Common Protein Component Research Articles

The cellular protrusions for inter-cellular material transfer: similarities between filopodia, cytonemes, tunneling nanotubes, viruses, and extracellular vesicles.

Extracellular vesicles (EVs) are crucial for transferring bioactive materials between cells and play vital roles in both health and diseases. Cellular protrusions, including filopodia and microvilli, are generated by the bending of the plasma membrane and are considered to be rigid structures facilitating various cellular functions, such as cell migration, adhesion, and environment sensing. Compelling evidence suggests that these protrusions are dynamic and flexible structures that can serve as sources of a new class of EVs, highlighting the unique role they play in intercellular material transfer. Cytonemes are specialized filopodia protrusions that make direct contact with neighboring cells, mediating the transfer of bioactive materials between cells through their tips. In some cases, these tips fuse with the plasma membrane of neighboring cells, creating tunneling nanotubes that directly connect the cytosols of the adjacent cells. Additionally, virus particles can be released from infected cells through small bud-like of plasma membrane protrusions. These different types of protrusions, which can transfer bioactive materials, share common protein components, including I-BAR domain-containing proteins, actin cytoskeleton, and their regulatory proteins. The dynamic and flexible nature of these protrusions highlights their importance in cellular communication and material transfer within the body, including development, cancer progression, and other diseases.

Endoribonucleolytic Cleavage of m6A-Containing RNAs by RNase P/MRP Complex.

N6-methyladenosine (m6A) is the most abundant internal modification in RNAs and plays regulatory roles in a variety of biological and physiological processes. Despite its important roles, the molecular mechanism underlying m6A-mediated gene regulation is poorly understood. Here, we show that m6A-containing RNAs are subject to endoribonucleolytic cleavage via YTHDF2 (m6A reader protein), HRSP12 (adaptor protein), and RNase P/MRP (endoribonucleases). We demonstrate that HRSP12 functions as an adaptor to bridge YTHDF2 and RNase P/MRP, eliciting rapid degradation of YTHDF2-bound RNAs. Transcriptome-wide analyses show that m6A RNAs that are preferentially targeted for endoribonucleolytic cleavage have an HRSP12-binding site and a RNase P/MRP-directed cleavage site upstream and downstream of the YTHDF2-binding site, respectively. We also find that a subset of m6A-containing circular RNAs associates with YTHDF2 in an HRSP12-dependent manner and is selectively downregulated by RNase P/MRP. Thus, our data expand the known functions of RNase P/MRP to endoribonucleolytic cleavage of m6A RNAs.

Comprehensive proteomic profiles of mouse AApoAII amyloid fibrils provide insights into the involvement of lipoproteins in the pathology of amyloidosis

Amyloidosis is a disorder characterized by extracellular fibrillar deposits of misfolded proteins. The amyloid deposits commonly contain several non-fibrillar proteins as amyloid-associated proteins, but their roles in amyloidosis pathology are still unknown. In mouse senile amyloidosis, apolipoprotein A-II (ApoA-II) forms extracellular amyloid fibril (AApoAII) deposits with other proteins (AApoAII-associated proteins) in many organs. We previously reported that R1.P1-Apoa2c mice provide a reproducible model of AApoAII amyloidosis. In order to investigate the sequential alterations of AApoAII-associated protein, we performed a proteomic analysis of amyloid fibrils extracted from mouse liver tissues that contained different levels of AApoAII deposition. We identified 6 AApoAII-associated proteins that constituted 20 of the top-ranked proteins in mice with severe AApoAII deposition. Although the amount of AApoAII-associated proteins increased with the progression of amyloidosis, the relative abundance of AApoAII-associated proteins changed little throughout the progression of amyloidosis. On the other hand, plasma levels of these proteins showed dramatic changes during the progression of amyloidosis. In addition, we confirmed that AApoAII-associated proteins were significantly associated with lipid metabolism based on functional enrichment analysis, and lipids were co-deposited with AApoAII fibrils from early stages of development of amyloidosis. Thus, these results demonstrate that lipoproteins are involved in AApoAII amyloidosis pathology. SignificanceThis study presented proteomic profiles of AApoAII amyloidosis during disease progression and it revealed co-deposition of lipids with AApoAII deposits based on functional analyses. The relative abundance of AApoAII-associated proteins in the amyloid fibril fractions did not change over the course of development of AApoAII amyloidosis pathology. However, their concentrations in plasma changed dramatically with progression of the disease. Interestingly, several AApoAII-associated proteins have been found as constituents of lipid-rich lesions of other degenerative diseases, such as atherosclerosis and age-related macular degeneration. The common protein components among these diseases with lipid-rich deposits could be accounted for by a lipoprotein retention model.

CircRNA-protein complexes: IMP3 protein component defines subfamily of circRNPs.

Circular RNAs (circRNAs) constitute a new class of noncoding RNAs in higher eukaryotes generated from pre-mRNAs by alternative splicing. Here we investigated in mammalian cells the association of circRNAs with proteins. Using glycerol gradient centrifugation, we characterized in cell lysates circRNA-protein complexes (circRNPs) of distinct sizes. By polysome-gradient fractionation we found no evidence for efficient translation of a set of abundant circRNAs in HeLa cells. To identify circRNPs with a specific protein component, we focused on IMP3 (IGF2BP3, insulin-like growth factor 2 binding protein 3), a known tumor marker and RNA-binding protein. Combining RNA-seq analysis of IMP3-co-immunoprecipitated RNA and filtering for circular-junction reads identified a set of IMP3-associated circRNAs, which were validated and characterized. In sum, our data suggest that specific circRNP families exist defined by a common protein component. In addition, this provides a general approach to identify circRNPs with a given protein component.

Podosomes and Invadopodia: Related structures with Common Protein Components that May Promote Breast Cancer Cellular Invasion.

A rate-limiting step in breast cancer progression is acquisition of the invasive phenotype, which can precede metastasis. Expression of cell-surface proteases at the leading edge of a migrating cell provides cells with a mechanism to cross tissue barriers. A newly appreciated mechanism that may be relevant for breast cancer cell invasion is the formation of invadopodia, well-defined structures that project from the ventral membrane and promote degradation of the extracellular matrix, allowing the cell to cross a tissue barrier. Recently, there has been some controversy and discussion as to whether invadopodia, which are associated with carcinoma cells, are related to a similar structure called podosomes, which are associated with normal cells. Invadopodia and podosomes share many common characteristics, including a similar size, shape, subcellular localization and an ability to promote invasion. These two structures also share many common protein components, which we outline herein. It has been speculated that podosomes may be precursors to invadopodia and by extension both structures may be relevant to cancer cell invasion. Here, we compare and contrast the protein components of invadopodia and podosomes and discuss a potential role for these proteins and the evidence that supports a role for invadopodia and podosomes in breast cancer invasion.

Ubiquitin-binding protein p62 is present in neuronal and glial inclusions in human tauopathies and synucleinopathies.

We examined the immunoreactivity of ubiquitin-binding protein p62 and its association with ubiquitin (Ub), alpha-synuclein, and paired helical filament (PHF)-tau in the affected brain areas of human tauopathies and synucleinopathies. Ubiquitin-binding protein p62 is a widely expressed protein that can bind to Ub noncovalently and is involved in several signalling pathways, making p62 a candidate regulator of Ub-mediated proteolysis. We show that p62 immunoreactivity co-localizes with neuronal and glial Ub-containing inclusions in Alzheimer's disease, Pick's disease, dementia with Lewy bodies, Parkinson's disease, and multiple system atrophy. This is the first demonstration of a common protein component, apart from Ub, that is present in both PHF-tau and alpha-synuclein inclusions. In both tauo- and synucleinopathies, the staining patterns for p62 and Ub were markedly similar, suggesting that a common mechanism which requires interaction of p62 and Ub contributes to the formation of PHF-tau and alpha-synuclein inclusions.

Tpx-1 is a component of the outer dense fibers and acrosome of rat spermatozoa.

Previously we reported the cloning of a member of the cysteine-rich secretory protein family, tpx-1, from a testis expression library using an outer dense fiber (ODF)-specific antiserum. Using immunohistochemical and immunoelectron microscopic techniques and Western blotting of purified sperm tail components, we have determined that tpx-1 exists as 25 and 27 kDa proteins in two components of rat spermatid: the ODFs and the acrosome. Tpx-1 mRNA is first expressed in the late pachytene spermatocytes, but the production of these tpx-1 proteins is translationally delayed for 4-5 days before being incorporated into the developing sperm acrosome, surrounding the elongating and condensing spermatid nucleus. Concurrent with sperm head formation, tpx-1 protein was incorporated into the developing sperm tail, and specifically the ODFs. The tpx-1 protein was seen within structures resembling granulated bodies in the cytoplasmic lobe of elongating spermatids and was incorporated subsequently into the growing tail in a manner consistent with ODF development. In addition, tpx-1 protein was localized at the ultrastructural level of the connecting piece of the neck and longitudinal columns of the fibrous sheath, suggesting common protein components in these cytoskeletal structures. As such, tpx-1 may have functional significance in the processes of sperm head development and tail function.

Distinct transport vesicles mediate the delivery of plasma membrane proteins to the apical and basolateral domains of MDCK cells.

Immunoisolation techniques have led to the purification of apical and basolateral transport vesicles that mediate the delivery of proteins from the trans-Golgi network to the two plasma membrane domains of MDCK cells. We showed previously that these transport vesicles can be formed and released in the presence of ATP from mechanically perforated cells (Bennett, M. K., A. Wandinger-Ness, and K. Simons, 1988. EMBO (Euro. Mol. Biol. Organ.) J. 7:4075-4085). Using virally infected cells, we have monitored the purification of the trans-Golgi derived vesicles by following influenza hemagglutinin or vesicular stomatitis virus (VSV) G protein as apical and basolateral markers, respectively. Equilibrium density gradient centrifugation revealed that hemagglutinin containing vesicles had a slightly lower density than those containing VSV-G protein, indicating that the two fractions were distinct. Antibodies directed against the cytoplasmically exposed domains of the viral spike glycoproteins permitted the resolution of apical and basolateral vesicle fractions. The immunoisolated vesicles contained a subset of the proteins present in the starting fraction. Many of the proteins were sialylated as expected for proteins existing the trans-Golgi network. The two populations of vesicles contained a number of proteins in common, as well as components which were enriched up to 38-fold in one fraction relative to the other. Among the unique components, a number of transmembrane proteins could be identified using Triton X-114 phase partitioning. This work provides evidence that two distinct classes of vesicles are responsible for apical and basolateral protein delivery. Common protein components are suggested to be involved in vesicle budding and fusion steps, while unique components may be required for specific recognition events such as those involved in protein sorting and vesicle targeting.

Endoplasmic reticulum contains a common, abundant calcium-binding glycoprotein, endoplasmin.

The most abundant protein in microsomal membrane preparations from mammalian cells has been identified as a 100 X 10(3) Mr concanavalin A-binding glycoprotein. The glycosyl moiety of the glycoprotein is completely sensitive to endoglycosidase H, suggesting a predominantly endoplasmic reticulum localization in the cell. Using a monospecific antibody it was shown by binding and immunofluorescence studies that the glycoprotein is intracellular. Immunoelectron microscopy showed that the glycoprotein was at least 100 times more concentrated in the endoplasmic reticulum than in any other cellular organelle. It was found to be substantially overexpressed in cells and tissues rich in endoplasmic reticulum. Since it is the major common protein component associated with the endoplasmic reticulum we refer to it as endoplasmin. Calcium-binding studies show that endoplasmin is a major calcium-binding protein in cells, suggesting that at least one of its roles might be in the calcium-storage function of the endoplasmic reticulum. The amino-terminal sequence of endoplasmin is identical to that of a 100 X 10(3) Mr stress-related protein.

Structural and immunochemical characterization of human urine arylsulfatase A purified by affinity chromatography

Arylsulfatase A (aryl-sulfate sulfohydrolase, EC 3.1.6.1) was isolated from an ammonium sulfate precipitate of urinary proteins using two different affinity chromatography methods. One method involved the use of concanavalin A-Sepharose affinity chromatography at an early stage of purification, followed by preparative polyacrylamide gel electrophoresis. The other procedure employed arylsulfatase subunit affinity chromatography as the main step and resulted in a remarkably efficient purification. The enzyme had a specific activity of 63 U/mg. The final preparation of arylsulfatase A was homogeneous on the basis of polyacrylamide gel electrophoresis at pH 7.5 and by immunochemical analysis. However, when an enzyme sample obtained by either method of purification was subjected to sodium dodecyl sulfate polyacrylamide gel electrophoresis under reducing or non-reducing conditions, peptide subunits, of 63.5 and 54.5 kDa, were observed. Immunological tests with 125I-labeled enzyme established the presence of a common protein component in both of the electrophoretically separable peptide subunits of human urine arylsulfatase. The amino acid analysis of homogeneous human urine arylsulfatase A showed only a few differences between it and the human liver enzyme. However, immunological cross-reactivity studies using rabbit anti-human urine arylsulfatase revealed immunological difference between the human urine and liver arylsulfatase A enzymes.

Ribosomal recessive suppressors cause a respiratory deficiency in yeast Saccharomyces cerevisiae

Recessive suppressor mutations in yeast Saccharomyces cerevisiae alter a component of the cytoplasmic ribosomes, relaxing the control of translational fidelity. As a consequence ribosomes can misread nonsense codons as amino acids (Surguchov et al. 1980a). The suppressor mutants are often respiratory deficient, being unable to grow on non-fermentable substrates. The study of the cytochrome spectra has revealed that the cytochrome b and aa3 contents were lower in the mutants than in the parent strains. Furthermore, the suppressor mutations often cause hypersensitivity to paromomycin and neomycin on media with a non-fermentable source of carbon. Some of the suppressor mutants exhibited both erythromycin and chloramphenicol-dependent growth on media containing ethanol or glycerol as a sole carbon source. These results suggest that the mutations altering cytoplasmic ribosomes may simultaneously impair the mitochondrial translation. A coupling of cytoplasmic and mitochondrial protein synthesis in yeast cells is proposed. The existence of a common protein component participating both in mitochondrial and cytoplasmic protein synthesis apparatus is discussed.

Catabolism of 3- and 4-hydroxyphenylacetate by the 3,4-dihydroxyphenylacetate pathway in Escherichia coli.

Various strains of Escherichia coli (but not strain K-12) were found to grow on 3-hydroxyphenylacetate and 4-hydroxyphenylacetate. Both compounds were catabolized by the same pathway, with 3,4-dihydroxyphenylacetate as a substrate for fission of the benzene nucleus, and with pyruvate and succinate as products. All the necessay enzymes were demonstrated in cell extracts prepared from induced cells but were essentially absent from uninduced cells. Mutants unable to grow on 3- and 4-hydroxyphenylactetate were defective in particular enzymes of the pathway. The characteristics of certain mutants indicated that either uptake or hydroxylation of 3- and 4-hydroxyphenylacetate may involve a common protein component. E. coli also grew on 3,4-hydroxyphenylacetate, with induction of the enzyme necessary for its degradation but not those for the uptake-hydroxylation of 3- and 4-hydroxyphenylacetate.

Electrophoretic patterns of red-cell membrane protein from various mammalian species.

Summary. Electrophoresis of solubilized red‐cell membrane protein was carried out on eight mammalian species. Haemoglobin‐free membranes were extracted with n‐butanol to obtain the material for study. Four electrophoretic systems were used, viz.: starch gel at pH 3.2 and 8.6 and polyacrylamide disc and flat gels at pH 3.2. All four systems showed similarities as well as differences in the electrophoretic patterns of the species studied. The human and monkey samples showed a similar overall pattern as did those of the bovine, sheep and pig. The results obtained support the hypothesis that certain structural and functional properties common to all membranes owe their similarity to specific common protein components.

Disassembly of T-even bacteriophage into structural parts and subunits

The strength and type of interactions involved in (a) joining the structural parts of T-even bacteriophage, and (b) the formation of the surface lattices of structural parts from subunits were investigated. This was done by monitoring by electron microscopy the disjoining and dissociation of entire phage and of their structural parts. No covalent bonds, including disulfide bonds, were found to be involved. The interactions holding identical protomers and chemical subunits within surface lattices of structural parts could be arranged in a hierarchy of increasing strength: base-plates, tail tubes, capsids, tail fibers and contracted sheaths; this order was independent of the degrading agents used. The attachment of structural parts to each other is much weaker and responds differently to different agents. For example, sheath contraction in which the base-plates move with the contracted sheaths can be induced by many agents, including an anionic detergent. However, sheath contraction in which the base-plate remains at the tip of the tubes can be induced by cationic detergents. Serology and genetics showed that contracted sheaths and polysheaths contain at least one common protein component. The strengths of bonding are very different, with the polysheaths having the weakest and the contracted sheaths having the strongest interactions among the structural parts investigated. Polysheaths were found to contain a core, which could be selectively removed by 0.5 m-guanidine hydrochloride. The possible reassembly of contracted sheaths or polysheaths from subunits was re-investigated. Experimental observation reported previously was confirmed; however, the interpretation of earlier observations was experimentally disproved by the finding that the sheaths recovered were only those sheaths which “survive” the degrading action of alkali. An indication of reassembly of a structural part from dissociated subunits was found only in the case of the tail tube, where the interaction involved is so weak that its subunits can probably be dissociated without being completely denatured.

Ribosomal proteins of bacterial cells: strain- and species-specificity.

Abstract The 50 s ribosomal protein of Escherichia coli labelled with [ 3 H]lysine, and the 30 s protein labelled with [ 14 C]lysine were simultaneously analysed by carboxymethyl-cellulose column chromatography. The results of this study, together with re-analysis by polyacrylamide gel electrophoresis of chromatographically isolated proteins, revealed that the 50 and 30 s subunits which contain respectively at least 15 and 11 main protein components possess almost no common protein components. In addition to the main components several minor protein constituents were detected in both ribosomal subunits. [ 14 C]Lysine-labelled ribosomal protein of E. coli Q13 was compared with [ 3 H]lysine-labelled ribosomal protein of E. coli B by means of chromatography on a carboxymethyl cellulose column. The elution pattern of the 50 s protein was found to be indistinguishable between these two strains, while the 30 s protein of Q13 contained two components which differ chromatographically from those of strain B, the total number of components being the same in each. The same differences in the 30 s protein were found when strains K12 (W1895) and B were compared. The chromatographic comparison of the labelled ribosomal proteins of E. coli and Salmonella abony indicated that the general elution patterns were very similar to each other. Clear differences were however detected in the elution positions of several components of both the 50 s and the 30 s proteins of these two species. [ 3 H]Lysine-labelled protein from Bacillus subtilis ribosomes was compared chromatographically with [ 14 C]lysine-labelled protein from B. megaterium and B. cereus ribosomes to examine the relatedness of species in the genus Bacillus . The results reveal almost no apparent similarities of both the 50 and 30 s proteins among these species. The same situation was found in comparisons of E. coli ribosomal protein with that from several Bacillus species and Sarcina lutea .