Mechanisms for the incorporation of proteins in membranes and organelles

Protein Misfolding and Aggregation in Proteinopathies: Causes, Mechanism and Cellular Response

Proteins are central to life functions. Alterations in the structure of proteins are reflected in their function. Misfolded proteins and their aggregates present a significant risk to the cell. Cells have a diverse but integrated network of protection mechanisms. Streams of misfolded proteins that cells are continuously exposed to must be continually monitored by an elaborated network of molecular chaperones and protein degradation factors to control and contain protein misfolding problems. Aggregation inhibition properties of small molecules such as polyphenols are important as they possess other beneficial properties such as antioxidative, anti-inflammatory, and pro-autophagic properties and help neuroprotection. A candidate with such desired features is important for any possible treatment development for protein aggregation diseases. There is a need to study the protein misfolding phenomenon so that we can treat some of the worst kinds of human ailments related to protein misfolding and aggregation.

The Recruitment-Secretory Block ("R-SB") Phenomenon and Endoplasmic Reticulum Storage Diseases

In this article, we review the biological and clinical implication of the Recruitment-Secretory Block (“R-SB”) phenomenon. The phenomenon refers to the reaction of the liver with regard to protein secretion in conditions of clinical stimulation. Our basic knowledge of the process is due to the experimental work in animal models. Under basal conditions, the protein synthesis is mainly carried out by periportal (zone 1) hepatocytes that are considered the “professional” synthesizing protein cells. Under stimulation, midlobular and centrolobular (zones 2 and 3) hepatocytes, are progressively recruited according to lobular gradients and contribute to the increase of synthesis and secretion. The block of secretion, operated by exogenous agents, causes intracellular retention of all secretory proteins. The Pi MZ phenotype of Alpha-1-antitrypsin deficiency (AATD) has turned out to be the key for in vivo studies of the reaction of the liver, as synthesis and block of secretion are concomitant. Indeed, the M fraction of AAT is stimulated for synthesis and regularly exported while the Z fraction is mostly retained within the cell. For that reason, the phenomenon has been designated “Recruitment-Secretory Block” (“R-SB”). The “R-SB” phenomenon explains why: (a) the MZ individuals can correct the serum deficiency; (b) the resulting immonohistochemical and electron microscopic (EM) patterns are very peculiar and specific for the diagnosis of the Z mutation in tissue sections in the absence of genotyping; (c) the term carrier is no longer applicable for the heterozygous condition as all Pi MZ individuals undergo storage and the storage predisposes to liver damage. The storage represents the true elementary lesion and consequently reflects the phenotype-genotype correlation; (d) the site and function of the extrahepatic AAT and the relationship between intra and extracellular AAT; (e) last but not least, the concept of Endoplasmic Reticulum Storage Disease (ERSD) and of a new disease, hereditary hypofibrinogenemia with hepatic storage (HHHS). In the light of the emerging phenomenon, described in vitro, namely that M and Z AAT can form heteropolymers within hepatocytes as well as in circulation, we have reviewed the whole clinical and experimental material collected during forty years, in order to evaluate to what extent the polymerization phenomenon occurs in vivo. The paper summarizes similarities and differences between AAT and Fibrinogen as well as between the related diseases, AATD and HHHS. Indeed, fibrinogen gamma chain mutations undergo an aggregation process within the RER of hepatocytes similar to AATD. In addition, this work has clarified the intriguing phenomenon underlying a new syndrome, hereditary hypofibrinogenemia and hypo-APO-B-lipoproteinemia with hepatic storage of fibrinogen and APO-B lipoproteins. It is hoped that these studies could contribute to future research and select strategies aimed to simultaneously correct the hepatocytic storage, thus preventing the liver damage and the plasma deficiency of the two proteins.

Hepatic and Extrahepatic Sources and Manifestations in Endoplasmic Reticulum Storage Diseases

Alpha-1-antitrypsin (AAT) and fibrinogen are secretory acute phase reactant proteins. Circulating AAT and fibrinogen are synthesized exclusively in the liver. Mutations in the encoding genes result in conformational abnormalities of the two molecules that aggregate within the rough endoplasmic reticulum (RER) instead of being regularly exported. That results in AAT-deficiency (AATD) and in hereditary hypofibrinogenemia with hepatic storage (HHHS). The association of plasma deficiency and liver storage identifies a new group of pathologies: endoplasmic reticulum storage disease (ERSD).

The Discovery of Endoplasmic Reticulum Storage Disease. The Connection between an H&E Slide and the Brain

The revolutionary evolution in science and technology over the last few decades has made it possible to face more adequately three main challenges of modern medicine: changes in old diseases, the appearance of new diseases, and diseases that are unknown (mostly genetic), despite research efforts. In this paper we review the road travelled by pathologists in search of a method based upon the use of routine instruments and techniques which once were available for research only. The application to tissue studies of techniques from immunology, molecular biology, and genetics has allowed dynamic interpretations of biological phenomena with special regard to gene regulation and expression. That implies stepwise investigations, including light microscopy, immunohistochemistry, in situ hybridization, electron microscopy, molecular histopathology, protein crystallography, and gene sequencing, in order to progress from suggestive features detectable in routinely stained preparations to more characteristic, specific, and finally, pathognomonic features. Hematoxylin and Eosin (H&E)-stained preparations and appropriate immunohistochemical stains have enabled the recognition of phenotypic changes which may reflect genotypic alterations. That has been the case with hepatocytic inclusions detected in H&E-stained preparations, which appeared to correspond to secretory proteins that, due to genetic mutations, were retained within the rough endoplasmic reticulum (RER) and were deficient in plasma. The identification of this phenomenon affecting the molecules alpha-1-antitrypsin and fibrinogen has led to the discovery of a new field of cell organelle pathology, endoplasmic reticulum storage disease(s) (ERSD). Over fifty years, pathologists have wandered through a dark forest of complicated molecules with strange conformations, and by detailed observations in simple histopathological sections, accompanied by a growing background of molecular techniques and revelations, have been able to recognize and identify arrays of grotesque polypeptide arrangements.

Assistance for Folding of Disease-Causing Plasma Membrane Proteins

An extensive catalog of plasma membrane (PM) protein mutations related to phenotypic diseases is associated with incorrect protein folding and/or localization. These impairments, in addition to dysfunction, frequently promote protein aggregation, which can be detrimental to cells. Here, we review PM protein processing, from protein synthesis in the endoplasmic reticulum to delivery to the PM, stressing the main repercussions of processing failures and their physiological consequences in pathologies, and we summarize the recent proposed therapeutic strategies to rescue misassembled proteins through different types of chaperones and/or small molecule drugs that safeguard protein quality control and regulate proteostasis.

Cell-Inspired All-Aqueous Microfluidics: From Intracellular Liquid-Liquid Phase Separation toward Advanced Biomaterials

Living cells have evolved over billions of years to develop structural and functional complexity with numerous intracellular compartments that are formed due to liquid-liquid phase separation (LLPS). Discovery of the amazing and vital roles of cells in life has sparked tremendous efforts to investigate and replicate the intracellular LLPS. Among them, all-aqueous emulsions are a minimalistic liquid model that recapitulates the structural and functional features of membraneless organelles and protocells. Here, an emerging all-aqueous microfluidic technology derived from micrometer-scaled manipulation of LLPS is presented; the technology enables the state-of-art design of advanced biomaterials with exquisite structural proficiency and diversified biological functions. Moreover, a variety of emerging biomedical applications, including encapsulation and delivery of bioactive gradients, fabrication of artificial membraneless organelles, as well as printing and assembly of predesigned cell patterns and living tissues, are inspired by their cellular counterparts. Finally, the challenges and perspectives for further advancing the cell-inspired all-aqueous microfluidics toward a more powerful and versatile platform are discussed, particularly regarding new opportunities in multidisciplinary fundamental research and biomedical applications.

The topogenic function of S4 promotes membrane insertion of the voltage-sensor domain in the KvAP channel

Voltage-dependent K⁺ (K_V) channels control K⁺ permeability in response to shifts in the membrane potential. Voltage sensing in K_V channels is mediated by the positively charged transmembrane domain S4. The best-characterized K_V channel, KvAP, lacks the distinct hydrophilic region corresponding to the S3-S4 extracellular loop that is found in other K⁺ channels. In the present study, we evaluated the topogenic properties of the transmembrane regions within the voltage-sensing domain in KvAP. S3 had low membrane insertion activity, whereas S4 possessed a unique type-I signal anchor (SA-I) function, which enabled it to insert into the membrane by itself. S4 was also found to function as a stop-transfer signal for retention in the membrane. The length and structural nature of the extracellular S3-S4 loop affected the membrane insertion of S3 and S4, suggesting that S3 membrane insertion was dependent on S4. Replacement of charged residues within the transmembrane regions with residues of opposite charge revealed that Asp⁷² in S2 and Glu⁹³ in S3 contributed to membrane insertion of S3 and S4, and increased the stability of S4 in the membrane. These results indicate that the SA-I function of S4, unique among K⁺ channels studied to date, promotes the insertion of S3 into the membrane, and that the charged residues essential for voltage sensing contribute to the membrane-insertion of the voltage sensor domain in KvAP.

Passenger protein determines translocation versus retention in the endoplasmic reticulum for aromatase expression

Aromatase protein is overexpressed in the breasts of women affected with cancer. In the endoplasmic reticulum (ER), signal sequence and signal anchors (SAs) facilitate translocation and topology of proteins. To understand the function of type-I SAs (SA-Is), we evaluated translocation of aromatase, whose signal anchor follows a hydrophilic region. Aromatase SA-I mediates translocation of a short N-terminal hydrophillic domain to ER lumen and integrates the protein in the membrane, with the remainder of the protein residing in the cytosol. We showed that lack of a signal peptidase cleavage site is not responsible for the stop-transfer function of SA-I. However, SA-I could not block the translocation of a full-length microsomal secretory protein and was cleaved as part of the signal sequence. We propose that interaction between the translocon and the region after the signal anchor plays a critical role in directing the topology of the protein by SA-Is. The positive charges in the signal sequence helped it to override the function of signal anchor. Thus, when signal sequence follows SA-I immediately, the interaction with the translocon is perturbed and topology of the protein in ER is altered. If signal sequence is placed far enough from SA-I, then it does not affect membrane integration of SA-I. In summary, we conclude that it is not just the SA-I, but also the region following it, which together affect function of aromatase SA-I in ER.

Haploinsufficiency of the Sec7 guanine nucleotide exchange factor gea1 impairs septation in fission yeast

Membrane trafficking is essential to eukaryotic life and is controlled by a complex network of proteins that regulate movement of proteins and lipids between organelles. The GBF1/GEA family of Guanine nucleotide Exchange Factors (GEFs) regulates trafficking between the endoplasmic reticulum and Golgi by catalyzing the exchange of GDP for GTP on ADP Ribosylation Factors (Arfs). Activated Arfs recruit coat protein complex 1 (COP-I) to form vesicles that ferry cargo between these organelles. To further explore the function of the GBF1/GEA family, we have characterized a fission yeast mutant lacking one copy of the essential gene gea1 (gea1+/-), the Schizosaccharomyces pombe ortholog of GBF1. The haploinsufficient gea1+/- strain was shown to be sensitive to the GBF1 inhibitor brefeldin A (BFA) and was rescued from BFA sensitivity by gea1p overexpression. No overt defects in localization of arf1p or arf6p were observed in gea1+/- cells, but the fission yeast homolog of the COP-I cargo sac1 was mislocalized, consistent with impaired COP-I trafficking. Although Golgi morphology appeared normal, a slight increase in vacuolar size was observed in the gea1+/- mutant strain. Importantly, gea1+/- cells exhibited dramatic cytokinesis-related defects, including disorganized contractile rings, an increased septation index, and alterations in septum morphology. Septation defects appear to result from altered secretion of enzymes required for septum dynamics, as decreased secretion of eng1p, a β-glucanase required for septum breakdown, was observed in gea1+/- cells, and overexpression of eng1p suppressed the increased septation phenotype. These observations implicate gea1 in regulation of septum breakdown and establish S. pombe as a model system to explore GBF1/GEA function in cytokinesis.

Upstream start codon in segment 4 of North American H2 avian influenza A viruses

H2N2 influenza A virus was the cause of the 1957 pandemic. Due to its constant presence in birds, the H2 subtype remains a topic of interest. In this work, comparison of H2 leader sequences of influenza A segment 4 revealed the presence of an upstream in-frame start codon in a majority of North American avian strains. This AUG is located seven codons upstream of the conventional start codon and is in a good Kozak context. In vivo experiments, using a luciferase reporter gene fused to leader sequences derived from North American avian H2 strains, support the efficient use of the upstream start codon. These results were corroborated by in vitro translation data using full-length segment 4 mRNA. Phylogenic analyses indicate that the upstream AUG, first detected in 1976, is stably nested in the North American avian lineage of H2 strains nowadays. The possible consequences of the upstream AUG are discussed.

Structural diversity and differential light control of mRNAs coding for angiosperm glyceraldehyde-3-phosphate dehydrogenases

Subunits A and B of chloroplast glyceraldehyde-3-phosphate dehydrogenase are synthesized as higher molecular weight precursors when polyadenylylated mRNA from angiosperm seedlings is translated in vitro by wheat germ ribosomes. The in vivo levels of mRNA coding for these precursors are strongly light dependent, and the increase in translational activity stimulated by continuous white light, relative to dark-grown seedlings, is at least 5- to 10-fold for the seven plant species investigated. As opposed to this, light does not seem to change mRNA levels coding for cytosolic glyceraldehyde-3-phosphate dehydrogenase, and the polypeptides synthesized in vitro have the same size as the authentic subunits. In addition, precursors of the chloroplast enzyme were identified for 12 different angiosperm species and compared with their respective subunits synthesized in vivo. The patterns of the in vitro and in vivo products correlate in several major characteristics. They both display a remarkable interspecific heterogeneity with respect to size and number of polypeptides. The peptide extensions of the enzyme precursors calculated from these data vary between 4,000 and 12,000 daltons and seem to fall into three major size classes. The present data demonstrate that chloroplast glyceraldehyde-3-phosphate dehydrogenase, like its cytosolic counterpart, is encoded in the nucleus. Yet, the two dehydrogenases are controlled differently at both the ontogenetic and phylogenetic levels. They follow separate biosynthetic pathways with respect to light regulation, post-translational processing, and transport and also exhibit different evolutionary rates. The fast evolutionary change observed for the chloroplast enzyme contrasts sharply with the conservative structure and sequence of the cytosolic enzyme.

Efficient in vitro import of a cytosolic heat shock protein into pea chloroplasts

In order to further our understanding of the targeting of nuclear-encoded proteins into intracellular organelles, we have investigated the import of chimeric precursor proteins into pea chloroplasts. Two different chimeric precursor proteins were produced by in vitro expression of chimeric genes. One chimeric precursor contained the transit peptide of the small subunit of soybean ribulose 1,5-bisphosphate carboxylase and the mature peptide of the same protein from pea. The second contained the same transit peptide plus 13 amino acids of the pea mature peptide fused to a cytosolic heat shock protein. The extent of import and binding of the two chimeric proteins was examined by using quantitative assays and was compared to the import of pea small subunit precursor. Both precursor proteins imported well into pea chloroplasts, although the extent of import observed with the chimeric small-subunit-heat shock precursor was less than that observed with the soybean-pea small subunit precursor. The heat shock protein alone did not import into nor bind to chloroplasts. The binding of both the chimeric small-subunit-heat shock protein and the soybean-pea small subunit precursor to chloroplasts was physiologically significant, as shown by the fact that when chloroplasts with bound precursors were isolated, these bound precursors could subsequently be imported.

Effects of colchicine on localization of alkaline phosphatase in McA-RH 7777 rat hepatoma cells

We investigated the changes caused by microtubule disruption in cell contact-induced translocation of alkaline phosphatase (ALP) from the Golgi area to the plasma membrane in McA-RH 7777 cells. When the cells were treated with colchicine, the tubular structure of microtubules in the cytoplasm was lost. Colchicine treatment also resulted in the appearance of numerous dots containing mannosidase II (man II) throughout the cytoplasm. Moreover, ALP was distributed in small dots throughout the cytoplasm, as well as in all regions of the plasma membrane, although it was most concentrated at sites of intercellular contact. On the other hand, when the cells were incubated in basal medium after colchicine treatment, large spots containing ALP reappeared in the perinuclear cytoplasm more quickly than the accumulation of small dots containing man II. These findings suggest that colchicine causes disassembly of the Golgi complex into fragments, which scatter throughout the cytoplasm, but that it does not interfere with translocation of ALP to the plasma membrane. Furthermore, cytoplasmic ALP may be localized at sites other than the Golgi complex.

Biosynthesis and assembly of the largest and major intrinsic polypeptide of the small intestinal brush borders

The sucrase-isomaltase complex (SI) of the small intestinal brush border membrane accounts for approximately 9-10% of the intrinsic protein. The isomaltase subunit alone interacts with the membrane directly, via a highly hydrophobic segment at its N-terminal region. This segment has a helical conformation for more than 85% and crosses the membrane twice, the N-terminus being located at the outer, luminal side of the membrane. The sucrase subunit is attached to the membrane solely via its interactions with the isomaltase subunit. The sucrase-isomaltase complex is synthesized as a single, very long (Mr approximately 260 000) polypeptide chain (pro-SI, carrying the two sites of sucrase and isomaltase in an already enzymically active form), with the isomaltase portion corresponding to the N-terminal part of pro-SI. Pro-SI is processed into 'final' SI by pancreatic proteases. Recently the cell-free translation of pro-SI has been achieved in vitro. From a detailed knowledge of the anchoring of SI (and pro-SI) in the membrane it has been possible to suggest one particular mechanism as the most likely for the synthesis, insertion and assembly of pro-SI.

Biosynthesis and transport of plasma membrane glycoproteins in the rat intestinal epithelial cell: studies with sucrase-isomaltase

Sucrase-isomaltase (SI), an integral heterodimeric glycoprotein of the intestinal microvillus membrane, is synthesized as a single enzymically active precursor protein (pro-SI) of high relative molecular mass. After glycosylation in the Golgi complex pro-SI is transferred to the microvillus membrane where it is cleaved into the two subunits by pancreatic elastase. Pro-SI was purified by monoclonal antibody-affinity chromatography from microvillus membranes of fetal intestinal transplants in which SI is found exclusively in the non-cleaved precursor form. The N-terminal amino acid sequence of pro-SI was identical to that of the isomaltase subunit of SI which anchors the mature enzyme complex to the lipid bilayer, but it differed from the N-terminal sequence of the sucrase subunit of SI. This structural comparison indirectly gave insight into the mechanisms of membrane insertion and assembly of pro-SI during its biosynthesis. Subcellular fractionation studies indicate transient structural association of newly synthesized pro-SI with the basolateral membrane on its transfer from the Golgi complex to the microvillus membrane, suggesting that part of the basolateral membrane or its associated structures might be involved in the sorting-out processes of microvillar membrane proteins. This concept may have general relevance for the mechanisms of membrane insertion, intracellular transport and sorting of other microvillar membrane glycoproteins in the intestinal epithelial cell.

Problems in intracellular membrane traffic

Eukaryotic cells operate an extensive and well regulated traffic of membrane-bound vesicles to: (a) transport intracellularly, and eventually discharge by exocytosis, macromolecular products; (b) take up by endocytosis molecules and particles from the environment; (c) transport macromolecules across epithelial barriers; and (d) move membranes from their site of assembly to their final locations. Vesicular transport appears to be the equivalent of a discontinuous circulatory system in which vesicles recycle between the termini of each transport pathway, so that balanced membrane distribution is maintained among cell compartments and the cell's surface. Although the general outline of the process is reasonably clear, much remains to be learned about the number and types of pathways, the types and quantities of membranes, and the rates of vesicular movement. Since each vesicular carrier finds its specific terminus (and fuses with it), vesicular traffic is strictly controlled. By analogy with the control of intracellular protein traffic, it may be assumed that vesicular traffic is regulated by the mutual recognition of protein signals and receptors affixed, in this case, with appropriate asymmetry to the surface of the interacting membranes. Since vesicular transport operates without loss of specific chemistry and function of various cellular membranes, cells can counteract effectively the randomization of membrane proteins and lipids, which becomes possible whenever two membranes establish continuity of their fluid bilayers, and when membrane is removed from one or both termini of a recycling pathway. Specific selection of termini and prevention of randomization among membrane components are major unsolved problems in vesicular transport. Their solution in terms of molecular interactions requires further work.

Biogenesis of epithelial cell plasma membranes

Polarized monolayers of cultured epithelial cells, such as the kidney-derived MDCK cell line, when infected with enveloped viruses, provide a convenient model system for study of the intracellular routes followed by newly synthesized glycoproteins to reach specific domains of the plasma membrane. The polarized nature of the monolayers is reflected in the asymmetric assembly of enveloped viruses, some of which, such as influenza and simian virus 5 (SV5), bud from the apical surfaces of the cells, while others, such as vesicular stomatitis virus (VSV), emerge from the basolateral surfaces. MDCK cells can sustain double infection with viruses of different budding polarity, and within such cells the envelope glycoproteins of the two viruses are synthesized simultaneously and assembled into virions at different sites. Immunoelectron microscopic observations of doubly infected cells show that glycoproteins of influenza and VSV traverse the same Golgi apparatus. This indicates that critical sorting steps must take place during or after passage of the glycoproteins through the organelle. Following passage through the Golgi, the HA glycoprotein accumulates almost exclusively at the apical surface, where the influenza virions assemble. Significant amounts of the G protein, however, are detected on both plasma membranes in singly and doubly infected cells, although VSV virion assembly is limited to basolateral domains. These observations indicate that the site of VSV budding is not exclusively determined by the presence of G polypeptides on a given cell-surface domain. It is possible that other cellular or viral components are responsible for the selection of the appropriate budding domain or that the G protein found on the apical surface must be transferred to the basolateral domain before it becomes competent for assembly.

Structure of microvillar enzymes in different phases of their life cycles

Structural changes have been studied during the life cycles of three glycosidases: sucrase-isomaltase (EC 3.2.48-10), lactase-phlorizin hydrolase (EC 3.2.1.23-62), maltase-glucoamylase (EC 3.2.1.20); and three peptidases: aminopeptidase A (EC 3.4.11.7), aminopeptidase N (EC 3.4.11.2) and dipeptidyl peptidase IV (EC 3.4.14.5). The final forms of the enzymes can be divided into at least two groups: the sucrase-isomaltase type, characterized as dimers, which are asymmetric in their hydrophilic parts, have two types of active site and anchor only on one subunit; and the aminopeptidase N type, characterized as dimers, which are symmetric in their hydrophilic part, have only one type of active site and anchor on both subunits. These enzymes are likely to be synthesized on rough endoplasmic reticulum and simultaneously glycosylated into endoglycosidase H-sensitive forms. They are later reglycosylated to endoglycosidase H-resistant forms, which have relative molecular masses similar to the final forms. Enzymes of the sucrase-isomaltase type seem to be synthesized with a polypeptide-chain length corresponding to the sum of both subunits, whereas enzymes of the aminopeptidase N type seem to be synthesized with a polypeptide-chain length corresponding to the constituent subunits themselves. Not much is known about the catabolism of these enzymes. The enzyme activities and the amounts of enzyme protein decrease at the top of the villi, probably due to release into the lumen. The subunits of aminopeptidase N are cleaved by pancreatic proteases to smaller peptides, and sucrase-isomaltase may lose its sucrase polypeptide, while both enzymes remain bound to the membrane.

Chapter 6 Protein Sorting in the Secretory Pathway

This chapter focuses on protein sorting in the secretory pathway. From primary and secondary biosynthetic sites in the cytosol and mitochondrial matrix, respectively, proteins and lipids are distributed to more than 30 final destinations in membranes or membrane-bound spaces, where they carry out their programmed function. Molecular sorting is defined, in its most general sense, as the sum of the mechanisms that determine the distribution of a given molecule from its site of synthesis to its site of function in the cell. The final site of residence of a protein in a eukaryotic cell is determined by a combination of various factors, acting in concert: (1) site of synthesis, (2) sorting signals or zip codes, (3) signal recognition or decoding mechanisms, (4) cotranslational or posttranslational mechanisms for translocation across membranes, (5) specific fusion-fission interactions between intracellular vesicular compartments, and (6) restrictions to the lateral mobility in the plane of the bilayer. Improvements in cell fractionation, protein separation, and immune precipitation procedures in the past decade have made them possible. Very little is known about the mechanisms that mediate the localization and concentration of specific proteins and lipids within organelles. Various experimental model systems have become available for their study. The advent of recombinant DNA technology has shortened the time needed for obtaining the primary structure of proteins to a few months.

Change in localization of alkaline phosphatase and mannosidase II by colchicine treatment of primary cultures of fetal rat hepatocytes

We examined the changes in localization of alkaline phosphatase (ALP) and mannosidase II (man II), a Golgi marker, after colchicine treatment of primary cultures of fetal rat hepatocytes, using double immunofluorescence staining and confocal laser microscopy. In hepatocytes cultured in basal medium, ALP was localized in the perinuclear cytoplasm, and man II was observed in the Golgi region of the cytoplasm. When hepatocytes were cultured in dexamethasone-supplemented medium, ALP was also localized in the plasma membrane surrounding the bile canaliculus-like structure that was formed between adjacent cells. In hepatocytes cultured in the same medium containing colchicine, the structure of microtubules in the cytoplasm was lost, man II exhibited granular distribution scattering throughout the cytoplasm, and ALP was localized in coarse granular sites of the cytoplasm. However, ALP was not colocalized at the same sites as man II. The present study indicated that colchicine inhibits the dexamethasone-promoted translocation of ALP to the plasma membrane surrounding the bile canaliculus-like structure in primary cultures of fetal rat hepatocytes by disassembling microtubules and discomposing the Golgi complex.

Altered protein expression at early-stage rat hepatic neoplasia

Protein expression patterns were analyzed in a rat model of hepatic neoplasia to detect changes reflecting biological mechanism or potential therapeutic targets. The rat resistant hepatocyte model of carcinogenesis was studied, with a focus on the earliest preneoplastic lesion visible in the liver, the preneoplastic hyperplastic nodule. Expression differences were shown by two-dimensional polyacrylamide gel electrophoresis and image analysis. Polypeptide masses were measured by peptide mass fingerprinting using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF) and their sequences were obtained by tandem mass spectrometry. Alterations in expression of cytoskeletal and functional proteins were demonstrated, consistent with biological changes known to occur in the preneoplastic cells. Of particular interest was the differential expression of a serine protease inhibitor (serpin) with a role implicated in angiogenesis. Serpin, implicated in the inhibition of angiogenesis, is present in normal liver but has greatly reduced expression at the preneoplastic stage of liver cancer development. Immunofluorescence microscopy with antibodies to this serpin, kallistatin, supports the proteomic identification. Immunofluorescence microscopy with antibodies to the blood vessel marker von Willebrand factor provides evidence for neovascularization in the liver containing multiple preneoplastic nodules. These observations suggest that at an early stage of liver carcinogenesis reduction or loss of angiogenesis inhibitors may contribute to initiation of neoangiogenesis. A number of other identified proteins known to be associated with hepatomas are also present at early-stage neoplasia.

Characterization and cDNA cloning of aminopeptidase A from the venom of Gloydius blomhoffi brevicaudus

The aminopeptidase activities of snake venoms from Gloydius blomhoffi brevicaudus, Gloydius halys blomhoffii, Trimeresurus flavoviridis, Bothrops jararaca and Crotalus atrox were investigated. Aminopeptidase A (APA), aminopeptidase B and aminopeptidase N activities were present in all snake venoms. The strongest APA activity was found in venom from G. blomhoffi brevicaudus. The susceptibility to metallopeptidase inhibitors and the pH optimum of the partially purified enzyme from G. blomhoffi brevicaudus venom were similar to those of known APAs from mammals. A G. blomhoffi brevicaudus venom gland cDNA library was screened to isolate cDNA clones using probes based on highly conserved amino acid sequences in known APAs. Molecular cloning of APA from G. blomhoffi brevicaudus venom predicted that it was a type II integral membrane protein containing 958 amino acid residues with 17 potential N-linked glycosylation sites. It possessed a His-Glu-Xaa-Xaa-His-(Xaa)(18)-Glu zinc binding motif that allowed the classification of this protein as a member of the M1 family of zinc-metallopeptidases, or gluzincins. The deduced amino acid sequence shows approximately 60% sequence identity to mammalian APA sequences. This is the first study to report the primary structure of APA from a reptile.

Molecular Cloning and Expression of a Novel Cytochrome P450 from Turkey Liver with Aflatoxin B1Oxidizing Activity

Cytochromes P450 are members of a superfamily of oxidative hemoprotein enzymes that metabolize a variety of endogenous and exogenous compounds. Previous studies in our laboratory have shown that efficient P450-mediated activation underlies the extreme sensitivity of poultry, specifically turkeys, to the toxic effects of the mycotoxin aflatoxin B1 (AFB1). Using 3'- and 5'-rapid amplification of cDNA ends (RACE), we amplified from turkey liver RNA a full-length 1.73 kb cDNA predicted to be 528 amino acids with 94.7% sequence identity to a CYP1A5 from chicken liver. A truncated construct of the turkey CYP1A5 gene with 29 amino acids deleted from the hydrophobic NH2-terminal region was cloned and heterologously expressed in Escherichia coli. The expressed protein from E. coli membranes had a CO-binding spectrum typical of P450s, and it catalyzed the O-dealkylation of the CYP1A prototype substrates ethoxyresorufin and methoxyresorufin. CYP1A5-mediated O-dealkylation of methoxyresorufin was completely inhibited by alpha-naphthoflavone, a specific CYP1A inhibitor. Inhibitors to other mammalian P450s (3A4, 2D, 2E, and 3A1) either slightly inhibited this activity or not at all. CYP1A5 oxidized AFB1 to form two metabolites: the reactive intermediate, AFB1 -8,9-epoxide (AFBO), and aflatoxin M1 (AFM1). Because of the importance of AFBO and AFM1 in the toxicity of AFB1, we conclude that this P450 probably plays some role in the well-known hypersensitivity of turkeys to AFB1. To our knowledge, this is the first P450 cloned and sequenced from turkeys, the species in which the toxicity of AFB1 was first discovered.

IN AWE OF SUBCELLULAR COMPLEXITY: 50 Years of Trespassing Boundaries Within the Cell

In this review I describe the several stages of my research career, all of which were driven by a desire to understand the basic mechanisms responsible for the complex and beautiful organization of the eukaryotic cell. I was originally trained as an electron microscopist in Argentina, and my first major contribution was the introduction of glutaraldehyde as a fixative that preserved the fine structure of cells, which opened the way for cytochemical studies at the EM level. My subsequent work on membrane-bound ribosomes illuminated the process of cotranslational translocation of polypeptides across the ER membrane and led to the formulation, with Gunter Blobel, of the signal hypothesis. My later studies with many talented colleagues contributed to an understanding of ER structure and function and aspects of the mechanisms that generate and maintain the polarity of epithelial cells. For this work my laboratory introduced the now widely adopted Madin-Darby canine kidney (MDCK) cell line, and demonstrated the polarized budding of envelope viruses from those cells, providing a powerful new system that further advanced the field of protein traffic.

The C-terminal tail of the gp41 transmembrane envelope glycoprotein of HIV-1 clades A, B, C, and D may exist in two conformations: an analysis of sequence, structure, and function

In addition to the major ectodomain, the gp41 transmembrane glycoprotein of HIV-1 is now known to have a minor ectodomain that is part of the long C-terminal tail. Both ectodomains are highly antigenic, carry neutralizing and non-neutralizing epitopes, and are involved in virus-mediated fusion activity. However, data have so far been biologically based, and derived solely from T cell line-adapted (TCLA), B clade viruses. Here we have carried out sequence and theoretically based structural analyses of 357 gp41 C-terminal sequences of mainly primary isolates of HIV-1 clades A, B, C, and D. Data show that all these viruses have the potential to form a tail loop structure (the minor ectodomain) supported by three, β-sheet, membrane-spanning domains (MSDs). This means that the first (N-terminal) tyrosine-based sorting signal of the gp41 tail is situated outside the cell membrane and is non-functional, and that gp41 that reaches the cell surface may be recycled back into the cytoplasm through the activity of the second tyrosine-sorting signal. However, we suggest that only a minority of cell-associated gp41 molecules – those destined for incorporation into virions – has 3 MSDs and the minor ectodomain. Most intracellular gp41 has the conventional single MSD, no minor ectodomain, a functional first tyrosine-based sorting signal, and in line with current thinking is degraded intracellularly. The gp41 structural diversity suggested here can be viewed as an evolutionary strategy to minimize HIV-1 envelope glycoprotein expression on the cell surface, and hence possible cytotoxicity and immune attack on the infected cell.

Linear motifs: evolutionary interaction switches

Linear motifs are short sequence patterns associated with a particular function. They differ fundamentally from longer, globular protein domains in terms of their binding affinities, evolution and in how they are found experimentally or computationally. In this Minireview, we discuss various aspects of these critically important functional regions.

Identification of microsomal triglyceride transfer protein in intestinal brush-border membrane

Microsomal triglyceride transfer protein (MTP) is a heterodimeric complex consisting of a unique large 97-kDa protein and the multifunctional 58-kDa protein disulfide isomerase (PDI). It plays an essential role in the assembly of lipoproteins by shuttling lipids between phospholipid membranes. Based on cell fractionation, early studies have suggested the endoplasmic reticulum (ER) as the exclusive site of MTP. Focusing on the plasma membrane in this study, our attempts with immunoelectron microscopy and specific antibodies surprisingly revealed that labeling was not exclusively confined to the microsomes of rat absorptive cells. Immunogold labeling was also detected over the microvillus membrane of enterocytes. Western blot analysis and biochemical activity measurement confirmed MTP protein expression in brush-border membrane vesicles (BBMV) isolated from the intestinal epithelial cells of various species. Furthermore, MTP was coexpressed in microvilli membrane with PDI that is crucial to maintain the structure and activity of the MTP complex. The treatment of Caco-2 cells with nocodazole and colchicine blocked the appearance of MTP in the apical membrane. Similarly, the addition of BMS-197636, a known inhibitor of MTP transfer activity, suppressed the latter. In conclusion, the present studies suggest that MTP is present in the brush-border membrane of the enterocyte. Understanding the possible physiological role of MTP in this location may reveal additional functions.

Nodulin 22 from Phaseolus vulgaris protects Escherichia coli cells from oxidative stress

Plant genes that are induced during the formation and function of a root nodule are called nodulin genes. Cloning and functional analysis of nodule-specific gene products are of valuable help in establishing the role and requirements of the host plant for the specificity and effectiveness of the symbiosis. A cDNA clone (nod22) was isolated from Phaseolus vulgaris L. (common bean) cDNA library derived from Rhizobium-infected roots. Nodulin 22 (Nod22) transcripts are accumulated from early to late stages in root nodule development. RT-PCR in situ studies indicated that Nod22 transcripts are highly accumulated in cortical, vascular bundle and infected cells. The deduced Nod22 protein contains a highly hydrophobic N-terminus, with signal peptide characteristics, and a C-terminal extension with high identity to the alpha-crystallin domains found in alpha-crystallin lens chaperone, and other small heat-shock proteins. These domains have not been previously described in other known nodulins, but have been observed in small heat-shock proteins found in plant tissues exposed to elevated temperature and oxidative stress. Nod22, when it is over-expressed in Escherichia coli, cells confers protection against oxidative stress suggesting its possible role in plant host protection from oxidative toxicity during the Rhizobium-legume symbiosis.

Cooperation of transmembrane segments during the integration of a double-spanning protein into the ER membrane

While membrane insertion of single-spanning membrane proteins into the endoplasmic reticulum (ER) is relatively well understood, it is unclear how multi-spanning proteins integrate. We have investigated the cotranslational ER integration of a double-spanning protein that is derived from leader peptidase. Both transmembrane (TM) segments are inserted into the membrane by the Sec61 channel. While the first, long and hydrophobic TM segment (TM1) inserts into the lipid bilayer on its own, the second, shorter TM anchor (TM2) collaborates with TM1 during its integration. TM1 diffuses away from the Sec61 complex in the absence of TM2, but is close to Sec61 when TM2 arrives inside the channel. These data suggest that the exit of a weak TM segment from the Sec61 channel into the lipid phase can be facilitated by its interaction with a previously integrated strong and stabilizing TM anchor.

A novel gene, Btcl1, encoding CUB and LDLa domains is expressed in restricted areas of mouse brain

A variety of secreted and membrane proteins play key roles in the formation of neuronal circuits in the central nervous system. Using the signal sequence trap method, we isolated and characterized a novel gene, Btcl1 (brain-specific transmembrane protein containing two CUB and an LDLa domains). BTCL1 has significant homology with neuropilin-1 and -2 in their CUB domains. Domain structure of BTCL1 indicates that BTCL1 belongs to a new class of brain-specific CUB domain-containing protein. On Northern blot analysis, Btcl1 mRNA was observed as a single transcript of 3.7 kb specifically in the brain. In situ hybridization analysis revealed that Btcl1 mRNA was highly expressed in the hippocampal CA3 region, olfactory bulb, and neocortex in the adult brain. Expression pattern of mRNA and structural similarity with neuropilin suggest that BTCL1 plays a role in the development and/or maintenance of neuronal circuitry.

Progressive truncations C terminal to the membrane-spanning domain of simian immunodeficiency virus Env reduce fusogenicity and increase concentration dependence of Env for fusion

The simian immunodeficiency virus (SIV) transmembrane (TM) protein, gp41, has multiple functions, which include anchoring the glycoprotein complex in the lipid envelope of the virus and mediating fusion of the virus and host cell membranes. Recently, a series of mutants of the SIVmac239 TM protein that have truncations at the carboxyl terminus of the membrane-spanning domain (MSD) have been characterized (J. T. West, P. Johnston, S. R. Dubay, and E. Hunter, J. Virol. 75:9601-9612, 2001). These mutants retained membrane anchorage but demonstrated reduced fusogenicity and infectivity as the MSD length was shortened. We have established a novel three-color fluorescence assay, which allows qualitative confocal and quantitative flow cytometric analyses, to further characterize the nature of the fusion defect in five of the MSD mutants: TM185, TM186, TM187, TM188, and TM189. Our analysis showed that each mutant could mediate complete lipid and aqueous dye transfer at early time points after effector and target cell mixing. No hemifusion with only lipid dye flux was detected. However, another intermediate fusion stage, which appears to involve small-fusion-pore formation that allowed small aqueous dye transfer but prevented the exchange of large cytoplasmic components, was identified infrequently in mutant-Env-expressing cell and target cell mixtures. Quantitative flow cytometric analysis of these mutants demonstrated that the TM187, TM188, and TM189 mutants were significantly more fusogenic than TM185 and TM186 but remained significantly impaired compared to the wild type. Moreover, fusion efficiency showed an increased dependence on the expression level of glycoproteins, suggesting that, for these mutants, formation of an active fusion complex was an increasingly stochastic event.

Challenges for the oral delivery of macromolecules

The rapid integration of new technologies by the pharmaceutical industry has resulted in numerous breakthroughs in the discovery, development and manufacturing of pharmaceutical products. In particular, the commercial-scale production of high-purity recombinant proteins has resulted in important additions to treatment options for many large therapeutic areas. In addition to proteins, other macromolecules, such as the animal-derived mucopolysaccharide heparins, have also seen dramatic growth as injectable pharmaceutical products. To date, macromolecules have been limited as therapeutics by the fact that they cannot be orally delivered. This article will address the current status and future possibilities of oral macromolecular drug delivery.

Co-translational targeting and translocation of the amino terminus of opsin across the endoplasmic membrane requires GTP but not ATP

The tight coupling between ongoing translation and translocation across the mammalian endoplasmic reticulum has made it difficult to determine the requirements that are specific for translocation. We have developed an in vitro assay that faithfully mimics the co-translational targeting and translocation of the amino terminus of opsin without ongoing translation. Using this system we demonstrate that this post-translational targeting and translocation requires nucleotide triphosphates but not cytosolic proteins. The addition of GTP alone was sufficient to fully restore targeting. The addition of ATP was not specifically required, and non-hydrolyzable analogs of ATP that blocked 90% of the ATPase activity also had no inhibitory effect on translocation.

The tenth membrane region of band 3 is initially exposed to the luminal side of the endoplasmic reticulum and then integrated into a partially folded band 3 intermediate

Band 3 is a typical polytopic membrane protein that mediates anion exchange activity [anion exchanger 1 (AE1)]. Although the topology and topogenesis of approximately 40 residues just after transmembrane (TM) 9 have been extensively studied, the topogenesis of this region [tenth region (10thR)] has been unclear. Glycosylation sites created in the 10thR were efficiently glycosylated in a cell-free transcription/translation system, whereas the glycosylation efficiencies were quite low in a cultured cell system. When TM12-14 was deleted or when cycloheximide was added to the culture medium, however, the glycosylation efficiency in the cultured cells increased to the same level as in the cell-free system, indicating that TM12 is essential for the sequestration from oligosaccharyl transferase into membrane and that cycloheximide treatment of the cells can mimic the cell-free system by reducing the rate of chain elongation. The glycosylation efficiency in cultured cells also increased with deletion of TM1-3. These results suggest that the 10thR is transiently extruded into the lumen and then inserted into the membrane. Both TM12 and the distant TM1-3 affect the membrane insertion of the 10thR. This indicates that during the folding of the protein, the 10thR is inserted into the membrane after the TM1-12 segments are properly assembled.

The amino terminus of opsin translocates "posttranslationally" as efficiently as cotranslationally

Opsin, a member of the G-protein-coupled receptor family, is a polytopic membrane protein that does not encode a cleaved amino-terminal signal sequence. The amino terminus of opsin precedes the first known targeting information, suggesting that it translocates across the endoplasmic reticulum (ER) membrane after synthesis, uncoupled from translation. However, translocation across the mammalian ER is believed to be coupled to protein synthesis. In this study we show that opsin, within a range of nascent peptide lengths, targets and translocates equally efficiently co- and posttranslationally. Longer nascent opsin peptides have a lower efficiency of cotranslational translocation but an even lower efficiency of posttranslational translocation. We also show that SRP is required for both co- and posttranslational targeting.

NHE6 protein possesses a signal peptide destined for endoplasmic reticulum membrane and localizes in secretory organelles of the cell

The NHE6 protein is a unique Na(+)/H(+) exchanger isoform believed to localize in mitochondria. It possesses a hydrophilic N-terminal portion that is rich in positively charged residues and many hydrophobic segments. In the present study, signal sequences in the NHE6 molecule were examined for organelle localization and membrane topogenesis. When the full-length protein was expressed in COS7 cells, it localized in the endoplasmic reticulum and on the cell surface. Furthermore, the protein was fully N-glycosylated. When green fluorescent protein was fused after the second (H2) or third (H3) hydrophobic segment, the fusion proteins were targeted to the endoplasmic reticulum (ER) membrane. The localization pattern was the same as that of fusion proteins in which green fluorescent protein was fused after H2 of NHE1. In an in vitro system, H1 behaved as a signal peptide that directs the translocation of the following polypeptide chain and is then processed off. The next hydrophobic segment (H2) halted translocation and eventually became a transmembrane segment. The N-terminal hydrophobic segment (H1) of NHE1 also behaved as a signal peptide. Cell fractionation studies using antibodies against the 15 C-terminal residues indicated that NHE6 protein localized in the microsomal membranes of rat liver cells. All of the NHE6 molecules in liver tissue possess an endoglycosidase H-resistant sugar chain. These findings indicate that NHE6 protein is targeted to the ER membrane via the N-terminal signal peptide and is sorted to organelle membranes derived from the ER membrane.

Interindividual variability in inhibition and induction of cytochrome P450 enzymes

Drug interactions have always been a major concern in medicine for clinicians and patients. Inhibition and induction of cytochrome P450 (CYP) enzymes are probably the most common causes for documented drug interactions. Today, many pharmaceutical companies are predicting potential interactions of new drug candidates. Can in vivo drug interactions be predicted accurately from in vitro metabolic studies? Should the prediction be qualitative or quantitative? Although some scientists believe that quantitative prediction of drug interactions is possible, others are less optimistic and believe that quantitative prediction would be very difficult. There are many factors that contribute to our inability to quantitatively predict drug interactions. One of the major complicating factors is the large interindividual variability in response to enzyme inhibition and induction. This review examines the sources that are responsible for the interindividual variability in inhibition and induction of cytochrome P450 enzymes.

A novel low-density lipoprotein receptor-related protein mediating cellular uptake of apolipoprotein E-enriched beta-VLDL in vitro

We report here the identification of a novel member of the low-density lipoprotein receptor (the LDL receptor) family through signal sequence trap screening of a mouse lymphocyte cDNA library. The protein was termed LDL receptor-related protein 9 (LRP9). LRP9 is a type I membrane protein predicted to contain 696 amino acids with a calculated molecular mass of 74 764 Da. The NH(2)-terminal half of LRP9 contains two CUB domains separated by a single ligand-binding repeat. The second CUB domain is followed by a cluster of three additional ligand-binding repeats and a transmembrane domain. The COOH-terminal intracellular region contains a proline-rich region. LRP9 mRNA was expressed in the liver, kidney, lung, and heart at high levels, and in the spleen and brain at low levels. In situ hybridization analysis of mouse liver, kidney, and brain detected LRP9 transcripts in hepatocytes, sinusoidal lining cells, peritubular capillaries, choroid plexus, ependyma of the third ventricle, pia matter, and hippocampus. In particular, high levels of expression were observed in the vascular walls. Apolipoprotein E (apoE)-enriched beta-VLDL stimulated cellular cholesteryl ester formation in ldl-A7/LRP9. These results raise the possibility that this newly identified receptor, which is expressed in the liver, may play a physiological role in the uptake of apoE-containing lipoproteins.

A mechanistic analysis of carrier-mediated oral delivery of protein therapeutics

This article summarizes the results of a theoretical analysis of protein absorption into the systemic circulation from the small intestine, with and without molecular 'carriers' designed to enhance absorption. The predictions are compared with experimental systemic protein concentrations following intraduodenal delivery of insulin, interferon alpha-2b, and human growth hormone. The results show that, from the standpoint of improving oral absorption, the primary consequence of carrier molecules is to increase epithelial membrane permeability, thereby leading to higher bioavailability. Several possible mechanisms of this permeability enhancement are discussed.

Identification of a cytoplasmic targeting/retention signal in a retroviral Gag polyprotein

Retroviral capsid assembly can occur by either of two distinct morphogenic processes: in type C viruses, the capsid assembles and buds at the plasma membrane, while in type B and D viruses, the capsid assembles within the cytoplasm and is then transported to the plasma membrane for budding. We have previously reported that a single-amino-acid substitution of a tryptophan for an arginine in the matrix protein (MA) of Mason-Pfizer monkey virus (MPMV) converts its capsid assembly from that of a type D retrovirus to that of the type C viruses (S. S. Rhee and E. Hunter, Cell 63:77-86, 1990). Here we identify a region of 18 amino acids within the MA of MPMV that is responsible for type D-specific morphogenesis. Insertion of these 18 amino acids into the MA of type C Moloney murine leukemia virus causes it to assemble an immature capsid in the cytoplasm. Furthermore, fusion of the MPMV MA to the green fluorescent protein resulted in altered intracellular targeting and a punctate accumulation of the fusion protein in the cytoplasm. These 18 amino acids, which are necessary and sufficient to target retroviral Gag polyproteins to defined sites in the cytoplasm, appear to define a novel mammalian cytoplasmic targeting/retention signal.

Recognition of the carboxyl-terminal signal for GPI modification requires translocation of its hydrophobic domain across the ER membrane

A carboxyl-terminal hydrophobic domain is an essential component of the processed signal for attachment of the glycosyl-phosphatidylinositol (GPI) membrane anchor to proteins and it is linked to the site (omega) of GPI modification by a spacer domain. This study was designed to test the hypothesis that the hydrophobic domain interacts with the lipid bilayer of the endoplasmic reticulum (ER) membrane to optimally position the omega site for GPI modification. The hydrophobic domain of the GPI signal in the human folate receptor (FR) type alpha was substituted with the carboxyl-terminal segment of the low-density lipoprotein receptor (LDLR), including its membrane spanning region, without altering either the spacer or the omega site. The FR-alpha/LDLR chimera was not GPI modified but was attached to the plasma membrane by a polypeptide anchor. When the carboxyl-terminal half of the hydrophobic transmembrane polypeptide in the FR-alpha/LDLR chimera was altered by introduction of negatively charged (Asp) residues, or when the cytosolic domain in the chimera was deleted, the mutated proteins became GPI-anchored. On the other hand, attachment of a carboxyl-terminal segment of LDLR including the entire cytosolic domain to FR-alpha converted it into a transmembrane protein. The results indicate that in the FR-alpha/LDLR chimera the inability of the cellular machinery for GPI modification to recognize the hydrophobic domain is not due to the intrinsic nature of the peptide, but is rather due to the retention of the peptide within the lipid bilayer. It follows that the hydrophobic domain in the signal for GPI modification must traverse the ER membrane prior to recognition of the omega site by the GPI-protein transamidase. The results thus establish a critical topographical requirement for recognition of the GPI signal in the ER.