Isolation of a multigene family containing human alpha-tubulin sequences

The boundaries of the origin of polyoma DNA replication have been analyzed using a set of deletion mutants. The majority of these had small deletions, 5 to 30 base-pairs in size, which together removed most of the non-translated sequences of the genome. The phenotype of the mutants was characterized by analysis of infectivity, transforming ability and DNA synthesis. All mutants with reduced or abolished infectivity had corresponding defects of viral DNA synthesis. The effect of the deletion was cis-acting, since the replication of the mutants was not stimulated by the presence of wild-type DNA. Deletions causing a reduction of DNA synthesis were found at two sites. The first at the 32 base-pair inverted repeat sequence and the neighbouring A · T tract previously implicated in the initiation of DNA synthesis, and the second close to the late genes. The two sites were separated by at least 60 base-pairs of non-essential DNA. Only one mutant with a deletion at the second site was unable to express early gene functions.The mutants were constructed by linearization, shortening and recircularization of polyoma DNA inserted into the plasmid pBR322. The mutagenesis was directed at restriction endonuclease BglI or PvuII cleavage sites. The BglI-directed mutagenesis was focussed to polyoma DNA by using as a vector a derivative of pBR322 resistant to cleavage by BglI.     

Messenger RNAs from the transforming region of bovine papilloma virus type I

Messenger RNAs present in C127 mouse cells transformed by bovine papilloma virus type 1 (BPV-1) were studied by the S1 nuclease protection technique, Northern blotting, and electron microscopic heteroduplex analysis. The results revealed at least five classes of spliced mRNAs which we designate types 1 to 5. They had a common poly(A) addition site located at co-ordinate 53 and all mRNAs, except the type 3 mRNAs, contained an exon located between co-ordinates 41 and 53. In the type 1 mRNAs this exon was connected to a very short leader sequence located around co-ordinate 31. The type 2 mRNAs contained 220 to 400-nucleotide long leaders which were located approximately 1.5 X 10(3) base-pairs further upstream. Two different subclasses of type 2 molecules (2A and 2B) were identified and these had slightly different leaders. The type 4 mRNAs contained a bipartite leader, whereas the type 5 mRNAs carried an approximately 900-nucleotide long leader. The type 3 mRNAs consisted of a main exon located between co-ordinates 32 and 53, linked to the same leader as is present in the type 2A mRNAs. A cap site which presumably is utilized by the type 2A, type 3, type 4 and type 5 mRNAs was mapped at nucleotide 89 in the BPV-1 sequence. A putative cap site for the type 1 mRNAs was mapped at co-ordinate 31.     

Structure of the filamentous bacteriophage,Pf3, by X-ray fiber diffraction

Fiber diffraction data have been obtained for the filamentous bacteriophage Pf3. The virus crystallizes on a hexagonal net with lattice constants a = b = 5.61 nm and c = 7.50 nm at 0% relative humidity and a = 6 = 6.20 nm and c = 7.99 nm at 98% relative humidity. The X-ray diffraction pattern resembles those of two other bacteriophages, Pf 1 and Xf, and therefore belongs to class II. The data are consistent with a 27₅ helix symmetry with an axial rise of 0.277 (dry) to 0.296 (wet) nm.     

Molecular cloning and expression of cardiac-specific myosin heavy chain gene sequences in chick embryo

A recombinant DNA plasmid, pMHC8, that contains gene sequences for embryonic chick cardiac myosin heavy chain was constructed, identified and characterized. The identity of the clone was established by hybridization with labeled probes that afford screening of MHC²² with high specificity, by inhibition of MHC synthesis in the in vitro hybrid-arrested translation assay, and by tissue-specific hybridization of labeled pMHC8 DNA to MHC messenger RNA.The pMHC8 DNA probe is highly specific for chick heart muscle tissue, since it hybridized poorly to chick skeletal muscle RNA and did not detectably hybridize to adult rat heart RNA. Upon screening the embryonic chick heart cells in culture, no detectable level of MHC mRNA was observed in dividing myoblasts, but the mRNA appeared in differentiated cardiac myocytes paralleling morphogenetic changes in the embryonic cells.     

Conservation and DNA sequence arrangement of the DNA polymerase I gene region from Klebsiella aerogenes, Klebsiella pneumoniae and Escherichia coli

Linked multiple mutation is observed after treatment of Escherichia coli with methyl methanesulfonate, N-methyl-N′-nitro-N-nitrosoguanidine, ethyl methanesulfonate, and N-ethyl-N-nitro-N-nitrosoguanidine but not ultraviolet light. Induction of linked multiple mutations requires the uvrE⁺ gene product indicating the involvement of the mismatch repair system. The observation of linked multiple mutations is not due to mutagenesis occurring in a subpopulation of cells. Growing point mutagenesis also occurs after treatment with these mutagens but not with ultraviolet light. It is likely that the excess of mutations observed with these mutagens at growing points is at least partly a relative effect, rather than one due to an absolute increase of reactivity at the DNA growing point region. This relative effect may result from the operation of an inducible repair mechanism which removes O⁶-alkylguanine residues from the DNA distal to the bacterial growing point. The adaptive response, first described by Robins &; Cairns (1979) prefers O⁶-methylguanine over O⁶-ethylguanine.     

Structure and biochemistry of mouse hepatic gap junctions

A new method for the isolation of gap junctions from mouse liver is described. Particular attention has been directed to minimising the effects of proteolysis during isolation. The purified membrane fragments retain the typical morphological features found in junctions of the intact liver.The junctions show two major polypeptides upon polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulphate. The apparent molecular weights are 26,000 for the more abundant species and 21,000 for the minor component. Preliminary protein chemical characterisation by fingerprint analysis suggests that the two polypeptides are structurally related. While an in vivo origin of the 21,000 molecular weight species cannot be excluded, the sensitivity of the junction proteins to proteolytic degradation in vitro suggests that the 21,000 molecular weight molecule may be a breakdown product of the major component.Image reconstruction methods applied to micrographs of negatively stained isolated junctions show that the membrane contains a close-packed hexagonal lattice of components having marked 6-fold symmetry. It is suggested that these represent hexamers of the 26,000 molecular weight protein.Lipid analysis performed on gap junctions isolated by different procedures shows that the lipid composition is strongly affected by the detergents employed during the isolation. A large amount of phopholipid, but not cholesterol, can be extracted from the structure without affecting its gross morphology. This result suggests that cholesterol is tightly bound to the junction protein and may play a role in determining the structure of the gap junction.     

Kinetics and mechanism in the reaction of gene regulatory proteins with DNA

We have measured the kinetic properties of the Escherichia coli cAMP receptor protein (CAP) and lac repressor interacting with lac promoter restriction fragments. Under our reaction conditions (10 mM-Tris X HCl (pH 8.0 at 21 degrees C), 1 mM-EDTA, 10 microM-cAMP, 50 micrograms bovine serum albumin/ml, 5% glycerol), the association of CAP is at least a two-step process, with an initial, unstable complex formed with rate constant kappa a = 5(+/- 2.5) X 10(7) M-1 s-1. Subsequent formation of a stable complex occurs with an apparent bimolecular rate constant kappa a = 6.7 X 10(6) M-1 s-1. At low total DNA concentration, the dissociation rate constant for the specific CAP-DNA complex is 1.2 X 10(-4) s-1. The ratio of formation and dissociation rate constants yields an estimate of the equilibrium constant, Keq = 5 X 10(10) M-1, in good agreement with static results. We observed that the dissociation rate constant of both CAP-DNA and repressor-DNA complexes is increased by adding non-specific "catalytic" DNA to the reaction mixture. CAP dissociation by the concentration-dependent pathway is second-order in added non-specific DNA, consistent with either the simultaneous or the sequential participation of two DNA molecules in the reaction mechanism. The results imply a role for distal DNA in assembly-disassembly of specific CAP-DNA complexes, and are consistent with a model in which the subunits in the CAP dimer separate in the assembly-disassembly process. The dissociation of lac repressor-operator complexes was found to be DNA concentration-dependent as well, although in contrast to CAP, the reaction is first-order in catalytic DNA. Added excess operator-rich DNA gave more rapid dissociation than equivalent concentrations of non-specific DNA, indicating that the sequence content of the competing DNA influences the rate of repressor dissociation. The simplest interpretation of these observations is that lac repressor can be transferred directly from one DNA molecule to another. A comparison of the translocation rates calculated for direct transfer with those predicted by the one-dimensional sliding model indicates that direct transfer may play a role in the binding site search of lac repressor.     

Structure of the vanadate-induced crystals of sarcoplasmic reticulum Ca2+-ATPase

The projected structure of the vanadate-induced crystalline aggregates of Ca2+-ATPase molecules in isolated sarcoplasmic reticulum membranes has been determined. The molecules form tubular crystals with an oblique surface lattice having cell dimensions a = 65.9 A, b = 114.4 A and gamma = 77.9 degrees. The space group is P2. The crystalline tubules are formed through lateral aggregation of chains made up of dimers of Ca2+-ATPase molecules.     

Structure of the central spacer region of extrachromosomal ribosomal DNA in Physarum polycephalum

We have analyzed the sequence organization of the central spacer region of the extrachromosomal ribosomal DNA from two strains of the acellular slime mold Physarum polycephalum. It had been inferred previously from electron microscopy that this region, which comprises about one third of the 60 kb³ palindromic rDNA, contains a complex series of inverted repetitious sequences. By partial digestion of end-labeled fragments isolated from purified rDNA and from rDNA fragments cloned in Escherichia coli, we have constructed a detailed restriction map of this region. The 11 kb of spacer DNA of each half molecule of rDNA contains the following elements: (a) two separate regions, one of 1.1 kb and one of 2.1 kb, composed of many direct repeats of the same 30 base-pair unit; (b) a region of 4.4 kb composed of a complex series of inverted repeats of a 310 base-pair unit; (c) another region of 1.6 kb composed of inverted repeats of the same 310 base-pair unit located directly adjacent to the center of the rDNA; (d) two copies of a unique sequence of 0.85 kb, which probably contains a replication origin. Some of the CpG sequences in the spacer resist cleavage by certain restriction endonucleases and thus appear to be methylated. The lack of perfect symmetry about the central axis and the arrangement of inverted repeated sequences explain the complex pattern of branches and forks of the fold-back molecules previously observed by electron microscopy. Comparison of the rDNA restriction maps from the two strains of Physarum suggests that the repeat units in the spacer are undergoing concerted evolution. We propose a model to explain the evolutionary origin of the several palindromic axes in the Physarum rDNA spacer.     

Evidence for sub-families of actin genes in Dictyostelium as determined by comparisons of 3' end sequences

We have sequenced the 3′ end of five actin genomic clones and three actin complementary DNA clones from Dictyostelium. Comparison of the sequences shows that the protein coding regions are highly conserved, while the region corresponding to the 3′ untranslated regions are divergent. Additional analysis indicates regions of homology in the 3′ untranslated region between sets of actin genes. Southern DNA blot hybridization studies using labeled 3′ ends suggest that there are sub-families of actin genes that are related within the 3′ untranslated regions. No homology is found in the sequences outside the messenger RNA encoding regions. Analysis of the sequence data has shown that the difference in length between the ~1.25 × 10³ and ~1.35 × 10³ base actin messenger RNAs is in the lengths of the 3′ untranslated region.     

Structure of two adrenal polypeptides containing multiple enkephalin sequences

Two enkephalin-containing polypeptides of 4000 and 5000 daltons have been isolated from extracts of bovine adrenal medulla. Each polypeptide was purified to homogeneity and subjected to sequence analysis. The entire primary structure of the 4000-dalton polypeptide was established by a combination of automated Edman degradation and chemical analysis of its tryptic peptides. The polypeptide contains two copies of the [Met]-enkephalin sequence, one at the amino terminus and the other at the carboxyl terminus. Chemical analysis of the tryptic peptides and automated Edman degradation of the 5000-dalton polypeptide indicated the presence of a [Leu]enkephalin sequence at the carboxyl terminus and an internal [Met]enkephalin sequence. Both of the above enkephalin-containing polypeptides appear to be intermediates in the biosynthesis of the enkephalins.     

Structure of the cytochrome c oxidase dimer electron microscopy of two-dimensional crystals

We have studied the structure of beef heart mitochondrial cytochrome c oxidase dimers by image-processing of electron micrographs of the vesicle crystal form. Specimens were prepared by different procedures, which contrast different features of the crystals. Heavy-atom shadowing of freeze-dried crystals contrasts the exterior or M-side surface (mitochondrial matrix-side) and reveals a 100 Å long ellipsoidal dimer oriented with its long axis in the (?1, 1) direction of the 95 Å × 125 Å rectangular unit cell. The M-side surface structure correlates well with the intra-bilayer structure revealed by contrast matching extra-bilayer protein with glucose. Frozen suspensions of vesicle crystals fracture predominantly along hydrophilic surfaces revealing the interior C-side (mitochondrial cytoplasm-facing surface) of vesicle crystals. The C-side surface revealed in shadowed replicas of fracture surfaces shows the ends of the dimers furthest from the bilayer surface; they consist of two structural domains separated by 70 to 80 Å. We present a new interpretation of the structure of the cytochrome oxidase dimer based on these data and on the y-shaped monomer structure described by Fuller et al. (1979). A cytochrome oxidase dimer is formed from two y-shaped monomers joined along one set of identical M-domain arms with the other arms approximately 70 Å apart along a unit cell diagonal in the (?1, 1) direction. The arms of the monomers lie within and perpendicular to the phospholipid bilayer, and they protrude approximately 25 Å beyond the bilayer surface on the M-side. The y tails represent the C-side domains, which are closely apposed across the dimer 2-fold axis near the C-side bilayer surface. Further away from the bilayer surface, C-side domains split away from one another forming a large cleft.     

Purification and characterization of chitinase from the stable fly,Stomoxys calcitrans

Chitinase that appears as a single band by electrophoresis was purified from stable fly pupae. The chitinase has no cation requirements for activity, and a broad pH optimum around 5. The molecular weight of the chitinase, as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, is 48,000, and the isoelectric point is 4.85. Kinetic properties were determined using acetylated chitosan. The K_m is 33 mm and V is 1.21 μmol/min/mg protein. The insect growth regulator diflubenzuron had no effect on chitinase activity.     

Activation of a silent gene is accompanied by its demethylation

The phenomenon of gene activation by cell fusion makes it possible to study a gene when it passes from a silent to an active state. The relationship between methylation and activation of the mouse albumin gene has been investigated in two types of hybrid clones: mouse lymphoblastoma--rat hepatoma hybrids where activation is very frequent, and mouse L-cell--rat hepatoma hybrids where activation is a rare event. Analysis of the methylation pattern of seven MspI/HpaII sites that occur along the first 8000 bases of the mouse albumin gene has been performed. The entire 5' region is unmethylated only in albumin-producing cells (adult liver and hepatoma); in non-hepatic cells this region is heavily methylated. In hybrids between rat hepatoma cells and mouse cells of mesenchymal origin, the only regular change is the demethylation of the most 5' site (M1), which is systematically observed in clones where expression of the mouse albumin gene has been activated. Demethylation of this site, like activation of the mouse albumin gene, is gene dosage-dependent; it is systematic in the lymphoblastoma--hepatoma hybrids and rare in L-cell--hepatoma hybrids. We conclude that demethylation of this site is tightly coupled with activation of the gene and may well be a necessary prerequisite for activation.