Biomedical subjects
W F Anderson
Publications and source records attributed to W F Anderson.
Lack of site specific recombination of exogenous DNA in mouse L cells.
Plasmids were constructed containing the HSV thymidine kinase gene and two copies of X. borealis 5S rDNA. Mouse L TK- cells were transformed with these DNAs, with selection for the TK+ gene. Transformed cells were then analyzed by Southern blot hybridization and hybridization in situ to determine whether integration of the exogenous DNA occurred at regions of chromosomal homology i.e., at the 5S rDNA regions. Four cell lines were analyzed by Southern blots. Differences in restriction endonuclease specificity strongly suggested that integration was at a different site in each cell line. Two cell lines were further analyzed by hybridization in situ; each showed a single integration site, both different from each other and different from the mouse L cell 5S rDNA sites. Therefore, the presence of two copies of the 5S rDNA gene in the DNA introduced by gene transfer and approximately 300-350 copies of the mouse 5S rDNA gene was not sufficient in these experiments to produce homologous integration into a specific site.
Comparison of the structures of cro and lambda repressor proteins from bacteriophage lambda.
The three-dimensional structures of cro repressor protein and of the amino-terminal domain of lambda repressor protein, both from bacteriophage lambda, are compared. The second and third alpha-helices, alpha 2 and alpha 3, are shown to have essentially identical conformations in the two proteins, confirming the significance of the amino acid sequence homology previously noted between these and other DNA binding proteins in the region corresponding to these helices. The correspondence between the two-helical units in cro and lambda repressor protein is better than the striking agreement noted previously between two-helical units in cro and catabolite gene-activator protein. Parts of the first alpha-helices of repressor and cro show a structural correspondence that suggests a revised sequence homology between the two proteins in their extreme amino-terminal regions. In particular, there is a short loop between the alpha 1 and alpha 2 helices of lambda repressor that is missing from cro. This structural difference may account for the observed differences found with different cros and repressors in the pattern of phosphates whose ethylation prevents the binding of these proteins to their specific recognition sites. Although the two proteins have strikingly similar alpha 2-alpha 3 helical units that are presumed to bind to DNA in an essentially similar manner, stereochemical restrictions prevent the alpha 2-alpha 3 units of the respective proteins aligning on the DNA in exactly the same way.
DNA-binding proteins.
The structures of three proteins that regulate gene expression have been determined recently and suggest how these proteins may bind to their specific recognition sites on the DNA. One protein (Cro) is a repressor of gene expression, the second (CAP) usually stimulates gene expression, and the third (lambda repressor) can act as either a repressor or an activator. The three proteins contain a substructure consisting of two consecutive alpha helices that is virtually identical in each case. Structural and amino acid sequence comparisons suggest that this bihelical fold occurs in a number of proteins that regulate gene expression, and is an intrinsic part of the DNA-protein recognition event. The modes of repression and activation by Cro and lambda repressor are understood reasonably well, but the mode of action of CAP is still unclear.
Crystallographic data for complexes of the Cro repressor with DNA.
Complexes of the bacteriophage lambda Cro repressor with two DNA duplexes have been crystallized. The DNA sequences are equimolar mixtures of ApTpCpApCpC and its complementary strand and ApCpCpGpCpApApGpG and its complementary strand, which are both parts of the lambda OR3 operator. The space group of both co-crystals is C2221 with cell dimensions a = 81.1 A, b = 89.2 A, and c = 80.0 A. Analysis of dissolved crystals shows that they respectively contain approximately two hexamers per Cro dimer and one nonamer per dimer. The co-crystals diffract to about 3 A resolution and appear suitable for structural studies.
Many gene-regulatory proteins appear to have a similar alpha-helical fold that binds DNA and evolved from a common precursor.
Amino acid and DNA sequence comparisons suggest that many sequence-specific DNA-binding proteins have in common an homologous region of about 22 amino acids. This region corresponds to two consecutive alpha-helices that occur in both Cro and cI repressor proteins of bacteriophage lambda and in catabolite gene activator protein of Escherichia coli and are presumed to interact with DNA. The results obtained here suggest that this alpha-helical DNA-binding fold occurs in many proteins that regulate gene expression. It also appears that this DNA-binding unit evolved from a common evolutionary precursor.
A mouse model for beta-thalassemia.
A mutation that produces an absolute deficiency of normal beta-major globin polypeptides has been recovered from a DBA/2J male mouse. Most mice homozygous for the deficiency survived to adulthood and reproduced but were smaller at birth than their littermates and demonstrated a hypochromic, microcytic anemia with severe anisocytosis, poikilocytosis, and reticulocytosis and the presence of inclusion bodies in a high proportion of circulating erythrocytes. Mice heterozygous for the deficiency demonstrated a mild reticulocytosis but were not clinically anemic. Analysis of globin chain synthesis in vitro by 3H-leucine incorporation revealed that beta-globin synthesis was nearly normal (95%) in heterozygotes and about 75% of normal in deficiency homozygotes. Molecular characterization of the mutation by restriction analysis revealed a deletion of about 3.3 kb of DNA, including regulatory sequences and all coding blocks for beta-major globin. Based on genetic and hematological criteria, mice homozygous for the mutant allele, designated Hbbth-1, represent the first animal model of beta-thalassemia (Cooley's anemia), a severe genetic disease of humans.
High resolution structural studies of Cro repressor protein and implications for DNA recognition.
Cro repressor is a small dimeric protein that binds to specific sites on the DNA of bacteriophage lambda. The structure of Cro has been determined and suggests that the protein binds to its sequence-specific sites with a pair of two-fold related alpha-helices of the protein located within successive major grooves of the DNA. From the known three-dimensional structure of the repressor, model building and energy refinement have been used to develop a detailed model for the presumed complex between Cro and DNA. Recognition of specific DNA binding sites appears to occur via multiple hydrogen bonds between amino acid side chains of the protein and base pair atoms exposed within the major groove of DNA. The Cro:DNA model is consistent with the calculated electrostatic potential energy surface of the protein. From a series of amino acid sequence and gene sequence comparisons, it appears that a number of other DNA-binding proteins have an alpha-helical DNA-binding region similar to that seen in Cro. The apparent sequence homology includes not only DNA-binding proteins from different bacteriophages, but also gene-regulatory proteins from bacteria and yeast. It has also been found that the conformations of part of the presumed DNA-binding regions of Cro repressor, lambda repressor and CAP gene activator proteins are strikingly similar. Taken together, these results strongly suggest that a two-helical structural unit occurs in the DNA-binding region of many proteins that regulate gene expression. However, the results to date do not suggest that there is a simple one-to-one recognition code between amino acids and bases. Crystals have been obtained of complexes of Cro with six-base-pair and nine-basepair DNA oligomers, and X-ray analysis of these co-crystals is in progress.
Diagnostic use of CFU-E formation from peripheral blood in polycythemia vera.
Peripheral blood mononuclear cells from five patients with polycythemia vera (P. vera) and three with other polycythemias were cultured in a methylcellulose system. Colony-forming unit-erythroid (CFU-E) colonies appeared after seven days in the absence of added erythropoietin (Ep) in all P. vera cultures. A pattern of growth similar to the one seen for P. vera patients occurred in the culture from a patient in whom that disease was suspected. In the cultures from two of the patients with other polycythemias, erythroid colonies did not appear even in the presence of Ep. These findings emphasize the potential value of culturing peripheral blood for CFU-E colonies in diagnosing polycythemia vera.
Cro repressor protein and its interaction with DNA.
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Differential activation of the mouse beta-globin promoter by enhancers.
A series of plasmids was constructed to study the effect of two enhancers, the simian virus 40 72-base-pair repeat and the Harvey sarcoma virus 73-base-pair repeat, on the mouse beta maj-globin promoter. These plasmids contain the mouse beta maj-globin promoter linked to the Escherichia coli galK gene, thus allowing galactokinase enzyme activity to be used as a measure of promoter function. In CV-1 (primate) cells, it was found that an enhancer is required for optimal promoter activity and that the simian virus 40 (primate) enhancer increases galactokinase fourfold more than the Harvey sarcoma virus (mouse) enhancer. In L (mouse) cells, however, the Harvey sarcoma virus enhancer is 1.3-fold stronger than the simian virus 40 enhancer. These data support the hypothesis that enhancer activity can be species specific. Furthermore, when both enhancers are present on the same plasmid, their effect is additive on the beta-globin promoter whether the plasmid is in CV-1 cells or L cells.
Globin gene expression in somatic cell hybrids.
Fusions between somatic cell lines have previously yielded evidence for the existence of trans-acting gene regulatory factors. For this reason, we developed a cell line containing a "locked in" human 11-X translocation chromosome (containing the beta-globin-like gene cluster) in MEL cells. The human 11-X chromosome is stably integrated in the "M11-X" cell line, and single-copy human gamma and beta genes are present. After induction with HMBA, M11-X cells produced 500 copies per cell of correctly initiated, processed, and terminated human beta-globin mRNA; authentic human beta-globin chains were also produced at a low level. Despite the presence of normally arranged human gamma-globin genes, no gamma-globin mRNA could be detected after HMBA induction. However, cytosine residues near the gamma-globin gene promoters are completely methylated in these cells, suggesting that the gamma-globin genes may be repressed in part by DNA methylation. The pattern of human globin gene expression in M11-X cells may be affected by methylation and/or by trans-acting factors produced by these tetraploid cells.
Proposed alpha-helical super-secondary structure associated with protein-dna recognition.
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The molecular basis of DNA-protein recognition inferred from the structure of cro repressor.
Recognition by cro repressor protein of its specific DNA binding sites appears to occur via multidentate hydrogen bonds between amino acid side chains of the protein and base-pair atoms in the major groove of right-handed B-form DNA. Most of the sequence-specific interactions between cro and DNA, as well as a number of sequence-independent ones, are mediated by a two-alpha-helical unit which appears to be common to many proteins that regulate gene expression.
Mixed myeloid-Lymphoid colonies in a patient with polycythemia vera.
Peripheral blood mononuclear cells from a patient with polycythemia vera were cultured in a methylcellulose system employing human serum. Electron microscopy documented the appearance of mixed colonies containing lymphocytes, granulocytes, megakaryocytes, and erythrocytes. In vitro culture characteristics were similar to those seen for other patients with polycythemia ver, ie, colonies grew in the absence of added erythropoietin or other pathway-specific regulators. Plating efficiency was linearly related to the number of cells plated, which supports the concept that each colony arose from a single cell. The appearance of mixed myeloid-lymphoid colonies points to the existence of a primitive stem cell capable of giving rise to multiple hematopoietic cell lines.
Regulation of human globin gene expression in mouse erythroleukemia x human fibroblast hybrid cells.
A somatic cell hybrid, XX-8, was obtained from a fusion of tetraploid mouse erythroleukemia cells with human Lesch-Nyhan skin fibroblasts. This hybrid cell was previously shown (1) to produce human beta- but no human gamma-globin mRNA sequences after induction with dimethylsulfoxide. In this study we show that: (a) human beta- and gamma-globin genes are present in XX-8 cells in approximately equal numbers; (b) no human gamma-globin mRNA sequences can be detected in either the cytoplasmic or nuclear RNA fractions even with several different inducers; (c) after induction the human beta-globin gene is converted from a DNase I insensitive or closed structure to a DNase I open configuration, while the human gamma-globin gene remains closed; and (d) no human beta-globin polypeptide can be detected in the intact induced cells, indicating that fibroblast globin genes, even when induced to make mRNA in an erythroid environment, do not synthesize an RNA that is translated efficiently.
Structural similarity in the DNA-binding domains of catabolite gene activator and cro repressor proteins.
It is shown that there is a structural similarity between the presumed DNA-binding regions of the Escherichia coli catabolite gene activator protein ("CAP") and the cro repressor protein ("cro") from bacteriophage lambda. The correspondence between the two proteins is particularly striking for a structural unit consisting of two consecutive alpha-helices. The 24 alpha-carbon atoms that constitute the two-helical structural units in the two proteins can be superimposed with a root-mean-square disagreement of 1.1 A. It is shown that this agreement is very unlikely to be due to a chance correspondence. For both CAP activator and cro repressor proteins it is the second alpha-helix of the two-helical unit that has been proposed to bind within the major groove of left-handed or right-handed B DNA, respectively [McKay, D. B. & Steitz, T. A. (1981) Nature (London) 290, 744-749; Anderson, W. F., Ohlendorf, D. H., Takeda, Y. & Matthews, B. W. (1981) Nature (London) 290, 754-758]. The structural correspondence between CAP and cro seen here, together with other recent evidence of sequence homologies between cro, CAP, and other proteins that bind double-stranded DNA, suggests that the two-helical unit is likely to be a common feature of many DNA-binding proteins. The results also suggest that some principles of specific protein-double-stranded DNA interaction may be general and include recognition via alpha-helices fitting into the major groove of the DNA.
Structure of the DNA-binding region of lac repressor inferred from its homology with cro repressor.
It is shown that the amino acid sequence and the DNA gene sequence of the 25 amino-terminal residues of the lac repressor protein of Escherichia coli are homologous with the sequences of five DNA-binding proteins: the cro repressor proteins from phage lambda and phage 434, the cI and cII proteins from phage lambda, and the repressor protein from Salmonella phage P22. The region of homology between lac repressor and the other proteins coincides with the principal DNA-binding region of cro repressor. In particular, residues Tyr-17 through Gln-26 of lac repressor correspond to the alpha-helix Gln-27 through Ala-36 of cro repressor, which we have postulated to bind within the major groove of the DNA and to be primarily responsible for the recognition of the DNA operator region by the protein [Anderson, W. F., Ohlendorf, D. H., Takeda, Y. & Matthews, B. W. (1981) Nature (London) 290, 754--758]. By analogy with cro repressor, we propose that residues 17--26 of lac repressor are alpha-helical and that this helix and a twofold-related alpha-helix in an adjacent subunit bind within successive major grooves of the lac operator, which is in a right-handed Watson--Crick B-DNA conformation. Also, by analogy with cro repressor, we suggest that residues Thr-5 through Ala-13 of lac repressor form a second alpha-helix and contribute, in part, to DNA binding. The proposed structure for the DNA-binding region of lac repressor is consistent with chemical protection data and with genetic experiments identifying the probable locations of a number of the residues of the repressor protein that either do or do not participate in DNA binding.