Conserved intron positions in ancient protein modules

Background  

The timing of the origin of introns is of crucial importance for an understanding of early genome architecture. The Exon theory of genes proposed a role for introns in the formation of multi-exon proteins by exon shuffling and predicts the presence of conserved splice sites in ancient genes. In this study, large-scale analysis of potential conserved splice sites was performed using an intron-exon database (ExInt) derived from GenBank.     

Evolution of the response to heat shock in genus Drosophila

Thermotolerance was studied in a wide spectrum of Drosophila species and strains originating from different climatic zones and considerably differing from one another in the ambient temperature of their habitats. The species that lived in hot climate have a higher thermotolerance. Most species of the virilis group exhibited positive correlation between the HSP70 accumulation after heat exposure and thermotolerance; however, this correlation was absent in some species and strains. For example, the D. melanogaster Oregon R strain, which had the highest sensitivity to heat shock (HS) among all strains and species studied, displayed the maximum level of HSP70 proteins after HS. The patterns of induction of various heat shock protein (HSP) families after heat exposure in a wide spectrum of Drosophila species were compared. The results obtained suggest that the HSP40 and low-molecular-weight HSPs (lmwHSPs) play a significant role in thermotolerance and adaptation to hot climate. Polymorphism in hsp70 gene clusters of Drosophila and variation in the numbers of gene copies and hsp70 isoforms in group virilis were found. The evolutionary role of the variation in the number of hsp70 gene copies observed in the strains and species of genus Drosophila is discussed.     

A comparative analysis of the <Emphasis Type="Italic">hsp70</Emphasis> gene system in two species of the family stratiomyidae (Diptera)

The structure of the hsp70 gene cluster was investigated for two species of the family Stratiomyidae (Diptera), Stratiomys singularior and Oxycera pardalina. Their larvae inhabit nearshore-aquatic biotopes with contrasting temperature regimes, composition and concentration of salts. It was shown that the S. singularior hsp70 gene cluster contains five copies and has a compact structural organization (the interval length did not exceed 5 kb). The O. pardalina hsp70 gene cluster contains four copies located at larger distances in comparison with the S. singularior and also includes the hsp68 gene. High variability in the structure of the S. singularior hsp70 gene cluster was detected.     

Qualitative and quantitative analyses of the transpositions of P element--based genetic construction into the region of Drosophila melanogaster hsp70 genes

The hsp70 genes is among the main systems underlying the adaptation of organisms to adverse environmental factors. The ever increasing amount of data in literature demonstrates an important adaptive role of mobile genetic elements in microevolution. Drosophila hsp70 genes are potential target for transpositions of various mobile elements in natural populations. We have analyzed the frequency and localization of a P element-based genetic construction, EPgy2, in the region of Drosophila melanogaster hsp70 genes. A hot spot for the transposition was discovered in the promoter regions of genes hsp70Aa and hsp70Ab. No insertions of this construction in the coding or 3'-flanking regions of hsp70 genes have been recorded. It was demonstrated that the region of 161 to 7800 bp adjacent to the original construction is in certain cases also involved in the transposition. No transpositions of any other mobile elements have been observed. The inserts were shown to change the activity of hsp70 genes and the thermotolerance of transgenic strains.     

Sepsis progression and outcome: a dynamical model

Background  

Sepsis (bloodstream infection) is the leading cause of death in non-surgical intensive care units. It is diagnosed in 750,000 US patients per annum, and has high mortality. Current understanding of sepsis is predominately observational and correlational, with only a partial and incomplete understanding of the physiological dynamics underlying the syndrome. There exists a need for dynamical models of sepsis progression, based upon basic physiologic principles, which could eventually guide hourly treatment decisions.     

Small heat shock proteins and adaptation to hypertermia in various Drosophila species

Expression level and kinetics of accumulation of small heat shock proteins (21-27 kDa group) have been investigated in three Drosophila species differing significantly by temperature niche and thermosensitivity. It was shown that low-latitude thermotolerant species D. virilis exceeds the high-latitude thermosensitive closely-related species D. lummei as well as distant thermosensitive species D. melanogaster in terms of small heat shock proteins expression and accumulation after temperature elevation. The data obtained enable to postulate an important role of small heat shock proteins in organism basal thermotolerance and general adaptation to adverse conditions of environment.     

Interplay between recombinant Hsp70 and proteasomes: proteasome activity modulation and ubiquitin-independent cleavage of Hsp70

The heat shock protein 70 (Hsp70, human HSPA1A) plays indispensable roles in cellular stress responses and protein quality control (PQC). In the framework of PQC, it cooperates with the ubiquitin-proteasome system (UPS) to clear damaged and dysfunctional proteins in the cell. Moreover, Hsp70 itself is rapidly degraded following the recovery from stress. It was demonstrated that its fast turnover is mediated via ubiquitination and subsequent degradation by the 26S proteasome. At the same time, the effect of Hsp70 on the functional state of proteasomes has been insufficiently investigated. Here, we characterized the direct effect of recombinant Hsp70 on the activity of 20S and 26S proteasomes and studied Hsp70 degradation by the 20S proteasome in vitro. We have shown that the activity of purified 20S proteasomes is decreased following incubation with recombinant human Hsp70. On the other hand, high concentrations of Hsp70 activated 26S proteasomes. Finally, we obtained evidence that in addition to previously reported ubiquitin-dependent degradation, Hsp70 could be cleaved independent of ubiquitination by the 20S proteasome. The results obtained reveal novel aspects of the interplay between Hsp70 and proteasomes.     

A novel approach for multi-domain and multi-gene family identification provides insights into evolutionary dynamics of disease resistance genes in core eudicot plants

Background

Recent advances in DNA sequencing techniques resulted in more than forty sequenced plant genomes representing a diverse set of taxa of agricultural, energy, medicinal and ecological importance. However, gene family curation is often only inferred from DNA sequence homology and lacks insights into evolutionary processes contributing to gene family dynamics. In a comparative genomics framework, we integrated multiple lines of evidence provided by gene synteny, sequence homology and protein-based Hidden Markov Modelling to extract homologous super-clusters composed of multi-domain resistance (R)-proteins of the NB-LRR type (for NUCLEOTIDE BINDING/LEUCINE-RICH REPEATS), that are involved in plant innate immunity.

Results

To assess the diversity of R-proteins within and between species, we screened twelve eudicot plant genomes including six major crops and found a total of 2,363 NB-LRR genes. Our curated R-proteins set shows a 50% average for tandem duplicates and a 22% fraction of gene copies retained from ancient polyploidy events (ohnologs). We provide evidence for strong positive selection and show significant differences in molecular evolution rates (Ka/Ks-ratio) among tandem- (mean = 1.59), ohnolog (mean = 1.36) and singleton (mean = 1.22) R-gene duplicates. To foster the process of gene-edited plant breeding, we report species-specific presence/absence of all 140 NB-LRR genes present in the model plant Arabidopsis and describe four distinct clusters of NB-LRR “gatekeeper” loci sharing syntenic orthologs across all analyzed genomes.

Conclusion

By curating a near-complete set of multi-domain R-protein clusters in an eudicot-wide scale, our analysis offers significant insight into evolutionary dynamics underlying diversification of the plant innate immune system. Furthermore, our methods provide a blueprint for future efforts to identify and more rapidly clone functional NB-LRR genes from any plant species.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-966) contains supplementary material, which is available to authorized users.