Identification of Yolk Protein Factor 1, a Sequence-specific DNA-binding Protein from Drosophila melanogaster

Viral RNAi suppressor reversibly binds siRNA to outcompete Dicer and RISC via multiple turnover

RNA interference is a conserved gene regulatory mechanism employed by most eukaryotes as a key component of their innate immune response to viruses and retrotransposons. During viral infection, the RNase-III-type endonuclease Dicer cleaves viral double-stranded RNA into small interfering RNAs (siRNAs) 21-24 nucleotides in length and helps load them into the RNA-induced silencing complex (RISC) to guide the cleavage of complementary viral RNA. As a countermeasure, many viruses have evolved viral RNA silencing suppressors (RSS) that tightly, and presumably quantitatively, bind siRNAs to thwart RNA-interference-mediated degradation. Viral RSS proteins also act across kingdoms as potential immunosuppressors in gene therapeutic applications. Here we report fluorescence quenching and electrophoretic mobility shift assays that probe siRNA binding by the dimeric RSS p19 from Carnation Italian Ringspot Virus, as well as by human Dicer and RISC assembly complexes. We find that the siRNA:p19 interaction is readily reversible, characterized by rapid binding [(1.69 ± 0.07) × 10(8) M(-)(1) s(-1)] and marked dissociation (k(off)=0.062 ± 0.002 s(-1)). We also observe that p19 efficiently competes with recombinant Dicer and inhibits the formation of RISC-related assembly complexes found in human cell extract. Computational modeling based on these results provides evidence for the transient formation of a ternary complex between siRNA, human Dicer, and p19. An expanded model of RNA silencing indicates that multiple turnover by reversible binding of siRNAs potentiates the efficiency of the suppressor protein. Our predictive model is expected to be applicable to the dosing of p19 as a silencing suppressor in viral gene therapy.

Ku autoantigen: a multifunctional DNA-binding protein

Ku is a heterodimeric protein composed of approximately 70- and approximately 80-kDa subunits (Ku70 and Ku80) originally identified as an autoantigen recognized by the sera of patients with autoimmune diseases. Ku has high binding affinity for DNA ends and that is why originally it was known as a DNA end binding protein, but now it is known to also bind the DNA structure at nicks, gaps, hairpins, as well as the ends of telomeres. It has been reported also to bind with sequence specificity to DNA and with weak affinity to RNA. Ku is an abundant nuclear protein and is present in vertebrates, insects, yeast, and worms. Ku contains ssDNA-dependent ATPase and ATP-dependent DNA helicase activities. It is the regulatory subunit of the DNA-dependent protein kinase that phosphorylates many proteins, including SV-40 large T antigen, p53, RNA-polymerase II, RP-A, topoisomerases, hsp90, and many transcription factors such as c-Jun, c-Fos, oct-1, sp-1, c-Myc, TFIID, and many more. It seems to be a multifunctional protein that has been implicated to be involved directly or indirectly in many important cellular metabolic processes such as DNA double-strand break repair, V(D)J recombination of immunoglobulins and T-cell receptor genes, immunoglobulin isotype switching, DNA replication, transcription regulation, regulation of heat shock-induced responses, regulation of the precise structure of telomeric termini, and it also plays a novel role in G2 and M phases of the cell cycle. The mechanism underlying the regulation of all the diverse functions of Ku is still obscure.

Purification and characterization of a cellular protein that binds to the downstream activation sequence of the strict late UL38 promoter of herpes simplex virus type 1

Previous work on the strict late (gamma) UL38 promoter of herpes simplex virus type 1 identified three cis-acting elements required for wild-type levels of transcription: a TATA box at -31, a consensus mammalian initiator element at the transcription start site, and a downstream activation sequence (DAS) at +20 to +33. DAS is found in similar locations on several other late promoters, suggesting an important regulatory role in late gene expression. In this communication, we further characterize the interaction between DAS and a cellular protein which is found in both uninfected and infected nuclear extracts. This protein was purified from HeLa nuclear extracts and identified as the DNA binding component (Ku heterodimer) of DNA-dependent protein kinase (DNA-PK) by peptide mapping. Highly purified DNA-PK was able to stimulate UL38 transcription in vitro approximately 10-fold. DAS is similar in sequence to another element, nuclear regulatory element 1 (NRE1) of the glucocorticoid-responsive mouse mammary tumor virus long terminal repeat. NRE1 is known to specifically bind Ku in the absence of DNA ends. We demonstrated that NRE1 is able to substitute for DAS in the UL38 promoter to activate transcription as measured by in vitro transcription and in vivo during infection of tissue culture cells with recombinant virus. Also, we found that the binding of DNA-PK to DAS involves the bases demonstrated to be important in UL38 transcription and that the 70-kDa subunit of Ku binds to DAS.

DNA binding specificities of YPF1, a Drosophila homolog to the DNA binding subunit of human DNA-dependent protein kinase, Ku

YPF1, a heterodimeric protein from Drosophila melanogaster, is a homolog to Ku, the DNA binding subunit of human DNA-dependent protein kinase. This kinase is crucial in transcriptional activation, V(D)J recombination, double-strand break repair, and both topoisomerase and helicase activities. To investigate functional homology between YPF1 and Ku, we examined DNA binding properties of YPF1. Like Ku, at 100 mM KCl, YPF1 binding has no detectable DNA sequence specificity, requires a DNA terminus, and has a concentration-dependent stoichiometry consistent with subsequent translocation along DNA. YPF1 differs from Ku by having a 10(5)-fold higher affinity. At 400 mM KCl, YPF1 still prefers DNA termini but shows binding specificities not observed previously with Ku. In descending order of affinity, YPF1 binds to: specific DNA sequences with a specific polarity and spacing relative to DNA termini; nonspecific linear DNA; and circular DNA. At this higher ionic strength, binding stoichiometry is concentration independent, indicating that YPF1 remains bound to ends. These results demonstrate a strong functional homology between YPF1 and Ku at physiological ionic strength. The strong binding of YPF1 has also allowed us to detect underlying binding specificities that may be specific to YPF1 and its function.

Identification of ovarian enhancer-binding factors which bind to ovarian enhancer 1 of the Drosophila genes yp1 and yp2

It has been reported that three different DNA regions-the fat body enhancer and ovarian enhancers 1 and 2-direct the tissue-specific expression of yp1 and yp2 in Drosophila melanogaster. In the present study, we identified ovarian enhancer 1-specific binding proteins. Electrophoretic mobility shift assay revealed that these proteins are present in the adult ovary, but not in adult testis or fat body. Southwestern blot analysis showed that about 130 kDa and 40 kDa proteins, designated OEF1 and OEF2, respectively, from ovarian nuclear or crude extracts bind specifically to the ovarian enhancer 1. The two proteins were partially purified by streptavidin/agarose-DNA affinity chromatography, and their binding activity was confirmed by electrophoretic mobility shift assay. These ovarian enhancer factors may play an important role in the regulation of transcription of yp1 and yp2 in the ovary.

Two independent cis-acting elements regulate the sex- and tissue-specific expression of yp3 in Drosophila melanogaster

In Drosophila, the three yolk protein (yp) genes are transcribed in a sex-, tissue- and developmentally specific manner, providing an ideal system in which to investigate the factors involved in their regulation. The yolk proteins are synthesized in the fat body of adult females, and in the ovarian follicle cells surrounding the developing oocyte during stages 8-10 of oogenesis. We report here an analysis of the yolk protein 3 (yp3) gene and its flanking sequences by means of P-element mediated germ-line transformation and demonstrate that a 747 bp promoter region is sufficient to direct sex-specific expression in the female fat body and both the temporal- and cell-type-specificity of expression during oogenesis. Two elements that independently govern yp3 transcription in these tissues have been separated and no other sequences in the upstream, downstream or coding regions have been identified that are autonomously involved in yp3 expression.

The regulation of the yolk protein genes, a family of sex differentiation genes in Drosophila melanogaster

There are many obvious morphological and behavioural differences between male and female Drosophila, whose differing phenotypes are produced by a hierarchy of sex determination genes. These genes have been well characterised at the genetic and molecular level. Similarly, a number of sex-specific differentiation genes have been characterised, such as the chorion and vitelline membrane genes in females and the sex peptide and other accessory gland proteins in males. Despite the depth of these parallel studies, there is only one example of a direct link between the sex determination pathway and the downstream sex differentiation genes, namely the regulation of the female-specific yolk protein genes. The yolk proteins are synthesised in the fat body and ovarian follicle cells of the adult female and are subsequently transported to the oocyte where they are stored for utilization during embryogenesis. The expression of the yolk protein genes is not entirely controlled by the sex determination hierarchy, as several different regulatory pathways must interact to direct their correct sexual, temporal and spatial regulation during development.

Yolk polypeptide gene expression in cultured Drosophila cells

The transfer of chimaeric plasmids to Drosophila melanogaster cell lines has been examined as a system for investigation of the hormonal regulation of the genes coding for D. melanogaster yolk polypeptide 1 (YP1) and Locusta migratoria vitellogenin B (VgB). Constructs containing promoters and putative 5'-regulatory sequences from these genes, ligated to bacterial chloramphenicol acetyltransferase (CAT) coding DNA, were transfected into Drosophila Kc (Kc-H) and S3 cells, and transient expression of CAT was assayed. Activity was expressed both from the homologous promoter of pYP1CAT and from the heterologous locust promoter of pVgCAT at comparable levels. In S3 cells, with calcium phosphate-mediated transfer of pYP1CAT there was a twofold induction of CAT activity after the addition of 10(-6) M ecdysterone, but no hormonal stimulation was noted when the polycation polybrene was used to achieve transfection. For Kc cells, calcium phosphate was ineffective for transfection, and after transfection with polybrene neither pYP1CAT nor pVgCAT was induced by the juvenile hormone (JH) analog methoprene. It is concluded that S3 cells may be useful for investigating the molecular basis of gene regulation by ecdysteroids, but conditions suitable for the analysis of JH action have not yet been established.

Vitellogenin protein diversity in the Hawaiian Drosophila

Egg and female hemolymph proteins were resolved via SDS-polyacrylamide gel electrophoresis in a diverse array of 33 endemic Hawaiian drosophilids, encompassing 17 picture-winged species, 3 of the antopocerus species group, 9 fungus feeders, 1 species from each of the modified mouthparts, crassifemur and ciliated tarsus groups, and 1 Scaptomyza species. Molecular weights of the two (10 species) or three vitellogenin bands (22 species) were highly variable, spanning a 7-kD range. The largest vitellogenin, V1, was the most variable, showing a change of some 10% in its mean size of 47.6 kD. The smallest V3 vitellogenin, mean size 44.1 kD, was evolutionarily the most conservative in size. The species Drosophila hawaiiensis was found to be polymorphic for two/three vitellogenin bands and, also, polymorphic with respect to the size of the V1 protein. No inter- or intrapopulation variability in vitellogenin size was detected in 10 other species examined. The major features of vitellogenin protein evolution in the Hawaiian Drosophila are change in molecular weight and regulatory differences that result in quantitative differences between species in patterns of vitellogenin protein production.