnić et al., (2005) Curr. Genet. 47:289.). Several interesting findings emerged from that study and we decided to expand this analysis to palindromes present in >300 sequenced bacterial genomes. First we developed the mathematical framework to compare the actual and expected numbers of palindromes in each genome. This comparison revealed two main numerical trends: (i) palindromes longer than 10 nt are highly overrepresented in bacterial genomes and (ii) shorter palindromes are mainly overrepresented in GC-rich genomes, but highly underrepresented in the AT-rich genomes. Interestingly, the size of the largest palindromes found in a given genome does not correlate either with its size or GC content. Different processes and phenomena, like fidelity of DNA replication, codon usage, restriction-modification systems or gene expression control may regulate the incidence of palindromic sequences in bacterial genomes.

Izvorni jezik
Engleski

Znanstvena područja
Biologija, Biotehnologija

POVEZANOST RADA