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1

High divergence rate of sequences located on different DNA strands in closely related bacterial genomes

100%
Mackiewicz P., Mackiewicz D., Kowalczuk M., Dudkiewicz M., Dudek M. R., Cebrat S.
Journal of Applied Genetics
|
2003
|
vol. 44
|
issue 4
561-584
EN
One of the common features of bacterial genomes is a strong compositional asymmetry between differently replicating DNA strands (leading and lagging). The main cause of the observed bias is the mutational pressure associated with replication. This suggests that genes translocated between differently replicating DNA strands are subjected to a higher mutational pressure, which may influence their composition and divergence rate. Analyses of groups of completely sequenced bacterial genomes have revealed that the highest divergence rate is observed for the DNA sequences that in closely related genomes are located on different DNA strands in respect to their role in replication. Paradoxically, for this group of sequences the absolute values of divergence rate are higher for closely related species than for more diverged ones. Since this effect concerns only the specific group of orthologs, there must be a specific mechanism introducing bias into the structure of chromosome by enriching the set of homologs in trans position in newly diverged species in relatively highly diverged sequences. These highly diverged sequences may be of varied nature: (1) paralogs or other fast-evolving genes under weak selection; or (2) pseudogenes that will probably be eliminated from the genome during further evolution; or (3) genes whose history after divergence is longer than the history of the genomes in which they are found. The use of these highly diverged sequences for phylogenetic analyses may influence the topology and branch length of phylogenetic trees. The changing mutational pressure may contribute to arising of genes with new functions as well.
2

Determination of replication initiation site

100%
Zakrzewska-Czerwinska J., Mackiewicz P., Zawilak A., Cebrat S.
Biotechnologia
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2005
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issue 3
91-101
EN
Initiation of bacterial chromosome replication is mediated by a single initiator protein ? DnaA which interacts specifically with multiple DnaA boxes located within the origin of replication oriC. We have applied in silico methods: DNA asymmetry, DnaA box distribution and dnaA gene location to identify the putative replication origins in bacterial chromosomes. The three methods identify the same region as a putative origin in more than half of the analyzed chromosomes. The most universal method of putative oriC identification in bacterial chromosomes is DNA asymmetry, although in some cases it is necessary to apply all three methods. Interestingly, most bacterial chromosomes exhibit an overrepresentation of DnaA boxes; they contain at least one cluster of DnaA boxes in the vicinity of the oriC region that is probably involved in controlling replication initiation.
3

Asymmetry of nucleotide composition of prokaryotic chromosomes

75%
Mackiewicz P., Gierlik A., Kowalczuk M., Dudek M., Cebrat S.
|
1999
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vol. 40
|
issue 1
1-14
EN
We have analysed the causes of asymmetry in nucleotide composition of DNA complementary strands of prokaryotic chromosomes. Analysing DNA walks we have separated the effect of replication-associated processes from the effect introduced by transcription and coding functions. The asymmetry introduced by replication switches its polarity at the origin and at the terminus of replication, which is observed in both noncoding and coding sequences and varies with respect to positions in codons. Coding functions introduce very strong trends into protein coding ORFs, which are specific for each nucleotide position in the codon. Using detrended DNA walks we have eliminated the effect of coding density and we were able to distinguish between mutational pressure associated with replication and compositional bias for genes proximal and distal to the origin of replication.
4

Is there any mystery of ORPHANs ?

75%
Cebrat S., Dudek M., Mackiewicz P.
Journal of Applied Genetics
|
1997
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vol. 38
|
issue 4
365-372
EN
We have analysed the coding capacity of ORFs longer than 100 codons found in the yeast genome. Comparing the parameters describing the DNA asymmetry in the set of known genes and the set of all ORFs>100 codons we have found that there are about 4700 coding ORFs in the yeast genome. Since for more than 2300 ORFs recognisable functions have been already found and for about 2000 ORFs homology to known genes has been identified - only about 400 ORFs can be considered as orphans - ORFs without any known function or homology. This finding means that there is no mystery of orphans - a paradox showing that the fraction of orphans has been growing with the growing number of genes with known functions in the yeast genome.
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