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

BACKGROUND: Any 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. RESULTS: We 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. CONCLUSIONS: Parameters 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

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

<p>Abstract</p> <p>Background</p> <p>The 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.</p> <p>Results</p> <p>We 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.</p> <p>Conclusion</p> <p>The 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.</p

Controllable Hierarchical Mechanical Metamaterials Guided by the Hinge Design

In this work, we use computer simulations (Molecular Dynamics) to analyse the behaviour of a specific auxetic hierarchical mechanical metamaterial composed of square-like elements. We show that, depending on the design of hinges connecting structural elements, the system can exhibit a controllable behaviour where different hierarchical levels can deform to the desired extent. We also show that the use of different hinges within the same structure can enhance the control over its deformation and mechanical properties, whose results can be applied to other mechanical metamaterials. In addition, we analyse the effect of the size of the system as well as the variation in the stiffness of its hinges on the range of the exhibited auxetic behaviour (negative Poisson’s ratio). Finally, it is discussed that the concept presented in this work can be used amongst others in the design of highly efficient protective devices capable of adjusting their response to a specific application

Distributions of the correlation coefficients between pI value and length of proteins calculated separately for acidic and basic sets of proteomes

<p><b>Copyright information:</b></p><p>Taken from "The relationships between the isoelectric point and: length of proteins, taxonomy and ecology of organisms"</p><p>http://www.biomedcentral.com/1471-2164/8/163</p><p>BMC Genomics 2007;8():163-163.</p><p>Published online 12 Jun 2007</p><p>PMCID:PMC1905920.</p><p></p

Relationship between the pI bias and: (A) logarithm of proteome size and (B) genomic GC content for different ecological groups of prokaryotes

<p><b>Copyright information:</b></p><p>Taken from "The relationships between the isoelectric point and: length of proteins, taxonomy and ecology of organisms"</p><p>http://www.biomedcentral.com/1471-2164/8/163</p><p>BMC Genomics 2007;8():163-163.</p><p>Published online 12 Jun 2007</p><p>PMCID:PMC1905920.</p><p></p