Catalytic domains of tyrosine kinases determine the phosphorylation sites within c-Cbl

Catalytic (SH1) domains of protein tyrosine kinases (PTKs) demonstrate specificity for peptide substrates. Whether SH1 domains differentiate between tyrosines in a physiological substrate has not been confirmed. Using purified proteins, we studied the ability of Syk, Fyn, and Abl to differentiate between tyrosines in a common PTK substrate, c-Cbl. We found that each kinase produced a distinct pattern of c-Cbl phosphorylation, which altered the phosphotyrosine-dependent interactions between c-Cbl and CrkL or phosphatidylinositol 3'-kinase (PI3-K). Our data support the concept that SH1 domains determine the final sites of phosphorylation once PTKs reach their target proteins.     

A critical examination of possible fractionations of human DNA according to base composition.

Human DNA has been fractionated according to base composition by sedimentation equilibrium in an HgCl2/Cs2SO4 density gradient, followed by sedimentation equilibrium in an actinomycin/cesium formate density gradient. The fractions of different base composition resulting from this procedure were subsequently analyzed by sedimentation equilibrium in CsCl, DNA renaturation kinetics, and electron microscopy. All fractions contain similar kinetic classes of repeated DNA sequences as judged by renaturation studies. Short (300 nucleotides) interspersed repeated sequences are found in all fractions with no noticeable enrichment for these sequences in any fraction. Repeated sequences from fractions of different base composition are partially able to cross-hybridize, demonstrating that nearly identical repeated sequences occur in molecules of different base composition. These findings are critically compared to reports of successful density gradient fractionations of different human DNA sequence classes.     

Regions of the polyoma genome coding for T antigens.

The early region of the polyoma genome encodes three T antigens. We have analyzed the organization of the coding regions for the T antigens, using the nucleotide sequence of polyoma DNA and peptides derived from purified, radio-labeled T antigens, separated by two-dimensional electrophoresis and chromatography. We compared the peptides, predicted from the nucleotide sequence of the DNA, with those derived from the purified T antigens. We also compared chemically synthesized peptides, predicted from the DNA sequence, with observed peptides. The results show that the three polyoma T antigens are encoded in overlapping regions of the viral DNA, translated, in part, in two different reading frames.     

An electron microscope study of the DNA sequence organization of the human genome

The arrangements of inverted-repeated and repeated DNA sequences in the human genome have been investigated by an electron microscope method. The arrangement of the interspersed repeated DNA sequences is found to be similar to the corresponding arrangement found in Xenopus. This arrangement consists of 300-nucleotide-long repeated DNA sequences interspersed with roughly gene-size single-copy DNA sequences. The inverted-repeated sequences are also 300 nucleotides in length and are interspersed with the other DNA sequence classes.Most inverted-repeated sequences (64%) are spaced by another sequence which is recognized by electron microscopy as a single-stranded loop in a hairpin structure. The average length of this spacer loop is 1.6 kilobases. Although some pairs of inverted-repeated sequences are clustered, most seem to be randomly distributed throughout the genome. The average distance separating two pairs of inverted-repeated sequences is 10 to 20 kilobases. The interspersed repeated sequences and inverted-repeated sequences are arranged simultaneously in a portion of the human genome resulting in an interspersion of all three sequence classes.     

Tandem insertions of Alu elements

The technique of chromosomal orientation and direction fluorescence in situ hybridization (COD-FISH) was adapted for plant chromosomes in order to study long-range organization of two families of satellite repeats, VicTR-B of Vicia sativa and PisTR-B of Pisum sativum. The technique allowed FISH to be performed on mitotic chromosomes in a strand-specific manner, resulting in visualization of the repeat orientation along the chromosomes and with respect to the direction of telomeric repeats. The VicTR-B probe applied to V. sativa chromosomes produced signals on a single chromatid at most regions containing corresponding sequences, thus confirming a presence of long arrays of head-to-tail arranged repeat monomers which is typical for satellite DNA. However, hybridization signals of different or equal intensities on both chromatids were also detected at some loci, suggesting a more complex arrangement of the repeats. Similar observations were made for PisTR-B repeats on P. sativum chromosomes, although the proportion of loci displaying signals on both chromatids was lower. In contrast to VicTR-B, orientation of the PisTR-B clusters with respect to telomeric sequences appeared to be conserved among subtelomeric regions of metacentric chromosomes and of the short arms of acrocentric chromosomes.     

Large-scale analysis of the Alu Ya5 and Yb8 subfamilies and their contribution to human genomic diversity

We have utilized computational biology to screen GenBank for the presence of recently integrated Ya5 and Yb8 Alu family members. Our analysis identified 2640 Ya5 Alu family members and 1852 Yb8 Alu family members from the draft sequence of the human genome. We selected a set of 475 of these elements for detailed analyses. Analysis of the DNA sequences from the individual Alu elements revealed a low level of random mutations within both subfamilies consistent with the recent origin of these elements within the human genome. Polymerase chain reaction assays were used to determine the phylogenetic distribution and human genomic variation associated with each Alu repeat. Over 99 % of the Ya5 and Yb8 Alu family members were restricted to the human genome and absent from orthologous positions within the genomes of several non-human primates, confirming the recent origin of these Alu subfamilies in the human genome. Approximately 1 % of the analyzed Ya5 and Yb8 Alu family members had integrated into previously undefined repeated regions of the human genome. Analysis of mosaic Yb8 elements suggests gene conversion played an important role in generating sequence diversity among these elements. Of the 475 evaluated elements, a total of 106 of the Ya5 and Yb8 Alu family members were polymorphic for insertion presence/absence within the genomes of a diverse array of human populations. The newly identified Alu insertion polymorphisms will be useful tools for the study of human genomic diversity.     

A BCR-ABL Mutant Lacking Direct Binding Sites for the GRB2, CBL and CRKL Adapter Proteins Fails to Induce Leukemia in Mice

The BCR-ABL tyrosine kinase is the defining feature of chronic myeloid leukemia (CML) and its kinase activity is required for induction of this disease. Current thinking holds that BCR-ABL forms a multi-protein complex that incorporates several substrates and adaptor proteins and is stabilized by multiple direct and indirect interactions. Signaling output from this highly redundant network leads to cellular transformation. Proteins known to be associated with BCR-ABL in this complex include: GRB2, c-CBL, p62^DOK, and CRKL. These proteins in turn, link BCR-ABL to various signaling pathways indicated in cellular transformation. In this study we show that a triple mutant of BCR-ABL with mutations of the direct binding sites for GRB2, CBL, p62^DOK and CRKL, is defective for transformation of primary hematopoietic cells in vitro and in a murine CML model, while it retains the capacity to induce IL-3 independence in 32D cells. Compared to BCR-ABL, the triple mutant''s ability to activate the MAP kinase and PI3-kinase pathways is severely compromised, while STAT5 phosphorylation is maintained, suggesting that the former are crucial for the transformation of primary cells, but dispensable for transformation of factor dependent cell lines. Our data suggest that inhibition of BCR-ABL-induced leukemia by disrupting protein interactions could be possible, but would require blocking of multiple sites.