The human archain gene, ARCN1, has highly conserved homologs in rice and Drosophila

Cloning and tissue-specific expression of a delta-COP homologue in a freshwater and a brackish water-adapted strain of rainbow trout (Oncorhynchus mykiss)

In eukaryotic cells, intracellular transport is mediated by coated vesicular carriers. Coat proteins I (COPI) vesicles are involved in the retrograde transport from Golgi apparatus to the endoplasmic reticulum. The COPI complex is composed of ADP-ribosylation factor 1 and coatomer comprising seven subunits, termed alpha-zeta. We isolated and characterised a cDNA sequence from rainbow trout homolog to delta-subunit of COPI complex (delta-COP). Trout delta-COP gene encodes a protein of 509 aa including a characteristic Mu homology domain. Searches at the Ensemble Genome browser identified three additional teleostean delta-COP-like sequences from pufferfish, rice fish, and stickleback. Sequence identity of piscine delta-COP protein sequences is greater than 84%. Moreover, a phylogenetic analysis indicates that delta-COP protein sequences are strongly conserved among vertebrate species. delta-COP homologue is ubiquitously expressed in trout tissues. Quantitative Real-Time RT-PCR revealed that delta-COP is differentially expressed in liver and gill tissue of two rainbow trout strains, the freshwater strain STEELHEAD and the brackish water-adapted strain BORN.

Towards a proteomic analysis of atopic dermatitis: A two-dimensional-polyacrylamide gel electrophoresis/mass spectrometric analysis of cultured patient-derived fibroblasts

Atopic dermatitis (AD) is a chronic relapsing inflammatory skin disease typically characterized by a distribution of eczematous skin lesions with lichenification, pruritic excoriations, and dry skin with wide varieties of pathophysiologic aspects. Recently, AD was divided into extrinsic and intrinsic forms according to the presence or absence of an allergy. We investigated alterations in protein expression in primary cultured AD cells from the patient biopsy samples by two-dimensional gel electrophoresis (2-DE) and matrix-assisted laser desorption/ionization-time of flight. In the primary cultured fibroblasts, we obtained 31 candidate proteins from the two-dimensional gel image analysis in which 18 proteins were up-regulated, eight proteins were down-regulated and five proteins were post-translationally modified. From these 2-DE results, we found several candidate genes matched proteomic expression patterns by semiquantitative reverse transcription PCR. Since the exact mechanism of atopic alterations in fibroblasts remains unknown, our results may provide new clues to aid in understanding AD.

Microarray gene analysis and expression profiles of Dupuytren's contracture

Dupuytren's disease, although not altogether uncommon, has eluded scientists who have sought to explain the cause of this palmar fibroproliferative disorder. It can lead to severe limitations of hand function if left untreated. This study is the first broad genetic survey using microarray technology to find gene products that are overexpressed or underexpressed in diseased tissues. The authors found 23 genes with levels that differ consistently from control levels. Nine were selected for further verification using reverse transcription-polymerase chain reaction. These genes hold potential promise in explaining some of the demographic trends seen with disease, such as correlation with alcoholism and the striking predisposition for the male gender.

Lotus japonicus gene Ljsbp is highly conserved among plants and animals and encodes a homologue to the mammalian selenium-binding proteins

We have isolated and characterized a Lotus japonicus gene (Ljsbp) encoding a putative polypeptide with striking homology to the mammalian 56-kDa selenium-binding protein (SBP). cDNA clones homologous to LjSBP were also isolated from soybean, Medicago sativa, and Arabidopsis thaliana. Comparative expression studies in L japonicus and A. thaliana showed that sbp transcripts are present in various tissues and at different levels. Especially in L japonicus nodules and seedpods and A. thaliana siliques, sbp expression appears to be developmentally up-regulated. sbp Gene transcripts were localized by in situ hybridization in the infected cells and vascular bundles of young nodules, while in mature nodules, low levels of expression were only detected in the parenchymatous cells. Expression of sbp transcripts in young seedpods and siliques was clearly visible in vascular tissues and embryos, while in embryos, low levels of expression were detected in the root epidermis and the vascular bundles. Polyclonal antibodies raised against a truncated LjSBP recombinant protein recognized a polypeptide of about 60 kDa in nodule extracts. Immunohistochemical experiments showed that accumulation of LjSBP occurred in root hairs, in the root epidermis above the nodule primordium, in the phloem of the vasculature, and abundantly in the infected cells of young nodules. Irrespective of the presence of rhizobia, expression of SBP was also observed in root tips, where it was confined in the root epidermis and protophloem cells. We hypothesize that LjSBP may have more than one physiological role and can be implicated in controlling the oxidation/reduction status of target proteins, in vesicular Golgi transport, or both.

Adaptins: the final recount

Adaptins are subunits of adaptor protein (AP) complexes involved in the formation of intracellular transport vesicles and in the selection of cargo for incorporation into the vesicles. In this article, we report the results of a survey for adaptins from sequenced genomes including those of man, mouse, the fruit fly Drosophila melanogaster, the nematode Caenorhabditis elegans, the plant Arabidopsis thaliana, and the yeasts, Saccharomyces cerevisiae and Schizosaccharomyces pombe. We find that humans, mice, and Arabidopsis thaliana have four AP complexes (AP-1, AP-2, AP-3, and AP-4), whereas D. melanogaster, C. elegans, S. cerevisiae, and S. pombe have only three (AP-1, AP-2, and AP-3). Additional diversification of AP complexes arises from the existence of adaptin isoforms encoded by distinct genes or resulting from alternative splicing of mRNAs. We complete the assignment of adaptins to AP complexes and provide information on the chromosomal localization, exon-intron structure, and pseudogenes for the different adaptins. In addition, we discuss the structural and evolutionary relationships of the adaptins and the genetic analyses of their function. Finally, we extend our survey to adaptin-related proteins such as the GGAs and stonins, which contain domains homologous to the adaptins.

Differential gene expression in neoplastic and human papillomavirus-immortalized oral keratinocytes

We have previously demonstrated that normal human oral keratinocytes immortalized by transfection with human papillomavirus type-16 Dna became tumorigenic after exposure to a chemical carcinogen. In an effort to detect differentially regulated genes associated with this transition from the immortal to the malignant phenotype, we employed representational differences analysis (a PCR-coupled subtractive hybridization technique). After analysing 50 colonies, 12 putative messages were identified. Northern analysis comparison using the identified cDNAs as probes was made between normal human oral keratinocyte, papillomavirus-immortalized human oral keratinocytes (HOK-16B), a neoplastic cell line derived from HOK-16B (HOK-16B-BaP-T) and the human oral cancer cell lines Hep-2, SCC-9 and Tu-177. We found that mRNAs encoding for cyclophilin A, c-myc binding protein 1, the heat shock protein 90alpha and one unknown transcript were up-regulated in the oral cancer cell lines analysed as well as in HOK-16B cells. We also detected a downregulation of the mRNAs encoding the skin-derived antileukoproteinase SKALP/elafin, the translationally regulated p23 protein and one unknown transcript. Whether these messages are associated to the neoplastic conversion of human keratinocytes remains to be determined.

Regulation of membrane traffic in animal cells by COPI

Intracellular membrane transport is mediated predominantly by vesicles which bud from one compartment and fuse specifically with the next compartment in the pathway, resulting in delivery of cargo. COPI-coated vesicles were first identified as intermediates in intra-Golgi transport and subsequent work has shown that they are also involved in transport between the endoplasmic reticulum and the Golgi complex. The COPI coat components have been characterised in detail at the molecular level and a role for membrane proteins and lipids in membrane recruitment of COPI has been uncovered. However, precisely how these distinct membrane components regulate coat recruitment is still unclear and is currently a matter for debate. Furthermore, it is still not clear at exactly how many transport steps COPI is involved and whether it mediates secretory transport in the anterograde or retrograde direction or both. This review focuses on our understanding of COPI structure and function and describes recent findings on the sites of action of COPI in animal cells.

Functional domain mapping of the clathrin-associated adaptor medium chains mu1 and mu2

The clathrin-associated adaptors AP-1 and AP-2 are heterotetrameric complexes involved in the recognition of sorting signals present within the cytosolic domain of integral membrane proteins. The medium chains of these complexes, mu1 and mu2, have been implicated in two types of interaction: assembly with the beta1 and beta2 chains of the corresponding complexes and recognition of tyrosine-based sorting signals. In this study, we report the results of a structure-function analysis of the mu1 and mu2 chains aimed at identifying regions of the molecules that are responsible for each of the two interactions. Analyses using the yeast two-hybrid system and proteolytic digestion experiments suggest that mu1 and mu2 have a bipartite structure, with the amino-terminal one-third (residues 1-145 of mu1 and mu2) being involved in assembly with the beta chains and the carboxyl-terminal two-thirds (residues 147-423 of mu1 and 164-435 of mu2) binding tyrosine-based sorting signals. These observations support a model in which the amino-terminal one-third of mu2 is embedded within the core of the AP-2 complex, while the carboxyl-terminal two-thirds of the protein are exposed to the medium, placing this region in a position to interact with tyrosine-based sorting signals.

Architecture of coatomer: molecular characterization of delta-COP and protein interactions within the complex

Coatomer is a cytosolic protein complex that forms the coat of COP I-coated transport vesicles. In our attempt to analyze the physical and functional interactions between its seven subunits (coat proteins, [COPs] alpha-zeta), we engaged in a program to clone and characterize the individual coatomer subunits. We have now cloned, sequenced, and overexpressed bovine alpha-COP, the 135-kD subunit of coatomer as well as delta-COP, the 57-kD subunit and have identified a yeast homolog of delta-COP by cDNA sequence comparison and by NH2-terminal peptide sequencing. delta-COP shows homologies to subunits of the clathrin adaptor complexes AP1 and AP2. We show that in Golgi-enriched membrane fractions, the protein is predominantly found in COP I-coated transport vesicles and in the budding regions of the Golgi membranes. A knock-out of the delta-COP gene in yeast is lethal. Immunoprecipitation, as well as analysis exploiting the two-hybrid system in a complete COP screen, showed physical interactions between alpha- and epsilon-COPs and between beta- and delta-COPs. Moreover, the two-hybrid system indicates interactions between gamma- and zeta-COPs as well as between alpha- and beta' COPs. We propose that these interactions reflect in vivo associations of those subunits and thus play a functional role in the assembly of coatomer and/or serve to maintain the molecular architecture of the complex.