Genomic evidence for the absence of a functional cholesteryl ester transfer protein gene in mice and rats

Mice and rats are naturally deficient in cholesteryl ester transfer protein (CETP) activity, although the reason behind the deficiency in activity is unknown. A search of mouse genome databases revealed sequences resembling 7 of the 16 human exons. However, these sequences could not code for a functional CETP. Analysis of the rat genome using Southern blotting revealed sequences complementary to human CETP cDNA, but RNase protection assays were unable to detect any Cetp gene expression in liver, adipose, or muscle. A search of rat whole-genome shotgun databases revealed exon-like sequences that would be unable to code for a functional CETP. An Ap3s1 pseudogene lay immediately upstream of the CETP-like sequences in mouse, but was nearly identical to the functional gene and unlikely to have been inserted prior to mouse-rat divergence. In contrast, a deletion leading to a nonsense codon was found in the exon 11-like sequences of both rat and mouse and not in any other species. Thus, the lack of CETP activity in both the mouse and the rat is most likely due to an evolutionary event that occurred before these species diverged and not to altered regulation of the gene or function of the gene product.

Similar subunit interactions contribute to assembly of clathrin adaptor complexes and COPI complex: analysis using yeast three-hybrid system

Clathrin adaptor protein (AP) complexes are heterotetramers composed of two large, one medium, and one small subunits. By exploiting the yeast three-hybrid system, we have found that an interaction between the two large subunits of the AP-1 complex, gamma-adaptin and beta1-adaptin, is markedly enhanced in the presence of the small subunit, sigma1. Similarly, two large subunits of the AP-4 complex, epsilon-adaptin and beta4-adaptin, are found to interact with each other only in the presence of the small subunit, sigma4. Furthermore, we have found that an interaction between two large subunits of the COPI F subcomplex, gamma-COP and beta-COP, is detectable only in the presence of zeta-COP. Because these COPI subunits have common ancestral origins to the corresponding AP subunits, these three-hybrid data, taken together with the previous two-hybrid data, suggest that the AP complexes and the COPI F subcomplex assemble by virtue of similar subunit interactions.

Distinct and redundant functions of mu1 medium chains of the AP-1 clathrin-associated protein complex in the nematode Caenorhabditis elegans

In the nematode Caenorhabditis elegans, there exist two micro1 medium chains of the AP-1 clathrin-associated protein complex. Mutations of unc-101, the gene that encodes one of the micro1 chains, cause pleiotropic effects (). In this report, we identified and analyzed the second mu1 chain gene, apm-1. Unlike the mammalian homologs, the two medium chains are expressed ubiquitously throughout development. RNA interference (RNAi) experiments with apm-1 showed that apm-1 and unc-101 were redundant in embryogenesis and in vulval development. Consistent with this, a hybrid protein containing APM-1, when overexpressed, rescued the phenotype of an unc-101 mutant. However, single disruptions of apm-1 or unc-101 have distinct phenotypes, indicating that the two medium chains may have distinct functions. RNAi of any one of the small or large chains of AP-1 complex (sigma1, beta1, or gamma) showed a phenotype identical to that caused by the simultaneous disruption of unc-101 and apm-1, but not that by single disruption of either gene. This suggests that the two medium chains may share large and small chains in the AP-1 complexes. Thus, apm-1 and unc-101 encode two highly related micro1 chains that share redundant and distinct functions within AP-1 clathrin-associated protein complexes of the same tissue.

Fine physical and transcript mapping of a 1.8 Mb region spanning the locus for childhood acute lymphoblastic leukemia on chromosome 12p12. 3

Rearrangements of the short arm of chromosome 12 are frequently observed in hematological disorders. Previous studies of loss of heterozygosity identified a small genetic interval on chromosome 12p12.3 that is frequently deleted in childhood acute lymphoblastic leukemia (ALL). Two genes, ETV6/TEL and p27/KIP1, are located in this interval. Evidence has accumulated that an as-yet unidentified tumor suppressor gene is closely linked to these. To facilitate the identification of candidate genes, a long-range high-resolution restriction map of the ALL locus was constructed using a contig of YAC clones. Several marker loci, including 11 STS, three newly developed YAC end-based STS, six EST, and seven genes were unambiguously positioned in the new map. The map covers 1.8Mb and extends from the distal salivary proline-rich protein gene cluster to the proximal p27/KIP1 gene. The data confirmed the order tel-D12S358-p27/KIP1-cen and excluded p27/KIP1 as a candidate tumor suppressor gene. The critical region delimited by D12S89 and D12S358 is a 750kb CpG-island rich region that includes the 240kb TEL/ETV6 gene as well as CLAPS3 (clathrin-adaptor small chain 3). The new map provides a molecular framework for the identification of novel genes and transcriptional units in the ALL interval.

Interaction of insulin receptor substrate-1 with the sigma3A subunit of the adaptor protein complex-3 in cultured adipocytes

Signaling through the insulin receptor tyrosine kinase involves its autophosphorylation in response to insulin and the subsequent tyrosine phosphorylation of substrate proteins such as insulin receptor substrate-1 (IRS-1). In basal 3T3-L1 adipocytes, IRS-1 is predominantly membrane-bound, and this localization may be important in targeting downstream signaling elements that mediate insulin action. Since IRS-1 localization to membranes may occur through its association with specific membrane proteins, a 3T3-F442A adipocyte cDNA expression library was screened with non-tyrosine-phosphorylated, baculovirus-expressed IRS-1 in order to identify potential IRS-1 receptors. A cDNA clone that encodes sigma3A, a small subunit of the AP-3 adaptor protein complex, was demonstrated to bind IRS-1 utilizing this cloning strategy. The specific interaction between IRS-1 and sigma3A was further verified by in vitro binding studies employing baculovirus-expressed IRS-1 and a glutathione S-transferase (GST)-sigma3A fusion protein. IRS-1 and sigma3A were found to co-fractionate in a detergent-resistant population of low density membranes isolated from basal 3T3-L1 adipocytes. Importantly, the addition of exogenous purified GST-sigma3A to low density membranes caused the release of virtually all of the IRS-1 bound to these membranes, while GST alone had no effect. These results are consistent with the hypothesis that sigma3A serves as an IRS-1 receptor that may dictate the subcellular localization and the signaling functions of IRS-1.

A novel spliced transcript of human CLAPS2 encoding a protein alternative to clathrin adaptor protein AP17

Transcripts of genes encoding proteins of clathrin complexes have been reported to undergo tissue-specific alternative splicing. AP17, encoded by human CLAPS2 cDNA, is the small chain of the major clathrin adaptor complex AP-2 associated with mammalian plasma membranes. In this study, two cDNAs were isolated from a cDNA library of human blood cells. Whereas one cDNA encoded AP17, the other cDNA encoded a putative novel protein variant, termed AP17Delta. Both coding regions were completely sequenced. Consisting of 142aa residues, the predicted protein AP17Delta of 12kDa lacks 38aa residues of AP17. Using specific primers for RT-PCR, mRNAs for AP17Delta and AP17 were found in leukocytes and cultured leukemia cells. The finding of a putative intron in a human EST cDNA clone suggests that mRNAs for AP17 and AP17Delta are formed by alternative splicing. In addition, the identity of human and rat AP17 amino acid sequences is demonstrated.

Identification and characterization of novel clathrin adaptor-related proteins

We have identified a human approximately 87-kDa protein, designated as gamma2-adaptin, that is similar to gamma-adaptin (called gamma1-adaptin in this paper), a large chain of the AP-1 clathrin-associated adaptor complex, not only in the primary structure (60% amino acid identity) but also in the domain organization. Northern blot analysis has shown that its mRNA is expressed in a variety of tissues. Analysis using a yeast two-hybrid system has revealed that, similarly to gamma1-adaptin, gamma2-adaptin is capable of interacting not only with the sigma1 chain (called as sigma1A in this paper), the small chain of the AP-1 complex, but also with a novel sigma1-like protein, designated as sigma1B, which shows an 87% amino acid identity to sigma1A; and that, unlike gamma1-adaptin, it is unable to interact with beta1-adaptin, another large chain of the AP-1 complex. Immunofluorescence microscopy analysis has revealed that gamma2-adaptin is localized to paranuclear vesicular structures that are not superimposed on structures containing gamma1-adaptin. Furthermore, unlike gamma1-adaptin, gamma2-adaptin is recruited onto membranes in the presence of a fungal antibiotic, brefeldin A. These data suggest that gamma2-adaptin constitute a novel adaptor-related complex that participates in a transport step different from that of AP-1.

Characterization of the sequence coding for the clathrin coat assembly protein AP17 (sigma2) associated with the plasma membrane from Zea mays and constitutive expression of its gene

The cDNA and genomic sequences coding for the clathrin coat assembly protein AP17 (sigma2) from maize and its corresponding mRNA accumulation have been analyzed. This protein in yeast and mammals has been shown to be part of the associated protein (AP) complex of clathrin in the plasma membrane. The availability of this sequence as well as a previous AP19 in a plant allows one to propose that specific AP complexes exist in plants in the Golgi complex and in the plasma membrane. The AP17 protein is encoded in maize by a single gene, and its mRNA accumulates in all the organs studied. In the immature embryo, it displays a pattern of expression typical of constitutively expressed genes.

Molecular characterization of the AP19 gene family in Arabidopsis thaliana: components of the Golgi AP-1 clathrin assembly protein complex

AP19 is the smallest polypeptide component of AP-1, the clathrin associated protein complex found in clathrin-coated vesicles of the Golgi apparatus. Two genomic clones that encode homologues of AP19 were isolated from Arabidopsis thaliana (AAP19-1 and AAP19-2). Analysis of their nucleotide sequences predict proteins of 162 and 163 amino acids with mr of 18,913 and 18,758 respectively. Amino acid sequence comparisons with mammalian, yeast and plant clathrin associated sequences indicates that the Arabidopsis genes encode polypeptides that are more closely related to the AP19 proteins associated with clathrin-coated Golgi vesicles than to AP17, which is part of the AP-2 complex of endocytic clathrin-coated pits. Ribonuclease protection assays showed that both genes are expressed in all Arabidopsis tissues throughout development. Constitutive transcription of AAP19-1 was confirmed in transgenic Arabidopsis seedlings and plants containing an AAP19-1 promoter::beta-glucuronidase (GUS) fusion by ribonuclease protection assays and GUS histochemical staining.

AP-3: an adaptor-like protein complex with ubiquitous expression

We have identified two closely related human proteins (sigma3A and sigma3B) that are homologous to the small chains, sigma1 and sigma2, of clathrin-associated adaptor complexes. Northern and Western blot analyses demonstrate that the products of both the sigma3A and sigma3B genes are expressed in a wide variety of tissues and cell lines. sigma3A and sigma3B are components of a large complex, named AP-3, that also contains proteins of apparent molecular masses of 47, 140 and 160 kDa. In non-neuronal cells, the 47 kDa protein most likely corresponds to the medium chain homolog p47A, and the 140 kDa protein is a homolog of the neuron-specific protein beta-NAP. Like other members of the medium-chain family, the p47A chain is capable of interacting with the tyrosine-based sorting signal YQRL from TGN38. Immunofluorescence microscopy analyses show that the sigma3-containing complex is present both in the area of the TGN and in peripheral structures, some of which contain the transferrin receptor. These results suggest that the sigma3 chains are components of a novel, ubiquitous adaptor-like complex involved in the recognition of tyrosine-based sorting signals.

Cloning and expression of a plant homologue of the small subunit of the Golgi-associated clathrin assembly protein AP19 from Camptotheca acuminata

Clathrin-coated vesicles (CCVs) are involved in selective protein transport in eukaryotes. AP-1 and AP-2 are protein complexes found in the CCVs of the Golgi apparatus and the plasma membrane respectively. AP19 is the smallest polypeptide chain components of AP-1. We have identified a cDNA clone (CAP19) encoding a putative homologue for the assembly protein AP19 from the Chinese medicinal tree, Camptotheca acuminata. The deduced polypeptide contains 161 amino acids and has a predicted Mr of 18820. DNA blot analysis suggests that the AP19S of C. acuminata are encoded by a small gene family. CAP19 was expressed ubiquitously throughout the plant suggesting that it may be involved in general Golgi-mediated secretion.

Cloning, expression pattern and mapping to 12p 13.2 --> p13.1 of CLAPS3, a gene encoding a novel clathrin-adaptor small chain

From a human fetal-brain cDNA library we isolated a novel gene encoding a peptide homologous to clathrin-adaptor small chains in rat, mouse, and yeast. The cDNA, designated CLAPS3 (clathrin-associated/assembly/adaptor protein, small 3, 22 kDa), contained an open reading frame of 579 nucleotides encoding 193 amino acids. Northern-blot analysis revealed expression of a 1.35-kb transcript in all human tissues examined. This gene was mapped to chromosome bands 12p13.2 --> p13.1 by FISH.

Human CLAPS2 encoding AP17, a small chain of the clathrin-associated protein complex: cDNA cloning and chromosomal assignment to 19q13.2-->q13.3

We have cloned the cDNA for the human homolog of the rat AP17 gene, a small chain of the clathrin-associated protein complex AP-2. The cDNA is highly conserved between rat and human. Human AP17, gene symbol CLAPS2 (clathrin-associated/assembly/adaptor protein, small 3, 17 kDa), was assigned to chromosome region 19q13.2-->q13.3.

Targeting signals and subunit interactions in coated vesicle adaptor complexes

There are two clathrin-coated vesicle adaptor complexes in the cell, one associated with the plasma membrane and one associated with the TGN. The subunit composition of the plasma membrane adaptor complex is alpha-adaptin, beta-adaptin, AP50, and AP17; while that of the TGN adaptor complex is gamma-adaptin, beta'-adaptin, AP47, and AP19. To search for adaptor targeting signals, we have constructed chimeras between alpha-adaptin and gamma-adaptin within their NH2-terminal domains. We have identified stretches of sequence in the two proteins between amino acids approximately 130 and 330-350 that are essential for targeting. Immunoprecipitation reveals that this region determines whether a construct coassemblies with AP50 and AP17, or with AP47 and AP19. These observations suggest that these other subunits may play an important role in targeting. In contrast, beta- and beta'-adaptins are clearly not involved in this event. Chimeras between the alpha- and gamma-adaptin COOH-terminal domains reveal the presence of a second targeting signal. We have further investigated the interactions between the adaptor subunits using the yeast two-hybrid system. Interactions can be detected between the beta/beta'-adaptins and the alpha/gamma-adaptins, between the beta/beta'-adaptins and the AP50/AP47 subunits, between alpha-adaptin and AP17, and between gamma-adaptin and AP19. These results indicate that the adaptor subunits act in concert to target the complex to the appropriate membrane.

The Saccharomyces cerevisiae APS1 gene encodes a homolog of the small subunit of the mammalian clathrin AP-1 complex: evidence for functional interaction with clathrin at the Golgi complex

Clathrin-associated protein (AP) complexes have been implicated in the assembly of clathrin coats and the selectivity of clathrin-mediated protein transport processes. We have identified a yeast gene, APS1, encoding a homolog of the small (referred to herein as sigma) subunits of the mammalian AP-1 complex. Sequence comparisons have shown that Aps1p is more similar to the sigma subunit of the Golgi-localized mammalian AP-1 complex than Aps2p, which is more related to the plasma membrane AP-2 sigma subunit. Like their mammalian counterparts, Aps1p and Aps2p are components of distinct, large (> 200 kDa) complexes and a significant portion of the Aps proteins co-fractionate with clathrin-coated vesicles during gel filtration chromatography. Unexpectedly, even though the evolutionary conservation of AP small subunits is substantial (50% identity between mammalian and yeast proteins), disruptions of APS1 (aps1 delta) and APS2 (aps2 delta), individually or in combination, elicit no detectable mutant phenotypes. These data indicate that the Aps proteins are not absolutely required for clathrin-mediated selective protein transport in cells expressing wild type clathrin. However, aps1 delta accentuated the slow growth and alpha-factor pheromone maturation defect of cells carrying a temperature-sensitive allele of clathrin heavy chain (Chc) (chc1-ts). In contrast, aps1 delta did not influence the effects of chc1-ts on vacuolar protein sorting or receptor-mediated endocytosis. The aps2 delta mutation resulted in a slight effect on chc1-ts cell growth but had no additional effects. The growth defect of cells completely lacking Chc was compounded by aps1 delta but not aps2 delta. These results comprise evidence that Aps1p is involved in a subset of clathrin functions at the Golgi apparatus. The effect of aps1 delta on cells devoid of clathrin function suggests that Aps1p also participates in clathrin-independent processes.

Cloning of the YAP19 gene encoding a putative yeast homolog of AP19, the mammalian small chain of the clathrin-assembly proteins

Mouse brain AP19 is the smallest polypeptide chain component of AP-1, the clathrin-assembly protein complex located at the Golgi complex. We isolated a gene, termed YAP19, potentially encoding a homolog of AP19 from the genomic DNA of the yeast Saccharomyces cerevisiae. The deduced amino acid sequence, 156 amino acids long, shows 53% identity with the mouse brain AP19 protein, but 37% with Yap17p, a yeast homolog of the mammalian AP17 in AP-2, another clathrin-assembly protein complex located at the plasma membrane. The identification of YAP19 supports the proposal that yeast cells also contain the Golgi-associated clathrin-assembly protein complex.

AP17 and AP19, the mammalian small chains of the clathrin-associated protein complexes show homology to Yap17p, their putative homolog in yeast

AP17 and AP19 are the smallest polypeptide chain components of AP-2 and AP-1, the clathrin-associated protein complexes found in coated structures of the plasma membrane and Golgi apparatus of mammalian cells. cDNA clones representing the entire coding sequence of AP17 and AP19 were isolated from rat and mouse brain cDNA libraries, respectively. Determination of their nucleotide sequence predicts proteins of 142 and 158 amino acids with Mr 17,018 and 18,733. A sequence comparison of rat brain AP17 with mouse brain AP19 demonstrates that the small chains are highly related. A computer search for other related proteins has uncovered in yeast a previously unknown gene whose DNA sequence encodes a protein homologous to the small chain of AP complexes. The yeast sequence predicts Yap17p, a protein with 147 amino acids and a Mr of 17,373 that is slightly more related to the mammalian AP17 chain than to its AP19 counterpart.

Stabilization of clathrin coats by the core of the clathrin-associated protein complex AP-2

AP-2 is the class of clathrin-associated protein complex found in coated vesicles derived from the plasma membrane of eukaryotic cells. We demonstrate here, using a chemical method, that an AP-2 complex is an asymmetric structure consisting of one large alpha chain, one large beta chain, one medium AP50 chain, and one small AP17 chain. The complex has been shown to contain a core and two appendages. The AP core includes the small AP17 and the medium AP50 chains together with the amino-terminal domains of the large alpha and beta chains. One appendage corresponds to the carboxy-terminal domain of the beta chain. We find that as in the case of the beta chains, the carboxy-terminal portion of the alpha chains is an independently folded domain corresponding to the second appendage. We use limited tryptic proteolysis of clathrin/AP-2 coats to show the release of the appendages from the interior of the coats and the retention of the AP core by the remaining clathrin lattice. In addition, we find that the AP core stabilizes the coat and prevents its depolymerization. These results are consistent with the proposal that the AP core contains the binding site(s) for clathrin, while the alpha- and beta-chain appendages interact with membrane components of coated pits and coated vesicles.

Structural and functional division into two domains of the large (100- to 115-kDa) chains of the clathrin-associated protein complex AP-2

The clathrin-associated protein complex 2 (AP-2 complex) is a group of proteins associated with clathrin-coated vesicles and believed to interact with cytoplasmic domains of receptors found in the plasma membrane. AP-2 was purified as an assembly of several polypeptide chains (alpha, beta, AP50, and AP17), of which only the alpha and beta chains (100-115 kDa) show significant heterogeneity. We have obtained cDNA clones for two distinct rat brain beta chains. We have also studied the domain organization of bovine brain AP-2 complexes by selective proteolysis. Results of these studies show that the alpha and beta chains have a similar two-domain organization. Their amino-terminal domains are relatively invariant whereas their carboxyl-terminal domains are variable in both sequence and length. We propose that the variable domains select receptors for inclusion in coated vesicles.