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

Harmonization of Flow Cytometric Minimal Residual Disease Assessment in Multiple Myeloma in Centers of Polish Myeloma Consortium

Minimal residual disease (MRD) status is now considered as one of the most relevant prognostic factors in multiple myeloma (MM) while MRD negativity became an important endpoint in clinical trials. Here, we report the results of the first study evaluating the reproducibility of high-sensitivity flow cytometry MM MRD assessment in four laboratories in Poland. EuroFlow protocols for instrument setting standardization and sample preparation in MM MRD assessment were implemented in each laboratory. In the inter-laboratory reproducibility study, 12 bone marrow samples from MM patients were distributed and processed in participant laboratories. In the inter-operator concordance study, 13 raw data files from MM MRD measurements were analyzed by five independent operators. The inter-laboratory study showed high 95% overall concordance of results among laboratories. In the inter-operator study, 89% of MRD results reported were concordant, and the highest immunophenotype interpretation differences with regard to expression of CD27, CD45, CD81 were noticed. We confirmed the applicability and feasibility of the EuroFlow protocol as a highly sensitive method of MRD evaluation in MM. Results of our inter-center comparison study demonstrate that the standardization of MM MRD assessment protocols is highly desirable to improve quality and comparability of results within and between different clinical trials

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

Ratios of the observed to expected number of proteomes in a given class of pI bias for different ecological classifications: (A) oxygen, (B) temperature, (C) salinity, (D) habitat and (E) relation to host cell

<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

Statistical analysis of the pI bias of different groups of proteomes and their UPGMA-based clustering according to the median of the pI bias

<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> Numbers at nodes mean the percentage support based on subsampling method and asterisks denote results of WLS-LRT/F tests (both with p < 0.001)

Statistical analysis of the pI bias of mitochondrial proteomes and their UPGMA-based clustering according to the median of the pI bias

<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> Numbers at nodes mean the percentage support based on subsampling method and asterisks denote results of WLS-LRT/F tests (both with p < 0.001)