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PubMed1996

Role of directed growth and target selection in the formation of cortical pathways: prenatal development of the projection of area V2 to area V4 in the monkey.

In experiments combining retrograde tracers and histochemistry, we have looked at the prenatal development of the cortical pathway linking areas V2 and V4. Transient expression of acetylcholinesterase in fetal area V2 reveals the separate compartments that project to V4 (temporal directed pathway) and V5 (parietal directed pathway). During early stages of pathway formation, V2 neurons projecting to area V4 are clustered in the appropriate compartments. During the phase of rapid axonal growth, there is a selective increase of connections originating from the appropriate compartments leading to a strongly clustered organization at the peak of connectivity. During this phase, injections involving the white matter also showed clustering, but this was somewhat reduced in comparison to that of gray matter injections. The growth phase is followed by an elimination phase during which there is a tendency for a preferential loss of intercluster connections, which may sharpen the early formed pattern. These results demonstrate the primary role of axonal guidance and target recognition mechanisms followed by a limited extent of selective elimination during the formation of functional cortical pathways in the primate isocortex. Compared to previous findings, these results suggest that the developmental restriction of callosal connections is not a universal model of cortical development. In the present report, the directed growth and early specification of feed-forward connections contrast with the prolonged remodelling of monkey feedback projections, suggesting two distinct developmental strategies of pathway formation in the monkey.

Acetylcholinesterase↗
PubMed1996

In vitro protein-primed initiation of pneumococcal phage Cp-1 DNA replication occurs at the third 3' nucleotide of the linear template: a stepwise sliding-back mechanism.

Phage Cp-1 from Streptoccocus pneumoniae makes use of a protein-priming mechanism to start replication of its linear DNA: the first reaction consists of the addition of 5' dAMP to a molecule of the primer protein, an initiation event occurring at both DNA ends. After elongation of the initiation complex, the primer protein remains linked to the 5' end of the nascent DNA chain, and is subsequently referred to as terminal protein (TP). In this paper, using DNA-free extracts from Cp-1-infected S. pneumoniae, we provide evidence that the formation of the covalent complex TP-dAMP is a template-instructed reaction and that ssDNA molecules can serve as templates for TP-primed replication. A mutational analysis of the 3' terminal nucleotides of Cp-1 DNA reveals that a precise DNA sequence is required for efficient template recognition, and that in vitro initiation of Cp-1 DNA replication is directed by the third nucleotide of the template. However, the two terminal nucleotides are recovered during the first steps of elongation. A new variant of the sliding-back mechanism for protein-primed initiation, firstly described for Bacillus subtilis phage phi29, is proposed to account for the maintenance of Cp-1 DNA ends. The results presented here reinforce the hypothesis that sliding-back must be a common feature in all genomes that use protein-priming to initiate replication.

Bacillus Phages↗
PubMedDate not supplied

Structural studies with inhibitors of the cell cycle regulatory kinase cyclin-dependent protein kinase 2.

Components of the cell cycle machinery are frequently altered in cancer. Many of these alterations affect the cyclin-dependent kinases (CDKs) and their regulation. Staurosporine and 7-hydroxystaurosporine (UCN-01) are two natural product kinase inhibitors originally identified as potent protein kinase C inhibitors. Staurosporine is non-selective and too toxic for use in therapy, but UCN-01 shows greater selectivity, and is in clinical trials. We have determined the crystal structures of staurosporine bound to monomeric CDK2 and UCN-01 bound to active phospho-CDK2/cyclin A. Both compounds mimic the hydrogen bonds made by the adenine moiety of ATP, and both exploit the non-polar nature of the adenine-binding site. In the complex with UCN-01, a hydrogen-bonded water molecule is incorporated into the non-polar cavity, which provides a partial polar character in the environment of the 7-hydroxyl group. Comparison of the ATP-binding site of CDK2 with that of other kinases reveals that in Chk1 kinase, a major target for UCN-01 in the cell, one of the surrounding residues, Ala144 in CDK2, is a serine in Chk1, thus providing a possible explanation for the effectiveness of UCN-01 against this kinase. For cells to exit mitosis, the CDKs must be completely inactivated, firstly by the ubiquintin-mediated destruction of the cyclins, followed by dephosphorylation of phospho-Thr160 (in CDK2) catalysed by the kinase-associated phosphatase and protein phosphatase 2C. We describe the structure of phospho-CDK2 in complex with kinase-associated phosphatase, and discuss the substrate recognition promoted by interactions that are remote from the catalytic site.

CDC2-CDC28 Kinases↗
PubMed2003

The role of the 3' untranslated region in mRNA sorting to the vicinity of mitochondria is conserved from yeast to human cells.

We recently demonstrated, using yeast DNA microarrays, that mRNAs of polysomes that coisolate with mitochondria code for a subset of mitochondrial proteins. The majority of these mRNAs encode proteins of prokaryotic origin. Herein, we show that a similar association occurs between polysomes and mitochondria in human cells. To determine whether mRNA transport machinery is conserved from yeast to human cells, we examined the subcellular localization of human OXA1 mRNA in yeast. Oxa1p is a key component in the biogenesis of mitochondrial inner membrane and is conserved from bacteria to eukaryotic organelles. The expression of human OXA1 cDNA partially restores the respiratory capacity of yeast oxa1- cells. In this study, we demonstrate that 1) OXA1 mRNAs are remarkably enriched in mitochondrion-bound polysomes purified from yeast and human cells; 2) the presence of the human OXA1 3' untranslated region (UTR) is required for the function of the human Oxa1p inside yeast mitochondria; and 3) the accurate sorting of the human OXA1 mRNA to the vicinity of yeast mitochondria is due to the recognition by yeast proteins of the human 3' UTR. Therefore, it seems that the recognition mechanism of OXA1 3' UTR is conserved throughout evolution and is necessary for Oxa1p function.

Electron Transport Complex IV↗
PubMed1986

Information-processing abnormalities: trait- and state-dependent components.

Schizophrenics were compared to schizoaffective, bipolar, and nonpsychotic depressed patients in a visual masking paradigm in which an informational target stimulus was followed at varying intervals by a noninformational masking stimulus. In limiting the availability of the sensory signal provided by the target stimulus, the mask was used to probe how information from the environment enters and is processed by the central nervous system. The use of the masking paradigm was originally based on the hypothesis that thought disorder is a result of a more primary dysfunction in the processes that precede and result in thought. Results confirmed previous findings of a performance deficit in the schizophrenics when compared to nonpsychotic controls. Schizoaffective and bipolar patients also showed evidence of impaired processing, however. Results were interpreted in terms of a trait/state formulation in which impaired information processing is seen as a fundamental trait of schizophrenia spectrum disorders and as a state that can covary with psychotic illness in general. A unifying concept centers on the effects of psychopathological conditions on an individual's processing resources that results in either underprovision or overprovision of information from sensory input to complex cognitive operations dependent on the cerebral cortex. Findings from a variety of paradigms are consistent with those of the masking paradigm in revealing that the processing deficits of schizophrenics are time dependent and occur in the 500 ms following stimulus input.

Adult↗
PubMed2025

Charting the phenotypic landscape of mitochondrial diseases through a systematic evaluation of pathogenic mitochondrial DNA and nuclear gene variants.

PURPOSE: Primary mitochondrial diseases (PMD) arise from variants in the mitochondrial or nuclear genomes. Phenotype-based recognition of specific PMD genotypes remains difficult, prolonging the diagnostic odyssey. We expanded the MitoPhen database to characterize phenotypic variation across PMD more systematically. METHODS: Individual-level data on mitochondrial DNA disorders, nuclear-encoded mitochondrial diseases, and single large-scale mitochondrial DNA deletions were manually curated with Human Phenotype Ontology (HPO) terms to produce MitoPhen v2. Principal-component analysis summarized system-level abnormalities; HPO-level enrichment and mean phenotype-similarity scores were then used to distinguish common PMD genotypes. RESULTS: MitoPhen v2 adds 3940 individuals to the original release, now encompassing 1597 publications, 10,626 individuals, and 117 genotypes. Among 7586 affected cases, 72,861 HPO terms were recorded. Principal-component analysis revealed 6 phenotype dimensions capturing most system-level variance. At the HPO level, we observed genotype-specific enrichments and identified 111 gene-phenotype links absent from the current HPO database. Using MT-TL1, single large-scale mitochondrial DNA deletions, and POLG as exemplars, phenotype-similarity scores reliably separated individuals with these genotypes from those without. CONCLUSION: MitoPhen v2 enabled systematic, genotype-aware analysis of heterogeneous PMD phenotypes and highlighted the diagnostic value of structured, individual-level data. Phenotype-similarity metrics from such data sets can refine variant interpretation in large rare-disease cohorts and provide a transferable framework for other phenotypically complex genetic disorders.

Humans↗
PubMed1999

Characterization of a stage-specific Mr16000 schistosomular surface glycoprotein antigen of Schistosoma mansoni.

A 16 kDa Schistosoma mansoni schistosomular surface antigen (Sm16) was originally described as the target of a passively protective mAb (B3A). It appeared on the schistosomular surface after transformation of cercariae and was uniquely recognised by sera from animals exposed to attenuated cercariae. In this work sequential extractions of schistosomula with Triton X-114 and sodium dodecyl sulphate showed Sm16 to be an integral membrane structure which did not appear to be glycosylphosphatidylinositol-anchored as judged by experiments using phosphatidyl inositol-specific phospholipase C. The antigen was strongly reactive in Western blotting with rabbit irradiated vaccine sera. Sm16 was demonstrated in the hepatopancreas of S. mansoni-infected snails and was equally abundant in cercariae and mechanically- transformed schistosomula but was undetected in liver stage worms or eggs. Immunoelectron microscopy showed Sm16 to be localised, in cercariae, to what are believed to be subtegumental cell bodies packed with membraneous vesicles. Treatment with proteases and with sodium metaperiodate showed Sm16 to be a glycoprotein of which the epitope recognised by B3A was periodate sensitive. Two-dimensional electrophoresis gave a PI of 6. Neither the size or the recognition by B3A was affected by treatment with N-glycosidase F, endoglycosidase F or endo-alpha-N-acetylgalactosaminidase. Western blotting using a wide range of biotinylated lectins showed recognition only by peanut agglutinin and Ricinus communis agglutinin II (ricin). It is concluded that Sm16 has antigenic surface-exposed O-linked complex oligosaccharides which lack mannose/glucose, GlcNAc, L-fucose and sialic acid but contain terminal Gal beta (1-3) GalNAc and/or galactose.

Animals↗
PubMed1990

Fluorescence characterization of the interaction of various transfer RNA species with elongation factor Tu.GTP: evidence for a new functional role for elongation factor Tu in protein biosynthesis.

The ubiquity of elongation factor Tu (EF-Tu)-dependent conformational changes in amino-acyl-tRNA (aa-tRNA) and the origin of the binding energy associated with aa-tRNA.EF-Tu.GTP ternary complex formation have been examined spectroscopically. Fluorescein was attached covalently to the 4-thiouridine base at position 8 (s4U-8) in each of four elongator tRNAs (Ala, Met-m, Phe, and Val). Although the probes were chemically identical, their emission intensities in the free aa-tRNAs differed by nearly 3-fold, indicating that the dyes were in different environments and hence that the aa-tRNAs had different tertiary structures near s4U-8. Upon association with EF-Tu.GTP, the emission intensities increased by 244%, 57%, or 15% for three aa-tRNAs due to a change in tRNA conformation; the fourth aa-tRNA exhibited no fluorescence change upon binding to EF-Tu.GTP. Despite the great differences in the emission intensities of the free aa-tRNAs and in the magnitudes of their EF-Tu-dependent intensity increases, the emission intensity per aa-tRNA molecule was nearly the same (within 9% of the average) for the four aa-tRNAs when bound to EF-Tu-GTP. Thus, the binding of EF-Tu.GTP induced or selected a tRNA conformation near s4U-8 that was very similar, and possibly the same, for each aa-tRNA species. It therefore appears that EF-Tu functions, at least in part, by minimizing the conformational diversity in aa-tRNAs prior to their beginning the recognition and binding process at the single decoding site on the ribosome. Since an EF-Tu-dependent fluorescence change was also observed with fluorescein-labeled tRNA(Phe), the protein-dependent structural change is effected by direct interactions between EF-Tu and the tRNA and does not require the aminoacyl group. The Kd of the tRNA(Phe).EF-Tu.GTP ternary complex was determined, at equilibrium, to be 2.6 microM by the ability of the unacylated tRNA to compete with fluorescent Phe-tRNA for binding to the protein. Comparison of this Kd with that of the Phe-tRNA ternary complex showed that in this case the aminoacyl moiety contributed 4.3 kcal/mol toward ternary complex formation at 6 degrees C but that the bulk of the binding energy in the ternary complex was derived from direct protein-tRNA interactions.(ABSTRACT TRUNCATED AT 400 WORDS)

Escherichia coli↗
PubMed1984

Concentrations of prostaglandins E2, F2 alpha and 6-keto-prostaglandin F1 alpha in the utero-ovarian venous plasma of nonpregnant and early pregnant ewes.

The effect of pregnancy on concentrations of prostaglandins E2, F2 alpha and 6-keto-prostaglandin F1 alpha (PGE2, PGF2 alpha and 6-keto-PGF1 alpha) in utero-ovarian venous plasma was examined in ewes on Days 10 through 14 after estrus, an interval which includes the critical period for maternal recognition of pregnancy. The utero-ovarian vein ipsilateral to a corpus luteum was catheterized on Day 9 or 10 in 6 pregnant and 8 nonpregnant ewes. Five blood samples were collected at 30-min intervals for 2 h beginning at 0500 and 1700 h daily. Sampling began at 0500 h on the day after catheterization. The mean and variance within each 2-h collection period were calculated for each ewe. The natural logarithm of the variance in each collection period (ln variance) was used as an estimate of the fluctuations in secretory activity by the endometrial-conceptus complex. Patterns of the mean concentrations of PGE2 were different between pregnant and nonpregnant ewes (P less than 0.01); PGE2 being higher in the pregnant ewes beginning on Day 13. There was a trend for the patterns of ln variance in PGE2 to differ (P less than 0.1) with pregnancy status over the entire period; ln variance was greater in pregnant ewes beginning on Day 13. The patterns of the mean concentrations and ln variances for PGF2 alpha and 6-keto-PGF1 alpha did not differ between pregnant and nonpregnant ewes. There were significant increases in both of these prostaglandins over time, independent of pregnancy status (P less than 0.01). The association of higher concentrations of PGE2 in utero-ovarian venous plasma with early pregnancy is consistent with the hypothesis that PGE2, originating from the uterus and/or conceptus, is one factor involved in maintenance of the corpus luteum of pregnancy.

6-Ketoprostaglandin F1 alpha↗
PubMed2003

Electrostatic potential on human leukocyte antigen: implications for putative mechanism of chronic beryllium disease.

The pathobiology of chronic beryllium disease (CBD) involves the major histocompatibility complex class II human leukocyte antigen (HLA). Although occupational exposure to beryllium is the cause of CBD, molecular epidemiologic studies suggest that specific (Italic)HLA-DPB1(/Italic) alleles may be genetic susceptibility factors. We have studied three-dimensional structural models of HLA-DP proteins encoded by these genes. The extracellular domains of HLA-DPA1*0103/B1*1701, *1901, *0201, and *0401, and HLA-DPA1*0201/B1*1701, *1901, *0201, and *0401 were modeled from the X-ray coordinates of an HLA-DR template. Using these models, the electrostatic potential at the molecular surface of each HLA-DP was calculated and compared. These comparisons identify specific characteristics in the vicinity of the antigen-binding pocket that distinguish the different HLA-DP allotypes. Differences in electrostatics originate from the shape, specific disposition, and variation in the negatively charged groups around the pocket. The more negative the pocket potential, the greater the odds of developing CBD estimated from reported epidemiologic studies. Adverse impact is caused by charged substitutions in positions 55, 56, 69, 84, and 85, namely, the exact same loci identified as genetic markers of CBD susceptibility as well as cobalt-lung hard metal disease. These findings suggest that certain substitutions may promote an involuntary cation-binding site within a putatively metal-free peptide-binding pocket and therefore change the innate specificity of antigen recognition.

Amino Acid Sequence↗
PubMed1991

Covalent structure of the diheme cytochrome subunit and amino-terminal sequence of the flavoprotein subunit of flavocytochrome c from Chromatium vinosum.

The complete sequence of the 21-kDa cytochrome subunit of the flavocytochrome c (FC) from the purple phototrophic bacterium Chromatium vinosum has been determined to be as follows: EPTAEMLTNNCAGCHG THGNSVGPASPSIAQMDPMVFVEVMEGFKSGEIAS TIMGRIAKGYSTADFEKMAGYFKQQTYQPAKQSF DTALADTGAKLHDKYCEKCHVEGGKPLADEEDY HILAGQWTPYLQYAMSDFREERRPMEKKMASKL RELLKAEGDAGLDALFAFYASQQ. The sequence is the first example of a diheme cytochrome in a flavocytochrome complex. Although the locations of the heme binding sites and the heme ligands suggest that the cytochrome subunit is the result of gene doubling of a type I cytochrome c, as found with Azotobacter cytochrome c4, the extremely low similarity of only 7% between the two halves of the Chromatium FC heme subunit rather suggests that gene fusion is at the evolutionary origin of this cytochrome. The two halves also require a single residue internal deletion for alignment. The first half of the Chromatium FC heme subunit is 39% similar to the monoheme subunit of the FC from the green phototrophic bacterium Chlorobium thiosulfatophilum, but the second half is only 9% similar to the Chlorobium subunit. The N-terminal sequence of the Chromatium FC flavin subunit was determined up to residue 41 as AGRKVVVVGGGTGGATAAKYIKLADPSIEVTLIEP NTKYYT. It shows more similarity to the Chlorobium FC flavin subunit (60%) than do the two heme subunits. The N terminus of the flavin subunit is homologous to a number of flavoproteins, including succinate dehydrogenase, glutathione reductase, and monamine oxidase. There is no obvious homology to the Pseudomonas putida FC flavin subunit, which suggests that the two types of flavocytochrome c arose by convergent evolution. This is consistent with the dissimilar enzyme activities of FC as sulfide dehydrogenase in the phototrophic bacteria and as p-cresol methylhydroxylase in Pseudomonas. We also present a sequence "fingerprint" pattern for the recognition of FAD-binding proteins which is an extended version of the consensus sequence previously presented (Wierenga, R. K., Terpstra, P., and Hol, W. G. J. (1986) J. Mol. Biol. 187, 101-107) for nucleotide binding sites.

Amino Acid Sequence↗
PubMed1993

The roles of similarity in transfer: separating retrievability from inferential soundness.

Similarity is universally acknowledged to be central in transfer, but recent research suggests that its role is complex. The present research attempts to isolate and compare the determinants of similarity-based access to memory and the determinants of the subjective soundness and similarity of a match. We predicted, based on structure-mapping theory, that subjective soundness would depend on the degree of shared relational structure, particularly higher-order structure such as causal bindings. In contrast, we predicted that memory retrieval would be highly sensitive to surface similarities such as common object attributes. To assess retrievability, in three studies, subjects were asked to read a large set of stories and were later given a set of probe stories that resembled the original stories in systematically different ways; e.g., purely relational analogies, surface-similarity matches, or overall (literal similarity) matches. Subjects were told to write out any of the original stories that came to mind. To assess subjective soundness, independent subjects (and also the same reminding subjects) were asked to rate the inferential soundness of each pair; i.e., how well inferences true of one story would apply to the other. As predicted, subjective soundness was highly related to the degree of common relational structure, while retrievability was chiefly related to the degree of surface similarity. Ratings of the similarity of the pairs did not predict the retrievability ordering, arguing against the possibility that the retrieval ordering simply reflected overall similarity. Further, a fourth study demonstrated that subjects given a forced-choice recognition task could discriminate between possible matches on the basis of relational structure, ruling out the possibility that the poor relational retrieval resulted from forgetting or failing to encode the relational structure. We conclude that there is a dissociation between the similarity that governs access to long-term memory and that which is used in evaluating and reasoning from a present match. We describe a model, called MAC/FAC ("Many are called but few are chosen"), that uses a two-stage similarity retrieval process to model these findings. Finally, we speculate on the implications of this view for learning and transfer.

Adult↗
PubMed1994

The Escherichia coli prr region encodes a functional type IC DNA restriction system closely integrated with an anticodon nuclease gene.

The prr locus was originally described as coding a ribonuclease that is activated after phage T4 infection to cut within the anticodon of a specific tRNA, inactivating protein synthesis and thus blocking phage development. Wild-type T4 phage has two genes coding the enzymes polynucleotide kinase and RNA ligase, whose only function seems to be to repair the damage done by the anticodon nuclease. As the only apparent function of the prr ribonuclease is to combat phage infection, it can be considered as an RNA-based restriction enzyme. In non-infected cells, the prr enzyme is kept inactive in a complex with three other proteins which were predicted on the basis of DNA homologies to be the subunits of a type IC DNA restriction and modification system. Unlike other type IC systems so far characterized, prr is chromosomally rather than plasmid coded. However, sequences upstream from prr also have homology with sequences from the plasmid R124 and the prophage P1. We have now investigated the prr system and shown that it is indeed a bona fide type IC system which we call EcoprrI, and which is active both in vivo and in vitro. The system is fully functional even in the absence of the anticodon nuclease and seems to be a typical type I enzyme. EcoprrI recognizes the sequence CCA(N7)RTGC. One peculiarity is that, with low efficiency, EcoprrI will recognize and methylate variants of its recognition sequence such as CCT(N7)ATGC, which is methylated in one strand of the DNA only.

Amino Acid Sequence↗
PubMed2002

Five Lec1 CHO cell mutants have distinct Mgat1 gene mutations that encode truncated N-acetylglucosaminyltransferase I.

Lec1 CHO cell mutants lack N-acetylglucosaminyltransferase I (GlcNAc-TI) activity and do not synthesize complex or hybrid N-glycans. The origins of six independent lec1 mutations are shown to reside in the coding region of the Mgat1 gene, proving that GlcNAc-TI is mutated in Lec1 mutants. One mutant has Mgat1 gene transcripts of reduced size, whereas the others possess transcripts of approximately normal size and amount containing a unique insertion or transition mutation that leads to a premature stop codon in the Mgat1 gene coding region. The lec1 mutation in the Lec3.2.8.1 mutant, a line used to generate minimally glycosylated membrane glycoproteins for X-ray crystallography, is a G insertion that leads to a nonsense codon after amino acid 391. The Pro-Lec1.3C line from the ATCC and in laboratory stocks, a line used widely for diverse purposes, possesses a C insertion in the Mgat1 gene coding exon, causing a frame shift and producing a stable, truncated approximately 24-kDa product. Mgat1 gene mutations were confirmed by sequencing genomic DNA PCR products. Mutant cDNAs were reverted by site-directed mutagenesis and shown to confer wild-type lectin binding and GlcNAc-TI activity on Lec1 transfectants. Surprisingly, three Mgat1 gene nucleotide changes previously reported in Pro-Lec1.3C cells (Puthalakath et al. [1996] J. Biol. Chem., 271, 27818-27822) were not detected in this study. These Lec1 mutants provide a novel cohort for investigating the effects on Golgi trafficking and kin recognition of deletion mutants of GlcNAc-TI expressed at endogenous rather than nonphysiological levels.

Animals↗
PubMed1980

Fine specificity of alloimmune cytotoxic T lymphocytes directed against H-2K. A study with Kb mutants.

The fine specificity of alloimmune cytotoxic T lymphocytes (CTL) was investigated in CTL responses across the smallest known H-2 differences, those based on mutation at a single H-2 locus. CTL were generated in all possible mixed lymphocyte culture (MLC) combinations among seven H-2Kb mutants and the mouse strain of origin, C57BL/6 (B6-H-2b). CTL were also generated in all F1 hybrid responder/homozygous stimulator-cell combinations among four Kb mutants and B6-H-2b. CTL activity was measured in cell-mediated lympholysis (CML) against target cells from all Kb mutants and B6-H-2b. Cross-reactivity against targets other than the MLC stimulator was extensive and led to the distinction of 64 CML target determinants. Two Kb mutants (B6-H-2bm6 and B6.C-H-2bm9) showed identical typing for all 64 CML determinants. CML reactions after MLC between these two haplotypes were mutually negative. The mutants B6-H-2bm3 and B6.C-H-2bm11 showed identical typing for 47 of the 64 determinants. Their close relationship is in agreement with the finding that H-2bm3 anti-H-2bm11 CTL were the only ones that exclusively lysed target cells of stimulator-cell genotype. On the basis of CML typing, the sequence of relatedness of the mutants with H-2b is as follows: bm6/bm9-bm10-bm3-bm1-bm11, bm6/bm9 being the closest to, and bm11 the most distant from H-2b. The extensive cross-reactivity of alloimmune CTL appears to reflect immunogenetic complexity rather than lack of specificity. Comparison with other reports supports the notion that the system of Kb CML determinants, recognized by alloimmune CTL, is at least partially overlapping with the H-2Kb specificity repertoire involved in the associative T cell recognition of virus-infected cells.

Animals↗
PubMed1991

Interaction of a regulatory protein with a DNA target containing two overlapping binding sites.

The LexA repressor from Escherichia coli regulates the transcription of about 20 different genes upon binding to single or multiple operators. In this work we study the interaction of LexA with the control region of the caa gene (coding for the bacterial toxin colicin A) that contains two operators (O1 and O2) which overlap by at least 2 base pairs relevant for sequence specific DNA recognition. This arrangement raises the question of how the LexA molecules which bind to the central overlapping part of the two operators avoid steric clashes and further, of whether the interaction of LexA with the two operators is cooperative or not. To address these questions we have constructed two mutant operators (O1+O2- and O1-O2+) for which the two most strongly conserved base pairs in each of the external operator half-sites have been mutated. Using methylation interference with the complex formation of LexA with the wild-type and these two mutant operators we could show: 1) that the two mutant operators behave symmetrically in that the methylation of one crucial guanine base in both operator half-sites interferes strongly with complex formation, 2) but that in the wild-type operator (containing four functional operator half-sites) only the two external half-operators give rise to interference if this crucial guanine base is methylated, whereas methylation of the two equivalent guanine bases within the two central (overlapping) operator half-sites does not lead to interference with the formation of a complex where both operators are occupied simultaneously. These data suggest that the centrally bound LexA molecules adopt a somewhat different binding mode than those bound to the external half-operators in order to avoid steric clashes and/or to optimize protein-protein contacts which are likely to be at the origin of the binding cooperativity that we could demonstrate by quantitative DNase I footprinting and gel retardation experiments. While the methylation interference experiments revealed a non-equivalence for the binding of externally and centrally bound LexA molecules, both methylation protection and hydroxyl radical footprinting were unable to reveal this difference, suggesting that the difference between the two binding modes should be fairly subtle.

Bacterial Proteins↗
PubMed2005

Parallel evolution in ecological and reproductive traits to produce cryptic damselfly species across the holarctic.

The damselfly genus Enallagma originated in the Nearctic, and two Nearctic lineages recently underwent radiations partly associated with multiple independent habitat shifts from lakes dominated by fish predators into lakes dominated by dragonfly predators. A previous molecular study of four Palearctic morphospecies and all representative Nearctic species identified the presence of two cryptic species sets, with each set having Palearctic and Nearctic representatives. However, the cryptic species within each set are not sibling species. Here, we present quantitative data on ecologically important larval morphologies and behaviors involved in predator avoidance and on adult male morphological structures involved in mate recognition to quantify the phenotypic relationships among these cryptic species sets. For the adult stage, our data indicate strong parallel evolution of the structures involved in specific mate recognition-the male cerci. For the larval stage, morphometric analyses show that the Palearctic species evolved a nearly identical morphology to the sibling-clade members in the Nearctic that live in waters where dragonflies are the top predators. This implicates the importance of dragonfly predation in the history of the Palearctic clade. Behavioral analyses suggest population differentiation in response to the actual predator environment in the Palearctic clade, consistent with the species differentiation seen in the Nearctic. Our results suggest parallel evolution of adult traits that influence specific mate choice and larval traits that influence ecological performance underlie the striking similarity of Enallagma species across continents. This concurrent parallel evolution in both stages of a complex life cycle, especially when both stages do not share the same selective environment, may be a very unusual mechanism generating cryptic species.

Adaptation, Biological↗
PubMed1984

A murine T cell receptor gene complex: isolation, structure and rearrangement.

We describe here our efforts to develop a systematic strategy for the enumeration and isolation of genes encoding T cell-specific, membrane-associated polypeptides. Of particular importance among the cDNA clones that we have isolated is one which encodes the beta chain of the murine T cell receptor for antigen. The gene product is strikingly similar to immunoglobulin in its variable (V), constant (C), joining (J), and diversity (D) - like elements and the ability of the latter three types of element to assort independently during differentiation. The genomic organization of the constant region locus which encodes this molecule consists of two tandemly arrayed units of the form JC/JC, where the J clusters consist of fourteen distinct elements, many of which may be functional. The two constant regions differ by only four amino acids and both are apparently expressed in T cells of the same phenotype, so they probably do not represent isotypes in the classical sense. The sequences flanking the V, D and J elements are also similar to the conserved heptamer and nonomer sequences of immunoglobulins thought to be important in the recombination of the specific gene segments. These similarities indicate both the common evolutionary origins of these loci and the strong selective pressure that must be operative. The T cell receptor locus differs somewhat from immunoglobulins in the large number of possible J region elements and to some extent in the hypervariable-framework regions of the V region. We and others have mapped this gene to chromosome 6 of the mouse, in the same portion of the chromosome but not closely linked the kappa locus. The significance of the predicted protein structure of the beta chain and its support of the one-receptor model of MHC-antigen recognition are discussed.

Amino Acid Sequence↗