Gamma-crystallins of the human eye lens: expression analysis of five members of the gene family.

While only two gamma-crystallins have been identified in the human eye lens, molecular studies indicate that the human gamma-crystallins are encoded in a multigene family comprising at least seven closely related members. Sequence analysis of five of these genes has suggested that three (gamma 1-2, G3, and G4) are potentially active, while two (G1 psi and G2 psi) correspond to closely related pseudogenes. Here we report on the detailed structure of a sixth gamma-crystallin gene, G5, and our results obtained with transient expression assays to characterize both the promoter activity and translation products of five members of the gene family. We show that 5'-flanking sequences of G1 psi and G2 psi lacked detectable promoter activity, while the corresponding sequences of G3, G4, and G5 were able to direct high levels of expression of the bacterial chloramphenicol acetyltransferase gene in primary lens epithelia, but not in cultures of nonlens origin. Detailed sequence comparisons indicated that active genes contained several conserved sequence tracts 5' of the TATA box which may constitute functional elements of a lens-specific gamma-crystallin promoter. Expression of the gamma-crystallin coding sequences from the human metallothionein IIA promoter in nonlens cells facilitated characterization of the polypeptides encoded by individual gamma-genes and, in future studies, should permit comparison of these proteins with distinct gamma-crystallins in the human lens.     

Granule lattice protein 1 (Grl1p), an acidic, calcium-binding protein in Tetrahymena thermophila dense-core secretory granules, influences granule size, shape, content organization, and release but not protein sorting or condensation

The electron-dense cores of regulated secretory granules in the ciliate Tetrahymena thermophila are crystal lattices composed of multiple proteins. Granule synthesis involves a series of steps beginning with protein sorting, followed by the condensation and precise geometric assembly of the granule cargo. These steps may to various degrees be determined by the cargo proteins themselves. A prominent group of granule proteins, in ciliates as well as in vertebrate neuronal and endocrine cells, are acidic, heat-stable, and bind calcium. We focused on a protein with these characteristics named granule lattice protein 1 (Grl1p), which represents 16% of total granule contents, and we have now cloned the corresponding gene. Mutants in which the macronuclear copies of GRL1 have been disrupted continue to synthesize dense-core granules but are nonetheless defective in regulated protein secretion. To understand the nature of this defect, we characterized mutant and wild-type granules. In the absence of Grl1p, the sorting of the remaining granule proteins appears normal, and they condense to form a well-defined core. However, the condensed cores do not demonstrate a visible crystalline lattice, and are notably different from wild type in size and shape. The cellular secretion defect arises from failure of the aberrant granule cores to undergo rapid expansion and extrusion after exocytic fusion of the granule and plasma membranes. The results suggest that sorting, condensation, and precise granule assembly are distinct in their requirements for Grl1p.     

Cloning and tissue distribution of three murine alpha/beta hydrolase fold protein cDNAs

We have cloned 3 novel murine cDNAs encoding proteins containing an alpha/beta hydrolase fold; a catalytic domain found in a very wide range of enzymes. These proteins belong to the prosite UPF0017 uncharacterized protein family and we have named them lung alpha/beta hydrolase 1, 2, and 3 (LABH) since they were cloned from lung cDNA. All have 9 coding exons, encoding 412, 425, and 411 residue proteins respectively (46-48 kDa); LABH1 being closely related to LABH3 having 45% identity. All 3 proteins have a single predicted amino-terminus transmembrane domain. An alignment of family members from different phyla enabled the identification of the LABH1 catalytic triad as Ser211, Asp337, and His366. mRNA expression levels of LABH1 and 3 were highest in liver and LABH2 highest in testis. These findings suggest that the LABH proteins consist of a novel family of membrane bound enzymes whose function has yet to be determined.     

Two families of rep-like genes that probably originated by interspecies recombination are represented in viral, plasmid, bacterial, and parasitic protozoan genomes

Two families of genes related to, and including, rolling circle replication initiator protein (Rep) genes were defined by sequence similarity and by evidence of intergene family recombination. The Rep genes of circoviruses were the best characterized members of the "RecRep1 family." Other members of the RecRep1 family were Rep-like genes found in the genomes of the Canarypox virus, Entamoeba histolytica, and Giardia duodenalis and in a plasmid, p4M, from the Gram-positive bacterium, Bifidobacterium pseudocatenulatum. The "RecRep2 family" comprised some previously identified Rep-like genes from plasmids of phytoplasmas and similar Rep-like genes from the genomes of Lactobacillus acidophilus, Lactococcus lactis, and Phytoplasma asteris. Both RecRep1 and RecRep2 proteins have a nucleotide-binding domain significantly similar to the helicases (2C proteins) of picorna-like viruses. On the N-terminal side of the nucleotide binding domain, RecRep1 proteins have a domain significantly similar to one found in nanovirus Reps, whereas RecRep2 proteins have a domain significantly similar to one in the Reps of pLS1 plasmids. We speculate that RecRep genes have been transferred from viruses or plasmids to parasitic protozoan and bacterial genomes and that Rep proteins were themselves involved in the original recombination events that generated the ancestral RecRep genes.     

The receptor tyrosine phosphatase-like protein ICA512 binds the PDZ domains of beta2-syntrophin and nNOS in pancreatic beta-cells

Islet cell autoantigen (ICA) 512 of type I diabetes is a receptor tyrosine phosphatase-like protein associated with the secretory granules of neurons and endocrine cells including insulin-secreting beta-cells of the pancreas. Here we show that in a yeast two-hybrid assay its cytoplasmic domain binds beta2-syntrophin, a modular adapter which in muscle cells interacts with members of the dystrophin family including utrophin, as well as the signaling molecule neuronal nitric oxide synthase (nNOS). The cDNA isolated by two-hybrid screening corresponded to a novel beta2-syntrophin isoform with a predicted molecular mass of 28 kDa. This isoform included the PDZ domain, but not the C-terminal region, which in full-length beta2-syntrophin is responsible for binding dystrophin-related proteins. In vitro binding of the beta2-syntrophin PDZ domain to ICA512 required both ICA512's C-terminal region and an internal polypeptide preceding its tyrosine phosphatase-like domain. Immunomicroscopy and co-immunoprecipitations from insulinoma INS-1 cells confirmed the occurrence of ICA512-beta2-syntrophin complexes in vivo. ICA512 also interacted in vitro with the PDZ domain of nNOS and ICA512-nNOS complexes were co-immunoprecipitated from INS-1 cells. Finally, we show that INS-1 cells, like muscle cells, contain beta2-syntrophin-utrophin oligomers. Thus, we propose that ICA512, through beta2-syntrophin and nNOS, links secretory granules with the actin cytoskeleton and signaling pathways involving nitric oxide.     

Rho GTPase signaling in Dictyostelium discoideum: insights from the genome

Rho GTPases are ubiquitously expressed across the eukaryotes where they act as molecular switches participating in the regulation of many cellular processes. We present an inventory of proteins involved in Rho-regulated signaling pathways in Dictyostelium discoideum that have been identified in the completed genome sequence. In Dictyostelium the Rho family is encoded by 18 genes and one pseudogene. Some of the Rho GTPases (Rac1a/b/c, RacF1/F2 and RacB) are members of the Rac subfamily, and one, RacA, belongs to the RhoBTB subfamily. The Cdc42 and Rho subfamilies, characteristic of metazoa and fungi, are absent. The activities of these GTPases are regulated by two members of the RhoGDI family, by eight members of the Dock180/zizimin family and by a surprisingly large number of proteins carrying RhoGEF (42 genes) or RhoGAP (43 genes) domains or both (three genes). Most of these show domain compositions not found in other organisms, although some have clear homologs in metazoa and/or fungi. Among the (in many cases putative) effectors found in Dictyostelium are the CRIB domain proteins (WASP and two related proteins, eight PAK kinases and a novel gelsolin-related protein), components of the Scar/WAVE complex, 10 formins, four IQGAPs, two members of the PCH family, numerous lipid kinases and phospholipases, and components of the NADPH oxidase and the exocyst complexes. In general, the repertoire of Rho signaling components of Dictyostelium is similar to that of metazoa and fungi.     

Independent Transport and Sorting of Functionally Distinct Protein Families in Tetrahymena thermophila Dense Core Secretory Granules

Dense core granules (DCGs) in Tetrahymena thermophila contain two protein classes. Proteins in the first class, called granule lattice (Grl), coassemble to form a crystalline lattice within the granule lumen. Lattice expansion acts as a propulsive mechanism during DCG release, and Grl proteins are essential for efficient exocytosis. The second protein class, defined by a C-terminal β/γ-crystallin domain, is poorly understood. Here, we have analyzed the function and sorting of Grt1p (granule tip), which was previously identified as an abundant protein in this family. Cells lacking all copies of GRT1, together with the closely related GRT2, accumulate wild-type levels of docked DCGs. Unlike cells disrupted in any of the major GRL genes, ΔGRT1 ΔGRT2 cells show no defect in secretion, indicating that neither exocytic fusion nor core expansion depends on GRT1. These results suggest that Grl protein sorting to DCGs is independent of Grt proteins. Consistent with this, the granule core lattice in ΔGRT1 ΔGRT2 cells appears identical to that in wild-type cells by electron microscopy, and the only biochemical component visibly absent is Grt1p itself. Moreover, gel filtration showed that Grl and Grt proteins in cell homogenates exist in nonoverlapping complexes, and affinity-isolated Grt1p complexes do not contain Grl proteins. These data demonstrate that two major classes of proteins in Tetrahymena DCGs are likely to be independently transported during DCG biosynthesis and play distinct roles in granule function. The role of Grt1p may primarily be postexocytic; consistent with this idea, DCG contents from ΔGRT1 ΔGRT2 cells appear less adhesive than those from the wild type.In eukaryotes, the directional transport of lumenal proteins throughout the network of membrane-bound organelles depends on reversible assembly of multisubunit protein complexes in the cytoplasm. For example, the assembly of a localized clathrin coat at a cell''s surface facilitates both the concentration of specific transmembrane receptors together with their bound ligands at that site and the invagination and budding of the plasma membrane, resulting in endocytosis (18). Similarly, other cytosolic coats assemble and direct traffic at the endoplasmic reticulum (ER) and Golgi apparatus (4). For one protein trafficking pathway in eukaryotic cells, however, the determinative protein self-assembly occurs not in the cytoplasm but within the lumen of the secretory pathway itself. Dense core granules (DCGs) are secretory vesicles whose lumenal cargo consists of a condensed polypeptide aggregate. This cargo is secreted when the vesicles fuse with the plasma membrane in response to a specific extracellular stimulus, an event called regulated exocytosis. The aggregation of the cargo occurs progressively within the secretory pathway, beginning in the trans-Golgi network (TGN), and may be promoted by multiple factors including compartment-specific proton and calcium levels (23). Aggregation facilitates the vesicular storage of concentrated secretory proteins but also serves as a sorting mechanism to segregate DCG proteins from proteins that are secreted via other pathways. Evidence for this mechanism includes in vitro experiments showing that some proteins released via constitutive exocytosis remain soluble under TGN-like conditions that promote DCG protein aggregation (10). In vivo, sorting would result if aggregated and soluble proteins exit the TGN in different carriers. Importantly, there is no evidence that sorting of DCG proteins at the TGN requires assembly of cytosolic coat complexes.While aggregative sorting represents an attractively simple mechanism, relatively little is known about the structure or dynamic properties of the aggregates themselves. This is an interesting issue, as illustrated by several phenomena. First, aggregates in some cell types, like those formed by proinsulin in pancreatic β cells, can become reordered as protein crystals during a multistage process called granule maturation (13). Second, Aplysia bag cells can sort different subsets of DCG proteins into distinct granules, suggesting that aggregation can be finely regulated and that different aggregates have different properties in vivo (20). Both of these phenomena have also been observed within the DCGs of unicellular ciliates (3, 14). In addition, ciliate DCGs demonstrate another degree of subtlety in DCG formation because the granule cores in many of these organisms are divided into distinct domains (25). The domain organization indicates that DCG proteins in these cells can segregate from one another even as they are sorted to the same vesicular destination. While the structures of DCGs in many ciliates have been captured by electron microscopy, molecular studies have advanced in two species, Tetrahymena thermophila and Paramecium tetraurelia (30, 33).In many ciliates, the individual DCGs are organized in at least two distinct domains within the lumen. First, the bulk of the cargo is organized as a core crystal that expands, spring-like, upon exocytosis (28). This expansion can drive rapid extrusion of the DCG contents, which may be essential for hunting or defensive behaviors (17). In addition, many ciliate DCGs possess a single polarized tip structure that is involved in DCG docking to the plasma membrane and exocytic fusion (25). These tip structures are also filled with condensed, highly organized proteins, which appear by both genetic and morphological criteria to be different from proteins making up the expansible core (1, 21). The proteins that form the distinct domains are beginning to be identified and analyzed. Those that constitute the expansible springs are encoded by homologous families of genes named GRL (granule lattice) in Tetrahymena and tmp (trichocyst matrix) in Paramecium (11, 12, 15). Assembly of Grl proteins begins in the ER with formation of heterooligomers. This is an obligatory step, as shown by the fact that deletion of individual Grl proteins by targeted gene disruption resulted in the ER retention of remaining Grl proteins (12). Further assembly of Grl proteins to form a crystal occurs during DCG maturation and is accompanied by site-specific proprotein processing (34). Upon exocytosis, the expansion of the crystalline core is controlled by calcium binding to the fully processed Grl proteins (34).In addition to the GRL family-encoded proteins, 13 other lumenal DCG proteins have been putatively or definitively identified in Tetrahymena, and homologous proteins are predicted in the Paramecium genome (6). The entire set belongs to a gene family that is defined by a carboxy-terminal β/γ-crystallin domain, which may function as a DCG-targeting motif (16). Studies of two different members of this family in Tetrahymena, IGR1 (induced during granule regeneration 1) and GRT1 (granule tip 1), suggested that these proteins are functionally distinct from the spring-forming Grl proteins. First, whereas gene disruption of any of the highly transcribed GRL genes resulted in grossly aberrant spring formation, no such defect was seen upon disruption of IGR1 (16). However, this could be explained by the fact that IGR1 encodes a relatively low-abundance protein in DCGs, and furthermore its function could be redundant with that of the highly related gene, IGR2.The second protein in the β/γ-crystallin domain family that has been investigated is the 80-kDa product of the GRT1 gene. Grt1p was first detected as one of the most abundant DCG components released during exocytosis (32). Biochemical analysis showed that Grt1p differs in its solubility from the Grl proteins and also that it is packaged intact in DCGs rather than undergoing proteolytic processing (31). Since processing is essential for Grl protein assembly and function, this difference appears highly significant. Second, Grt1p accumulates at a single pole of each DCG, corresponding to the tip of the organelle that docks and then fuses with the plasma membrane (5). Two Mendelian mutants with defects in DCG maturation show delocalized Grt1p, and these mutant DCGs can dock but do not appear to undergo exocytosis (5). These results suggested that Grt1p might be involved in forming a DCG tip domain that interacted with the plasma membrane.We have now investigated the trafficking and function of Grt1p. Our data provide both direct biochemical and cell-biological evidence that Grt1p and Grl proteins form distinct complexes during DCG biogenesis in Tetrahymena. Together with earlier results, our experiments provide genetic evidence that Grl and Grt complexes can be independently trafficked to DCGs. Cells lacking GRT1, together with the closely related GRT2, still show rapid and efficient release of DCG contents upon stimulation with secretagogues, but the released DCG contents are subtly different from those of the wild type, suggesting that Grt1p may primarily serve a postexocytic function.     

The membrane skeleton in Paramecium: Molecular characterization of a novel epiplasmin family and preliminary GFP expression results

Previous attempts to identify the membrane skeleton of Paramecium cells have revealed a protein pattern that is both complex and specific. The most prominent structural elements, epiplasmic scales, are centered around ciliary units and are closely apposed to the cytoplasmic side of the inner alveolar membrane. We sought to characterize epiplasmic scale proteins (epiplasmins) at the molecular level. PCR approaches enabled the cloning and sequencing of two closely related genes by amplifications of sequences from a macronuclear genomic library. Using these two genes (EPI-1 and EPI-2), we have contributed to the annotation of the Paramecium tetraurelia macronuclear genome and identified 39 additional (paralogous) sequences. Two orthologous sequences were found in the Tetrahymena thermophila genome. Structural analysis of the 43 sequences indicates that the hallmark of this new multigenic family is a 79 aa domain flanked by two Q-, P- and V-rich stretches of sequence that are much more variable in amino-acid composition. Such features clearly distinguish members of the multigenic family from epiplasmic proteins previously sequenced in other ciliates. The expression of Green Fluorescent Protein (GFP)-tagged epiplasmin showed significant labeling of epiplasmic scales as well as oral structures. We expect that the GFP construct described herein will prove to be a useful tool for comparative subcellular localization of different putative epiplasmins in Paramecium.     

PC1/3, PC2 and PC5/6A are targeted to dense core secretory granules by a common mechanism

There are seven members of the proprotein convertase (PC) family of secreted serine proteases that cleave their substrates at basic amino acids, thereby activating a variety of hormones, growth factors, and viruses. PC1/3, PC2 and PC5/6A are the only members of the PC family that are targeted to dense core secretory granules, where they carry out the processing of proteins that are secreted from the cell in a regulated manner. Previous studies have identified alpha-helices in the C-termini of the PC1/3 and PC2 proteases that are required for this subcellular targeting. In the current study, we demonstrate that a predicted alpha-helix in the C-terminus of PC5/6A is also critical for the ability of this domain to target a heterologous protein to the regulated secretory pathway of mouse endocrine AtT-20 cells. Analysis of the subcellular distribution of fusion proteins containing the C-terminal domains of PC1/3, PC2 and PC5/6A confirmed that all three domains have the capacity to redirect a constitutively secreted protein to the granule-containing cytoplasmic extensions. Analysis of the predicted structures formed by these three granule-sorting helices shows a correlation between their granule-sorting efficiency and the clustering of hydrophobic amino acids in their granule-targeting helices.     

Identification of a CD20-, FcepsilonRIbeta-, and HTm4-related gene family: sixteen new MS4A family members expressed in human and mouse

CD20, high-affinity IgE receptor beta chain (FcepsilonRIbeta), and HTm4 are structurally related cell-surface proteins expressed by hematopoietic cells. In the current study, 16 novel human and mouse genes that encode new members of this nascent protein family were identified. All family members had at least four potential membrane-spanning domains, with N- and C-terminal cytoplasmic domains. This family was therefore named the membrane-spanning 4A gene family, with at least 12 subgroups (MS4A1 through MS4A12) currently representing at least 21 distinct human and mouse proteins. Each family member had unique patterns of expression among hematopoietic cells and nonlymphoid tissues. Four of the 6 human MS4A genes identified in this study mapped to chromosome 11q12-q13.1 along with CD20, FcepsilonRIbeta, and HTm4. Thus, like CD20 and FcepsilonRIbeta, the other MS4A family members are likely to be components of oligomeric cell surface complexes that serve diverse signal transduction functions.     

COG3926 and COG5526: a tale of two new lysozyme-like protein families

We have identified two new lysozyme-like protein families by using a combination of sequence similarity searches, domain architecture analysis, and structural predictions. First, the P5 protein from bacteriophage phi8, which belongs to COG3926 and Pfam family DUF847, is predicted to have a new lysozyme-like domain. This assignment is consistent with the lytic function of P5 proteins observed in several related double-stranded RNA bacteriophages. Domain architecture analysis reveals two lysozyme-associated transmembrane modules (LATM1 and LATM2) in a few COG3926/DUF847 members. LATM2 is also present in two proteins containing a peptidoglycan binding domain (PGB) and an N-terminal region that corresponds to COG5526 with uncharacterized function. Second, structure prediction and sequence analysis suggest that COG5526 represents another new lysozyme-like family. Our analysis offers fold and active-site assignments for COG3926/DUF847 and COG5526. The predicted enzymatic activity is consistent with an experimental study on the zliS gene product from Zymomonas mobilis, suggesting that bacterial COG3926/DUF847 members might be activators of macromolecular secretion.     

ADAM-TS5, ADAM-TS6, and ADAM-TS7, novel members of a new family of zinc metalloproteases. General features and genomic distribution of the ADAM-TS family.

We report the primary structure of three novel, putative zinc metalloproteases designated ADAM-TS5, ADAM-TS6, and ADAM-TS7. All have a similar domain organization, comprising a preproregion, a reprolysin-type catalytic domain, a disintegrin-like domain, a thrombospondin type-1 (TS) module, a cysteine-rich domain, a spacer domain without cysteine residues, and a COOH-terminal TS module. These genes are differentially regulated during mouse embryogenesis and in adult tissues, with Adamts5 highly expressed in the peri-implantation period in embryo and trophoblast. These proteins are similar to four other cognate gene products, defining a distinct family of human reprolysin-like metalloproteases, the ADAM-TS family. The other members of the family are ADAM-TS1, an inflammation-induced gene, the procollagen I/II amino-propeptide processing enzyme (PCINP, ADAM-TS2), and proteins predicted by the KIAA0366 and KIAA0688 genes (ADAM-TS3 and ADAM-TS4). Individual ADAM-TS members differ in the number of COOH-terminal TS modules, and some have unique COOH-terminal domains. The ADAM-TS genes are dispersed in human and mouse genomes.