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In the current paper, two presumable mechanisms of protein folding are discussed; one of them, the 'nucleation mechanism', is exemplified by 3β-corner domains containing proteins, while the other, 'structural units mechanism', is exemplified by serine proteases. The analysis of the spatial structure of 3β-corners and of the common features of the amino acid sequences encoding them made it possible to conclude, that 3β-corners are capable of assuming their unique structures on their own and can serve as the nuclei or preformed structural units in the process of protein folding. The high order protein structures may be obtained by the further successive addition of β strands to a 3β-corner acting as a nucleus, according to certain rules and restrictions. On the other hand, 3β-corner may serve as a preformed structural unit, and the association of two 3β-corners may result in the formation of such 3D structures, which can be found in the domains of serine proteases and similar proteins. [ABSTRACT FROM AUTHOR]

Abstract: Aspergillus versicolor is common on moldy building materials. Asp v 13, the principal allergen is produced by strains collected from across Canada. In this paper, we report a 1833bp Asp v 13 open reading frame predicted to encode a protein of 403 amino acids in length with three introns. A BLAST search of Asp v 13, a phylogenic tree calculation and alignment with its homologous proteins from other species indicated that Asp v 13 is a secretory, subtilisin-like serine protease widely distributed in Aspergillus species. His-tagged Asp v 13 was over-expressed in Escherichia coli and purified using Ni-NTA columns with a yield of 1mg/L. Based on immuno binding assay of recombinant protein both antibodies developed against the natural protein, and human sera IgE, the recombinant protein was similar to the natural form. Six IgE- and seven IgG-binding epitopes were also identified with selected human sera along the entire amino acid sequence of Asp v 13. Most residues binding these epitopes are exposed on the surface and correspond to charged regions of the molecule. [Copyright &y& Elsevier]

Abstract: FVII is a vitamin K dependent serine protease that plays a key role in extrinsic coagulation pathway. In this paper, we report the full-length cDNA sequences of rhesus monkey FVII. The full-length cDNA has 2424 bp, and predicts an open reading frame of 1416 bp corresponding to 472 amino acids. The deduced protein sequence of rhesus monkey FVII indicates the functional domains including signal peptide, Gla domain, two EGF domains, and catalytic domain. Rhesus monkey FVII is highly homologous to human FVII with amino acid identity of 91.0%. Comparison of three-dimensional protein structure shows high conservation between them. The important functional sites such as the N-terminal γ-carboxyglutamic acids of the Gla domain, the Ca2+ binding region of the EGF I domain, the TF binding region, the active site binding cleft, and the macromolecular substrate binding exosite of trypsin domain are all well conserved in FVII of rhesus monkey. Prothrombin time test shows rhesus monkey FVII has a similar clotting time with that of human. This study of rhesus monkey FVII might be helpful for understanding the function compatibility of human and rhesus monkey FVII, which is beneficial for the study of xenotransplantation. [Copyright &y& Elsevier]

Background: In this paper, we describe cDNA cloning of a new anionic trypsin and a collagenolytic serine protease from king crab Paralithodes camtschaticus and the elucidation of their primary structures. Constructing the phylogenetic tree of these enzymes was undertaken in order to prove the evolutionary relationship between them. Results: The mature trypsin PC and collagenolytic protease PC contain 237 (Mcalc 24.8 kDa) and 226 amino acid residues (Mcalc 23.5 kDa), respectively. Alignments of their amino acid sequences revealed a high degree of the trypsin PC identity to the trypsin from Penaeus vannamei (approximately 70%) and of the collagenolytic protease PC identity to the collagenase from fiddler crab Uca pugilator (76%). The phylogenetic tree of these enzymes was constructed. Conclusions: Primary structures of the two mature enzymes from P. camtschaticus were obtained and compared with those of other proteolytic proteins, including some enzymes from brachyurans. A phylogenetic analysis was also carried out. These comparisons revealed that brachyurins are closely related to their vertebrate and bacterial congeners, occupy an intermediate position between them, and their study significantly contributes to the understanding of the evolution and function of serine proteases. [ABSTRACT FROM AUTHOR]

Jellyfish is a common toxic zooplankton in ocean. We successfully captured a kind of jellyfish 200 m underwater in Antarctica, and identified it as a jellyfish Cyanea sp. through morphological examination and MT-CO1 phylogenetic analysis. A total of 40,468 unigenes were harvested through transcriptome sequencing. We also successfully annotated 12,955 (32.01%) unigenes with the NR database, 10,882 (26.89%) unigenes with the SWISSPROT database, 4951 (12.23%) unigenes with the GO database, and 4901 (12.11%) unigenes with the KEGG database. In the proteomic analysis, a total of 11,159 peptides and 2630 proteins were harvested using the constructed transcriptome as the database. A number of 771 (29.31%) and 841 (31.98%) proteins were annotated against the GO and KEGG database, respectively. Moreover, a number of 29 toxic proteins matched from the 145 toxin-related unigenes were successfully screened, including 6 metalloproteinases, 4 phospholipases, 2 serine proteases, 1 serine protease inhibitor, 7 toxin-related venom and 9 other toxins. Our study is the first to identify a polar jellyfish Cyanea sp. with transcriptomics and proteomics, and these data can further serve as a public database for the identification of potential polar jellyfish-derived lead compounds feasibly functioning in the cold environment. With increasing discussions on marine biodiversity and global warming, polar species have gradually become a focus for research. To the best of our knowledge, there is only one paper in pubMed about the mitochondrial genome of the Antarctic stalked jellyfish Haliclystus antarcticus Pfeffer. In this study, we captured a type of jellyfish (named BD-4) from the Southern Ocean (60°29′57" S, 52°11′44"W) on the scientific expedition ship "Xue Long" at the end of 2016. Although the samples were stored and transported by the ship at only −20 °C for more than two month, we successfully extracted the total RNA, and performed molecular species identification and combined analyses of de novo transcriptomics and proteomics. In addition to conventional bioinformatics techniques such as GO and KEGG annotation, we screened and listed toxic proteins, aligned the sequences, simulated three-dimensional structures and performed molecular phylogenetic analysis for typical components, including metalloproteinase and serine proteinase. Our study is the first to identify a polar jellyfish Cyanea sp. with de novo transcriptomics and proteomics, and these data can further serve as a public database for the identification of potential polar jellyfish-derived lead compounds. Species identification. (A) Geographical distribution (left) of the jellyfish captured from Antarctica (60°29′57 "S, 52°11′44" W) and image of the jellyfish that was preliminarily named BD-4 (right). The sampling location is marked in red circles. (B) Phylogenetic tree constructed using mtDNA sequences of cytochrome c oxidase subunit I (MT-COI, CO1) by using MEGA 7 with the Neighbor-Joining method. BD-4 is marked with red circles, lophotrochozoa are marked with dark blue circles, cnidaria are marked with light blue circles and the identity values are indicated on the right of each species name. (C) Two amino acid sequences of CO1 from Cyanea tzetlinii and Cyanea capillata aligned with the CO1 amino acids of BD-4 transformed from the DNA sequence by blastx. At the bottom of the columns, asterisks (*) show conserved positions, and colons (:) show conserved substitutions and points. (D) Phylogenetic tree constructed using the CO1 amino acid sequences of BD-4 and 7 other species using using MEGA 7 with the Neighbor-Joining method. BD-4 is marked with red circles, and the identity values are indicated to the right of each species name. Unlabelled Image • We have luckily captured an Antarctic jellyfish by the Chinese "Xuelong" scientific ship, and naturally did the investigations on it by CO1 molecular identification, combined analysis of transcriptomics and proteomics, as well as its toxin screening. The sample is very precious and this study is the first to identify the polar jellyfish, and its toxin screening. • Our study is the first to identify a polar jellyfish Cyanea sp. with transcriptomics and proteomics, and these data can further serve as a public database for the identification of potential polar jellyfish-derived lead compounds that feasibly function well in the cold environment. [ABSTRACT FROM AUTHOR]

Xylem plays a role not only in the transport of water and nutrients but also in the regulation of growth and development through the transport of biologically active substances. In addition to mineral salts, xylem sap contains hormones, organic nutrients and proteins. However, the physiological functions of most of those substances remain unclear. To explore genes involved in xylem sap production, we identified Arabidopsis genes expressed in the root stele of the root hair zone from gene-trap lines by randomly inserting the β-glucuronidase gene into the genome. Among 26 000 gene-trap lines, we found that 10 lines had β-glucuronidase (GUS) staining predominantly in the root stele of the root hair zone and no GUS staining in the shoots. Of these 10 lines, 2 lines showed that gene-trap tags inserted into the promoter region of the same gene, denoted Arabidopsis thaliana subtilase 4.12( AtSBT4.12). Analysis of AtSBT4.12 promoter using an pAtSBT4.12::β-glucuronidase transgenic line showed that the AtSBT4.12 gene was expressed only in the root stele of the root hair zone. AtSBT4.12 expression in roots was increased by application of methyl jasmonate. Subtilase proteins are commonly detected in proteomic analyses of xylem sap from various plant species, including Brassica napus, a relative of Arabidopsis. These results suggest that AtSBT4.12 may be a protein localized in the apoplast of root stele including xylem vessel and involved in stress responses in Arabidopsis roots. [ABSTRACT FROM AUTHOR]