Dorota Mackiewicz

The relationships between the isoelectric point and: length of proteins, taxonomy and ecology of organisms

BackgroundThe distribution of isoelectric point (pI) of proteins in a proteome is universal for all organisms. It is bimodal dividing the proteome into two sets of acidic and basic proteins. Different species however have different abundance of acidic and basic proteins that may be correlated with taxonomy, subcellular localization, ecological niche of organisms and proteome size.ResultsWe have analysed 1784 proteomes encoded by chromosomes of Archaea, Bacteria, Eukaryota, and also mitochondria, plastids, prokaryotic plasmids, phages and viruses. We have found significant correlation in more than 95% of proteomes between the protein length and pI in proteomes – positive for acidic proteins and negative for the basic ones. Plastids, viruses and plasmids encode more basic proteomes while chromosomes of Archaea, Bacteria, Eukaryota, mitochondria and phages more acidic ones. Mitochondrial proteomes of Viridiplantae, Protista and Fungi are more basic than Metazoa. It results from the presence of basic proteins in the former proteomes and their absence from the latter ones and is related with reduction of metazoan genomes. Significant correlation was found between the pI bias of proteomes encoded by prokaryotic chromosomes and proteomes encoded by plasmids but there is no correlation between eukaryotic nuclear-coded proteomes and proteomes encoded by organelles. Detailed analyses of prokaryotic proteomes showed significant relationships between pI distribution and habitat, relation to the host cell and salinity of the environment, but no significant correlation with oxygen and temperature requirements. The salinity is positively correlated with acidicity of proteomes. Host-associated organisms and especially intracellular species have more basic proteomes than free-living ones. The higher rate of mutations accumulation in the intracellular parasites and endosymbionts is responsible for the basicity of their tiny proteomes that explains the observed positive correlation between the decrease of genome size and the increase of basicity of proteomes. The results indicate that even conserved proteins subjected to strong selectional constraints follow the global trend in the pI distribution.ConclusionThe distribution of pI of proteins in proteomes shows clear relationships with length of proteins, subcellular localization, taxonomy and ecology of organisms. The distribution is also strongly affected by mutational pressure especially in intracellular organisms.

Flip-flop around the origin and terminus of replication in prokaryotic genomes

A response to Evidence for symmetric chromosomal inversions around the replication origin in bacteria by JA Eisen, JF Heidelberg, O White, SL Salzberg. Genome Biology 2000, 1:research0011.1-0011.9.

High correlation between the turnover of nucleotides under mutational pressure and the DNA composition

BackgroundAny DNA sequence is a result of compromise between the selection and mutation pressures exerted on it during evolution. It is difficult to estimate the relative influence of each of these pressures on the rate of accumulation of substitutions. However, it is important to discriminate between the effect of mutations, and the effect of selection, when studying the phylogenic relations between taxa.ResultsWe have tested in computer simulations, and analytically, the available substitution matrices for many genomes, and we have found that DNA strands in equilibrium under mutational pressure have unique feature: the fraction of each type of nucleotide is linearly dependent on the time needed for substitution of half of nucleotides of a given type, with a correlation coefficient close to 1. Substitution matrices found for sequences under selection pressure do not have this property. A substitution matrix for the leading strand of the Borrelia burgdorferi genome, having reached equilibrium in computer simulation, gives a DNA sequence with nucleotide composition and asymmetry corresponding precisely to the third positions in codons of protein coding genes located on the leading strand.ConclusionsParameters of mutational pressure allow us to count DNA composition in equilibrium with this mutational pressure. Comparing any real DNA sequence with the sequence in equilibrium it is possible to estimate the distance between these sequences, which could be used as a measure of the selection pressure. Furthermore, the parameters of the mutational pressure enable direct estimation of the relative mutation rates in any DNA sequence in the studied genome.

How many protein-coding genes are there in the Saccharomyces cerevisiae genome?

We have compared the results of estimations of the total number of protein‐coding genes in the Saccharomyces cerevisiae genome, which have been obtained by many laboratories since the yeast genome sequence was published in 1996. We propose that there are 5300–5400 genes in the genome. This makes the first estimation of the number of intronless ORFs longer than 100 codons, based on the features of the set of genes with phenotypes known in 1997 to be correct. This estimation assumed that the set of the first 2300 genes with known phenotypes was representative for the whole set of protein‐coding genes in the genome. The same method used in this paper for the approximation of the total number of protein‐coding sequences among more than 40 000 ORFs longer than 20 codons gives a result that is only slightly higher. This suggests that there are still some non‐coding ORFs in the databases and a few dozen small ORFs, not yet annotated, which probably code for proteins. Copyright

The Differential Killing of Genes by Inversions in Prokaryotic Genomes

We have elaborated a method which has allowed us to estimate the direction of translocation of orthologs which have changed, during the phylogeny, their positions on chromosome in respect to the leading or lagging role of DNA strands. We have shown that the relative number of translocations which have switched positions of genes from the leading to the lagging DNA strand is lower than the number of translocations which have transferred genes from the lagging strand to the leading strand of prokaryotic genomes. This paradox could be explained by assuming that the stronger mutation pressure and selection after inversion preferentially eliminate genes transferred from the leading to the lagging DNA strand.

Replication associated mutational pressure generating long-range correlation in DNA

There are many biological mechanisms which introduce long-range correlations into the DNA molecule. One of the most important is replication of chromosomes, its mechanisms and topology. Replication associated mutational pressure, defined as specific preferences in nucleotide substitutions during replication, generates asymmetry in the genome. On the other hand, substitution rates, which determine the evolutionary turnover time of a nucleotide, are highly correlated with the fraction of that nucleotide in the genome. Assuming the Azbel hypothesis that the number of mutations per genome per generation is invariant and universal, a general rule for mutational pressure can be formulated: the half-time of a nucleotide turnover in the genome is linearly dependent on the number of this nucleotide in the genome.

Sympatric speciation as intrinsic property of the expanding population

Sympatric speciation is still debatable, though some well documented empirical data that support it already exist. Our computer modeling reveals that sympatric speciation is an intrinsic property of the expanding populations with differentiated inbreeding—higher at the edges and lower inside the territory. At the edges of expanding populations, the probability of forming deleterious phenotypes by placing two defective alleles in the corresponding loci is relatively high even with low genetic load. Thus, the winning strategy is to use rather the complementary haplotypes to form zygotes. This strategy leads to a very fast sympatric speciation and specific distribution of recombination activity along the chromosomes—higher at the subtelomeric regions (close to the ends of chromosomes) and lower in the middle of chromosomes, which is also observed in all human chromosomes (excluding Y).

Optimisation of Asymmetric Mutational Pressure and Selection Pressure Around the Universal Genetic Code

One of hypotheses explaining the origin of the genetic code assumes that its evolution has minimised the deleterious effects of mutations in coded proteins. To estimate the level of such optimization, we calculated optimal codes for genes located on differently replicating DNA strands separately assuming the rate of amino acid substitutions in proteins as a measure of codes susceptibility to errors. The optimal code for genes located on one DNA strand was simultaneously worse than the universal code for the genes located on the other strand. Furthermore, we generated 20 million random codes of which only 23 were better than the universal one for genes located on both strands simultaneously while about two orders of magnitude more codes were better for each of the two strands separately. The result indicates that the existing universal code, the mutational pressure, the codon and amino acid compositions are highly optimised for the both differently replicating DNA strands.

Correlation between mutation pressure, selection pressure, and occurrence of amino acids

With the help of the empirical mutation table for nucleotides in the Borrelia burgdorferi genome we have performed Monte Carlo simulation of the pure mutation pressure experienced by the genes of the genome. We have examined the divergence of the mutated genes from the ancestral ones and we have constructed MPM1 matrix (Mutation Probability Matrix) of the substitution rates between amino acids of the diverging genes. The results have been compared to mutation data matrix PAM1 PET91 representing mutation and selection data of 16130 homologous genes od different organisms. We have found that the effective survival time of amino acids in organisms follows a power law with respect to frequency of their occurrence in genes. This makes possible to find the effect of the pure mutational pressure and the selection on the amino acid composition of genes. The results are universal in the sense that the survival time of amino acids calculated from the higher order PAMk matrices (k > 1) follows the same power law as in the case of PAM1 matrices.

Distribution of Recombination Hotspots in the Human Genome – A Comparison of Computer Simulations with Real Data

Recombination is the main cause of genetic diversity. Thus, errors in this process can lead to chromosomal abnormalities. Recombination events are confined to narrow chromosome regions called hotspots in which characteristic DNA motifs are found. Genomic analyses have shown that both recombination hotspots and DNA motifs are distributed unevenly along human chromosomes and are much more frequent in the subtelomeric regions of chromosomes than in their central parts. Clusters of motifs roughly follow the distribution of recombination hotspots whereas single motifs show a negative correlation with the hotspot distribution. To model the phenomena related to recombination, we carried out computer Monte Carlo simulations of genome evolution. Computer simulations generated uneven distribution of hotspots with their domination in the subtelomeric regions of chromosomes. They also revealed that purifying selection eliminating defective alleles is strong enough to cause such hotspot distribution. After sufficiently long time of simulations, the structure of chromosomes reached a dynamic equilibrium, in which number and global distribution of both hotspots and defective alleles remained statistically unchanged, while their precise positions were shifted. This resembles the dynamic structure of human and chimpanzee genomes, where hotspots change their exact locations but the global distributions of recombination events are very similar.