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PubMed1989

Production of human adrenocorticotropin by cleavage of alkaline-phosphatase-derived fusion proteins containing repetitive recognition sequences for collagenases.

Recombinant plasmids coding for fusion proteins which consist of human adrenocorticotropin joined to N-terminal sequences of Escherichia coli alkaline phosphatase via collagenase-sensitive linkers were constructed and used for the production of these proteins by transformed E. coli cells. It was shown that repetitive linkers of the form -Gly-(Pro-Xaa-Gly)n-Pro- with n greater than or equal to 2 were cleaved by clostridiopeptidase A (Clostridium histolyticum) by orders of magnitude faster than corresponding nonrepetitive sequences (n = 1). The C-terminal cleavage product was Gly-Pro-adrenocorticotropin which could be converted to the authentic hormone by dipeptidyl peptidase IV. On the basis of these enzymatic reactions a procedure for the preparation of pure adrenocorticotropin was developed. Derivatives of alkaline phosphatase containing similar repetitive linker sequences were cleaved by clostridiopeptidase A as efficiently as the adrenocorticotropin fusion proteins.

Adrenocorticotropic Hormone↗
PubMedDate not supplied

[Mechanism determining the variability of the immunologic specificity spectrum of antibodies and other immunoglobulins (theory)].

An analysis of the theories of immunity-the germ line theory, the translocations and recombinations theory, the somatic mutation theory, and the reverse translation theory advanced earlier shows that their postulates afford no answer to any of the central questions of immunology, such as: 1) The origin of genetic information which codes the entire multimillion totality of immunologically different antibodies and antigen-recognizing receptors of the immunological system B and T cells. 2) The causes of sharp differences in both, the resolving power and mechanisms of recognition of antigenic determinant by antibodies and B cell receptors, on the one hand, and of macromolecular antigens as such by antigen-recognizing receptors of T cells, on the other 3) The essence of the mechanisms by means of which the T cell receptors recognize and distinguish the macro-molecular antigens as such. A new theory is advanced which in terms of the principle of cross stereocomplementarycity determining the regularities of mutual specific recognition by polynucleotides and polypeptides coded by them and also on the basis of some biophysical, virological phenomena explains the physico-chemical and genetic basis of immunological phenomena mentioned above.

Antibody Specificity↗
PubMed1990

Simultaneous manipulation of propositional and analog codes in picture memory.

Revealing a picture as a whole or as momentarily displayed strips presumably manipulated the propositional coding of the picture. Analog manipulation employed superimposition of a grid pattern. Effectiveness of simultaneous manipulations was tested via recognition with three foil categories, each of which presumably tapped the analog or propositional codes mainly, or both of them in detection. While figural units' perspective reversals should presumably be detected via the analog code, their locational displacements should be detected via the propositional code. Foils with novel item substitution should be detected by both codes. On the basis of such presumptions about encoding and recognition manipulations, certain predictions were made for scan and grid effects in "reversal," "displacement," and "novelty" foil categories. Full confirmation of these predictions was then taken as evidence that both analog and propositional codes do exist. Once such evidence was established, other issues were tackled, showing that target detection involves the propositional code only, while foil detection involves both codes. Further, recognition hypermnesia, where performance improves with repeated testing, was obtained only when both codes were attenuated. Data suggested that subjects might be switching from analog to propositional codes when both codes were strong, thereby preventing hypermnesia.

Adult↗
PubMed1987

Molecular cloning and sequencing of a cDNA encoding the acyl carrier protein and its flanking domains in the mammalian fatty acid synthetase.

Cloned cDNAs containing coding sequences for domains proximal to the carboxy terminus of the rat fatty acid synthetase have been isolated using an expression vector and domain-specific antibodies. The coding regions were assigned to specific domains of the multifunctional complex by identification of sequences coding for characterized peptide fragments and by recognition of sequences homologous to other monofunctional enzymes. Two clones contain the entire coding region for the acyl carrier protein domain. The sequence is flanked at the 3'-end by a region coding for the thioesterase domain and at the 5'-end by a sequence coding for a reductase, most likely the ketoreductase domain. Thus the ordering of these domain-coding regions in the fatty acid synthetase mRNA is established. The acyl carrier protein domain exhibits about 25% homology with that of the discrete monofunctional acyl carrier proteins of Escherichia coli, spinach and barley, the ketoreductase domain exhibits about 25% homology with bacterial dihydrofolate reductases and the active site of the thioesterase domain exhibits both primary and secondary structural features common to the serine proteases. These findings lend support to the hypothesis that the polyfunctional fatty acid synthetase probably arose by a complex evolutionary process involving fusion of genes coding for seven individual enzymes.

Acyl Carrier Protein↗
PubMed1975

A possible model for cell-cell recognition via surface macromolecules.

Alternative possibilities for the establishment of the proper cell distribution during embryogenesis are summarized at the beginning, followed by an assessment of the examples known so far where cell-cell recognition is known to be mediated via cell surface components. In the second part the species-specific recognition process which occurs during the sorting-out of dissociated sponge cells is analysed since it may serve as a possible model for cell-cell recognition in higher animals. Three possible mechanisms for the establishment of proper cell distribution are considered. These include, first, chemotaxis: secondly, guidance of cell or cell sheet movement by extracellular matrix or by surrounding cells and thirdly, random movement followed by recognition at the final point of destination. Recognition is necessary for both of the two latter processes, i.e. for cell guidance as well as for locking the cells into their final position after random movement. Two basically different recognition mechanisms should be distinguished from each other. On the one hand cells may recognize each other with the help of macromolecules situated in or just outside of the plasmamembrane which fit to each other like enzymes and substrates or antibodies and antigens. On the other hand, cells may exchange information by exchanging cytoplasmatic components via vesicles or gap junctions. The species-specific aggregation of dissociated sponge cells is considered to be a possible model for cell-cell recognition in higher animals. A proteoglycan-like intercellular macromolecule called aggregation factor seems to mediate recognition of a given species of cells in the reaggregation process of dissociated cells. The data available at the present time suggest that a monovalent surface macromolecule (baseplate) may mediate the recognition process probably by recognizing the carbohydrate side chains of the multivalent proteoglycan aggregation factor. A cell-free system was devised to mimic this aggregation process. Addition of aggregation factor to baseplate-coated sepharose beads of approximately the size of the original sponge cells has essentially the same characteristics as the cellular system. Macromolecule-coded surface information for the recognition between cells has not been established during the embryogenesis of higher animals and remains an interesting challenge.

Animals↗
PubMed1992

T cells and human autoimmune thyroid disease: emerging data show lack of need to invoke suppressor T cell problems.

Human T cells recognize self and foreign antigens when such antigens are processed into small peptides and bound to molecules coded for by genes of the HLA region on chromosome 6. The part of the T-cell surface which is responsible for such recognition is a set of molecules coded for by a variety of genes and known as the T-cell-receptor complex. In animal models, T cells are able to transfer autoimmune thyroiditis and T cells have, therefore, long been implicated in the etiology of human autoimmune thyroid disease (AITD). Information gained from the study of intrathyroidal T cells and thyroid antigen-specific T-cell clones has shown that in patients with Graves' disease, mainly helper T-cell clones have been obtained, whereas in autoimmune (Hashimoto's) thyroiditis cytolytic T-cell clones may be predominant. Such thyroid antigen-specific T cells have now been shown to recognize one or other of the three major thyroid-specific antigens; thyroglobulin, thyroid peroxidase, or the TSH receptor and efforts are currently in progress to characterize the T-cell epitopes of these major thyroid autoantigens. Recent findings of restricted T-cell receptor V gene use amongst intrathyroidal T cells confirm the primary role of T cells in human thyroid autoimmune processes leading to AITD. However, the mechanisms whereby such autoreactive T cells escape deletion and anergy, and how they become activated, remain uncertain. There is compelling evidence that the thyroid cell itself, by expressing HLA molecules, and presenting antigen directly to the T cells, may initiate disease, perhaps after an external insult.

Amino Acid Sequence↗
PubMed1987

Immunoglobulin variable region heptamer-nonamer recognition sequence joined to rearranged D-J segment: implications for the immunoglobulin recombinase mechanism.

We have found a novel immunoglobulin gene rearrangement in a murine hybridoma in which a heavy chain variable region (VH) heptamer-nonamer recognition sequence is joined to the diversity segment (D) through head-to-head fusion. The heptamer-nonamer recognition sequence and its adjacent 5' DNA are derived from the downstream flanking region of a germline VH gene. Sequence analysis indicates that this adjacent DNA is homologous to the downstream flank of VH108B, and it has characteristics of RNA processing that may suggest it was derived from an mRNA intermediate; these unusual features indicate that the segment is a processed gene. Because of head-to-head fusion, the recognition sequence and the flanking sequence are in opposite transcriptional polarity to D. The latter is joined correctly at its 3' border to a joining (J) gene segment. A gamma 1 constant region (but not mu) is located further downstream. Thus this fragment has several features common to normal immunoglobulin heavy chain gene rearrangement despite the unusual joining event involving V-D. Linkage of the VH heptamer-nonamer recognition sequence to D has not been observed previously. Although the recognition sequence described is inverted with respect to D and J, the endonucleolytic process that cleaved the recognition sequence at the 5' border of the heptamer before rearranging it to D was accurate. We suggest that of the three functions associated with the recombinase reaction; recognition, cutting, and ligation, only recognition and cutting may be limited to specific structures, and the ligation step may be less restricted because it is not confined to forming coding-to-coding or flank-to-flank joints. This aberrant ligation product suggests that the information leading to normal rearrangements may be found in structures that include more than the recognition sequences or coding regions alone, because the joining described here has spliced the incorrect end of a recognition sequence to a coding region to yield a nonproductive recombination.

Animals↗
PubMed1989

DNA synthesis in CD4- and CD8-positive cells in synovial fluid of patients with reactive and rheumatoid arthritis.

The occurrence of MHC class I antigens and microbial antigens derived from the triggering infection of the diseased joints in reactive arthritis (ReA) seems to set the stage for local immune activation. In this report activated lymphocytes are demonstrated by using an avidin-biotin-peroxidase complex (ABC) method combined with autoradiography that identifies DNA synthesis and, thus, activation. Most of the activated T lymphocytes in reactive arthritis were found to belong to the CD8 suppressor/cytotoxic T-lymphocyte subset. In striking contrast, the majority of the activated T lymphocytes detected in rheumatoid arthritis (RA) synovial fluid belonged to the CD4 helper/inducer subset. These findings agree well with the assumption that CD8-positive cells identify the foreign antigen in the context of class I antigens, whereas CD4-positive cells are found to be associated with the recognition of MHC locus II coded HLA antigens.

Adult↗
PubMed1979

Interferon effect on ribosomal ribonucleic acid related to chromosome 21 ploidy.

Antiviral and cell-growth-inhibitory activities of human interferon were shown to be related to the activity of a gene or genes present on chromosome 21. The 18s rRNA is vital to cell growth; it is capable of a viral-mRNA-recognition function and it is coded for by genes a portion of which are present on chromosome-21. A previously reported ability of human interferon to affect rRNA metabolism is characterized by a decrease in the sucrose-gradient-peak ratio of radiolabelled 28S to 18S rRNA in extracts from the cytoplasm of interferon-treated human fibroblasts. In the present report, interferon dose-response curves are presented demonstrating a direct relationship between a decrease in this ratio and interferon concentrations in the media. By using this virus-independent cytoplasmic rRNA assay, eight human fibroblast lines, differing in chromosome 21 ploidy, were tested for sensitivity to human interferon. Two monosomy-21, two euploid-21 and four trisomy-21 cell lines were tested. The monosomy-21 cell populations were significantly less sensitive to interferon than the other six cell types tested. Of the cell lines tested, the most sensitive, by a wide margin, was a trisomy-21 line. Trisomy-21 cell monolayer sensitivity, however, varied widely within the range from normal to supersensitive. These observations suggest that interferon's ability to affect rRNA metabolism is related to the activity of a gene or genes present on chromosome 21.

Cell Line↗
PubMed1986

A peptide to DNA conversion program.

A modification and extension of the computer program REVCUT (Blumenthal et al, Nucl. Acids Res. 10, 91-101 (1982) is described. The new program searches for restriction endonuclease recognition sites that are not coding DNA sequences of a protein of known aminoacid sequence using bit patterns. The modifications make the program more accurate and extend the range of the restriction endonucleases.

Amino Acid Sequence↗
PubMed1990

The yeast Yarrowia lipolytica has two, functional, signal recognition particle 7S RNA genes.

Cells containing a deletion of either the SCR1 or SCR2 genes, which code for the 7SL RNA component of the signal recognition particle (SRP) homologue, were found to be viable. Two independent approaches demonstrated that cells containing deletions of both genes were inviable. Therefore, Yarrowia lipolytica contains two (and only two) functional 7SL RNA genes.

Blotting, Southern↗
PubMed1988

'Recognition units' at the top of a neuronal hierarchy? Prepacemaker neurons in Eigenmannia code the sign of frequency differences unambiguously.

The electric fish, Eigenmannia, is able to discriminate the sign of the frequency difference, Df, between a neighbor's electric organ discharges (EODs) and its own. The fish lowers its EOD frequency for positive Dfs and raises its frequency for negative Dfs to minimize jamming of its electrolocation ability by a neighbor's EODs of similar frequency. This jamming avoidance response (JAR) is controlled by a group of 'sign-selective' neurons in the prepacemaker nucleus (PPN) that is located at the boundary of the midbrain and the diencephalon (Fig. 1). Extracellular recordings from a total of 35 neurons revealed a great similarity between behavioral and neuronal response properties: 1. All neurons fired vigorously for negative Dfs and were almost silent for positive Dfs, regardless of the orientation of the jamming stimulus, and thus discriminated the sign of Df unambiguously (Fig. 2). 2. In accordance with behavioral observations, individual neurons failed to discriminate the sign of Df when the jamming stimulus had the same field geometry as the signal mimicking the animal's own EOD (Fig. 3). 3. Df magnitudes which evoke strongest JARs, usually 4 to 8 Hz, also induced most vigorous responses in sign-selective neurons (Fig. 5). 4. Behavioral and neuronal thresholds for the detection of small jamming signals were similar. Threshold for sign selectivity was reached when the amplitude ratio of the jamming signal to the EOD mimic, measured near the head surface, was 0.001. This value corresponds to a maximal temporal disparity (a necessary cue for performing a correct JAR) of 1 to 2 microseconds for signals received by the two sides of the body in a transverse jamming field (Fig. 7). 5. The effects of two jamming fields, offered orthogonally to each other, may interact nonlinearly at the behavioral as well as at the neuronal level. A positive Df presented in one field may suppress behavioral and neuronal responses to modulations of the sign of Df in the other field (Fig. 8c).

Animals↗
PubMed1992

Assessment of protein coding measures.

A number of methods for recognizing protein coding genes in DNA sequence have been published over the last 13 years, and new, more comprehensive algorithms, drawing on the repertoire of existing techniques, continue to be developed. To optimize continued development, it is valuable to systematically review and evaluate published techniques. At the core of most gene recognition algorithms is one or more coding measures--functions which produce, given any sample window of sequence, a number or vector intended to measure the degree to which a sample sequence resembles a window of 'typical' exonic DNA. In this paper we review and synthesize the underlying coding measures from published algorithms. A standardized benchmark is described, and each of the measures is evaluated according to this benchmark. Our main conclusion is that a very simple and obvious measure--counting oligomers--is more effective than any of the more sophisticated measures. Different measures contain different information. However there is a great deal of redundancy in the current suite of measures. We show that in future development of gene recognition algorithms, attention can probably be limited to six of the twenty or so measures proposed to date.

Algorithms↗
PubMed1978

Nuclear volume control by nucleoskeletal DNA, selection for cell volume and cell growth rate, and the solution of the DNA C-value paradox.

The 40,000-fold variation in eukaryote haploid DNA content is unrelated to organismic complexity or to the numbers of protein-coding genes. In eukaryote microorganisms, as well as in animals and plants, DNA content is strongly correlated with cell volume and nuclear volume, and with cell cycle length and minimum generation time. These correlations are simply explained by postulating that DNA has 2 major functions unrelated to its protein-coding capacity: (1) the control of cell volume by the number of replicon origins, and (2) the determination of nuclear volume by the overall bulk of the DNA: cell growth rates are determined by the cell volume and by the area of the nuclear envelope available for nucleocytoplasmic transport of RNA, which in turn depends on the nuclear volume and therefore on the DNA content. During evolution nuclear volume, and therefore DNA content, has to be adjusted to the cell volume to allow reasonable growth rates. The great diversity of cell volumes and growth rates, and therefore of DNA contents, among eukaryotes results from a varying balance in different species between r-selection, which favours small cells and rapid growth rates and therefore low DNA C-values, and K-selection which favours large cells and slow growth rates and therefore high DNA C-values. In multicellular organisms cell size needs to vary in different tissues: size differences between somatic cells result from polyteny, endopolyploidy, or the synthesis of nucleoskeletal RNA. Conflict between the need for large ova and small somatic cells explains why lampbrush chromosomes, nurse cells, chromatin diminution and chromosome elimination evolved. Similar evolutionary considerations clarify the nature of polygenes, the significance of the distribution of haploidy, diploidy and dikaryosis in life cycles and of double fertilization in angiosperms, and of heteroploidy despite DNA constancy in cultured cells, and other puzzles in eukaryote chromosome biology. Eukaryote DNA can be divided into genic DNA (G-DNA), which codes for proteins (or serves as recognition sites for proteins involved in transcription, replication and recombination), and nucleoskeletal DNA (S-DNA) which exists only because of its nucleoskeletal role in determining the nuclear volume (which it shares with G-DNA, and performs not only directly, but also indirectly by coding for nucleoskeletal RNA). Mechanistic and evolutionary implications of this are discussed.

Animals↗
PubMed1986

Structure of rat calmodulin processed genes with implications for a mRNA-mediated process of insertion.

Two distinct processed calmodulin genes of rat (lambda SC8 and lambda SC9) were identified, cloned and their DNA sequences determined. The existence of direct repeats of 19 base-pairs for lambda SC8 or 9 base-pairs for lambda SC9 at both ends of the coding plus non-coding regions suggested a possible involvement of a mRNA-mediated process of insertion. Total genomic Southern hybridization suggested the existence of at least three different calmodulin-related genes in the rat genome. The other gene was the bona fide calmodulin gene (lambda SC4) which was split into at least five exons. lambda SC9 contained insertions of one nucleotide and two 17 base-pair direct repeats in the coding region. These insertions cause frameshift mutations probably preventing it from encoding a functional calmodulin. It also carried an insertion of a rat middle repetitive sequence, identifier sequence (IDS: Sutcliffe et al., 1982) in the 3'-non-coding region. Otherwise, it consisted of an almost identical DNA sequence to that of the bona fide calmodulin gene (lambda SC4), including the 3'-non-coding region down to the poly(A) recognition signal, A-A-T-A-A-A. On the other hand, lambda SC8 did not possess frameshift mutations in the coding region, and hence was capable of encoding a functional protein. In fact, a probe specific to the lambda SC8 sequence identified a band in Northern blotting whose size was 300 nucleotides smaller than that of authentic calmodulin mRNA. Comparison of the nucleotide sequences showed that only the coding regions of these two processed genes were homologous, indicating that the divergence of these two processed genes from the common ancestor calmodulin was an ancient event.

Amino Acid Sequence↗
PubMedDate not supplied

Cloning and sequencing of the yeast Saccharomyces cerevisiae SEC1 gene localized on chromosome IV.

The SEC1 gene of yeast Saccharomyces cerevisiae was cloned by complementing the temperature-sensitive mutation of sec1-1 at 37 degrees C, and its nucleotide sequence was determined. SEC1 is a single copy gene and encodes a protein of 724 amino acids and 83,490 daltons with a predicted pI value of 6.11. Hydrophobicity plotting showed no clearly hydrophobic regions suggesting a soluble nature for the protein. Amino acid sequence comparisons revealed no obvious homologies with the proteins in the SWISSPROT databank. Two consensus sequence for the cdc2 encoded protein kinase recognition site were revealed within Sec1p. The codon usage suggests a low expression level for SEC1. The 5' non-translated region contains two TATA-like sequences at -52 and -215 nucleotides from the translation start site. Two potential regulatory sequences for DNA binding proteins were found in the non-coding 5' region: a HAP2/HAP3 consensus recognition sequence at nucleotide-154 and a BAF1 consensus recognition sequence at nucleotide-136. The SEC1 specific probe detected a 2400 nucleotides long transcript, which was in reasonable agreement with the 2172 nucleotides long open reading frame.

Amino Acid Sequence↗
PubMedDate not supplied

Avoidance of DNA methylation. A virus-encoded methylase inhibitor and evidence for counterselection of methylase recognition sites in viral genomes.

The ocr+ gene of bacterial virus T7 codes for the first protein recognized to inhibit a specific group of DNA methylases. The recognition sequences of several other DNA methylases, not susceptible to Ocr inhibition, are significantly suppressed in the virus genome. The bacterial virus T3 encodes an Ado-Met hydrolase, destroying the methyl donor and causing T3 DNA to be totally unmethylated. These observations could stimulate analogous investigations into the regulation of DNA methylation patterns of eukaryotic viruses and cells. For instance, an underrepresentation of methylation sites (5'-CG) is also true for animal DNA viruses. Moreover, we were able to disclose some novel properties of DNA restriction-modification enzymes concerning the protection of DNA recognition sequences in which only one strand can be methylated (e.g., type III enzyme EcoP15) and the primary resistance of (unmethylated) DNA recognition sites towards type II restriction endonuclease EcoRII.

Base Sequence↗