Uses of Staphylococcus aureus GeneChips in genotyping and genetic composition analysis.

Understanding the relatedness of strains within a bacterial species is essential for monitoring reservoirs of antimicrobial resistance and for epidemiological studies. Pulsed-field gel electrophoresis (PFGE), ribotyping, and multilocus sequence typing are commonly used for this purpose. However, these techniques are either nonquantitative or provide only a limited estimation of strain relatedness. Moreover, they cannot extensively define the genes that constitute an organism. In the present study, 21 oxacillin-resistant Staphylococcus aureus (ORSA) isolates, representing eight major ORSA lineages, and each of the seven strains for which the complete genomic sequence is publicly available were genotyped using a novel GeneChip-based approach. Strains were also subjected to PFGE and ribotyping analysis. GeneChip results provided a higher level of discrimination among isolates than either ribotyping or PFGE, although strain clustering was similar among the three techniques. In addition, GeneChip signal intensity cutoff values were empirically determined to provide extensive data on the genetic composition of each isolate analyzed. Using this technology it was shown that strains could be examined for each element represented on the GeneChip, including virulence factors, antimicrobial resistance determinants, and agr type. These results were validated by PCR, growth on selective media, and detailed in silico analysis of each of the sequenced genomes. Collectively, this work demonstrates that GeneChips provide extensive genotyping information for S. aureus strains and may play a major role in epidemiological studies in the future where correlating genes with particular disease phenotypes is critical.

Transrepression of RNA polymerase II promoters by the simian virus 40 small t antigen.

Simian virus 40 (SV40) small t antigen (t) can activate transcription from certain RNA polymerase II and III promoters (M. Loeken, I. Bikel, D. M. Livingston, and J. Brady, Cell 55:1171-1177, 1988). Here we report a new function of t, its ability to repress human c-fos promoter and AP-1 transcriptional activity in CV-1P cells. This function is the product of a discrete N-terminal domain of t, because the large T antigen (T)/t-common polypeptide, which contains only the first 82 amino acids common to both T and t of SV40, was, like the intact protein, an active repressor. The data further suggest that the t- and T/t-common-mediated repression of c-fos expression was most likely manifest at the level of transcription. In keeping with the possibility that t affects the expression of the genomic c-fos promoter, it also led to repression of AP-1 formation. Thus, SV40 is both an activator and a repressor of transcription. Its ability to inhibit c-fos expression should be considered in light of the natural history of SV40 in its natural host.

The T/t common region of simian virus 40 large T antigen contains a distinct transformation-governing sequence.

Simian virus 40 large T antigen (T) can transform cultured cells, but the mechanisms by which it functions are not entirely understood. Several lines of evidence have suggested that the amino-terminal approximately 130 residues of T may be sufficient to confer the transforming capability. Oligonucleotide-directed mutagenesis was used to generate a series of deletion and substitution mutants within the amino-terminal 82 residues of T, the segment which is shared with simian virus 40 small t antigen (t). Results of stability and transformation assays of these mutants strongly suggest that the 1-to-82 region of T contains sequences which govern T transforming activity and affect in vivo stability. Instability and a defect in transforming activity could be separated from one another genetically. Thus, the 1-to-82 region appears to contain a specific region that contributes to the transforming function of the protein. This segment operates by means other than the simple binding of pRb and/or p107.

An N-terminal transformation-governing sequence of SV40 large T antigen contributes to the binding of both p110Rb and a second cellular protein, p120.

In addition to Rb and p53, a third cellular protein, p120 in monkey and p118 in human cells, forms a specific complex with SV40 large T antigen (T). p118/120 is not a product of the Rb-gene. As was shown with T/Rb complex formation, the interaction between T and p120 is dependent on the intact nature of a ten residue, transformation-controlling domain in T (residues 105-114). In mouse cells, a readily detectable protein of 115 kd was detected, which, like murine Rb, also forms a stable complex with T. Like p118/120, p115 binding is also dependent on the intact nature of the 105-114 sequence. Given their similar size and T antigen binding sequence dependence, p115 and p118/120 may be products of the same gene in different species. These results suggest that interactions between T and p115/118/120, as well as T and Rb, contribute to the SV40 transforming mechanism.

SV40 large tumor antigen forms a specific complex with the product of the retinoblastoma susceptibility gene.

Monkey cells synthesizing SV40 large T antigen were lysed and the extracts immunoprecipitated with either monoclonal anti-T antibody or monoclonal antibody to p110-114, the product of the retinoblastoma susceptibility gene (Rb). T and p110-114 coprecipitated in each case, implying that the proteins are complexed with each other. Substitution and internal deletion mutants of T that contain structural alterations in a ten residue, transformation-controlling domain failed to complex with p110-114. In contrast, T mutants bearing structural changes outside of this domain bound to p110-114. These results are consistent with a model for transformation by SV40 which, at least in part, involves T/p110-114 complex formation and the perturbation of Rb protein and/or T function.

Methylation of the alpha 2(I) collagen gene in chemically transformed rat liver epithelial cells.

W8 cells, 2-N-(acetoxyacetyl)aminofluorene-transformed rat liver epithelial-like cells, secrete no alpha 2(I) collagen chains. This paper reports the first demonstration of DNA methylation in the promoter-5' region of an alpha 2(I) collagen gene which occurs in W8 cells. Since inhibition of methylation by azacytidine induces transcription of the alpha 2(I) gene, DNA methylation of W8 alpha 2(I) promoter-5' region could contribute to altered collagen production in these cells.

Absence of procollagen alpha 2(I) mRNA in chemically transformed rat liver epithelial cells.

The W8 cell line, a chemically transformed variant of K16 rat liver epithelial cells, does not produce a normal type I collagen but instead secretes alpha 1(I) trimer and no alpha 2(I) chains (Smith, B.D., and Niles, R. (1980) Biochemistry 19, 1820-1825). Analysis of total cellular RNA from the K16 and W8 cells by cell-free translation in a rabbit reticulocyte lysate demonstrates the specific absence of translatable pro-alpha 2(I) collagen mRNA. No alpha 2(I) collagen mRNA sequences were detected by Northern hybridization analysis using cloned rat alpha 2(I) cDNAs as a probe. The total amount of alpha 1(I) collagen mRNAs, however, was the same in both cell types, suggesting a lack of coordinate control of alpha 1(I) and alpha 2(I) mRNAs in the transformed cells.