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PubMed1992

Alternative topogenic signals in peroxisomal citrate synthase of Saccharomyces cerevisiae.

The tripeptide serine-lysine-leucine (SKL) occurs at the carboxyl terminus of many peroxisomal proteins and serves as a peroxisomal targeting signal. Saccharomyces cerevisiae has two isozymes of citrate synthase. The peroxisomal form, encoded by CIT2, terminates in SKL, while the mitochondrial form, encoded by CIT1, begins with an amino-terminal mitochondrial signal sequence and ends in SKN. We analyzed the importance of SKL as a topogenic signal for citrate synthase, using oleate to induce peroxisomes and density gradients to fractionate organelles. Our experiments revealed that SKL was necessary for directing citrate synthase to peroxisomes. C-terminal SKL was also sufficient to target a leaderless version of mitochondrial citrate synthase to peroxisomes. Deleting this tripeptide from the CIT2 protein caused peroxisomal citrate synthase to be missorted to mitochondria. These experiments suggest that the CIT2 protein contains a cryptic mitochondrial targeting signal.

Amino Acid Sequence↗
PubMed2005

Identification of splicing silencers and enhancers in sense Alus: a role for pseudoacceptors in splice site repression.

Auxiliary splicing signals in introns play an important role in splice site selection, but these elements are poorly understood. We show that a subset of serine/arginine (SR)-rich proteins activate a cryptic 3' splice site in a sense Alu repeat located in intron 4 of the human LST1 gene. Utilization of this cryptic splice site is controlled by juxtaposed Alu-derived splicing silencers and enhancers between closely linked short tandem repeats TNFd and TNFe. Systematic mutagenesis of these elements showed that AG dinucleotides that were not preceded by purine residues were critical for repressing exon inclusion of a chimeric splicing reporter. Since the splice acceptor-like sequences are present in excess in exonic splicing silencers, these signals may contribute to inhibition of a large number of pseudosites in primate genomes.

Alternative Splicing↗
PubMed1998

Characterization of the phytopathogen Pseudomonas syringae pathovar ribicola NCPPB 963.

In 1939, a bacterial spot caused severe defoliation of Ribes aureum (Golden Currant) The causal agent is now recognized as Pseudomonas syringae pathovar ribicola. This communication extends the phenotype of the only identified strain of P. syringae pv. ribicola, which is reminiscent of those of other pathovars, and provides a molecular biological characterization. A minimum size of 5.55 Mb for the bacterial genome was obtained using pulsed-field electrophoresis. The SDS-PAGE outer-membrane profile contained seven major bands, and has obvious similarities to that of P. aeruginosa. SDS-PAGE of concentrated mid-log phase culture supernatants revealed large amounts of a single, cryptic 24.0 kD protein. The amino acid composition and 57 residues in the N-terminus of this protein. were determined. The protein sequence was nearly identical to the translation of a region of unknown function in the P. aeruginosa genome. Extensive similarity in N-terminal sequence, composition and subunit size to a secreted hydrophilic Vibrio cholerae protein of unknown function was also found. Neither protein has been directly associated with disease development.

Amino Acid Sequence↗
PubMed1997

Removal of a cryptic intron and subcellular localization of green fluorescent protein are required to mark transgenic Arabidopsis plants brightly.

The green fluorescent protein (GFP) from the jellyfish Aequorea victoria is finding wide use as a genetic marker that can be directly visualized in the living cells of many heterologous organisms. We have sought to express GFP in the model plant Arabidopsis thaliana, but have found that proper expression of GFP is curtailed due to aberrant mRNA processing. An 84-nt cryptic intron is efficiently recognized and excised from transcripts of the GFP coding sequence. The cryptic intron contains sequences similar to those required for recognition of normal plant introns. We have modified the codon usage of the gfp gene to mutate the intron and to restore proper expression in Arabidopsis. GFP is mainly localized within the nucleoplasm and cytoplasm of transformed Arabidopsis cells and can give rise to high levels of fluorescence, but it proved difficult to efficiently regenerate transgenic plants from such highly fluorescent cells. However, when GFP is targeted to the endoplasmic reticulum, transformed cells regenerate routinely to give highly fluorescent plants. These modified forms of the gfp gene are useful for directly monitoring gene expression and protein localization and dynamics at high resolution, and as a simply scored genetic marker in living plants.

Agrobacterium tumefaciens↗
PubMed1996

The nature of cryptic epitopes within the self-antigen myelin basic protein.

Mechanisms that allow potentially autoreactive T cells to escape central tolerance and persist in the peripheral lymphoid organs of healthy individuals are poorly defined. It has been proposed that such cells are specific for epitopes which normally are not well presented to the immune system or, in other words, are cryptic. We have used synthetic peptides to define potential T cell epitopes within the N-terminal portion of myelin basic protein (MBP). These were defined in terms of their relative affinity for the MHC-restriction element I-Au and their ability to activate T cells in mice of the H-2(u) haplotype. Three epitopes were identified, one of which corresponded to the known dominant N-terminal epitope (Ac1-9). The other two epitopes (9-20 and 5-20) bound to their MHC-restriction element with relatively high affinity but were cryptic, as defined by the poor response to these epitopes following immunization with intact MBP. Even the longer of these two epitopes did not induce autoimmune encephalomyelitis in H-2(u) mice. These results demonstrate that antigen processing can control both the induction of and effector function of autoreactive T cells, and is therefore a principal mechanism involved in limiting the autoreactive T cell repertoire.

Amino Acid Sequence↗
PubMed1997

The active transport of myelin basic protein into the nucleus suggests a regulatory role in myelination.

The myelin basic proteins (MBPs) are a set of membrane proteins that function to adhere the cytoplasmic leaflets of the myelin bilayer. During oligodendrocyte maturation prior to compact myelin formation, however, certain MBPs have been observed within the cell body and nucleus. We explored the parameters of the translocation of the exon II-containing MBPs (MBPexII) from the site of synthesis in the cell cytoplasm into the nucleus and in some experiments used GFP as a molecular reporter to monitor the intracellular distribution of MBP-GFP fusion proteins in living cells. We show here that the transport of MBPexII into cell nuclei is an active process, which is temperature and energy dependent, and may be regulated by phosphorylation state. Further, MBPexII can direct the entry of macromolecular complexes into cell nuclei, revealing that the exon II peptide segment may provide a nuclear localization signal (NLS), perhaps a novel one, or may induce a conformational change in the full-length protein that exposes a cryptic NLS. The MBPexII are thus very unusual in that they are plasma membrane proteins that are also targeted to the nucleus. In oligodendrocytes and Schwann cells, where the MBPs are naturally expressed, it is likely that karyophilic MBPs subserve a regulatory function in implementing the myelination program.

Biological Transport, Active↗
PubMed2004

Activation of cryptic 3' splice sites within introns of cellular genes following gene entrapment.

Gene trap vectors developed for genome-wide mutagenesis can be used to study factors governing the expression of exons inserted throughout the genome. For example, entrapment vectors consisting of a partial 3'-terminal exon [i.e. a neomycin resistance gene (Neo), a poly(A) site, but no 3' splice site] were typically expressed following insertion into introns, from cellular transcripts that spliced to cryptic 3' splice sites present either within the targeting vector or in the adjacent intron. A vector (U3NeoSV1) containing the wild-type Neo sequence preferentially disrupted genes that spliced in-frame to a cryptic 3' splice site in the Neo coding sequence and expressed functional neomycin phosphotransferase fusion proteins. Removal of the cryptic Neo 3' splice site did not reduce the proportion of clones with inserts in introns; rather, the fusion transcripts utilized cryptic 3' splice sites present in the adjacent intron or generated by virus integration. However, gene entrapment with U3NeoSV2 was considerably more random than with U3NeoSV1, consistent with the widespread occurrence of potential 3' splice site sequences in the introns of cellular genes. These results clarify the mechanisms of gene entrapment by U3 gene trap vectors and illustrate features of exon definition required for 3' processing and polyadenylation of cellular transcripts.

Animals↗
PubMed2001

A cryptic plasmid from Pasteurella multocida has a predicted protein nearly identical to a transport protein from Actinobacillus actinomycetemcomitans.

Several plasmids from Pasteurella multocida have been shown to carry antibiotic resistance genes but no other genes possibly related to the organism's pathogenesis. We report here that sequence from the plasmid pLEM from a fowl isolate of P. multocida, strain 1059, contained one open reading frame that had significant identity with a predicted protein from pVT745, a plasmid that was isolated from a human oral isolate of Actinobacillus actinomycetemcomitans. This predicted protein had significant homology at the amino acid level to cation transport proteins.

Aggregatibacter actinomycetemcomitans↗
PubMed2004

Activated vitronectin as a target for anticancer therapy with human antibodies.

The formation of a provisional extracellular matrix represents an important step during tumor growth and angiogenesis. Proteins that participate in this process become activated and undergo conformational changes that expose biologically active cryptic sites. Activated matrix proteins express epitopes not found on their native counterparts. We hypothesized that these epitopes may have a restricted tissue distribution, rendering them suitable targets for therapeutic human monoclonal antibodies (huMabs). In this study, we exploited phage antibody display technology and subtractive phage selection to generate human monoclonal antibody fragments that discriminate between the activated and native conformation of the extracellular matrix protein vitronectin. One of the selected antibody fragments, scFv VN18, was used to construct a fully human IgG/kappa monoclonal antibody with an affinity of 9.3 nM. In immunohistochemical analysis, scFv and huMab VN18 recognized activated vitronectin in tumor tissues, whereas hardly any activated vitronectin was detectable in normal tissues. Iodine 123-radiolabeled huMabVN18 was shown to target to Rous sarcoma virus-induced tumors in chickens, an animal model in which the epitope for huMab VN18 is exposed during tumor development. Our results establish activated vitronectin as a potential target for tumor therapy in humans.

Animals↗
PubMed2003

Cryptic clues as to how water-soluble protein toxins form pores in membranes.

Pore-forming protein toxins possess the remarkable property that they can exist either in a stable water-soluble state or as an integral membrane pore. In order to convert from the water-soluble to the membrane state, the toxin must undergo large conformational changes. Recent work on a class of pore-forming toxins that are rich in beta-sheet content suggests a common mechanism of membrane insertion may exist despite these toxins possessing very different primary, tertiary and quaternary structures.

Amino Acid Sequence↗
PubMed1996

Cryptic domains of a 60 kDa heat shock protein of Helicobacter pylori bound to bovine lactoferrin.

Bovine lactoferrin binds to a 60 kDa heat shock protein of Helicobacter pylori. Binding ability was related to human immunoglobulin G because bovine lactoferrin binding proteins were isolated by extraction of cell surface associated proteins with distilled water, applied on IgG-Sepharose and nickel sulphate chelate affinity chromatography. Binding was demonstrated by Western blot after purified protein was digested with alpha-chymotrypsin and incubated with peroxidase-labeled bovine lactoferrin. Binding was inhibited by bovine lactoferrin, lactose, rhamnose, galactose, and two iron-containing proteins, ferritin and haptoglobin. Helicobacter pylori binds ferritin and haptoglobin via charge or hydrophobic interactions because this binding was not inhibited by specific and various glycoproteins or carbohydrates. Carbohydrate moieties of bovine lactoferrin molecules seem to be involved in binding because glycoproteins with similar carbohydrate structures strongly inhibited binding. Scatchard plot analysis of the binding of peroxidase-labeled bovine lactoferrin to H. pylori cells yielded a kd 2.88 x 10(-6) M. In addition, binding of H. pylori cells to bovine lactoferrin was enhanced when bacteria treated with pepsin or alpha-chymotrypsin after isolation from iron-restricted and iron-containing media.

Animals↗
PubMed2026

A functional atlas of transposon-encoded products and their integration into host networks.

Transposable elements (TEs) are pervasive genomic components that propagate via self-encoded factors, yet the nature, regulation, and function of these factors remain largely unresolved. Here, we integrated extensive long- and short-read transcriptome data, regulatory network analyses, deep proteomics, and structural predictions to construct a comprehensive atlas of TE products in Arabidopsis. We show that TE expression is embedded within host regulatory circuits, with DNA methylation and transcription factors jointly shaping TE transcriptional activity. Proteomic analyses confirm the production of over a hundred of high-confidence TE-encoded proteins, and structure-guided analyses of the transcript-informed TE proteome predict previously uncharacterized structural folds, multimerization capacity, and host protein interaction potential. Structural alignments further uncover cryptic homologies between TE-encoded proteins and host factors, including cases of domestications and co-options. Together, our study reveals the functional integration of TEs into cellular pathways and underscores the role of TEs as active drivers of genome function and innovation.

Arabidopsis↗
PubMed1997

The self-association and fibronectin-binding sites of fibulin-1 map to calcium-binding epidermal growth factor-like domains.

Fibulin-1 is a modular glycoprotein with amino-terminal anaphylatoxin-like modules followed by nine epidermal growth factor (EGF)-like modules and, depending on alternative splicing, four possible carboxyl termini. Fibulin-1 has been shown to self-associate as well as to bind calcium, fibronectin (FN), laminin, nidogen, and fibrinogen. To map ligand-binding sites within fibulin-1, polypeptides corresponding to various regions of fibulin-1 were expressed recombinantly and evaluated for their capacity to bind calcium, FN, or fibulin-1. A calcium-binding site(s) was mapped to EGF-like modules 5-9. A fibulin-1 self-association site was localized to EGF-like modules 5 and 6 (amino acid residues 356-440), as was a binding site for FN. The self-association interaction mediated by this pair of modules involved calcium since divalent cation chelators reduced the binding affinity of the interaction. By contrast, FN binding to EGF-like modules 5 and 6 was unaffected by the presence of divalent cation chelators. It can be concluded that EGF-like modules 5 and 6 bind calcium and mediate homotypic interaction between EGF-like modules 5 and 6 present in different fibulin-1 molecules and heterotypic interaction between EGF-like modules 5 and 6 and type III repeats 13 and 14 in FN. While additional binding sites for calcium or FN were not detected, another fibulin-1 self-association site was found within amino acid residues 30-173. However, unlike the self-association site in EGF-like modules 5 and 6, which was functional in the native protein, the amino-terminal site was cryptic and revealed only after the protein was denatured.

Binding Sites↗
PubMed2005

Recent advances in GFP folding reporter and split-GFP solubility reporter technologies. Application to improving the folding and solubility of recalcitrant proteins from Mycobacterium tuberculosis.

We have improved our green fluorescent protein (GFP) folding reporter technology [Waldo et al., (1999) Nat. Biotechnol. 17, 691-695] to evolve recalcitrant proteins from Mycobacterium tuberculosis. The target protein is inserted into the scaffolding of the GFP, eliminating false-positive artifacts caused by expression of truncated protein variants from internal cryptic ribosome binding sites in the target RNA. In parallel, we have developed a new quantitative fluorescent protein tagging and detection system based on micro-domains of GFP. This split-GFP system, which works both in vivo and in vitro, is amenable to high-throughput assays of protein expression and solubility [Cabantous et al., (2005) Nat. Biotechnol. 23, 102-107]. Together, the GFP folding reporter and split-GFP technologies offer a comprehensive system for manipulating and improving protein folding and solubility.

Bacterial Proteins↗
PubMed1996

Overcoming the crypticity of a viral T cell determinant by insertion into a chimeric bacterial protein.

Among the potential T cell determinants contained in a protein antigen, the T cell response only focuses on a few immunodominant T cell determinants, whereas cryptic epitopes remain hidden to the immune system. In the present work, we have studied the antigen processing and presentation of the C3:93-115 sequences of Mahoney poliovirus VP1 protein, which is immunodominant in H-2d but cryptic in H-2s and H-2q mouse MHC haplotypes. For this purpose, we genetically inserted the C3 determinant into five internal sites of a bacterial protein, the maltose binding protein of Escherichia coli (MalE). In four out of five insertion sites of MalE, the C3 determinant retained its immunodominance when the purified hybrid proteins were injected to BALB/c (H-2d) mice. Moreover, in SJL/J (H-2s) mice, in three out of five MalE-C3 constructs, the new structural environment of the cryptic C3 epitope rescued its processing and its in vivo presentation to T cells. In contrast, in DBA/1 (H-2q) mice, although MalE-C3 chimeric proteins were correctly processed in vitro, the C3 epitope remained cryptic in vivo. In this case, the impairment to stimulate a T cell response in vivo was correlated with a short time persistence of C3 peptides bound to Aq molecules at the surface of live antigen-presenting cells. These results emphasize the role of flanking residues on the lack of processing of cryptic determinants and the importance of the life span of peptide-MHC complexes to stimulate T cell responses.

ATP-Binding Cassette Transporters↗
PubMed1985

Maximizing gene expression from plasmid vectors containing the lambda PL promoter: strategies for overproducing transcription termination factor rho.

We have constructed two plasmids in which transcription of the rho gene from Escherichia coli K-12 is under the control of the lambda phage PL promoter. In p31-356, the normal rho promoter is deleted, but the remainder of the rho leader region, including the ribosome binding site, is present. In p39-AS, the rho leader is completely absent, and the lambda cII ribosome binding site replaces that of rho. Under noninducing conditions, expression of rho protein from these plasmids is repressed by the lambda cI protein in hosts carrying lambda cryptic prophage. Induction using mitomycin C or nalidixic acid in a cryptic lysogen carrying the cI+ repressor resulted in the overproduction of rho protein to levels of 3%-5% of the total cellular protein with p31-356, and to levels of approximately equal to 40% with p39-AS. The overproduced protein is functionally indistinguishable from the rho protein isolated from the K-12 strain W3110, and it can be obtained from cells harboring p39-AS in yields of up to 25 mg of rho per g of cells. In contrast to chemical induction, heat induction in four cryptic lambda lysogens carrying the thermolabile cI857 repressor failed to yield the same high levels of rho protein (with either plasmid). Our results show that chemical induction of PL-containing plasmid expression vectors can serve as a convenient and useful alternative to the commonly used method of heat induction.

Bacteriophage lambda↗
PubMed1990

Transcriptional regulation of 3-methylcholanthrene-inducible P-450 gene responsible for metabolic activation of aromatic carcinogenes.

We have investigated the transcriptional regulation of 3-methylcholanthrene (3MC)-inducible P-450c gene which is involved in the metabolic activation of polycyclic aromatic carcinogens. Reverse genetic study using the fusion gene composed of the 5' upstream sequence of P-450c gene and the structure gene for bacterial chloramphenicol acetyltransferase (CAT) and a cultured cell line of Hepa-1 cells localized two kinds of cis-acting regulatory DNA elements. One is designated XRE or xenobiotic responsive element which is responsible for the inducibility of the gene and is distributed 5 times in the region from -3.0 to -0.5 kb. The other is BTE or basal transcription element whose deletion reduces a low level of the constitutive CAT expression to a background level, and which is localized immediately upstream of the TATA sequence. Both kinds of regulatory elements are necessary for a high level of inducible expression. Gel mobility shift assay strongly suggests that the binding protein to the XRE is an Ah receptor with a specific affinity for 3MC or 2,3,7,8,tetrachlorodibenzo-p-dioxin (TCDD). Without inducer treatment, cryptic form of the binding protein occurs only in the cytoplasm of the Hepa-1 cells. Upon treatment with the inducer, the cryptic form of the binding protein exhibits binding activity to XRE and, at the same time, translocates to the nuclei. The BTE-binding protein is an ubiquitous nuclear factor and its cDNA cloning reveals the DNA-binding feature with zinc finger motifs.

Animals↗