Background frequencies for residue variability estimates: BLOSUM revisited

<p>Abstract</p> <p>Background</p> <p>Shannon entropy applied to columns of multiple sequence alignments as a score of residue conservation has proven one of the most fruitful ideas in bioinformatics. This straightforward and intuitively appealing measure clearly shows the regions of a protein under increased evolutionary pressure, highlighting their functional importance. The inability of the column entropy to differentiate between residue types, however, limits its resolution power.</p> <p>Results</p> <p>In this work we suggest generalizing Shannon's expression to a function with similar mathematical properties, that, at the same time, includes observed propensities of residue types to mutate to each other. To do that, we revisit the original construction of BLOSUM matrices, and re-interpret them as mutation probability matrices. These probabilities are then used as background frequencies in the revised residue conservation measure.</p> <p>Conclusion</p> <p>We show that joint entropy with BLOSUM-proportional probabilities as a reference distribution enables detection of protein functional sites comparable in quality to a time-costly maximum-likelihood evolution simulation method (rate4site), and offers greater resolution than the Shannon entropy alone, in particular in the cases when the available sequences are of narrow evolutionary scope.</p

Selective Pressure to Increase Charge in Immunodominant Epitopes of the H3 Hemagglutinin Influenza Protein

The evolutionary speed and the consequent immune escape of H3N2 influenza A virus make it an interesting evolutionary system. Charged amino acid residues are often significant contributors to the free energy of binding for protein–protein interactions, including antibody–antigen binding and ligand–receptor binding. We used Markov chain theory and maximum likelihood estimation to model the evolution of the number of charged amino acids on the dominant epitope in the hemagglutinin protein of circulating H3N2 virus strains. The number of charged amino acids increased in the dominant epitope B of the H3N2 virus since introduction in humans in 1968. When epitope A became dominant in 1989, the number of charged amino acids increased in epitope A and decreased in epitope B. Interestingly, the number of charged residues in the dominant epitope of the dominant circulating strain is never fewer than that in the vaccine strain. We propose these results indicate selective pressure for charged amino acids that increase the affinity of the virus epitope for water and decrease the affinity for host antibodies. The standard PAM model of generic protein evolution is unable to capture these trends. The reduced alphabet Markov model (RAMM) model we introduce captures the increased selective pressure for charged amino acids in the dominant epitope of hemagglutinin of H3N2 influenza (R2 > 0.98 between 1968 and 1988). The RAMM model calibrated to historical H3N2 influenza virus evolution in humans fit well to the H3N2/Wyoming virus evolution data from Guinea pig animal model studies

Dichotomy in the NRT Gene Families of Dicots and Grass Species

A large proportion of the nitrate (NO3−) acquired by plants from soil is actively transported via members of the NRT families of NO3− transporters. In Arabidopsis, the NRT1 family has eight functionally characterised members and predominantly comprises low-affinity transporters; the NRT2 family contains seven members which appear to be high-affinity transporters; and there are two NRT3 (NAR2) family members which are known to participate in high-affinity transport. A modified reciprocal best hit (RBH) approach was used to identify putative orthologues of the Arabidopsis NRT genes in the four fully sequenced grass genomes (maize, rice, sorghum, Brachypodium). We also included the poplar genome in our analysis to establish whether differences between Arabidopsis and the grasses may be generally applicable to monocots and dicots. Our analysis reveals fundamental differences between Arabidopsis and the grass species in the gene number and family structure of all three families of NRT transporters. All grass species possessed additional NRT1.1 orthologues and appear to lack NRT1.6/NRT1.7 orthologues. There is significant separation in the NRT2 phylogenetic tree between NRT2 genes from dicots and grass species. This indicates that determination of function of NRT2 genes in grass species will not be possible in cereals based simply on sequence homology to functionally characterised Arabidopsis NRT2 genes and that proper functional analysis will be required. Arabidopsis has a unique NRT3.2 gene which may be a fusion of the NRT3.1 and NRT3.2 genes present in all other species examined here. This work provides a framework for future analysis of NO3− transporters and NO3− transport in grass crop species

Cube - An online tool for comparison and contrasting of protein sequences

When comparing sequences of similar proteins, two kinds of questions can be asked, and the related two kinds of inference made. First, one may ask to what degree they are similar, and then, how they differ. In the first case one may tentatively conclude that the conserved elements common to all sequences are of central and common importance to the protein's function. In the latter case the regions of specialization may be discriminative of the function or binding partners across subfamilies of related proteins. Experimental efforts - mutagenesis or pharmacological intervention - can then be pointed in either direction, depending on the context of the study. Cube simplifies this process for users that already have their favorite sets of sequences, and helps them collate the information by visualization of the conservation and specialization scores on the sequence and on the structure, and by spreadsheet tabulation. All information can be visualized on the spot, or downloaded for reference and later inspection. Server homepage: http://eopsf.org/cub

Gene structure and expression pattern analysis of three monodehydroascorbate reductase (Mdhar) genes in Physcomitrella patens: Implications for the evolution of the MDHAR family in plants

The original publication can be found at www.springerlink.comThe ascorbate–glutathione pathway plays a major role in the detoxification of reactive oxygen species (ROS) in vascular plants. One of the key enzymes in this pathway is monodehydroascorbate reductase (MDHAR), a FAD enzyme that catalyses the reduction of the monodehydroascorbate radical. To elucidate the evolution and functional role of MDHAR we identified and characterised MDHARs from the moss Physcomitrella patens. Expressed sequence tag (EST) databases containing approximately 100.000 ESTs from Physcomitrella were searched and three isoforms of monodehydroascorbate reductase (PpMDHAR1, PpMDHAR2 and PpMDHAR3) were identified. In vascular plants MDHAR is found in the cytosol, chloroplast, mitochondria and peroxisome. Surprisingly, all three PpMDHARs resembled the cytosolic isoforms from vascular plants lacking the NH ₂-terminal or COOH-terminal extension found in organelle targeted MDHARs. The number and position of introns was also conserved between PpMDHARs and cytosolic MDHARs from vascular plants. Phylogenetic analysis revealed that cytosolic MDHARs are monophyletic in origin and the ancestral gene evolved before the divergence of bryophytes more than 400 million years ago. Transcript analyses showed that expression of PpMdhar1 and PpMdhar3 was increased up to 5-fold under salt stress, osmotic stress or upon exposure to abscisic acid. In contrast, PpMdhar transcription levels were unchanged upon chilling, UV-B exposure or oxidative stress. The conservation of cytosolic MDHAR in the land-plant lineage and the transcriptional upregulation under water deficiency suggest that the evolution of cytosolic MDHAR played an essential role in stress protection for land plants when they inhabited the dry terrestrial environment.Christina Lunde, Ute Baumann, Neil J. Shirley, Damian P. Drew and Geoffrey B. Finche