scholarly journals Cloning of cDNAs encoding two related 100-kD coated vesicle proteins (alpha-adaptins).

1989 ◽  
Vol 108 (3) ◽  
pp. 833-842 ◽  
Author(s):  
M S Robinson

Coat proteins of approximately 100-kD (adaptins) are components of the adaptor complexes which link clathrin to receptors in coated vesicles. The alpha-adaptins, which are found exclusively in endocytic coated vesicles, separate into two bands on SDS gels, designated A and C (Robinson, M. S., 1987. J. Cell Biol. 104:887-895). Two distinct cDNAs (sequences 1 and 2) encoding the two alpha-adaptins were cloned from a mouse brain cDNA library. Southern blotting indicates that there is one copy of each of the two alpha-adaptin genes, and that there are no additional closely related genes. Based on the size of the predicted protein products of the two genes (108 and 104 kD), the relative abundance of the two messages in brain and liver, and the reactivity of a sequence 1 fusion protein with different antibodies, it was possible to conclude that sequence 1 codes for A and sequence 2 for C. The two protein sequences are strikingly homologous to each other (84% identical amino acids), the major difference being an additional stretch of 41 amino acids, rich in prolines and acidic residues, inserted into the COOH-terminal half of A. In situ hybridization carried out on mouse brain sections indicates that the same cell type may express both transcripts, but that their relative expressions vary. Antipeptide antibodies are now being raised to find out whether the proteins are localized in functionally distinct populations of endocytic coated vesicles.

1998 ◽  
Vol 201 (10) ◽  
pp. 1595-1613 ◽  
Author(s):  
J Prince ◽  
T G Nolen ◽  
L Coelho

The marine snail Aplysia californica obtains its defensive ink exclusively from a diet of red seaweed. It stores the pigment (phycoerythrobilin, the red algal photosynthetic pigment, r-phycoerythrin, minus its protein) in muscular ink-release vesicles within the ink gland. Snails fed a diet of green seaweed or romaine lettuce do not secrete ink and their ink-release vesicles are largely devoid of ink. Successive activation of individual ink-release vesicles by ink motor neurons causes them to secrete approximately 55 % of their remaining ink (similar to the percentage of ink reserves released from the intact gland). The peripheral activation of vesicles appears to be cholinergic: 70 % of isolated vesicles were induced to squeeze ink from their valved end by solutions of acetylcholine at concentrations of 0.5 mmol l-1 or below. Ultrastructural analysis commonly found three cell types in the ink gland. The RER cells, the most numerous, were characterized by an extensive rough endoplasmic reticulum with greatly distended cisternae. This cell type is probably the site for synthesis of the high molecular mass protein of secreted ink. The granulate cells, less common than RER cells, had nuclear and cell areas significantly larger than those of RER cells. In addition, granulate cells of red-algal-fed snails had 4-14 vacuoles that contained electron-dense material with staining characteristics similar to that of ink in mature ink-release vesicles. The granulate cell's plasma membrane was regularly modified into grated areas, which both localized and expanded the surface area for coated vesicle formation and provided a sieve structure that prevented large particles in the hemolymph either from being taken up by, or from occluding, the coated vesicles. Electron-dense particles within coated vesicles were similar in size to those in granulate vacuoles but larger (on average by approximately 1 nm) than those that make up the ink. In green-seaweed-fed snails, granulate cells and their vacuoles were present but the vacuoles were empty. The third cell type, the vesicle cell, expands markedly, with its nucleus enlarging concurrent with cell growth until it is on average 50 times larger in cross-sectional area than the nuclei of either RER or granulate cells; the cytoplasm eventually becomes filled with ink, which obscures the mitochondria, vacuoles and nucleus. Continued cell expansion ceases with the appearance of an encircling layer of muscle and 1-3 layers of cells of unknown origin, thereby becoming the ink-release vesicle itself. The absorption spectra of the soluble contents of mature ink-release vesicles from snails fed red algae had peaks characteristic of the red algal pigment r-phycoerythrin or/and phycoerythrobilin. Immunogold localization of r-phycoerythrin showed no statistical difference in the amount of label within the ink-release vesicles, RER or granulate cell types. Furthermore, there was no localization of phycoerythrin immunoreactivity within the various cellular compartments of either the RER or granulate cells (nucleus, endoplasmic reticulum, mitochondria, vacuoles). Immunogold labeling in the ink gland ranged from 11 to 16 % of that for the digestive vacuoles of the rhodoplast digestive cells lining the tubules of the digestive gland. Our observations suggest (a) that the main form of the ink pigment in the gland is phycoerythrobilin or/and a non-antigenic form of phycoerythrin, and (b) that separation of the bilin from phycoerythrin (or its modification so that it is no longer antigenic) occurs before it reaches the ink gland, probably within the vacuoles of the rhodoplast digestive cells of the digestive gland. We propose the following model. The ink pigment, phycoerythrobilin, is cleaved from its protein in rhodoplast digestive vacuoles in the digestive gland. (ABSTRACT TRUNCATED)


1994 ◽  
Vol 107 (4) ◽  
pp. 945-953 ◽  
Author(s):  
S.E. Holstein ◽  
M. Drucker ◽  
D.G. Robinson

Plant clathrin-coated vesicles (CCV), suitably protected against proteolysis, were isolated from zucchini hypocotyls, and screened for the presence of adaptin-like polypeptides using monoclonal antibodies prepared against alpha, beta(beta') and gamma-adaptins of bovine brain. An immunoreactive polypeptide in plant CCV was only detected in the case of the beta(beta')-adaptin antibody. This polypeptide has a molecular mass of 108 kDa in SDS-PAGE, and gives rise to a major cleavage product of 70 kDa after proteolysis with trypsin. Gel filtration of 0.75 M MgCl2-dissociated coat proteins showed that the plant beta(beta')-type adaptin eluted with other polypeptides in a manner similar to the adaptor complexes of brain CCV. Upon subsequent hydroxyapatite chromatography the immunoreactive polypeptide eluted in fractions corresponding to Golgi (HA-I) rather than plasma membrane (HA-II) brain adaptor complexes. In addition, this polypeptide did not shift to a higher molecular mass when subjected to urea-SDS-PAGE. Confirmation of the presence of a beta-type adaptin in plants was provided by dot and Southern blotting experiments using genomic DNA from zucchini hypocotyls and a beta-adaptin cDNA clone from human fibroblasts.


2012 ◽  
Vol 197 (1) ◽  
pp. 141-160 ◽  
Author(s):  
Georg H.H. Borner ◽  
Robin Antrobus ◽  
Jennifer Hirst ◽  
Gary S. Bhumbra ◽  
Patrycja Kozik ◽  
...  

Despite recent advances in mass spectrometry, proteomic characterization of transport vesicles remains challenging. Here, we describe a multivariate proteomics approach to analyzing clathrin-coated vesicles (CCVs) from HeLa cells. siRNA knockdown of coat components and different fractionation protocols were used to obtain modified coated vesicle-enriched fractions, which were compared by stable isotope labeling of amino acids in cell culture (SILAC)-based quantitative mass spectrometry. 10 datasets were combined through principal component analysis into a “profiling” cluster analysis. Overall, 136 CCV-associated proteins were predicted, including 36 new proteins. The method identified >93% of established CCV coat proteins and assigned >91% correctly to intracellular or endocytic CCVs. Furthermore, the profiling analysis extends to less well characterized types of coated vesicles, and we identify and characterize the first AP-4 accessory protein, which we have named tepsin. Finally, our data explain how sequestration of TACC3 in cytosolic clathrin cages causes the severe mitotic defects observed in auxilin-depleted cells. The profiling approach can be adapted to address related cell and systems biological questions.


BMC Biology ◽  
2020 ◽  
Vol 18 (1) ◽  
Author(s):  
Elin Lundin ◽  
Chenglin Wu ◽  
Albin Widmark ◽  
Mikaela Behm ◽  
Jens Hjerling-Leffler ◽  
...  

Abstract Background Adenosine-to-inosine (A-to-I) RNA editing is a process that contributes to the diversification of proteins that has been shown to be essential for neurotransmission and other neuronal functions. However, the spatiotemporal and diversification properties of RNA editing in the brain are largely unknown. Here, we applied in situ sequencing to distinguish between edited and unedited transcripts in distinct regions of the mouse brain at four developmental stages, and investigate the diversity of the RNA landscape. Results We analyzed RNA editing at codon-altering sites using in situ sequencing at single-cell resolution, in combination with the detection of individual ADAR enzymes and specific cell type marker transcripts. This approach revealed cell-type-specific regulation of RNA editing of a set of transcripts, and developmental and regional variation in editing levels for many of the targeted sites. We found increasing editing diversity throughout development, which arises through regional- and cell type-specific regulation of ADAR enzymes and target transcripts. Conclusions Our single-cell in situ sequencing method has proved useful to study the complex landscape of RNA editing and our results indicate that this complexity arises due to distinct mechanisms of regulating individual RNA editing sites, acting both regionally and in specific cell types.


1990 ◽  
Vol 111 (1) ◽  
pp. 19-29 ◽  
Author(s):  
S Ahle ◽  
E Ungewickell

We have identified a new coat protein in clathrin-coated vesicles from bovine brain by urea-SDS gel electrophoresis. The protein was purified from Tris-solubilized coat proteins either by combination of hydroxyapatite chromatography and gel filtration or more rapidly in a single step by immunoaffinity chromatography. The purified protein binds to clathrin triskelia and thereby promotes clathrin assembly into regular 50-100-nm cages. We propose for the new protein the name auxilin (Latin auxilium, meaning support). Auxilin migrates as a 110-kD polypeptide in standard type SDS-PAGE, but in the presence of 6 M urea shifts to a position corresponding to 126 kD. Gel filtration in 6 M guanidinium hydrochloride gives a molecular weight of approximately 86,000. The native protein is monomeric in 0.5 M Tris. Antigenic reactivity and two-dimensional peptide maps gave no evidence of gross similarities between auxilin and any of the other known coated vesicle-associated proteins. Since the structural organization of auxilin does not resemble that of the ubiquitous heterotetrameric HA1 and HA2 adaptor complexes, that are believed to connect clathrin to receptors, it is unlikely that it functions as an adaptor. Immunoblotting did not reveal the presence of auxilin in tissues other than brain. If auxilin and AP 180 are indeed both confined to neuronal cells, as the immunochemical evidence suggests, it might be inferred that both serve to adapt clathrin-coated vesicles to an as yet undisclosed function unique to this cell type.


Author(s):  
G.P.A. Vigers ◽  
R.A. Crowther ◽  
B.M.F. Pearse

Clathrin forms the polyhedral cage of coated vesicles, which mediate the transfer of selected membrane components within eukaryotic cells. Clathrin cages and coated vesicles have been extensively studied by electron microscopy of negatively stained preparations and shadowed specimens. From these studies the gross morphology of the outer part of the polyhedral coat has been established and some features of the packing of clathrin trimers into the coat have also been described. However these previous studies have not revealed any internal details about the position of the terminal domain of the clathrin heavy chain, the location of the 100kd-50kd accessory coat proteins or the interactions of the coat with the enclosed membrane.


2020 ◽  
Vol 15 (2) ◽  
pp. 121-134 ◽  
Author(s):  
Eunmi Kwon ◽  
Myeongji Cho ◽  
Hayeon Kim ◽  
Hyeon S. Son

Background: The host tropism determinants of influenza virus, which cause changes in the host range and increase the likelihood of interaction with specific hosts, are critical for understanding the infection and propagation of the virus in diverse host species. Methods: Six types of protein sequences of influenza viral strains isolated from three classes of hosts (avian, human, and swine) were obtained. Random forest, naïve Bayes classification, and knearest neighbor algorithms were used for host classification. The Java language was used for sequence analysis programming and identifying host-specific position markers. Results: A machine learning technique was explored to derive the physicochemical properties of amino acids used in host classification and prediction. HA protein was found to play the most important role in determining host tropism of the influenza virus, and the random forest method yielded the highest accuracy in host prediction. Conserved amino acids that exhibited host-specific differences were also selected and verified, and they were found to be useful position markers for host classification. Finally, ANOVA analysis and post-hoc testing revealed that the physicochemical properties of amino acids, comprising protein sequences combined with position markers, differed significantly among hosts. Conclusion: The host tropism determinants and position markers described in this study can be used in related research to classify, identify, and predict the hosts of influenza viruses that are currently susceptible or likely to be infected in the future.


2020 ◽  
Vol 528 (13) ◽  
pp. 2218-2238 ◽  
Author(s):  
Attilio Iemolo ◽  
Patricia Montilla‐Perez ◽  
I‐Chi Lai ◽  
Yinuo Meng ◽  
Syreeta Nolan ◽  
...  

2020 ◽  
Author(s):  
Sumit Handa ◽  
Andres Reyna ◽  
Timothy Wiryaman ◽  
Partho Ghosh

Abstract Diversity-generating retroelements (DGRs) vary protein sequences to the greatest extent known in the natural world. These elements are encoded by constituents of the human microbiome and the microbial ‘dark matter’. Variation occurs through adenine-mutagenesis, in which genetic information in RNA is reverse transcribed faithfully to cDNA for all template bases but adenine. We investigated the determinants of adenine-mutagenesis in the prototypical Bordetella bacteriophage DGR through an in vitro system composed of the reverse transcriptase bRT, Avd protein, and a specific RNA. We found that the catalytic efficiency for correct incorporation during reverse transcription by the bRT-Avd complex was strikingly low for all template bases, with the lowest occurring for adenine. Misincorporation across a template adenine was only somewhat lower in efficiency than correct incorporation. We found that the C6, but not the N1 or C2, purine substituent was a key determinant of adenine-mutagenesis. bRT-Avd was insensitive to the C6 amine of adenine but recognized the C6 carbonyl of guanine. We also identified two bRT amino acids predicted to nonspecifically contact incoming dNTPs, R74 and I181, as promoters of adenine-mutagenesis. Our results suggest that the overall low catalytic efficiency of bRT-Avd is intimately tied to its ability to carry out adenine-mutagenesis.


1951 ◽  
Vol 193 (1) ◽  
pp. 205-217
Author(s):  
MaxE. Rafelson ◽  
RichardJ. Winzler ◽  
HaroldE. Pearson
Keyword(s):  

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