[YPK1 overexpression resulted salt stress hypersensitivity in Saccharomyces cerevisiae is dependent on TOR1]

Serine/threonine protein kinase YPK1, a homologue of mammalian protein kinase serum and glucocorticoid-inducible kinase (SGK), plays important physiological roles in Saccharomyces cerevisiae. It involves in cell wall maintenance, actin cytoskeleton dynamics, endocytosis, translation during nitrogen starvation and nutrient sensing.

OBJECTIVE

In order to further explore the cellular function of YPK1 and the its transduction pathway.

METHODS

We overexpressed YPK1 in wild type and tor1 mutant cells and monitored the cell growth responding to salt stress.

RESULTS

We found that YPK1 overexpression resulted salt stress hypersensitivity in wild type cells and this hypersensitivity was abolished by tor1 mutant.

CONCLUSION

Our results indicate that YPK1 may interact with target of rapamycin (TOR1) to regulate the salt stress response.

Comparative genomics of elastin: Sequence analysis of a highly repetitive protein

Due to the low complexity associated with their sequences, uncovering the evolutionary and functional relationships in highly repetitive proteins such as elastin, spider silks, resilin and abductin represents a significant challenge. Using the polymeric extracellular protein elastin as a model system, we present a novel computational approach to the study of sequence, function and evolutionary relationships in repetitive proteins. To address the absence of accurate sequence annotation for repetitive proteins such as elastin, we have constructed a new database repository, ElastoDB (http://theileria.ccb.sickkids.ca/elastin), dedicated to the storage and retrieval of elastin sequence- and meta-data. To analyse their sequence relationships we have devised an innovative new method, based on the identification of overrepresented 'fuzzy' motifs. Applying this method to elastin sequences derived from mammals, chicken, Xenopus and zebrafish resulted in the identification of both highly conserved, and taxon and species specific motifs that likely represent important functional and/or structural elements. The relative spacing and organization of these elements suggest that exon duplication events have played an important role in the evolution of elastin. Clustering of similarity profiles generated for sets of exons and introns, revealed a pattern of putative duplication events involving exons 15-30 in mammalian and chicken elastins, exons 20-31 in both zebrafish elastins, exons 15-20 in fugu elastin and exons 35-50 in Xenopus elastin 1. The success of this approach for elastin offers a promising route to the elucidation of sequence, structure, function and evolutionary relationships for many other proteins with sequences of low complexity.

Proline and Glycine Control Protein Self-Organization into Elastomeric or Amyloid Fibrils

Elastin provides extensible tissues, including arteries and skin, with the propensity for elastic recoil, whereas amyloid fibrils are associated with tissue-degenerative diseases, such as Alzheimer's. Although both elastin-like and amyloid-like materials result from the self-organization of proteins into fibrils, the molecular basis of their differing physical properties is poorly understood. Using molecular simulations of monomeric and aggregated states, we demonstrate that elastin-like and amyloid-like peptides are separable on the basis of backbone hydration and peptide-peptide hydrogen bonding. The analysis of diverse sequences, including those of elastin, amyloids, spider silks, wheat gluten, and insect resilin, reveals a threshold in proline and glycine composition above which amyloid formation is impeded and elastomeric properties become apparent. The predictive capacity of this threshold is confirmed by the self-assembly of recombinant peptides into either amyloid or elastin-like fibrils. Our findings support a unified model of protein aggregation in which hydration and conformational disorder are fundamental requirements for elastomeric function.

Differential expression of two tropoelastin genes in zebrafish

Elastin is the extracellular matrix protein responsible for properties of extensibility and elastic recoil in large blood vessels, lung and skin of most vertebrates. Elastin is synthesized as a monomer, tropoelastin, but is rapidly transformed into its final polymeric form in the extracellular matrix. Until recently information on sequence and developmental expression of tropoelastins was limited to mammalian and avian species. We have recently identified and characterized two expressed tropoelastin genes in zebrafish. This was the first example of a species with multiple tropoelastin genes, raising the possibility of differential expression and function of these tropoelastins in elastic tissues of the zebrafish. Here we have investigated the temporal expression and tissue distribution of the two tropoelastin genes in developing and adult zebrafish. Expression was detected early in skeletal cartilage structures of the head, in the developing outflow tract of the heart, including the bulbus arteriosus and the ventral aorta, and in the wall of the swim bladder. While the temporal pattern of expression was similar for both genes, the upregulation of eln2 was much stronger than that of eln1. In general, both genes were expressed and their gene products deposited in most of the elastic tissues examined, with the notable exception of the bulbus arteriosus in which eln2 expression and its gene product was predominant. This finding may represent a sub-specialization of eln2 to provide the unique architecture of elastin and the specific mechanical properties required by this organ.

Sequences and domain structures of mammalian, avian, amphibian and teleost tropoelastins: Clues to the evolutionary history of elastins

Tropoelastin is the monomeric form of elastin, a polymeric extracellular matrix protein responsible for properties of extensibility and elastic recoil in connective tissues of most vertebrates. As an approach to investigate how sequence and structural characteristics of tropoelastin assist in polymeric assembly and account for the elastomeric properties of this polymer, and to better understand the evolutionary history of elastin, we have identified and characterized tropoelastins from frog (Xenopus tropicalis) and zebrafish (Danio rerio), comparing these to their mammalian and avian counterparts. Unlike other species, two tropoelastin genes were expressed in zebrafish. All tropoelastins shared a predominant and characteristic alternating domain arrangement, as well as the fundamental crosslinking sequence motifs. However, zebrafish and frog tropoelastins had several unusual characteristics, including increased exon numbers and protein molecular weights, and decreased hydropathies. For all tropoelastins there was evidence of evolutionary expansion of the proteins by extensive replication of a hydrophobic-crosslinking exon pair. This was particularly apparent for zebrafish and frog tropoelastin genes, where remnants of sequence similarity were also seen in introns flanking the replicated exon pair. While overall alignment of mammalian, avian, frog and zebrafish tropoelastin sequences was not possible because of sequence variability, the C-terminal exon was well-conserved in all species. In addition, good sequence alignment was possible for several exons just upstream of the putative region of replication, suggesting that these conserved domains may represent 'primordial' core sequences present in the ancestral sequence common to all tropoelastins and in some way essential to the structure/function of elastin.

Structural determinants of cross-linking and hydrophobic domains for self-assembly of elastin-like polypeptides

Elastin is a major structural protein found in large blood vessels, lung, ligaments, and skin, imparting the physical properties of extensibility and elastic recoil to these tissues. To achieve the required structural durability of the elastic matrix, the elastin monomer, tropoelastin, undergoes ordered assembly into a covalently cross-linked, fibrillar polymeric structure. Human tropoelastin consists of 34 exons coding for alternating hydrophobic and cross-linking domains. Using a series of well-defined recombinant polypeptides based on human elastin sequences mimicking native elastin, we have previously investigated the role of sequence and context of hydrophobic domains in elastin self-assembly. Here, we demonstrate that the structure of both cross-linking and hydrophobic domains have significant effects on the assembly of these polypeptides. Removing a putative flexible hinge region in the center of a cross-linking domain substantially increased the alpha-helical content and strongly promoted their self-aggregation. However, while trifluoroethanol (TFE) promoted and urea inhibited self-assembly of these polypeptides, these effects were not predominantly due to altered alpha-helicity of the polypeptides. Our results suggest that, while increased alpha helicity also favors this process, the major effect of TFE to promote organized self-assembly of elastin-like polypeptides is likely related to direct effects of this cosolvent on hydrophobic domains. Such simple elastin polypeptide models can provide an important tool for understanding the relationships between sequence, structure, and polymeric assembly of elastin.

Sequence and structure determinants for the self-aggregation of recombinant polypeptides modeled after human elastin

Elastin is a polymeric structural protein that imparts the physical properties of extensibility and elastic recoil to tissues. The mechanism of assembly of the tropoelastin monomer into the elastin polymer probably involves extrinsic protein factors but is also related to an intrinsic capacity of elastin for ordered assembly through a process of hydrophobic self-aggregation or coacervation. Using a series of simple recombinant polypeptides based on elastin sequences and mimicking the unusual alternating domain structure of native elastin, we have investigated the influence of sequence motifs and domain structures on the propensity of these polypeptides for coacervation. The number of hydrophobic domains, their context in the alternating domain structure of elastin, and the specific nature of the hydrophobic domains included in the polypeptides all had major effects on self-aggregation. Surprisingly, in polypeptides with the same number of domains, propensity for coacervation was inversely related to the mean Kyte-Doolittle hydropathy of the polypeptide. Point mutations designed to increase the conformational flexibility of hydrophobic domains had the unexpected effect of suppressing coacervation and promoting formation of amyloid-like fibers. Such simple polypeptides provide a useful model system for understanding the relationship between sequence, structure, and mechanism of assembly of polymeric elastin.

Monodithiolene molybdenum(V, VI) complexes: a structural analogue of the oxidized active site of the sulfite oxidase enzyme family

The active sites of the xanthine oxidase and sulfite oxidase enzyme families contain one pterin-dithiolene cofactor ligand bound to a molybdenum atom. Consequently, monodithiolene molybdenum complexes have been sought by exploratory synthesis for structural and reactivity studies. Reaction of [MoO(S(2)C(2)Me(2))(2)](1-) or [MoO(bdt)(2)](1-) with PhSeCl results in removal of one dithiolate ligand and formation of [MoOCl(2)(S(2)C(2)Me(2))](1-) (1) or [MoOCl(2)(bdt)](1-) (2), which undergoes ligand substitution reactions to form other monodithiolene complexes [MoO(2-AdS)(2)(S(2)C(2)Me(2))](1-) (3), [MoO(SR)(2)(bdt)](1-) (R = 2-Ad (4), 2,4,6-Pr(i)(3)C(6)H(2) (5)), and [MoOCl(SC(6)H(2)-2,4,6-Pr(i)(3))(bdt)](1-) (6) (Ad = 2-adamantyl, bdt = benzene-1,2-dithiolate). These complexes have square pyramidal structures with apical oxo ligands, exhibit rhombic EPR spectra, and 3-5 are electrochemically reducible to Mo(IV)O species. Complexes 1-6 constitute the first examples of five-coordinate monodithiolene Mo(V)O complexes; 6 approaches the proposed structure of the high-pH form of sulfite oxidase. Treatment of [MoO(2)(OSiPh(3))(2)] with Li(2)(bdt) in THF affords [MoO(2)(OSiPh(3))(bdt)](1-) (8). Reaction of 8 with 2,4,6-Pr(i)(3)C(6)H(2)SH in acetonitrile gives [MoO(2)(SC(6)H(2)-2,4,6-Pr(i)(3))(bdt)](1-) (9, 55%). Complexes 8 and 9 are square pyramidal with apical and basal oxo ligands. With one dithiolene and one thiolate ligand of a square pyramidal Mo(VI)O(2)S(3) coordination unit, 9 closely resembles the oxidized sites in sulfite oxidase and assimilatory nitrate reductase as deduced from crystallography (sulfite oxidase) and Mo EXAFS. The complex is the first structural analogue of the active sites in fully oxidized members of the sulfite oxidase family. This work provides a starting point for the development of both structural and reactivity analogues of members of this family.

[Trace elements and extracellular matrix]

OBJECTIVE

To investigate the effects of trace elements on the metabolism of extracellular matrix and explore the physiological and pathological mechanism of trauma.

METHODS

Based on the experimental and clinical data, it was studied that the action of trace elements in the metabolism of extracellular matrix in trauma repairing.

RESULTS

During wound healing, the trace elements were the components of many kinds of enzymes, carriers and proteins. They took part in the synthesis of hormones and vitamins as well as the transmission of information system. They activated many different kinds of enzymes and regulate the levels of free radicals. The trace elements had the complicated effects on the synthesis, decompose, deposition and reconstruction of collagen and other extracellular matrix.

CONCLUSION

The trace elements play an important role in regulating the metabolism of extracellular matrix.

Isolation and characterization of skin-type, type I antifreeze polypeptides from the longhorn sculpin, Myoxocephalus octodecemspinosus

The antifreeze polypeptides (AFPs) are found in several marine fish and have been grouped into four distinct biochemical classes (type I-IV). Recently, the new subclass of skin-type, type I AFPs that are produced intracellularly as mature polypeptides have been identified in the winter flounder (Pleuronectes americanus) and the shorthorn sculpin (Myoxocephalus scorpius). This study demonstrates the presence of skin-type AFPs in the longhorn sculpin (Myoxocephalus octodecemspinosus), which produces type IV serum AFPs. Using polymerase chain reaction-based methods, a clone that encoded for a type I AFP was identified. The clone lacked a signal sequence, indicating that the mature polypeptide is produced in the cytosol. A recombinant protein was produced in Escherichia coli and antifreeze activity was characterized. Four individual Ala-rich polypeptides with antifreeze activity were isolated from the skin tissue. One polypeptide was completely sequenced by tandem MS. This study provides the first evidence of a fish species that produces two different biochemical classes of antifreeze proteins (type I and type IV), and enforces the notion that skin-type AFPs are a widespread biological phenomenon in fish.

The rat ortholog of the presumptive flounder antifreeze enhancer-binding protein is a helicase domain-containing protein

The expression of winter flounder liver-type antifreeze protein (wflAFP) genes is tissue-specific and under seasonal and hormonal regulation. The only intron of the major wflAFP gene was demonstrated to be a liver-specific enhancer in both mammalian cell lines and flounder hepatocytes. Element B, the core enhancer sequence, was shown to interact specifically with a liver-enriched transcription factor, CCAAT/enhancer-binding protein alpha (C/EBPalpha), as well as a presumptive antifreeze enhancer-binding protein (AEP). In this study, the identity of the rat AEP ortholog was revealed via its DNA-protein interaction with element B. It is a helicase-domain-containing protein, 988 amino acids in length, and is homologous to mouse Smubp-2, hamster Rip-1 and human Smubp-2. The specific binding between element B and AEP was confirmed by South-Western analysis and gel retardation assays. Residues in element B important to this interaction were identified by methylation interference assays. Mutation on one of the residues disrupted the binding between element B and AEP and its enhancer activity was significantly reduced, suggesting that AEP is essential for the transactivation of the wflAFP gene intron. The rat AEP is ubiquitously expressed in various tissues, and the flounder homolog is present as shown by genomic Southern analysis. The potential role of AEP in regulating the flounder AFP gene expression is discussed.

Oxo/sulfidotungstate(VI) as precursors to W(VI)O2, W(VI)OS, and W(VI)S2 complexes and W(IV)-dithiolene chelate rings

Synthetic models leading to oxosulfidotungsten(VI) groups and dithiolene chelate rings have been investigated. The heterogeneous reaction systems [WO4-nSn]2-/2Ph3SiCl/Me4phen (n = 0-2) in acetonitrile afford the complexes [WQ2(OSiPh3)2(Me4phen)] (1-3) in the indicated yields containing the groups W(VI)O2 (1; 86%), W(VI)O2 (2; 45%), and W(VI)S2 (3; 83%). In the crystalline state these complexes have imposed C2 symmetry, with cis-oxo/sulfido and trans-silyloxide ligands. 1H NMR spectra indicate that this stereochemistry is retained in solution. The colors of 2 (yellow, 367 nm) and 3 (orange, 451 nm) arise from LMCT absorptions at the indicated wavelengths. These results demonstrate that the silylation procedure previously introduced for the preparation of molecules with the Mo(VI)OS group (Thapper, et al. Inorg. Chem. 1999, 38, 4104) extends to tungsten. Methods for the formation of dithiolene chelate rings MS2C2R2 in reactions with sulfide-bound M = Mo or W precursors are summarized. In a known reaction type, 3 and activated acetylenes rapidly form [W(IV)(OSiPh3)2(Me4phen)(S2C2R2)] (R = CO2Me, 4, 83%, and Ph, 5, 98%). In a new reaction type not requiring the isolation of an intermediate, the systems [MO2S2]2-/2Ph3SiCl/Me4phen/PhC=CPh in acetonitrile afford 5 (68%) and [Mo(IV)(OSiPh3)2(Me4phen)(S2C2Ph2)] (6; 61%). Complexes 5 and 6 are isostructural, maintain the trans-silyloxide stereochemistry, and exhibit chelate ring dimensions indicative of ene- 1,2-dithiolate coordination. Reductions in the -1.4 to -1.7 V range are described as metal-centered. It remains to be seen whether the oxo/sulfidotungsten(VI) groups in 1-3 eventuate in the active sites of tungstoenzymes. (Me4phen = 3,4,7,8-tetramethyl-1,10-phenanthroline.)

Vicia root micronucleus assay on the clastogenicity of water samples from the Xiaoqing River in Shandong Province of the People's Republic of China

Vicia root micronucleus assay was used to determine the clastogenicity of water samples from Xiaoqing River that passes through Jinan City. Positive results were obtained from eight water collecting sites. This indicates that the water in most areas of this river was polluted with industrial waste and municipal sewage. Results of this study proves that biomonitoring with Vicia root micronucleus test is an efficient way to assess the water quality of this river.

Skin-type antifreeze protein from the shorthorn sculpin, Myoxocephalus scorpius. Expression and characterization of a Mr 9, 700 recombinant protein

A cDNA clone encoding a presumptive antifreeze protein was isolated from a skin library from shorthorn sculpin, Myoxocephalus scorpius. The clone encodes a 92-residue mature polypeptide (sssAFP-2) without any signal and prosequence, which suggests an intracellular localization. It is the largest alanine-rich, alpha-helical type I antifreeze protein known. A recombinant fusion protein containing an N-terminal-linked His-tag was produced and purified from Escherichia coli. This protein is alpha-helical at 0 degreesC and exhibits significant antifreeze activity. Northern blot and reverse transcription-polymerase chain reaction analyses indicate that sssAFP-2 mRNA has limited tissue distribution and is present in peripheral tissues such as skin and dorsal fin, but is notably absent in the liver. These studies reinforce recent evidence that indicate that the external tissues of cold water marine fishes are major organs for antifreeze protein synthesis and are likely the first line of defense against the threat of freezing.

Identification of nuclear proteins interacting with the liver-specific enhancer B element of the antifreeze protein gene in winter flounder

The intron of the winter flounder antifreeze protein (AFP) gene contains a liver-specific enhancer element B as demonstrated by transient expression in mammalian cells. Element B interacts with rat C/EBPalpha and a novel protein, tentatively designated as the antifreeze enhancer-binding protein (AEP). Present studies revealed that nuclear proteins from the winter flounder liver interact similarly and specifically to element B as shown by footprinting analysis and gel retardation assays. The presence of C/EBP in the flounder liver was confirmed by Western blot analysis. In vitro transcription assays in its homologous system further demonstrated the transactivation activity of the AFP gene intron. The present findings suggest that the mechanisms for regulating liver-specific transcription are evolutionarily conserved.

The skin-type antifreeze protein gene intron of the winter flounder is a ubiquitous enhancer lacking a functional C/EBPalpha binding motif

The winter flounder antifreeze protein (AFP) intron contains a liver-specific enhancer (Element B) which was shown earlier to bind CCAAT/enhancer binding protein (C/EBP)alpha. In contrast, as demonstrated in the present studies, the intron of the skin-type AFP gene acted as a ubiquitous enhancer and contained a TA insertion at similar region to Element B (Element S) which destroyed its interaction with C/EBPalpha. Furthermore, a TA insertion of Element B by site-directed mutagenesis decreased its liver enhancer activity. The presence or absence of C/EBPalpha binding motifs in Element B and Element S, respectively, may provide a mechanism for their differential expression.

The role of CCAAT/enhancer-binding protein alpha and a protein that binds to the activator-protein-1 site in the regulation of liver-specific expression of the winter flounder antifreeze protein gene

Winter flounder, Pleuronectes americanus, produces antifreeze proteins (AFPs) to avoid freezing during winter. The AFP in the blood is synthesized by the liver and its annual level is regulated by environmental factors and somatotropin. The only intron (+106 to +602) of the AFP gene contains putative binding sites for liver-enriched transcription activators. Due to the lack of an appropriate fish liver cell line, a mammalian model system was used to demonstrate the liver-specific enhancer activity of the intron. Deletion analysis of the intron indicated nucleotide sequences between +192 bp and +334 bp were important for the enhancer activity. Further refinement showed that the element B (+303 to +322 bp) resided in this region interacted with proteins from rat nuclear extracts by DNase I footprinting and mobility shift analysis. Gel retardation with competition and supershift experiments defined element B to include binding sites for CCAAT/enhancer binding protein a (C/EBP alpha), a liver-enriched transcription factor, and a novel activator protein-1 (AP-1) site binding protein, designated as antifreeze enhancer binding protein (AEP). Residues important to DNA-protein interaction in element B were mapped by methylation interference. Mutations in element B by site-directed mutagenesis destroyed the enhancer activity of the intron. Ultraviolet crosslinking experiments using element B revealed the specific binding of two proteins of approximately 43 and 80 kDa. The present findings provide a mechanism(s) by which the tissue specificity of AFP gene expression can be achieved. Integration of the present information with the somatotropin-mediated signal transduction pathways has generated a working model for the hormonal regulation and seasonal expression of the AFP gene.