Faculty Bibliography

A set of yeast strains based on Saccharomyces cerevisiae S288C in which commonly used selectable marker genes are deleted by design based on the yeast genome sequence has been constructed and analysed. These strains minimize or eliminate the homology to the corresponding marker genes in commonly used vectors without significantly affecting adjacent gene expression. Because the homology between commonly used auxotrophic marker gene segments and genomic sequences has been largely or completely abolished, these strains will also reduce plasmid integration events which can interfere with a wide variety of molecular genetic applications. We also report the construction of new members of the pRS400 series of vectors, containing the kanMX, ADE2 and MET15 genes.

Replication of Moloney murine leukemia virus requires a readthrough translation mechanism to generate the Gag-Pol polyprotein. One of the final products of this polyprotein is the protease (PR), which is required to generate the mature virion proteins. The assembly of Gag and Gag-Pol polyprotein into a virion followed by activation of the viral protease is necessary to produce a mature, infectious particle. These events are believed to occur near the cell membrane just prior to the budding of the virion. We report here the autoproteolytic activity of the viral PR when a Gag-PR fusion protein is expressed in E. coli. Efficient cleavage at the p12/CA, CA/NC and NC/PR junctions was observed. Thus the Moloney murine leukemia virus PR is capable of cleaving its substrates in the absence of specific host factors.

The yeast Ty1 LTR retrotransposon replicates by reverse transcription and integration; the process shows many similarities to the retroviral life cycle. However, we show that plus strand strong-stop DNA transfer in yeast Ty1 elements differs from the analogous retroviral process. By analysis of the native structure of the Ty1 primer binding site and by a series of manipulations of this region and assessment of the effects on retrotransposition, we show that primer binding site inheritance is not from the tRNA primer, which is inconsistent with classical retroviral models. This unusual inheritance pattern holds even when the Ty1 primer binding site is lengthened in order to be more retrovirus-like. Finally, the distantly related Ty3 element has an inheritance pattern like Ty1, indicating evolutionary conservation of the alternative pathway used by Ty1. Based on these results we arrive at a plus strand primer recycling model that explains Ty1 plus strand strong-stop DNA transfer and inheritance patterns in the primer binding site.

The yeast Saccharomyces cerevisiae and the one- and two-hybrid systems are essential genetic tools for studying the macromolecular interactions that define all living organisms. Newly developed variations on this theme can now address an even bigger set of questions. Reverse one- and two-hybrid systems can identify factors that dissociate or abrogate defined macromolecular interactions. Different forms of three-hybrid systems can evaluate the complex interplay of proteins with RNAs, peptide ligands, small organic ligands or protein kinases. Finally, the ubiquitin-based split-protein sensor and the Sos recruitment systems promise to overcome some limitations of conventional two-hybrid systems.

Proviral integration is essential for HIV-1 replication and represents an important potential target for antiviral drug design. Although much is known about the integration process from studies of purified integrase (IN) protein and synthetic target DNA, provirus formation in virally infected cells remains incompletely understood since reconstituted in vitro assays do not fully reproduce in vivo integration events. We have developed a novel experimental system in which IN-mutant HIV-1 molecular clones are complemented in trans by Vpr-IN fusion proteins, thereby enabling the study of IN function in replicating viruses. Using this approach we found that (i) Vpr-linked IN is efficiently packaged into virions independent of the Gag-Pol polyprotein, (ii) fusion proteins containing a natural RT/IN processing site are cleaved by the viral protease and (iii) only the cleaved IN protein complements IN-defective HIV-1 efficiently. Vpr-mediated packaging restored IN function to a wide variety of IN-deficient HIV-1 strains including zinc finger, catalytic core and C-terminal domain mutants as well as viruses from which IN was completely deleted. Furthermore, trans complemented IN protein mediated a bona fide integration reaction, as demonstrated by the precise processing of proviral ends (5'-TG...CA-3') and the generation of an HIV-1-specific (5 bp) duplication of adjoining host sequences. Intragenic complementation between IN mutants defective in different protein domains was also observed, thereby providing the first evidence for IN multimerization in vivo.

The gypsy retroelement of Drosophila moves at high frequency in the germ line of the progeny of females carrying a mutation in the flamenco (flam) gene. This high rate of de novo insertion correlates with elevated accumulation of full-length gypsy RNA in the ovaries of these females, as well as the presence of an env-specific RNA. We have prepared monoclonal antibodies against the gypsy Pol and Env products and found that these proteins are expressed in the ovaries of flam females and processed in the manner characteristic of vertebrate retroviruses. The Pol proteins are expressed in both follicle and nurse cells, but they do not accumulate at detectable levels in the oocyte. The Env proteins are expressed exclusively in the follicle cells starting at stage 9 of oogenesis, where they accumulate in the secretory apparatus of the endoplasmic reticulum. They then migrate to the inner side of the cytoplasmic membrane where they assemble into viral particles. These particles can be observed in the perivitelline space starting at stage 10 by immunoelectron microscopy using anti-Env antibodies. We propose a model to explain flamenco-mediated induction of gypsy mobilization that involves the synthesis of gypsy viral particles in the follicle cells, from where they leave and infect the oocyte, thus explaining gypsy insertion into the germ line of the subsequent generation.

We have previously shown that a molecule consisting of a fusion of a Ca(2+)-dependent nuclease (from Staphylococcus aureus) to a retroviral coat protein specifies a potent antiviral specific for that retrovirus. Genes specifying such fusion proteins can be delivered to virus-susceptible cells, providing an antiviral gene therapy aimed at limiting virus spread. We report here the results of experiments to vary the nuclease moiety of such fusion proteins. We found that one nuclease. Serratia marcescens nuclease, was extremely toxic to host cells and hence not likely to be useful for therapeutic purposes. A second nuclease, Escherichia coli RNase Hl was found to be nontoxic and highly effective against a murine leukemia virus when it was fused to the leukemia virus coat protein. The fusion protein was enzymatically active and stably expressed, without apparent toxicity to host cells. Reduction in infectious virus output was as high as 97-99%. These studies provide a model system for the development of gene therapeutic agents aimed at combating retroviral infections in vivo.

Repetitive DNA is a significant component of eukaryotic genomes. We have developed a strategy to efficiently and accurately sequence repetitive DNA in the nematode Caenorhabditis elegans using integrated artificial transposons and automated fluorescent sequencing. Mapping and assembly tools represent important components of this strategy and facilitate sequence assembly in complex regions. We have applied the strategy to several cosmid assembly gaps resulting from repetitive DNA and have accurately recovered the sequences of these regions. Analysis of these regions revealed six novel transposon-like repetitive elements, IR-1, IR-2, IR-3, IR-4, IR-5, and TR-1. Each of these elements represents a middle-repetitive DNA family in C. elegans containing at least 3-140 copies per genome. Copies of IR-1, IR-2, IR-4, and IR-5 are located on all (or most) of the six nematode chromosomes, whereas IR-3 is predominantly located on chromosome X. These elements are almost exclusively interspersed between predicted genes or within the predicted introns of these genes, with the exception of a single IR-5 element, which is located within a predicted exon. IR-1, IR-2, and IR-3 are flanked by short sequence duplications resembling the target site duplications of transposons. We have established a website database (http:(/)/www.welch.jhu.edu/approximately devine/RepDNAdb.html) to track and cross-reference these transposon-like repetitive elements that contains detailed information on individual element copies and provides links to appropriate GenBank records. This set of tools may be used to sequence, track, and study repetitive DNA in model organisms and humans.