hsp70 genes in the human genome: Conservation and differentiation patterns predict a wide array of overlapping and specialized functions

<p>Abstract</p> <p>Background</p> <p>Hsp70 chaperones are required for key cellular processes and response to environmental changes and survival but they have not been fully characterized yet. The human <it>hsp70</it>-gene family has an unknown number of members (eleven counted over ten years ago); some have been described but the information is incomplete and inconsistent. A coherent body of knowledge encompassing all family components that would facilitate their study individually and as a group is lacking. Nowadays, the study of chaperone genes benefits from the availability of genome sequences and a new protocol, chaperonomics, which we applied to elucidate the human <it>hsp70 </it>family.</p> <p>Results</p> <p>We identified 47 hsp70 sequences, 17 genes and 30 pseudogenes. The genes distributed into seven evolutionarily distinct groups with distinguishable subgroups according to phylogenetic and other data, such as exon-intron and protein features. The N-terminal ATP-binding domain (ABD) was conserved at least partially in the majority of the proteins but the C-terminal substrate-binding domain (SBD) was not. Nine proteins were typical Hsp70s (65–80 kDa) with ABD and SBD, two were lighter lacking partly or totally the SBD, and six were heavier (>80 kDa) with divergent C-terminal domains. We also analyzed exon-intron features, transcriptional variants and protein structure and isoforms, and modality and patterns of expression in various tissues and developmental stages. Evolutionary analyses, including human <it>hsp70 </it>genes and pseudogenes, and other eukaryotic <it>hsp70 </it>genes, showed that six human genes encoding cytosolic Hsp70s and 27 pseudogenes originated from retro-transposition of HSPA8, a gene highly expressed in most tissues and developmental stages.</p> <p>Conclusion</p> <p>The human <it>hsp70</it>-gene family is characterized by a remarkable evolutionary diversity that mainly resulted from multiple duplications and retrotranspositions of a highly expressed gene, HSPA8. Human Hsp70 proteins are clustered into seven evolutionary Groups, with divergent C-terminal domains likely defining their distinctive functions. These functions may also be further defined by the observed differences in the N-terminal domain.</p

Chaperonin genes on the rise: new divergent classes and intense duplication in human and other vertebrate genomes

<p>Abstract</p> <p>Background</p> <p>Chaperonin proteins are well known for the critical role they play in protein folding and in disease. However, the recent identification of three diverged chaperonin paralogs associated with the human Bardet-Biedl and McKusick-Kaufman Syndromes (BBS and MKKS, respectively) indicates that the eukaryotic chaperonin-gene family is larger and more differentiated than previously thought. The availability of complete genome sequences makes possible a definitive characterization of the complete set of chaperonin sequences in human and other species.</p> <p>Results</p> <p>We identified fifty-four chaperonin-like sequences in the human genome and similar numbers in the genomes of the model organisms mouse and rat. In mammal genomes we identified, besides the well-known CCT chaperonin genes and the three genes associated with the MKKS and BBS pathological conditions, a newly-defined class of chaperonin genes named CCT8L, represented in human by the two sequences CCT8L1 and CCT8L2. Comparative analyses from several vertebrate genomes established the monophyletic origin of chaperonin-like MKKS and BBS genes from the CCT8 lineage. The CCT8L gene originated from a later duplication also in the CCT8 lineage at the onset of mammal evolution and duplicated in primate genomes. The functionality of CCT8L genes in different species was confirmed by evolutionary analyses and in human by expression data. Detailed sequence analysis and structural predictions of MKKS, BBS and CCT8L proteins strongly suggested that they conserve a typical chaperonin-like core structure but that they are unlikely to form a CCT-like oligomeric complex. The characterization of many newly-discovered chaperonin pseudogenes uncovered the intense duplication activity of eukaryotic chaperonin genes.</p> <p>Conclusions</p> <p>In vertebrates, chaperonin genes, driven by intense duplication processes, have diversified into multiple classes and functionalities that extend beyond their well-known protein-folding role as part of the typical oligomeric chaperonin complex, emphasizing previous observations on the involvement of individual CCT monomers in microtubule elongation. The functional characterization of newly identified chaperonin genes will be a challenge for future experimental analyses.</p

Concurrent Kleene Algebra: Free Model and Completeness

Concurrent Kleene Algebra (CKA) was introduced by Hoare, Moeller, Struth and Wehrman in 2009 as a framework to reason about concurrent programs. We prove that the axioms for CKA with bounded parallelism are complete for the semantics proposed in the original paper; consequently, these semantics are the free model for this fragment. This result settles a conjecture of Hoare and collaborators. Moreover, the techniques developed along the way are reusable; in particular, they allow us to establish pomset automata as an operational model for CKA.Comment: Version 2 includes an overview section that outlines the completeness proof, as well as some extra discussion of the interpolation lemma. It also includes better typography and a number of minor fixes. Version 3 incorporates the changes by comments from the anonymous referees at ESOP. Among other things, these include a worked example of computing the syntactic closure by han

Elucidating drivers of oral epithelial dysplasia formation and malignant transformation to cancer using RNAseq

Oral squamous cell carcinoma (OSCC) is a prevalent cancer with poor prognosis. Most OSCC progresses via a non-malignant stage called dysplasia. Effective treatment of dysplasia prior to potential malignant transformation is an unmet clinical need. To identify markers of early disease, we performed RNA sequencing of 19 matched HPV negative patient trios: normal oral mucosa, dysplasia and associated OSCC. We performed differential gene expression, principal component and correlated gene network analysis using these data. We found differences in the immune cell signatures present at different disease stages and were able to distinguish early events in pathogenesis, such as upregulation of many HOX genes, from later events, such as down-regulation of adherens junctions. We herein highlight novel coding and non-coding candidates for involvement in oral dysplasia development and malignant transformation, and speculate on how our findings may guide further translational research into the treatment of oral dysplasia

HSPD1 (Heat Shock 60kDa Protein 1)

The HSPD1 gene encodes a protein known as HSP60 or Hsp60, also commonly referred to as Cpn60. This protein is a molecular chaperone typically localized inside mitochondria where it forms a chaperoning machine with HSP10 (encoded by the HSPE1 gene), also called Cpn10, to assist protein folding inside the organelle. Hsp60 also occurs in the cytosol, plasma-cell membrane, intercellular space, and blood. Its functions in all these extramitochondrial locations are poorly understood. While the canonical functions of Hsp60 are considered to be cytoprotective, anti-stress and maintenance of protein homeostasis, other roles are currently being investigated. For example, Hsp60 participates in the pathogenesis of diseases in various ways in certain types of cancer, and chronic inflammatory and autoimmune pathological conditions. These are considered chaperonopathies by mistake, in which a normal chaperone (normal at least as far as it can be determined by current methods to study the structure of a molecule available only at extremely low concentrations and quantities) turns against the organism instead of protecting it, favouring the growth and dissemination of cancer cells, or the initiation-progression of inflammation, for instance. In addition, Hsp60 mutations cause at least two types of severe genetic chaperonopathies. All this knowledge is expanding nowadays clearly pointing to Hsp60 as a potential target for chaperonotherapy by replacement when it is defective or by inhibition when it is pathogenic

Water induced sediment levitation enhances downslope transport on Mars

On Mars, locally warm surface temperatures (~293 K) occur, leading to the possibility of (transient) liquid water on the surface. However, water exposed to the martian atmosphere will boil, and the sediment transport capacity of such unstable water is not well understood. Here, we present laboratory studies of a newly recognized transport mechanism: “levitation” of saturated sediment bodies on a cushion of vapor released by boiling. Sediment transport where this mechanism is active is about nine times greater than without this effect, reducing the amount of water required to transport comparable sediment volumes by nearly an order of magnitude. Our calculations show that the effect of levitation could persist up to ~48 times longer under reduced martian gravity. Sediment levitation must therefore be considered when evaluating the formation of recent and present-day martian mass wasting features, as much less water may be required to form such features than previously thought

The complete mitochondrial genome of the foodborne parasitic pathogen Cyclospora cayetanensis

Cyclospora cayetanensis is a human-specific coccidian parasite responsible for several food and water-related outbreaks around the world, including the most recent ones involving over 900 persons in 2013 and 2014 outbreaks in the USA. Multicopy organellar DNA such as mitochondrion genomes have been particularly informative for detection and genetic traceback analysis in other parasites. We sequenced the C. cayetanensis genomic DNA obtained from stool samples from patients infected with Cyclospora in Nepal using the Illumina MiSeq platform. By bioinformatically filtering out the metagenomic reads of non-coccidian origin sequences and concentrating the reads by targeted alignment, we were able to obtain contigs containing Eimeria-like mitochondrial, apicoplastic and some chromosomal genomic fragments. A mitochondrial genomic sequence was assembled and confirmed by cloning and sequencing targeted PCR products amplified from Cyclospora DNA using primers based on our draft assembly sequence. The results show that the C. cayetanensis mitochondrion genome is 6274 bp in length, with 33% GC content, and likely exists in concatemeric arrays as in Eimeria mitochondrial genomes. Phylogenetic analysis of the C. cayetanensis mitochondrial genome places this organism in a tight cluster with Eimeria species. The mitochondrial genome of C. cayetanensis contains three protein coding genes, cytochrome (cytb), cytochrome C oxidase subunit 1 (cox1), and cytochrome C oxidase subunit 3 (cox3), in addition to 14 large subunit (LSU) and nine small subunit (SSU) fragmented rRNA genes

Morphological evidence for geologically young thaw of ice on Mars: a review of recent studies using high-resolution imaging data

Liquid water is generally only meta-stable on Mars today; it quickly freezes, evaporates or boils in the cold, dry, thin atmosphere (surface pressure is about 200 times lower than on Earth). Nevertheless, there is morphological evidence that surface water was extensive in more ancient times, including the Noachian Epoch (~4.1 Ga to ~3.7 Ga bp), when large lakes existed and river-like channel networks were incised, and early in the Hesperian Epoch (~3.7 Ga to ~2.9 Ga bp), when megafloods carved enormous channels and smaller fluvial networks developed in association with crater-lakes. However, by the Amazonian Epoch (~3.0 Ga to present), most surface morphogenesis associated with liquid water had ceased, with long periods of water sequestration as ice in the near-surface and polar regions. However, inferences from observations using imaging data with sub-metre pixel sizes indicate that periglacial landscapes, involving morphogenesis associated with ground-ice and/or surface-ice thaw and liquid flows, has been active within the last few million years. In this paper, three such landform assemblages are described: a high-latitude assemblage comprising features interpreted to be sorted clastic stripes, circles and polygons, non-sorted polygonally patterned ground, fluvial gullies, and solifluction lobes; a mid-latitude assemblage comprising gullies, patterned ground, debris-covered glaciers and hillslope stripes; and an equatorial assemblage of linked basins, patterned ground, possible pingos, and channel-and-scarp features interpreted to be retrogressive thaw-slumps. Hypotheses to explain these observations are explored, including recent climate change, and hydrated minerals in the regolith ‘thawing’ to form liquid brines at very low temperatures. The use of terrestrial analogue field sites is also discussed

System analysis and robustness

Software is increasingly embedded in a variety of physical contexts. This imposes new requirements on tools that support the design and analysis of systems. For instance, modeling embedded and cyberphysical systems needs to blend discrete mathematics, which is suitable for modeling digital components, with continuous mathematics, used for modeling physical components. This blending of continuous and discrete creates challenges that are absent when the discrete or the continuous setting are considered in isolation. We consider robustness, that is, the ability of an analysis of a model to cope with small amounts of imprecision in the model. Formally, we identify analyses with monotonic maps between complete lattices (a mathematical framework used for abstract interpretation and static analysis) and define robustness for monotonic maps between complete lattices of closed subsets of a metric space.</p