Quantitative image analysis identifies pVHL as a key regulator of microtubule dynamic instability

The product of the von Hippel-Lindau tumor suppressor gene stabilizes microtubules by inhibiting GTPase activity

Proteome sequence features carry signatures of the environmental niche of prokaryotes

<p>Abstract</p> <p>Background</p> <p>Prokaryotic environmental adaptations occur at different levels within cells to ensure the preservation of genome integrity, proper protein folding and function as well as membrane fluidity. Although specific composition and structure of cellular components suitable for the variety of extreme conditions has already been postulated, a systematic study describing such adaptations has not yet been performed. We therefore explored whether the environmental niche of a prokaryote could be deduced from the sequence of its proteome. Finally, we aimed at finding the precise differences between proteome sequences of prokaryotes from different environments.</p> <p>Results</p> <p>We analyzed the proteomes of 192 prokaryotes from different habitats. We collected detailed information about the optimal growth conditions of each microorganism. Furthermore, we selected 42 physico-chemical properties of amino acids and computed their values for each proteome. Further, on the same set of features we applied two fundamentally different machine learning methods, Support Vector Machines and Random Forests, to successfully classify between bacteria and archaea, halophiles and non-halophiles, as well as mesophiles, thermophiles and mesothermophiles. Finally, we performed feature selection by using Random Forests.</p> <p>Conclusions</p> <p>To our knowledge, this is the first time that three different classification cases (domain of life, halophilicity and thermophilicity) of proteome adaptation are successfully performed with the same set of 42 features. The characteristic features of a specific adaptation constitute a signature that may help understanding the mechanisms of adaptation to extreme environments.</p

Proteomic Properties Reveal Phyloecological Clusters of <em>Archaea</em>

<div><p>In this study, we propose a novel way to describe the variety of environmental adaptations of <em>Archaea</em>. We have clustered 57 <em>Archaea</em> by using a non-redundant set of proteomic features, and verified that the clusters correspond to environmental adaptations to the archaeal habitats. The first cluster consists dominantly of hyperthermophiles and hyperthermoacidophilic aerobes. The second cluster joins together halophilic and extremely halophilic <em>Archaea</em>, while the third cluster contains mesophilic (mostly methanogenic) <em>Archaea</em> together with thermoacidophiles. The non-redundant subset of proteomic features was found to consist of five features: the ratio of charged residues to uncharged, average protein size, normalized frequency of beta-sheet, normalized frequency of extended structure and number of hydrogen bond donors. We propose this clustering to be termed phyloecological clustering. This approach could give additional insights into relationships among archaeal species that may be hidden by sole phylogenetic analysis.</p> </div

Assessing predictive power of phyloecological clustering.

<p>We added five new species to the dataset and preformed hierarchical clustering with the established parameters. The new species became a part of the clusters defined with similar environmental conditions as it is found in their respective niches. One archaeon joined the “red” cluster with other mesophilic methanogens; two species merged with the members of halophilic ”blue” cluster; and two hyperthermoacidophilic organisms became members of the corresponding “yellow” cluster.</p

Genetic deletion of the long isoform of the von Hippel-Lindau tumour suppressor gene product alters microtubule dynamics

The von Hippel-Lindau tumour suppressor protein (pVHL) controls distinct cellular responses ranging from targeting hypoxia inducible factor α (HIFα) subunits for degradation and promotion of chromosomal stability to the regulation of microtubule dynamics. pVHL is produced in mammalian cells as a long and a short isoform, derived from alternate translational initiation sites in a single Vhl mRNA. However, it is unclear whether these isoforms have different cell biological activities that may represent different tumour suppressor activities of pVHL. Through a knock-in strategy to mutate the first translational initiation site from methionine to leucine (M1L) we have genetically deleted the pVHL long protein isoform in mice, allowing dissection of isoform-specific functions of pVHL. Vhl(M1L/M1L) mice exhibit no obvious phenotypic abnormalities. While numerous pVHL-mediated activities, including degradation of HIFα transcription factors, are unaffected, microtubule dynamics are altered in primary cells derived from Vhl(M1L/M1L) mice to an extent similar to that seen following complete loss of pVHL function. We conclude that the microtubule-regulating function and the HIFα-regulating function of pVHL are separable activities mediated by different protein isoforms

Unstructured hydrophilic sequences in prokaryotic proteomes correlate with dehydration tolerance and host association

Water loss or desiccation is among the most life-threatening stresses. It leads to DNA double-strand breakage, protein aggregation, cell shrinkage, and low water activity precluding all biological functions. Yet, in all kingdoms of life, rare organisms are resistant to desiccation through prevention or reversibility of such damage. Here, we explore possible hallmarks of prokaryotic desiccation tolerance in their proteomes. The content of unstructured, low complexity (LC) regions was analyzed in a total of 460 bacterial and archaeal proteomes. It appears that species endowed with proteomes abundant in unstructured hydrophilic LC regions are desiccation-tolerant or sporulating bacteria, halophilic archaea and bacteria, or host-associated species. In the desiccation- and radiation-resistant bacterium Deinococcus radiodurans, most proteins that contain large hydrophilic LC regions have unassigned function, but those with known function are mostly involved in diverse cellular recovery processes. Such LC regions are typically absent in orthologous proteins in desiccation-sensitive species. D. radiodurans encodes also special LC proteins, akin to those associated with desiccation resistance of plant seeds and some plants and animals. Therefore, we postulate that large unstructured hydrophilic LC regions and proteins provide for cellular resistance to dehydration and we discuss mechanisms of their protective activity.</p

Abundances of environmental phenotypes within the clusters.

<p>The table presents abundances of specific environmental phenotypes. It is hard to infer adaptation to a single condition as the dominant phenotype for each main cluster. Perhaps only one environmental phenotype could be emphasized, and that is halophilicity, which is dominant within the “blue” cluster. The bolded numbers depict phenotypes that are prevailing within the respective clusters, however, they are mainly coupled with another adaptation; e.g. mesophilic methanogens in the “red” cluster or hyperthermoacidophiles in the “yellow” cluster.</p

Heat map visualization of archaeal proteomic properties across phyloecological clusters.

<p>In this heat map, the rows correspond to each species and the columns correspond to the proteomic features; therefore, each row depicts the subset of 5 proteomic features per given archaeon. Normalized values of each feature are associated with the colors in the heat map as shown on the legend on the left side. The cluster tree was built with correlation metric and average linkage, same as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0048231#pone-0048231-g001" target="_blank"><b>Fig. 1</b></a>. Three main phyloecological clusters are highlighted with three different colors of the branches (yellow: hyperthermophiles and hyperthermoacidophiles; blue: halophiles and extreme halophiles; red: mesophilic methanogens and thermoacidophiles).</p

Phyloecological cluster tree of <i>Archaea</i>.

<p><b>A.</b> The cluster tree was built with average linkage of distances based on correlation metric by using the 5-features subset. Cut-off distance for the formation of clusters was 1.0. The tree is divided into three main phyloecological clusters. The first cluster (highlighted in yellow) is comprised of hyperthermophilic species, non-halophilic or halotolerant, and aerobic hyperthermoacidophiles. The members of the second cluster (highlighted in blue) are halophilic and extremely halophilic <i>Archaea</i>, growing in the various temperature ranges (mesophilic, thermophilic or hyperthermophilic values), and conditions of neutral pH or alkaliphilic. The third cluster (highlighted in red) contains mesophilic (mostly methanogens) and thermoacidophilic <i>Archaea</i>, non-halophiles or halotolerant. <b>B.</b> Leaves of the tree display names of phyla for each species from <b>A</b>.</p