The second PDZ domain of INAD is a type I domain involved in binding to eye protein kinase C. Mutational analysis and naturally occurring variants.

INAD is a scaffolding protein containing five PSD95/dlg/zonular occludens-1 (PDZ) domains that tether NORPA (phospholipase Cbeta(4)), the TRP calcium channel, and eye-PKC in Drosophila photoreceptors. We previously showed that eye-PKC interacted with the second PDZ domain (PDZ2) of INAD. Sequence comparison with a prototypical type I PDZ domain predicts that PDZ2 is the best candidate among the five PDZ domains to recognize eye-PKC that contains a type I PDZ ligand, Ile-Thr-Ile-Ile, at its carboxyl terminus. Replacement of Ile(-3) in eye-PKC with charged residues resulted in a drastic reduction of the PDZ2 interaction. Substitution of a conserved His with Arg at the second alpha-helix of PDZ2 led to a reduced binding; however, a Leu replacement resulted in an enhanced eye-PKC association. We isolated and sequenced the InaD gene. The coding sequence of InaD contains nine exons spanning 3 kilobases. Translation of coding sequences from three wild-type alleles revealed three SNPs affecting residues, 282, 319, and 333 of INAD. These polymorphisms are localized in PDZ2. Interestingly, we found two of three PDZ2 variants displayed a greater affinity for eye-PKC. In summary, we evaluated the molecular basis of the eye-PKC and PDZ2 association by mutational analysis and concluded that PDZ2 of INAD is a type I domain important for the eye-PKC interaction.

Reversible phosphorylation of the signal transduction complex in Drosophila photoreceptors.

In the Drosophila visual cascade, the transient receptor potential (TRP) calcium channel, phospholipase Cbeta (no-receptor-potential A), and an eye-specific isoform of protein kinase C (eye-PKC) comprise a multimolecular signaling complex via their interaction with the scaffold protein INAD. Previously, we showed that the interaction between INAD and eye-PKC is a prerequisite for deactivation of a light response, suggesting eye-PKC phosphorylates proteins in the complex. To identify substrates of eye-PKC, we immunoprecipitated the complex from head lysates using anti-INAD antibodies and performed in vitro kinase assays. Wild-type immunocomplexes incubated with [(32)P]ATP revealed phosphorylation of TRP and INAD. In contrast, immunocomplexes from inaC mutants missing eye-PKC, displayed no phosphorylation of TRP or INAD. We also investigated protein phosphatases that may be involved in the dephosphorylation of proteins in the complex. Dephosphorylation of TRP and INAD was partially suppressed by the protein phosphatase inhibitors okadaic acid, microcystin, and protein phosphatase inhibitor-2. These phosphatase activities were enriched in the cytosol of wild-type heads, but drastically reduced in extracts prepared from glass mutants, which lack photoreceptors. Our findings indicate that INAD functions as RACK (receptor for activated PKC), allowing eye-PKC to phosphorylate INAD and TRP. Furthermore, dephosphorylation of INAD and TRP is catalyzed by PP1/PP2A-like enzymes preferentially expressed in photoreceptor cells.

An improved alkaline lysis method for minipreparation of plasmid DNA.

This study is to improve the digestion pattern of miniprepped plasmid analyzed on gel. Frequently, some ambiguous DNA bands, which are suspected to be denatured DNA molecules, appear during electrophoresis of enzyme digested miniprepped plasmids. By employing Southern hybridization of two identical gels, one had been treated with denaturation-neutralization step and another without such treatment, we confirmed that many of these ambiguous DNA bands were single-stranded (SS) DNA molecules. The presence of SS DNA was due to the use of excess amount of NaOH during plasmid DNA purification with the conventional alkaline lysis method. We, therefore, modified the procedure and recommend that a half amount of NaOH (0.1N instead of 0.2N) should be used when isolating small quantity of plasmid DNA with the method.

A unique isoform of phospholipase Cbeta4 highly expressed in the cerebellum and eye.

We report a unique isoform of PLCbeta4 in rat, PLCbeta4c, that has an additional 37-nucleotide exon inserted between nucleotides 3459-3460 of the previously published PLCbeta4a coding sequence. This insertion results in replacement of 22 amino acid residues at the carboxyl terminal tail of PLCbeta4a with 41 unique residues. A human EST for PLCbeta4 also contains this exon and this exon was mapped to within a 5.5 kb intron of the human PLCbeta4 gene. PLCbeta4c is the third PLCbeta4 isoform to be identified which has a unique carboxyl-terminal tail. PLCbeta4b differs from PLCbeta4a by truncation 162 amino acid residues from the carboxyl terminus which are replaced with 10 distinct amino acid residues. Reverse transcription-polymerase chain reaction experiments show that both PLCbeta4a and PLCbeta4c mRNA are expressed throughout the rat brain and that PLCbeta4c mRNA is highly expressed in the eye and cerebellum. RNase protection assays demonstrate that both PLCbeta4a and PLCbeta4c transcripts are abundant in the cerebellum. The different carboxyl terminal tails of PLCbeta4 isoforms may allow for differential targeting and subcellular localization, contributing to regulation of PLC beta4-mediated signal transduction.

Interaction of eye protein kinase C and INAD in Drosophila. Localization of binding domains and electrophysiological characterization of a loss of association in transgenic flies.

Drosophila eye-specific protein kinase C (eye-PKC) is involved in light adaptation and deactivation. eye-PKC, NORPA (phospholipase Cbeta), and transient-receptor-potential (TRP) (calcium channel) are integral components of a signal transduction complex organized by INAD, a protein containing five PDZ domains. We previously demonstrated the direct association between the third PDZ domain of INAD with TRP in addition to the carboxyl-terminal half of INAD with the last three residues of NORPA. In this work, the molecular interaction between eye-PKC and INAD is defined via the yeast two-hybrid and ligand overlay assays. We show that the second PDZ domain of INAD interacts with the last three residues in the carboxyl-terminal tail of eye-PKC, Thr-Ile-Ile. The association between eye-PKC and INAD is disrupted by an amino acid substitution (Ile-700 to Asp) at the final residue of eye-PKC. In flies lacking endogenous eye-PKC (inaCp215), normal visual physiology is restored upon expression of wild-type eye-PKC, whereas the eye-PKCI700D mutant is completely inactive. Flies homozygous for inaCp209 and InaDp215, a mutation that causes a loss of the INAD-TRP association, were generated. These double mutants display a more severe response inactivation than either of the single mutants. Based on these findings, we conclude that the in vivo activity of eye-PKC depends on its association with INAD and that the sensitivity of photoreceptors is cooperatively regulated by the presence of both eye-PKC and TRP in the signaling complex.

Association of INAD with NORPA is essential for controlled activation and deactivation of Drosophila phototransduction in vivo.

Visual transduction in Drosophila is a G protein-coupled phospholipase C-mediated process that leads to depolarization via activation of the transient receptor potential (TRP) calcium channel. Inactivation-no-afterpotential D (INAD) is an adaptor protein containing PDZ domains known to interact with TRP. Immunoprecipitation studies indicate that INAD also binds to eye-specific protein kinase C and the phospholipase C, no-receptor-potential A (NORPA). By overlay assay and site-directed mutagenesis we have defined the essential elements of the NORPA-INAD association and identified three critical residues in the C-terminal tail of NORPA that are required for the interaction. These residues, Phe-Cys-Ala, constitute a novel binding motif distinct from the sequences recognized by the PDZ domain in INAD. To evaluate the functional significance of the INAD-NORPA association in vivo, we generated transgenic flies expressing a modified NORPA, NORPAC1094S, that lacks the INAD interaction. The transgenic animals display a unique electroretinogram phenotype characterized by slow activation and prolonged deactivation. Double mutant analysis suggests a possible inaccessibility of eye-specific protein kinase C to NORPAC1094S, undermining the observed defective deactivation, and that delayed activation may similarly result from NORPAC1094S being unable to localize in close proximity to the TRP channel. We conclude that INAD acts as a scaffold protein that facilitates NORPA-TRP interactions required for gating of the TRP channel in photoreceptor cells.

Identification of a naturally occurring peroxidase-lipoxygenase fusion protein.

A distant relative of catalase that is specialized for metabolism of a fatty acid hydroperoxide was identified. This heme peroxidase occurs in coral as part of a fusion protein, the other component of which is a lipoxygenase that forms the hydroperoxide substrate. The end product is an unstable epoxide (an allene oxide) that is a potential precursor of prostaglandin-like molecules. These results extend the known chemistry of catalase-like proteins and reveal a distinct type of enzymatic construct involved in the metabolism of polyunsaturated fatty acids.

Purification and molecular cloning of an 8R-lipoxygenase from the coral Plexaura homomalla reveal the related primary structures of R- and S-lipoxygenases.

Lipoxygenases that form S configuration fatty acid hydroperoxides have been purified or cloned from plant and mammalian sources. Our objectives were to characterize one of the lipoxygenases with R stereospecificity, many of which are described in marine and freshwater invertebrates. Characterization of the primary structure of an R-specific enzyme should help provide a new perspective to consider the enzyme-substrate interactions that are the basis of the specificity of all lipoxygenases. We purified an 8R-lipoxygenase of the prostaglandin-containing coral Plexaura homomalla by cation and anion exchange chromatography. This yielded a colorless enzyme preparation, a band of approximately 100 kDa on SDS-polyacrylamide gel electrophoresis, and turnover numbers of 4000 min-1 of 8R-lipoxygenase activity in peak chromatographic fractions. The full-length cDNA was cloned by PCR using peptide sequence from the purified protein and by 5'- and 3'-rapid amplification of cDNA ends. The cDNA encodes a polypeptide of 715 amino acids, including over 70 amino acids identified by peptide microsequencing. A peptide presequence of 52 amino acids is cleaved to give the mature protein of 76 kDa; the difference from the estimated size by SDS-PAGE implies a post-translational modification of the P. homomalla enzyme. All of the iron-binding histidines of S-lipoxygenases are conserved in the 8R-lipoxygenase. However, the C-terminal amino acid is a threonine, as opposed to the isoleucine that provides the carboxylate ligand to the iron in all known S-lipoxygenases. These results establish that the 8R-lipoxygenase is related in primary structure to the S-lipoxygenases. A model of the basis of R and S stereospecificity is described.

Regulation of the TRP Ca2+ channel by INAD in Drosophila photoreceptors.

Drosophila vision involves a G protein-coupled phospholipase C-mediated signaling pathway that leads to membrane depolarization through activation of Na+ and Ca2+ channels. InaD mutant flies have a M442K point mutation and display a slow recovery of the Ca2+ dependent current. We report that anti-INAD antibodies coimmunoprecipitate TRP, identified by its electrophoretic mobility, cross reactivity with anti-TRP antibody, and absence in a null allele trp mutant. This interaction is abolished by the InaD point mutation in vitro and in vivo. Interaction was localized to the 19 amino acid C-terminus of TRP by overlay assays, and to the PDZ domain of INAD, encompassing the point mutation. Given the impaired electrophysiology of the InaD mutant, this novel interaction suggests that INAD functions as a regulatory subunit of the TRP Ca2+ channel.

A novel protein encoded by the InaD gene regulates recovery of visual transduction in Drosophila.

InaDp215 is a point mutation that affects photoreceptor function in Drosophila. To understand the molecular basis of the defect, we isolated the InaD gene and found it encodes a photoreceptor-specific polypeptide of 674 residues. Within its sequence are two repeats that share remarkable homology with a family of cytoskeleton-associated proteins that are involved in signal transduction. Patch-clamp recordings from isolated photoreceptor cells of InaDp215 show a slow deactivation of the light-induced current. This defective deactivation of InaD appears dependent on calcium influx; removal of extracellular calcium masks its abnormal phenotype. Moreover, InaD photoreceptors show increases sensitivity to dim light. We propose that InaD is involved in the negative feedback regulation of the light-activated signaling cascade in Drosophila photoreceptors.

Evidence for linkage of the apolipoprotein A-II locus to plasma apolipoprotein A-II and free fatty acid levels in mice and humans.

Although it has been hypothesized that the synteny between mouse and human genes provides an approach to the localization of genes that determine quantitative traits in humans, this has yet to be demonstrated. We tested this approach with two quantitative traits, plasma apolipoprotein A-II (apoAII) and free fatty acid (FFA) levels. ApoAII is the second most abundant protein of high density lipoprotein particles, but its function remains largely unknown. We now show that, in a backcross between strains Mus spretus and C57BL/6J, apoAII levels correlate with plasma FFA concentrations on both chow (P < 0.0001) and high-fat (P < 0.0003) diets and that apoAII levels are linked to the apoAII gene (P < 0.0002). To test whether variations of the apoAII gene influence plasma lipid metabolism in humans, we studied 306 individuals in 25 families enriched for coronary artery disease. The segregation of the apoAII gene was followed by using an informative simple sequence repeat in the second intron of the gene and two nearby genetic markers. Robust sib-pair linkage analysis was performed on members of these families using the SAGE linkage programs. The results suggest linkage between the human apoAII gene and a gene controlling plasma apoAII levels (P = 0.03). Plasma apoAII levels were also significantly correlated with plasma FFA levels (P = 0.007). Moreover, the apoAII gene exhibited linkage with a gene controlling FFA levels (P = 0.003). Evidence for nonrandom segregation was seen with markers as far as 6-12 centimorgans from the apoAII structural locus. These data provide evidence, in two species, that the apoAII gene is linked to a gene that controls plasma apoAII levels and that apoAII influences, by an unknown mechanism, plasma FFA levels. The results illustrate the utility of animal studies for analysis of complex traits.

Localization of the gene-encoding upstream stimulatory factor (USF) to human chromosome 1q22-q23.

The upstream stimulatory factor, USF, is a ubiquitously expressed cellular transcription factor that binds to a symmetrical DNA sequence that is found in a variety of viral and cellular promoters. A full-length cDNA encoding the 43-kDa USF protein has previously been isolated. USF contains both helix-loop-helix and leucine repeats, which are involved in regulating its DNA binding and dimerization properties. We report the use of mouse-human somatic cell hybrids and in situ hybridization in localizing the gene-encoding USF to human chromosome 1q22-q23.

Localization of the transcription factor SP1 gene to human chromosome 12q12-->q13.2.

The cellular transcription factor SP1 binds to critical regulatory elements in a variety of cellular and viral promoters. The gene encoding the approximately 100-kDa SP1 protein contains zinc finger DNA-binding domains and glutamine-activation domains. Since SP1 is involved in the regulation of a variety of cellular genes, we wished to determine its chromosomal localization. Southern blot analysis of genomic DNA from a panel of mouse x human somatic cell hybrids indicated that SP1 was localized to chromosome 12. In situ hybridization allowed the localization of the gene encoding SP1 to human chromosome 12q12-->q13.2, with 12q13.1 being the most probable location.

Genetic dissection of cyclophilin function. Saturation mutagenesis of the Drosophila cyclophilin homolog ninaA.

Cyclophilins, the intracellular receptors for the widely used immunosuppressant cyclosporin A have been found to be peptidyl-prolyl cis/trans isomerases and have been implicated in intracellular protein folding and trafficking. The Drosophila ninaA gene encodes a photoreceptor-specific cyclophilin homolog involved in rhodopsin biogenesis. ninaA mutants have a 90% reduction in the levels of Rh1 rhodopsin. To gain insight into the role of cyclophilins in vivo, we carried out a genetic screen designed to identify functionally important regions in the ninaA protein. Over 700,000 mutagenized flies were screened for a visible ninaA phenotype and 70 independent mutations in ninaA were isolated and characterized. These mutations provide a detailed dissection of the structure/function relationships in cyclophilin. We also show that mammalian cyclophilins engineered to contain missense mutations found in two temperature-sensitive ninaA alleles display temperature-sensitive prolyl cis/trans isomerase activity.

Mapping of the gene for the cardiac sarcolemmal Na(+)-Ca2+ exchanger to human chromosome 2p21-p23.

The cardiac sarcolemmal Na(+)-Ca2+ exchanger is the primary mechanism for extrusion of calcium from the cardiac myocyte and therefore is important in regulating cardiac contractility. As part of an effort to determine whether the exchanger is associated with any genetic disorders of the heart or blood pressure, we have assigned the exchanger gene (designated NCX1) to human chromosome 2p21-p23 by analysis of a panel of mouse-human somatic cell hybrids and by in situ hybridization.

The cyclophilin homolog ninaA is a tissue-specific integral membrane protein required for the proper synthesis of a subset of Drosophila rhodopsins.

Mutations in the Drosophila ninaA gene cause dramatic reductions in rhodopsin levels, leading to impaired visual function. The ninaA protein is a homolog of peptidyl-prolyl cis-trans isomerases. We find that ninaA is unique among this family of proteins in that it is an integral membrane protein, and it is expressed in a cell type-specific manner. We have used transgenic animals misexpressing different rhodopsins in the major class of photoreceptor cells to demonstrate that ninaA is required for normal function by two homologous rhodopsins, but not by a less conserved member of the Drosophila rhodopsin gene family. This demonstrates in vivo substrate specificity in a cyclophilin-like molecule. We also show that vertebrate retina contains a ninaA-related protein and that ninaA is a member of a gene family in Drosophila. These data offer insights into the in vivo role of this important family of proteins.

Isolation and structure of an arrestin gene from Drosophila.

A Drosophila gene encoding a homologue of vertebrate arrestin was isolated by subtractive hybridization and identified as a member of a set of genes that are preferentially expressed in the visual system. This gene encodes a 364-amino acid protein that displays greater than 40% amino acid sequence identity with human and bovine arrestin. Interestingly, the Drosophila homologue lacks the C-terminal sequences that were postulated to interact with rhodopsin during the quenching of the phototransduction cascade in the vertebrate visual response. These findings are discussed in terms of invertebrate phototransduction. The Drosophila gene was mapped cytogenetically to chromosomal position 36D1-2, near the ninaD locus. However, the arrestin gene does not appear to be the ninaD locus, as sequence analysis of three ethylmethane sulfate-induced ninaD mutant alleles reveals no alteration in amino acid sequence.

The use of alpha 2-antiplasmin as a model for the demonstration of complex reversibility in serpins.

Human alpha 2-antiplasmin readily forms 1:1 complexes with either trypsin or chymotrypsin at independent but overlapping reactive sites. In the absence of alpha 2-macroglobulin, complex dissociation and enzyme release can be demonstrated without regeneration of inhibitory activity. However, in the presence of this inhibitor the dissociation of alpha 2-antiplasmin-chymotrypsin complexes or alpha 2-antiplasmin-trypsin complexs yields functionally active inhibitors which can now inactivate trypsin and chymotrypsin, respectively. These results clearly indicate that Serpin-proteinase complexes can dissociate to give both active inhibitor and enzyme. If the enzyme is trapped by alpha 2-macroglobulin, in vivo, it is possible that the inhibitor may be recycled for further use.

The ninaA gene required for visual transduction in Drosophila encodes a homologue of cyclosporin A-binding protein.

Mutations of the Drosophila melanogaster ninaA gene affect phototransduction: ninaA mutant flies have a 10-fold reduction in the levels of rhodopsin in the R1-R6 photoreceptor cells. The ninaA gene was isolated and found to encode a 237-amino-acid protein that has over 40% amino-acid sequence identity with the vertebrate cyclosporin A-binding protein, cyclophilin, a protein that seems to be involved in T-lymphocyte activation. The remarkable evolutionary conservation of cyclophilin in two phylogenetically distant organisms and its involvement in diverse transduction processes suggests that this protein plays an important role in cellular metabolism. Indeed, cyclophilin has recently been shown to be a prolyl cis-trans isomerase that catalyses, in vitro, rate-limiting steps in the folding of a number of proteins. Here, we present evidence for the involvement of cyclophilin-like molecules in a defined cellular process. The availability of mutations in a cyclophilin gene provides a new model system for the study of cyclophilin and cyclosporin action.

The functional role of acute phase plasma proteinase inhibitors.

Human plasma contains an array of proteinase inhibitors which are utilized in the regulation of a host of biological activities, including coagulation, fibrinolysis, connective tissue turnover, and complement activation. The concentration of several of these inhibitors increase at varying rates in the acute phase state while others remain constant or actually decrease. Increases are presumably an attempt to retain rigid control over certain critical reactions, while decreases are probably due to inhibitor turnover either through consumption during complex formation or inactivation by other endogenous proteinases. Virtually all of these latter reactions take place in a reactive site loop which is an exposed region present in at least eight related serine proteinase inhibitors (Serpins) in plasma. Complex formation and inhibitor inactivation presumably act as signals for inhibitor production and turnover in the acute phase state. However, exactly how this initial stimulus for increased protein synthesis is manifested at the protein level remains to be established.