Structure of human cholecystokinin gene and its chromosomal location.

We have determined the entire structure of human cholecystokinin (CCK) gene, which is 7 kb in size and separated into three exons. S1 endonuclease analysis has shown two putative transcription initiation sites that are preceded by 'TATA' equivalent sequences located 39 bp and 35 bp upstream from these sites. The promoter region contains five 'G-C box'-like sequences, which are believed to be sp 1-binding sites. By chromosome sorting in combination with velocity sedimentation and Southern hybridization, the human cck gene was mapped on the short arm of human chromosome 3.

Nine unique repeating sequences in a region essential for replication and incompatibility of the mini-F plasmid.

The nucleotide sequence of a 2248 bp portion of the plasmid mini-F has been determined. This region includes the replication origin and all of the plasmid-coded information required for replication. The same region is also capable of expressing incompatibility. A striking feature of the sequence is the presence of nine 19-bp repeating units. Four of these repeats, all arranged in one direction, comprise a cluster, and the remaining five, all arranged in the opposite direction, comprise another cluster. These clusters are separated by a region of about 850 bp that encodes a hypothetical 29-kd polypeptide. This region has sequences highly homologous to those found in the origin regions of the Escherichia coli (Sugimoto et al., 1979; Meijer et al., 1979) and Salmonella typhimurium (Zyskind and Smith, 1980) genomes.

A new packing for separation of DNA restriction fragments by high performance liquid chromatography.

TSK-GEL SW was found to be useful as a packing in high performance liquid chromatography for the separation of double-stranded DNA restriction fragments. DNA fragments smaller than 300 base pairs were separated as discrete peaks depending solely upon difference in chain length. The recovery of DNA fragments was higher than 90%.

Role of an autorepression system in the control of lambda dv plasmid copy number and incompatibility.

The lambda dv plasmid genome is composed of two regions: (1) the autorepressor region which consists of promoter-operator (pRoR) and autorepressor (tof) and (2) the origin region which consists of the origin of replication (ori) and two initiator genes (O and P) (Matsubara 1976). Replication of this plasmid is directly connected with transcription from pRoR. Using lambda dvs having various mutations in pRoR, the transcription ability was examined in detail in connection with the control mechanism of replication. The transcription ability of the autorepressor region is controlled by the binding affinity of the tof protein and pRoR. Thus, at steady-state, lambda dvs carrying a highly-constitutive ('strong') pRoR produced the autorepressor at high levels, whereas those carrying a low-constitutive ('weak') pRoR produced the autorepressor at low levels. This relationship did not change even when a fragment of lambda dv genome covering the autorepressor region was cloned into the plasmids pBR322 and pSC138, which could be maintained in a fixed amount within a cell. It was also shown that the autorepressor level at steady-state is a function of copy number of the DNA carrying the region for autorepression. These observations fit the autorepression model of Sompayrac and Maaløe (1973), which predicts that a decreased level of autorepressor activates pRoR and initiates transcription which leads to the production of tof protein until a new steady-state is established. By the same token, if the affinity of autorepressor and pRoR is decreased, pRoR remains active until a higher level of autorepressor is produced. Transcription of the autorepressor region directly affects the level of transcription of the origin region which is located distal to the promoter. Thus, the ability to replicate is connected with an ability to produce autorepressor. The lambda dv plasmids with 'strong' or 'weak' pRoR were maintained at a high or low copy number, respectively. The phenomenon of incompatibility of lambda dv was also examined using pBR322 and pSC138 plasmids carrying the cloned autorepressor region of lambda dv. The chimeric plasmids with 'strong' pRoR exhibited strong incompatibility with lambda dv, whereas those with 'weak' pRoR showed weak incompatibility. This indicates that interaction of the autorepressor and pRoR is related to the incompatibility of lambda dv plasmids.

Chromosomal assignment of human genes for gastrin, thyrotropin (TSH)-beta subunit and C-erbB-2 by chromosome sorting combined with velocity sedimentation and Southern hybridization.

Human genes for gastrin, thyrotropin (THS)-beta subunit and c-erbB-2 were assigned to specific chromosomes using a single-laser cell sorter. For this purpose, condensed human chromosomes prepared from a karyotypically normal lymphoblastoid cell line were preliminarily fractionated by velocity sedimentation, and then sorted using a fluorescence-activated cell sorter. DNA was then extracted from the chromosomes, cleaved by restriction enzymes, and subjected to Southern hybridization using gene-specific radioactive probes. When the assignment of specific chromosomes was not possible due to chromosomal size overlapping, sorted chromosomes from cell lines carrying chromosomal translocation or from hybrid cells carrying known human chromosomes were used in addition. The results indicate that human genes for gastrin, TSH-beta, and c-erbB-2 are located on chromosomes 17, 1 and 17, respectively.

Purification and properties of the mini-F plasmid-encoded E protein needed for autonomous replication control of the plasmid.

Mini-F plasmid encodes a protein, E protein, that is indispensable for its autonomous replication. We have constructed a plasmid that overproduces the E protein and have purified the protein to apparent homogeneity. Using nitrocellulose filter binding and nuclease digestion assays, we demonstrated that the E protein binds to three unique regions of the mini-F DNA sequence: the replication origin (ori2) and an incompatibility locus (incB), another incompatibility locus (incC), and the promoter for the E gene. These binding sites have a common 8-base-pair sequence. These findings suggest the direct role of the E protein in initiation of mini-F replication and copy number control. They are also in line with the in vivo evidence that the incompatibility phenotype caused by incB and incC DNA is due to titration of a factor(s) indispensable for replication and that the production of the E initiator protein of the mini-F plasmid is under autoregulatory control.

Identification of the minimal essential region for the replication origin of miniF plasmid.

The minimal replication origin of miniF plasmid was found to lie within a region of 217 bp in length. This region contains an AT cluster and the four 19 bp direct repeats responsible for incompatibility, termed incB. Its location coincides with hat of ori2 of plasmid F, previously inferred to be the replication starting point by electron microscopic analysis (Eichenlaub et al. 1981).

Mini-F protein that binds to a unique region for partition of mini-F plasmid DNA.

A mini-F-coded protein, named F2 protein, binds specifically to mini-F DNA. This protein has a molecular weight of 37,000 and is coded by the A2 segment of the mini-F genome (47.3 to 49.4 kilobases on the F coordinate map). The binding site is located also in the A2 segment of mini-F. This binding site is lost by spontaneous deletion when the A2 segment alone, but not A2 together with its neighboring segment, is cloned in a multicopy plasmid pBR322. These data are discussed in connection with incompatibility and plasmid stability.

Replication of mini-F plasmid in vitro promoted by purified E protein.

An in vitro system for replication of mini-F plasmid DNA was constructed. This system consists of an ammonium sulfate fraction II (Fuller et al. 1981) from Escherichia coli extract, exogenously added purified E protein encoded by mini-F plasmid, and mini-F DNA in a closed circular form. Experiments with this system showed that the 217 bp DNA region which contains the A + T rich cluster and the four 19 bp direct repeats responsible for incB incompatibility is essential for mini-F DNA replication.

Role of nine repeating sequences of the mini-F genome for expression of F-specific incompatibility phenotype and copy number control.

An autonomously replicating 2,248-base-pair DNA segment of the mini-F plasmid carries nine 19-base-pair repeating sequences. Five of the repeats are arranged in one direction and form the right cluster, whereas the remaining four repeats are arranged in the opposite direction and form the left cluster (Murotsu et al., Gene 15:257-271, 1981). Each cluster, cloned separately into the multicopy plasmid vector pBR322, exhibited a strong F-specific incompatibility phenotype (FIP). These clusters were thought to be responsible for the expression of IncB and IncC phenotypes, causing a switchoff function on mini-F replication. Mini-F DNA fragments containing two, three, or more than four repeats were inserted into pBR322. Cells carrying these recombinant plasmids exhibited, respectively, no, intermediate, and strong FIP intensity. Cloning of five repeats into pSC101, whose copy number is about 6 in contrast to 20 for pBR322, resulted in an FIP of intermediate intensity. Thus, the intensity of FIP reflects the dosage of repeats in a cell. The five repeats in the right cluster were eliminated from the mini-F derivative without impairing its autonomous-replicating ability (Bergquist et al., J. Bacteriol. 147:888-889, 1981; Kline and Palchavdhuri, Plasmid 4:281-289). Such deletion, however, caused a sixfold elevation of the copy number. When the eliminated cluster of repeats was reinserted in the derivative, the copy number was lowered to the original value, viz., 1 to 2. The position and orientation of this insertion was not important in the copy number control. Thus, the repeats are also related to copy number control. A model to account for the role of the repeating sequences in the control of copy number and FIP is discussed.

Operational variables in high-performance gel filtration of DNA fragments and RNAs.

Double-stranded DNA fragments and ribosomal and transfer RNAs were measured by high-performance gel filtration on TSK-GEL G2000SW, G3000SW, G4000SW and G5000PW columns to investigate the separation range and resolution of these columns and the effects of eluent ionic strength and flow-rate on retention and resolution. These columns could separate double-stranded DNA fragments up to ca 1 X 10(6) and rRNAs up to ca 5 X 10(6) daltons in molecular weight. However, it was found that the selection of the column is very important to achieve optimum separation, depending on the molecular weight of the sample. Elution is delayed as the eluent ionic strength is increased. An eluent ionic strength of 0.3-0.5 seemed appropriate in most cases. Resolution is greatly increased as the flow-rate is decreased.

Detection and mapping of six miniF-encoded proteins by cloning analysis of dissected miniF segments.

Various DNA subfragments were derived from miniF DNA by complete or partial PstI cleavage, and cloned in the plasmid vectors pBR322 or lambda dv1. The recombinant plasmids obtained were introduced into an Escherichia coli minicell-producing strain, and the plasmid-coded proteins were radiolabeled and analyzed by gel electrophoresis. Six miniF-encoded proteins, larger than 11 000 daltons, were detected and their coding regions were mapped on the F plasmid genome. Three of them were assigned by taking into account the known nucleotide sequences (Murotsu et al. 1981; K. Yoshioka, personal communication). The coding directions of some proteins were determined by inserting the lac promotor into one of the recombinant plasmids and analyzing the increase in production of the proteins. The coding direction of the five proteins analyzed so far was uniform. Comparison of these results with a functional map of miniF suggested possible roles of the proteins.

Purification and properties of a lambda operator-binding protein which is expected to be autorepressor (tof protein) from E. coli carrying lambdadv plasmid.

In order to study the mode of action of the tof gene product, which is an "autorepressor" of the bacteriophage lambda and plasmid lambdadv, we have purified a DNA-binding protein which is specifically produced in bacteria carrying lambdadv. This protein possesses characteristics expected for the product of the tof gene, since it is produced under conditions where cI-repressor is not made, and since it binds to oL and oR operators on the lambda phage genome. The molecular weight of the native protein is 16,000-17,000 daltons, and the monomeric molecular weight as measured by gel electrophoresis in the presence of sodium dodecyl sulfate is about 10,000 daltons. Denaturation and renaturation experiments demonstrated that the native protein is a dimer of 10,000-dalton monomers. The lambdaDNA-specific binding protein is not produced in cells carrying i21dv or ø80dv.

Primary structure of human pancreatic secretory trypsin inhibitor (PSTI) gene.

The human pancreatic secretory trypsin inhibitor (PSTI) gene was isolated from a human gene library. Restriction endonuclease mapping and DNA sequencing analysis revealed that this gene is approximately 7.5 kb long and is separated into four exons by three introns. The gene has multiple transcription start points and examination with a single-laser cell-sorter showed that it is located on chromosome 5.

Chromosomal translocation and inverted duplication associated with integrated hepatitis B virus in hepatocellular carcinomas.

Integrated hepatitis B virus (HBV) DNA is found in hepatocellular carcinomas which develop in HBV carriers. Presented here are the results of analyses of four integrants that show chromosomal rearrangements associated with the integrated HBV DNA. Two clones (p4 and C15) were found to have large inverted repeating structures, each consisting of HBV genome along with flanking cellular sequences. The structure must have arisen by duplication of the primary integrant, including the flanking cellular DNA, followed by recombination within the viral DNA. One of the two viral arms in each clone joins to the other viral arm at the "cohesive end region." Two clones (DA2-2 and DA2-6) were found to have integrated HBV sequences, each flanked by cellular DNAs from different chromosomes (chromosome X joined to 17 and chromosome 5 joined to 9). They must be the products of cellular DNA translocations using the integrated HBV DNA as the switch point. The viral DNA in each clone is a continuous stretch of a single virus genome with one end in the cohesive end region. These complex structures seem to have been produced by activation of the cohesive end of an integrant viral genome, followed by its recombination with another chromosomal DNA.

Human gene coding for granulocyte-colony stimulating factor is assigned to the q21-q22 region of chromosome 17.

Granulocyte-colony stimulating factor (G-CSF) is a member of colony stimulating factors which regulate the proliferation and differentiation of hematopoietic progenitor cells. A full-length cDNA clone coding human G-CSF was used as a hybridization probe to detect homologous sequence in human-mouse somatic cell hybrids, flow-sorted human chromosomes, and in situ human metaphase chromosomes. The results indicate that the gene encoding human G-CSF is on the q21-q22 region of chromosome 17, which is involved in translocation of t(15;17) (q23;21) in human acute promyelocytic leukemia.

Assignment of human pepsinogen C (PGC) gene to chromosome 6.

cDNA of rat pepsinogen C (PGC) hybridizes to, among others, a 3.2-kb band in Southern blot analysis of BamHI-cleaved human genomic DNA. This property was employed to localize the human PGC gene. Use of flow-sorted human chromosomes and 12 human x mouse somatic cell hybrid lines demonstrated that the gene is located on chromosome 6.

Isolation and characterization of the active cDNA of the human cell cycle gene (RCC1) involved in the regulation of onset of chromosome condensation.

The human RCC1 gene was cloned after DNA-mediated gene transfer into the tsBN2 cell line, which shows premature chromosome condensation at nonpermissive temperatures (39.5-40 degrees C). This gene codes for a 2.5-kb poly(A)+ RNA that is well conserved in hamsters and humans. We isolated 15 cDNA clones from the Okayama-Berg human cDNA library, and found two that can complement the tsBN2 mutation with an efficiency comparable to that of the genomic DNA clone. The base sequences of these two active cDNA clones differ at the 5' proximal end, yet both have a common open reading frame, encoding a protein of 421 amino acids with a calculated molecular weight of 44,847 and with seven homologous repeated domains of about 60 amino acids. This human RCC1 gene was located to human chromosome 1 using sorted chromosomal fractions.