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Identification and functional analysis of the transcriptional enhancer of the human T cell receptor beta gene.

The productive rearrangement and transcription of T cell receptor (TcR) beta genes is confined to T lymphocytes and is subject to both tissue-specific and developmental regulation. In addition to their function in transcriptional control, cis-acting elements are likely to play a role in the regulation of the rearrangement process. In this report we describe the location of a strong and inducible transcriptional enhancer 3' to the human TcR C beta 2 gene segment. The core enhancer, defined by deletion analysis using a transient transfection assay, resided within 362 bp of DNA. This enhancer core was able to activate transcription from a heterologous promoter and functioned well in T and B lymphocytes, but only minimally in HeLa cells. In contrast, a longer fragment containing the enhancer core showed marked T cell specificity. The enhancer was highly inducible by phorbol esters, the molecular basis for the inducibility residing within a 118-bp region of the enhancer core. This inducibility may be important in modulation of TcR beta gene expression during T cell differentiation and/or activation.

Base Sequence↗

Chimeric enzymes. Structure-function analysis of segments of sn-1,2-diacylglycerol choline- and ethanolaminephosphotransferases.

The Saccharomyces cerevisiae CPT1 and EPT1 genes represent structural genes that encode distinct choline- and choline/ethanolaminephosphotransferases, respectively. To explore the function of linear segments of these enzymes, a series of 14 EPT1-CPT1 chimeric gene constructs and the parental wild-type genes were expressed in a cpt1 ept1 double null mutant background completely devoid of phosphoamino alcohol transferase activity. Eleven of the chimeric genes expressed functional enzymes. The CDP-amino alcohol and sn-1,2-diacylglycerol (DAG) substrate specificities and essential phospholipid cofactor requirements of the parental and chimeric enzymes were investigated using a mixed micellar assay system. Chimeric enzymes exhibited a pattern of CDP-amino alcohol affinities that defined a structural domain sufficient to confer CDP-amino alcohol specificity. When wild-type enzymes were investigated using a chemically defined series of DAGs, each possessed a distinct characteristic pattern of utilization. Chimeric enzymes exhibited DAG acyl chain specificity profiles that either conformed to parental wild-type patterns or represented novel substrate specificities. Correlation of these outcomes with their underlying structural modifications permitted the assignment of an internal, linear region of 218 amino acids sufficient to confer DAG acyl chain specificity; this region contained three predicted transmembrane segments. Neither wild-type enzyme showed significant acyl chain selectivity with respect to phospholipid activation when a homologous series of chemically defined phosphatidylcholines were employed, suggesting that enzyme recognition of the fatty acyl moieties of the DAG substrate and phospholipid activator is fundamentally different. Analysis of chimeric enzymes dependence on phospholipid activators suggested the involvement of discontinuous protein segments participating in the interaction with phospholipid cofactors.

Amino Alcohols↗

Biochemical and functional analysis of mice deficient in expression of the CD45-associated phosphoprotein LPAP.

The role of the CD45-associated phosphoprotein (LPAP / CD45-AP) during an immune response remains unclear. To understand better the function of LPAP we generated LPAP-deficient mice by disrupting exon 2 of the LPAP gene. LPAP-null mice were healthy and did not show gross abnormalities compared to their wild-type littermates. However, immunofluorescence analysis of T and B lymphocytes revealed a reduced expression of CD45, which did not affect a particular subpopulation. In contrast to a recent report (Matsuda et al., J. Exp. Med. 1998. 187: 1863 - 1870) we neither observed significant alterations of the assembly of the CD45 / lck-complex nor of polyclonal T-cell responses. However, lymphnodes from LPAP-null mice showed increased cellularity, which could indicate that expression of LPAP might be required to prevent expansion of lymphocytes in particular lymphatic organs rather than potentiating immune responses.

Animals↗

Intracellular targeting and functional analysis of single-chain Fv fragments in mammalian cells.

In the past decade, intracellular antibodies have proven to be a useful tool in obtaining the phenotypic knock-out of selected gene function in different animal and plant systems. This strategy is based on the ectopic expression of recombinant forms of antibodies targeted towards different intracellular compartments, exploiting specific targeting signals to confer the new intracellular location. The functional basis of this technology is closely linked to the ability of intracellular antibodies to interact with their target antigens in vivo. This interaction allows either a direct neutralising effect or the dislodgement of the target protein from its normal intracellular location and, by this mechanism, the inactivation of its function. By using this approach, the function of several antigens has been inhibited in the cytoplasm, the nucleus, and the secretory compartments. In this article, we shall describe all the steps required for expressing single-chain Fv fragments in different subcellular compartments of mammalian cells and their subsequent use in knock-out experiments, starting from a cloned single-chain Fv fragment. This will include the analysis of the solubility properties of the new scFv fragment in transfected mammalian cells, the intracellular distribution of the antigen-antibody complex, and the resulting phenotype.

Animals↗

Functional analysis of capsaicin receptor (vanilloid receptor subtype 1) multimerization and agonist responsiveness using a dominant negative mutation.

The recently cloned vanilloid receptor subtype 1 (VR1) is a ligand-gated channel that is activated by capsaicin, protons, and heat. We have attempted to develop a dominant negative isoform by targeting several mutations of VR1 at highly conserved amino acids or at residues of potential functional importance and expressing the mutants in Chinese hamster ovary cells. Mutation of three highly conserved amino acid residues in the putative sixth transmembrane domain disrupts activation of the VR1 receptor by both capsaicin and resiniferatoxin. The vanilloid binding site in this mutant is intact, although the affinity for [(3)H]resiniferatoxin (RTX) is diminished by nearly 40-fold. Interestingly, this mutant retains a significant but diminished response to protons, supporting the existence of multiple gating mechanisms for different stimuli. The mutant appears to function by interfering with the gating induced by vanilloids rather than the expression level or permeability of the receptor. In addition, this mutant was found to function as a strong dominant negative mutation when coexpressed with wild-type VR1, providing functional evidence that the VR1 receptor forms a multimeric complex. Analysis of both current density and [(3)H]RTX affinity in cells cotransfected with different ratios of wild-type and mutant VR1 is consistent with tetrameric stoichiometry for the native capsaicin receptor.

Amino Acid Substitution↗

Capsid assembly and involved function analysis of twelve core protein mutants of duck hepatitis B virus.

The roles of different regions of the duck hepatitis B virus (DHBV) core protein on viral capsid assembly and related functions were examined. Twelve deletion and insertion mutations which covered 80% of the DHBV C open reading frame were constructed and expressed in Escherichia coli. The N-terminal region (amino acids 3 to 66) of DHBV core protein was important for its tertiary structure and function in E. coli. The expressed core mutants without this region apparently inhibited E. coli growth. The results of transmission electron microscopy of E. coli thin sections, capsid agarose gel, and sucrose gradient sedimentation demonstrated that a few DHBV core mutants with insertion in the N terminus and deletion in the C terminus retained the ability to form core-like particles in E. coli. However, other mutations in most of N-terminal and central regions strongly inhibited the self-assembly ability of DHBV core protein in E. coli. In addition, the mutant with a C-terminal region deletion (amino acids 181 to 228) lost most of the nucleic acid-binding activity of the DHBV core protein.

Amino Acid Sequence↗

Functional analysis of the human variants of breast cancer resistance protein: I206L, N590Y, and D620N.

Previous studies have shown that the V12M and Q141K variants of breast cancer resistance protein (BCRP) can affect expression and function of the transporter. In this study, the effects of the I206L, N590Y, and D620N variants on protein expression, plasma membrane localization, and transport activity of BCRP were investigated. Wild-type BCRP and the three variants were stably expressed in human embryonic kidney (HEK) cells. Confocal microscopy analysis showed that the three variants were predominantly routed to the plasma membrane of HEK cells. The expression level of I206L in the plasma membrane was approximately 45% of that of wild-type protein, whereas the N590Y and D620N levels were increased approximately 3.6-fold and 2.4-fold, respectively, as determined by immunoblotting. All three variants transported mitoxantrone, pheophorbide a, and BODIPY FL-prazosin. After normalization for differences in BCRP expression, I206L, N590Y, and D620N exhibited approximately 2-fold, 0.3-fold, and 0.5-fold wild-type efflux activities, respectively. The variants also conferred resistance to mitoxantrone and topotecan. Mitoxantrone and topotecan resistance by I206L and N590Y was approximately 2-fold and 0.3-fold of the wild-type BCRP resistance levels, respectively. Although D620N conferred a topotecan resistance similar to that of the wild-type protein, its level of mitoxantrone resistance was decreased by 50%. After normalization to BCRP expression levels, ATPase activities of I206L were not significantly different from those of wild-type protein, whereas N590Y and D620N exhibited approximately 30% and 50% of wild-type ATPase activities, respectively. These results suggest that I206L has the lowest protein expression and the highest activity, whereas N590Y and D620N display higher expression and lower activity, relative to wild-type BCRP.

ATP Binding Cassette Transporter, Subfamily G, Mem↗

Regulation of the TRP4 gene of Saccharomyces cerevisiae at the transcriptional level and functional analysis of its promotor.

The TRP4 gene of Saccharomyces cerevisiae, which encodes anthranilate phosphoribosyl transferase (E.C. 2.4.2.18), is subject to the general control of amino acid biosynthesis. The regulation takes place at the transcriptional level by increasing the amount of initiation and not by changing the stability of mRNA. We have observed a change in the utilization of TRP4 mRNA start sites, depending on whether cells were grown under repressing or derepressing conditions. The function of promoter elements has been tested by deletion analysis with a plasmid-encoded TRP4 gene. A routinely practicable method was used for copy-number calibration of plasmids based on 2 micron DNA. Promoter structures and spacing problems in the TRP4 promoter region are discussed.

Anthranilate Phosphoribosyltransferase↗

Molecular cloning and functional analysis of Photobacterium damselae subsp. piscicida haem receptor gene.

A haem receptor gene from Photobacterium damselae subsp. piscicida (formerly known as Pasteurella piscicida) has been cloned, sequenced and analysed for its function. The gene, designated as pph, has an open reading frame consisting of 2154 bp, a predicted 718 amino acid residues and exists as a single copy. It is homologous with the haem receptors of Vibrio anguillarum hupA, V. cholerae hutA, V. mimicus mhuA and V. vulnificus hupA at 32.7, 32.7, 45.6 and 30.9%, respectively, and is highly conserved, consisting of a Phe-Arg-Ala-Pro sequence (FRAP), an iron transport related molecule (TonB) and a Asn-Pron-Asn-Leu sequence (NPNL), binding motifs associated with haem receptors. As a single gene knockout mutant P. damselae subsp. piscicida was able to bind haem in the absence of pph, suggesting that other receptors may be involved in its iron transport system. This study shows that the P. damselae subsp. piscicida pph belongs to the haem receptor family, is conserved and that its iron-binding system may involve more than one receptor.

Amino Acid Motifs↗

Structural dissection and functional analysis of the complex promoter of the streptokinase gene from Streptococcus equisimilis H46A.

The overlapping tandem promoters of the streptokinase gene, P1 and P2, identified previously by S1 nuclease transcript mapping were functionally dissected by mutagenesis of their -10 regions and fused transcriptionally with or without the 202-bp upstream region (USR) to the luciferase reporter gene (luc) from Photinus pyralis to analyze the contribution of the different sequence elements to promoter activity in Escherichia coli and the homologous Streptococcus equisimilis strain H46A. In E. coli, virtually the entire promoter activity derived from the upstream promoter P1. In S. equisimilis, luc expression increased in the following order of the involved sequence elements: P2 approximately equal to P2 + USR < P1 < P1 + P2 < P1 + USR < P1 + P2 + USR. This shows that (1) in the homologous system, P1 and P2 alone are extremely weak, (2) in the USR-less arrangement, only the combined core promoters have substantial activity, and (3) the USR stimulates only P1 and the combination of P1 + P2. Thus, the tandem promoters presumably function by mutual contributary action and their full activity strongly depends on the AT-rich and statically bent upstream region. The distinctive feature determining the strength of P1 in both hosts appears to be its extended -10 region which matches the consensus TRTGN established for strong S. pneumoniae and Bacillus subtilis promoters.

Base Sequence↗

Functional analysis of point mutations in human flap endonuclease-1 active site.

Human flap endonuclease-1 (hFEN-1) is highly homologous to human XPG, Saccharomyces cerevisiae RAD2 and S.cerevisiae RTH1 and shares structural and functional similarity with viral exonucleases such as T4 RNase H, T5 exonuclease and prokaryotic DNA polymerase 5'nucleases. Sequence alignment of 18 structure-specific nucleases revealed two conserved nuclease domains with seven conserved carboxyl residues and one positively charged residue. In a previous report, we showed that removal of the side chain of each individual acidic residue results in complete loss of flap endonuclease activity. Here we report a detailed analysis of substrate cleavage and binding of these mutant enzymes as well as of an additional site-directed mutation of a conserved acidic residue (E160). We found that the active mutant (R103A) has substrate binding and cleavage activity indistinguishable from the wild type enzyme. Of the inactive mutants, one (D181A) has substrate binding properties comparable to the wild type, while three others (D34A, D86A and E160A) bind with lower apparent affinity (2-, 9- and 18-fold reduced, respectively). The other mutants (D158A, D179A and D233A) have no detectable binding activity. We interpret the structural implications of these findings using the crystal structures of related enzymes with the flap endonuclease activity and propose that there are two metal ions (Mg2+or Mn2+) in hFEN enzyme. These two metal coordinated active sites are distinguishable but interrelated. One metal site is directly involved in nucleophile attack to the substrate phosphodiester bonds while the other may stabilize the structure for the DNA substrate binding. These two sites may be relatively close since some of carboxyl residues can serve as ligands for both sites.

Amino Acid Sequence↗

Stoichiometric structure-function analysis of the prolactin receptor signaling domain by receptor chimeras.

The intracellular domain of the prolactin (PRL) receptor (PRLr) is required for PRL-induced signaling and proliferation. To identify and test the functional stoichiometry of those PRLr motifs required for transduction and growth, chimeras consisting of the extracellular domain of either the alpha or beta subunit of human granulocyte-macrophage colony-stimulating factor (GM-CSF) receptor (GM-CSFr) and the intracellular domain of the rat PRLr were synthesized. Because the high-affinity binding of GM-CSF results from the specific pairing of one alpha- and one beta-GM-CSFr, use of GM-CSFr/PRLr chimera enabled targeted dimerization of the PRLr intracellular domain. To that end, the extracellular domains of the alpha- and beta-GM-CSFr were conjugated to one of the following mutations: (i) PRLr C-terminal truncations, termed alpha278, alpha294, alpha300, alpha322, or beta322; (ii) PRLr tyrosine replacements, termed Y309F, Y382F, or Y309+382F; or, (iii) PRLr wild-type short, intermediate, or long isoforms. These chimeras were cotransfected into the cytokine-responsive Ba/F3 line, and their expression was confirmed by ligand binding and Northern and Western blot analyses. Data from these studies revealed that heterodimeric complexes of the wild type with C-terminal truncation mutants of the PRLr intracellular domain were incapable of ligand-induced signaling or proliferation. Replacement of any single tyrosine residue (Y309F or Y382F) in the dimerized PRLr complex resulted in a moderate reduction of receptor-associated Jak2 activation and proliferation. In contrast, trans replacement of these residues (i.e., alphaY309F and betaY382F) markedly reduced ligand-driven Jak2 activation and proliferation, while cis replacement of both tyrosine residues in a single intracellular domain (i.e., alphaY309+382F) produced an inactive signaling complex. Analysis of these GM-CSFr-PRLr complexes revealed equivalent levels of Jak2 in association with the mutant receptor chains, suggesting that the tyrosine residues at 309 and 382 do not contribute to Jak association, but instead to its activation. Heterodimeric pairings of the intracellular domains from the known PRLr receptor isoforms (short-intermediate, short-long, and intermediate-long) also yielded inactive receptor complexes. These data demonstrate that the tyrosine residues at 309 and 382, as well as additional residues within the C terminus of the dimerized PRLr complex, contribute to PRL-driven signaling and proliferation. Furthermore, these findings indicate a functional requirement for the pairing of Y309 and Y382 in trans within the dimerized receptor complex.

Animals↗

Use of chimeric human immunodeficiency virus types 1 and 2 reverse transcriptases for structure-function analysis and for mapping susceptibility to nonnucleoside inhibitors.

The human immunodeficiency virus type 1 and type 2 (HIV-1 and HIV-2) reverse transcriptases (RTs) are evolutionary related. To study the effect of homologous sequence replacements on polymerase function and to map the determinants of the lack of susceptibility of HIV-2 RT to nonnucleoside drugs, a series of chimeric HIV-1/HIV-2 RTs were constructed. Analysis of the chimeric RTs showed that wild-type levels of RNA-dependent DNA polymerase activity were retained when both finger and palm subdomains were exchanged as a unit between the two parental RTs. Analysis of enzymatically active chimeras for inhibition by the thiobenzimidazolone derivative TIBO R82150 showed that a segment of HIV-2 RT at 212-250, when placed in the HIV-1 RT context, conferred a 40-fold decrease in susceptibility to TIBO R82150. Site-directed mutagenesis of this segment found Tyr227 to be a key residue in this segment for the natural resistance of HIV-2 RT to TIBO R82150.

Amino Acids↗

Assay and functional analysis of the ARL3 effector RP2 involved in X-linked retinitis pigmentosa.

Mutations in RP2 cause X-linked retinitis pigmentosa and also macular and peripapillary atrophy. RP2 is a functional homologue of the tubulin folding cofactor, cofactor C, as it can replace the beta tubulin GTPase stimulating activity of cofactor C in an in vitro assay. An important difference between RP2 and cofactor C is their subcellular localization. RP2 is targeted to the cytoplasmic face of the plasma membrane by dual N-terminal acylation, and this post-translational modification is important for protein function. The activity of tubulin folding cofactors is modulated by certain ADP ribosylation factor-like (Arl) proteins. It has been shown that RP2 can interact directly with Arl3. Here we describe the methodologies that we have developed to analyze the interaction of RP2 with Arl3 and to investigate the effect of RP2 post-translational modifications on its subcellular and tissue localization.

ADP-Ribosylation Factors↗

Comparative structural and functional analysis of photoreceptor neurons of Rho-/- mice reveal increased survival on C57BL/6J in comparison to 129Sv genetic background.

To explore the possible influence of defined genetic backgrounds on photoreceptor viability and function in mice carrying a targeted disruption of the rhodopsin gene, the severities of retinopathies in Rho-/- mice on C57BL/6J and 129Sv congenic backgrounds were compared by light microscopy and electroretinography and qualitatively by in situ end labeling of DNA in apoptotic photoreceptor nuclei of retinal sections. Cone photoreceptor viability and function were shown to deteriorate more slowly on the C57BL/6J background in comparison to that of the 129Sv, with significantly greater numbers of outer nuclear layer nuclei in the retinas of C57BL/6J mice at 3 and 4 months of age. Both amplitude and waveform features of the ERG were shown to be remarkably different in the two strains, indicating an approximately 6-fold difference in C57BL/6J Rho-/- mice compared to 129Sv Rho-/- mice at 80 days. Thus, in comparison with the 129Sv strain, genetic modifiers appear to constitute a component of the C57BL/6J background, the expression of which significantly protects cone photoreceptors from apoptotic death in a mutation-induced murine retinopathy. The differences in phenotype revealed in this study are sufficient in principle to provide a basis for comparisons to be made between QTLs in light-induced and mutation-induced systems.

Aging↗

Functional analysis of the glycosylation of murine acid sphingomyelinase.

Glycosylation plays a crucial role in glycoprotein stability and its correct folding. Murine acid sphingomyelinase (ASM) is a lysosomal glycoprotein. We studied the functional role of its individual N-linked oligosaccharides needed to maintain enzymatic activity and protein stability. Mutagenized cDNA constructs were heterologously expressed. All six potential N-glycosylation sites were modified. Incomplete glycosylation of the most distant C-terminal site resulted in two isoforms. Oligosaccharides at N-84, N-173, and N-611 were found to be of minor importance for enzymatic activity. The glycosylation defect at N-333 or N-393 reduced the enzymatic activity to 40% and at N-518 to less than 20%. These mutations did not effect the Km value. Glycosylation at N-333 and N-393 mainly contributed to the enzyme stability and prevented degradation at lysosomal acidic pH, whereas the low residual enzymatic activity of mutant ASM deficient in glycosylation at N-518 was caused by protein misfolding. The mutant protein was also prone to proteolysis when trapped in the endoplasmic reticulum/cis-Golgi after brefeldin A application. Insufficiently glycosylated ASM formed a stable complex with BiP, an immunoglobulin heavy chain-binding protein, and thus remained in the endoplasmic reticulum. 32PO4 labeling revealed that the glycosylation mutants of ASM were phosphorylated predominantly at mannose residues of oligosaccharides linked to N-84, N-333, and N-393.

Animals↗

Structural and functional analysis of integrin alpha2I domain interaction with echovirus 1.

Integrins are cell surface receptors for several microbial pathogens including echovirus 1 (EV1), a picornavirus. Cryo-electron microscopy revealed that the functional domain (alpha(2)I) of human alpha(2)beta(1) integrin binds to a surface depression on the EV1 capsid. This three-dimensional structure of EV1 bound to alpha(2)I domain provides the first structural details of an integrin interacting with a picornavirus. The model indicates that alpha(2)beta(1) integrin cannot simultaneously bind both EV1 and the physiological ligand collagen. Compared with collagen binding to the alpha(2)I domain, the virus binds with a 10-fold higher affinity but in vitro uncoating of EV1 was not observed as a result of attachment of alpha(2)I. A molecular model, constructed on the basis of the EV1-integrin complex, shows that multiple alpha(2)beta(1) heterodimers can bind at adjacent sites around the virus 5-fold symmetry axes without steric hindrance. In agreement with this, virus attachment to alpha(2)beta(1) integrin on the cell surface was found to result in integrin clustering, which can give rise to signaling and facilitate the initiation of the viral entry process that takes place via caveolae-mediated endocytosis.

Capsid↗

Yeast regulatory protein LEU3: a structure-function analysis.

Eleven mutations resulting in partially deleted or truncated LEU3 protein were generated by linker insertion or other modifications at restriction sites, deletion of restriction fragments, or oligonucleotide-directed mutagenesis. Functional studies of these mutants showed the following: (i) A specific DNA binding region is contained within the 173 N-terminal residues, but other regions of the protein are required for optimal binding. (ii) Activation of LEU2 expression depends on the C-terminal 113 residues of the LEU3 protein. (iii) Deletion of part or all of a central section of LEU3 eliminates the ability of the LEU3 protein to respond to the co-activator alpha-isopropylmalate, i.e. creates an unmodulated activator. (iv) Overproduction of unmodulated activator slows down cell growth. (v) Specific deletion of two short acidic regions, including one with net charge - 19, has only minor effects on activation and modulation.

Amino Acid Sequence↗