Otu Gene Research Articles

<i>Otu</i> and <i>Rif<sup>1</sup></i> double mutant enables analysis of satellite DNA in polytene chromosomes of ovarian germ cells in <i>Drosophila melanogaster</i>

Polytene chromosomes in Drosophila serve as a classical model for cytogenetic studies. However, heterochromatic regions of chromosomes are typically under-replicated, hindering their analysis. Mutations in the Rif1 gene lead to additional replication of heterochromatic sequences, including satellite DNA, in salivary gland cells. Here, we investigated the impact of the Rif1 mutation on heterochromatin in polytene chromosomes formed in ovarian germ cells due to the otu gene mutation. By the analysis of otu11; Rif11 double mutants, we found that, in the presence of the Rif1 mutation, ovarian cells undergo additional polytenization of pericentromeric regions. This includes the formation of large chromatin blocks composed of satellite DNA. Thus, the effects of the Rif1 mutation were similar in salivary gland and germ cells. The otu11; Rif11 system opens new possibilities for studying factors associated with heterochromatin during oogenesis.

Otu and Rif1 Double Mutant Enables Analysis of Satellite DNA in Polytene Chromosomes of Ovarian Germ Cells in Drosophila melanogaster.

Polytene chromosomes in Drosophila serve as a classical model for cytogenetic studies. However, heterochromatic regions of chromosomes are typically under-replicated, hindering their analysis. Mutations in the Rif1 gene lead to additional replication of heterochromatic sequences, including satellite DNA, in salivary gland cells. Here, we investigated the impact of the Rif1 mutation on heterochromatin in polytene chromosomes formed in ovarian germ cells due to the otu gene mutation. By the analysis of otu11; Rif11 double mutants, we found that, in the presence of the Rif1 mutation, ovarian cells undergo additional polytenization of pericentromeric regions. This includes the formation of large chromatin blocks composed of satellite DNA. Thus, the effects of the Rif1 mutation are similar in salivary gland and germ cells. The otu11; Rif11 system opens new possibilities for studying factors associated with heterochromatin during oogenesis.

Genome-Wide Identification and Gene Expression Analysis of the OTU DUB Family in Oryza sativa.

Ovarian tumor domain (OTU)-containing deubiquitinating enzymes (DUBs) are an essential DUB to maintain protein stability in plants and play important roles in plant growth development and stress response. However, there is little genome-wide identification and analysis of the OTU gene family in rice. In this study, we identified 20 genes of the OTU family in rice genome, which were classified into four groups based on the phylogenetic analysis. Their gene structures, conserved motifs and domains, chromosomal distribution, and cis elements in promoters were further studied. In addition, OTU gene expression patterns in response to plant hormone treatments, including SA, MeJA, NAA, BL, and ABA, were investigated by RT-qPCR analysis. The results showed that the expression profile of OsOTU genes exhibited plant hormone-specific expression. Expression levels of most of the rice OTU genes were significantly changed in response to rice stripe virus (RSV), rice black-streaked dwarf virus (RBSDV), Southern rice black-streaked dwarf virus (SRBSDV), and Rice stripe mosaic virus (RSMV). These results suggest that the rice OTU genes are involved in diverse hormone signaling pathways and in varied responses to virus infection, providing new insights for further functional study of OsOTU genes.

Structural Basis for Ubiquitin Recognition by the Otu1 Ovarian Tumor Domain Protein

Ubiquitination of proteins modifies protein function by either altering their activities, promoting their degradation, or altering their subcellular localization. Deubiquitinating enzymes are proteases that reverse this ubiquitination. Previous studies demonstrate that proteins that contain an ovarian tumor (OTU) domain possess deubiquitinating activity. This domain of approximately 130 amino acids is weakly similar to the papain family of proteases and is highly conserved from yeast to mammals. Here we report structural and functional studies on the OTU domain-containing protein from yeast, Otu1. We show that Otu1 binds polyubiquitin chain analogs more tightly than monoubiquitin and preferentially hydrolyzes longer polyubiquitin chains with Lys(48) linkages, having little or no activity on Lys(63)- and Lys(29)-linked chains. We also show that Otu1 interacts with Cdc48, a regulator of the ER-associated degradation pathway. We also report the x-ray crystal structure of the OTU domain of Otu1 covalently complexed with ubiquitin and carry out structure-guided mutagenesis revealing a novel mode of ubiquitin recognition and a variation on the papain protease catalytic site configuration that appears to be conserved within the OTU family of ubiquitin hydrolases. Together, these studies provide new insights into ubiquitin binding and hydrolysis by yeast Otu1 and other OTU domain-containing proteins.

Morphological Oogenesis in the out1 Mutant of Drosophila melanogaster Meigen (Diptera: Drosophilidae)

ABSTRACT The sex‐linked, recessive otu1 mutant of Drosophila melanogaster was studied cytologically to reveal the effect of the otu gene mutation on oogenesis. Consequently, the germarium of the otu1 mutant was found to be larger as compared to the normal fertile one and contains many undifferentiated tumor cells resembling cystocytes. Each ovary consists of three types of ovarioles; ovarioles with only a germarium, ovarioles with a germarium and one tumor chamber, and ovarioles with a germarium and two tumor chambers. In the otu1 germarium, the mesodermal follicle cells invade the clusters of different number of tumor cells at the posterior region of the germarium in order to make the tumor chamber and the dividing frequency of the tumor cells in the first tumor chamber was six times more than in the second tumor chamber. Follicle cells surrounding the tumor chamber are morphologically normal, but the number of the follicle cells becomes less as the tumor chambers move down contrary to the fertile one. The otu1 mutant female never lays the egg and the formation of the vitelline membrane is incomplete. The otu1 mutant tumor cells also showed characteristics of certain rapidly dividing cells and its nucleus is lobulated.

Drosophila OVO regulates ovarian tumor transcription by binding unusually near the transcription start site.

Evolutionarily conserved ovo loci encode developmentally regulated, sequence-specific, DNA-binding, C(2)H(2)-zinc-finger proteins required in the germline and epidermal cells of flies and mice. The direct targets of OVO activity are not known. Genetic experiments suggest that ovo acts in the same regulatory network as ovarian tumor (otu), but the relative position of these genes in the pathway is controversial. Three OVO-binding sites exist in a compact regulatory region that controls germline expression of the otu gene. Interestingly, the strongest OVO-binding site is very near the otu transcription start, where basal transcriptional complexes must function. Loss-of-function, gain-of-function and promoter swapping constructs demonstrate that OVO binding near the transcription start site is required for OVO-dependent otu transcription in vivo. These data unambiguously identify otu as a direct OVO target gene and raise the tantalizing possibility that an OVO site, at the location normally occupied by basal components, functions as part of a specialized core promoter.

Nurse cell polytene chromosomes of Drosophila melanogaster otu mutants: morphological changes accompanying interallelic complementation and position effect variegation.

Combinations of certain mutant alleles of the ovarian tumor gene permit the production of viable eggs. Two alleles that behave in this way are otu7 and otu11. Females homozygous for either allele are sterile, and their ovarian nurse cells (NC) contain giant polytene chromosomes of various morphologies. Fertile flies (otu+/otu+, otu+/otu7, otu+/otu11) have endopolyploid nurse cells with typical dispersed chromosomes. Fertile hybrids (otu7/otu11) produce large numbers of polytene chromosomes comparable to, and often larger than, classic salivary gland (SG) chromosomes. Therefore, these otu hybrids provide a unique system for studying, at the chromosomal level, the activation and expression of genes functioning during oogenesis. The otu gene encodes a long and a short isoform. The normal long isoform appears to be responsible for the dispersion of chromosomes during the endomitolic DNA replications occurring in ovarian NCs. The genetic inactivation of euchromatic genes placed next to pericentric heterochromatin by a chromosomal rearrangement is accompanied by the compaction of corresponding chromosome regions. A comparative study of the manifestation of position-effect variegation for the polytene chromosomes of SG cells and NCs was made using the Dp(1;1)pn 2b and Dp(1;f)1337 rearrangements. The percentage frequencies of block formation in the SG and NC nuclei for Dp(1;1)pn 2b rearrangement were 92.6% vs. 15.8%, respectively; for Dp(1;f) 1337, these values were 56.8% vs. 9.7%. Therefore heterochromatin belonging to germ line chromosomes is in a configuration that is far less likely to inactivate inserted segments of euchromatin than is heterochromatin from somatic chromosomes.

Developmental analysis of the ovarian tumor gene during Drosophila oogenesis.

Severe alleles of the ovarian tumor (otu) and ovo genes result in female sterility in Drosophila melanogaster, producing adult ovaries that completely lack egg chambers. We examined the developmental stage in which the agametic phenotype first becomes apparent. Germ cell development in embryos was studied using a strategy that allowed simultaneous labeling of pole cells with the determination of embryonic genotype. We found that ovo- or otu- XX embryonic germ cells were indistinguishable in number and morphology from those present in wild-type siblings. The effects of the mutations were not consistently manifested in the female germline until pupariation, and there was no evidence that either gene was required for germ cell viability at earlier stages of development. The requirement for otu function in the pupal and adult ovary is supported by temperature-shift experiments using a heat-inducible otu gene construct. We demonstrate that otu activity limited to prepupal stages was not sufficient to support oogenesis, while induction during the pupal and adult periods caused suppression of the otu mutant phenotype.

The Ovarian Tumor Protein Isoforms of Drosophila melanogaster Exhibit Differences in Function, Expression, and Localization

The Drosophila melanogaster ovarian tumor ( otu gene, required for normal proliferation and differentiation of the female germ-line, encodes two cytoplasmic protein isoforms, 98 and 104 kDa. Mutants with defects in this gene are typically grouped into one of three phenotypic classes: quiescent (germ cells do not proliferate), oncogenic or tumorous (germ-line cells proliferate uncontrollably), and differentiated (germ-line cells initiate but do not complete differentiation). Analysis of transformants expressing only one of the otu isoforms showed that the 104-kDa isoform (otu-104) can rescue all classes of otu mutants, whereas only differentiated mutants are rescued to a significant extent by the 98-kDa isoform (otu-98). Western analysis of protein extracts prepared from ovaries of various developmental stages indicated that otu-104 predominates in predifferentiated stages, while otu-98 is prevalent in differentiated egg chambers. Immunolocalization experiments demonstrated that otu protein is present in the cytoplasm of oogonial stem cells that populate third instar larvae and in all germ-line-derived cells until late in oogenesis. In stage 10 egg chambers, otu protein shifts to the subcortical region of nurse cells. This type of analysis also showed that upon formation of a 16-cell syncytium otu-104, but not otu-98, preferentially accumulates in the developing oocyte cytoplasm. The otu 11 mutant protein does not show this pattern of enhanced accumulation, nor does it occur in ovaries of egalitarian and Bicaudal-D mutants, which are defective in oocyte determination. Thus, these studies indicate that the 104-kDa isoform is required for normal proliferation of female germ-line cells and perhaps for oocyte differentiation. The 98-kDa isoform appears to be dispensable but can provide an otu function needed for the completion of oocyte maturation.

Structure and expression of hybrid dysgenesis-induced alleles of the ovarian tumor (otu) gene in Drosophila melanogaster.

Mutations at the ovarian tumor (otu) gene of Drosophila melanogaster cause female sterility and generate a range of ovarian phenotypes. Quiescent (QUI) mutants exhibit reduced germ cell proliferation; in oncogenic (ONC) mutants germ cells undergo uncontrolled proliferation generating excessive numbers of undifferentiated cells; the egg chambers of differentiated (DIF) mutants differentiate to variable degrees but fail to complete oogenesis. We have examined mutations caused by insertion and deletion of P elements at the otu gene. The P element insertion sites are upstream of the major otu transcription start sites. In deletion derivatives, the P element, regulatory regions and/or protein coding sequences have been removed. In both insertion and deletion mutants, the level of otu expression correlates directly with the severity of the phenotype: the absence of otu function produces the most severe QUI phenotype while the ONC mutants express lower levels of otu than those which are DIF. The results of this study demonstrate that the diverse mutant phenotypes of otu are the consequence of different levels of otu function.

Identification of a genomic DNA fragment containing the Drosophila melanogaster ovarian tumor gene ( otu) and localization of regions governing its expression

We have identified a genomic DNA fragment which restores fertility to mutants of the ovarian tumor locus ( otu) of Drosophila melanogaster. Germ-line transformants bearing this fragment express otu mRNA with the same tissue specificity as, and at levels comparable to, the wild-type otu gene. Transcription from the otu promoter, P otu, which lacks a TATA element, appears to be initiated at multiple transcription start points ( tsp) within an 80-bp region. Deletion of sequences upstream of the tsp indicates that a region between nucleotides −190 and −310 is required for proper expression from the otu gene. A DNA fragment containing 452 bp upstream and 126 bp downstream from the tsp is able to direct expression of the Escherichia coli lacZ gene in the germ cells of the ovary and testis, indicating that cis-acting regulatory elements governing these expression patterns are located in a 578-bp region surrounding the multiple tsp.

Sequence and Structure of the Drosophila melanogaster Ovarian Tumor Gene and Generation of an Antibody Specific for the Ovarian Tumor Protein

Sequencing cDNA and genomic DNA from the ovarian tumor gene revealed a gene with seven introns spanning 4.5 kilobases. The proline-rich, hydrophilic otu protein is novel. An antibody prepared to a beta-gal-otu fusion protein recognized a 110-kilodalton ovarian protein which was altered in the ovaries of otu gene mutants.

Sequence and structure of the Drosophila melanogaster ovarian tumor gene and generation of an antibody specific for the ovarian tumor protein.

Sequencing cDNA and genomic DNA from the ovarian tumor gene revealed a gene with seven introns spanning 4.5 kilobases. The proline-rich, hydrophilic otu protein is novel. An antibody prepared to a beta-gal-otu fusion protein recognized a 110-kilodalton ovarian protein which was altered in the ovaries of otu gene mutants.

Molecular localization and developmental expression of the otu locus of Drosophila melanogaster.

The female-sterile ovarian tumor gene, otu, is located in cytological region 7F1 on the Drosophila melanogaster chromosome map. We have mapped the gene at the molecular level by using four dysgenic alleles and two revertant derivatives of these alleles as well as an ethyl methanesulfonate-induced allele. The insertional (dysgenic) changes were all associated with one restriction fragment, and its size was restored after phenotypic reversion. One ethyl methanesulfonate-induced allele had a deletion in the restriction fragment adjacent (distal) to the fragment altered in the insertional alleles. These two restriction fragments were immediately adjacent to the s38 chorion gene. Associated with the two altered restriction fragments were two RNA species, an abundant 3.2-kilobase (kb) poly(A)+ RNA and a minor 4.0-kb RNA. Several other less-abundant RNA species were detectable with more-sensitive single-stranded RNA probes. The otu gene was transcribed proximal to distal relative to the centromere; this was opposite to the direction of transcription of the adjacent s38 gene. During development, the 3.2-kb RNA was absent in larvae, first appeared in the pupal stages, and persisted in adult females, in which it was most prevalent in the ovaries. The DNA that hybridized to the 3.2-kb ovarian RNA hybridized to four different RNAs found in the testes but not in the rest of the adult male. These testis-enriched RNAs were transcribed from the same strand of DNA as the ovarian transcripts.

Molecular localization and developmental expression of the otu locus of Drosophila melanogaster.

The female-sterile ovarian tumor gene, otu, is located in cytological region 7F1 on the Drosophila melanogaster chromosome map. We have mapped the gene at the molecular level by using four dysgenic alleles and two revertant derivatives of these alleles as well as an ethyl methanesulfonate-induced allele. The insertional (dysgenic) changes were all associated with one restriction fragment, and its size was restored after phenotypic reversion. One ethyl methanesulfonate-induced allele had a deletion in the restriction fragment adjacent (distal) to the fragment altered in the insertional alleles. These two restriction fragments were immediately adjacent to the s38 chorion gene. Associated with the two altered restriction fragments were two RNA species, an abundant 3.2-kilobase (kb) poly(A)+ RNA and a minor 4.0-kb RNA. Several other less-abundant RNA species were detectable with more-sensitive single-stranded RNA probes. The otu gene was transcribed proximal to distal relative to the centromere; this was opposite to the direction of transcription of the adjacent s38 gene. During development, the 3.2-kb RNA was absent in larvae, first appeared in the pupal stages, and persisted in adult females, in which it was most prevalent in the ovaries. The DNA that hybridized to the 3.2-kb ovarian RNA hybridized to four different RNAs found in the testes but not in the rest of the adult male. These testis-enriched RNAs were transcribed from the same strand of DNA as the ovarian transcripts.

Multiplicity of functions for the otu gene products during Drosophila oogenesis.

The ovarian tumor gene behaves as if it encodes a product (OGP), which is required during several early steps in the transformation of oogonia into functional oocytes. Seventeen ethyl methane sulfonate-induced mutations have been studied, and their mutant phenotypes can be explained as graded responses by individual germ cells to different levels of OGP synthesized by the mutant germ cells themselves. The lowest and highest levels of OGP appear to be produced by otu10 and otu14, respectively. The 15 mutants with intermediate OGP levels are temperature sensitive; subnormal temperatures improve ovarian development, while above-normal temperatures suppress it. A subgroup of these mutants are unable to form a system of actin microfilament bundles in the cortical cytoplasm of their nurse cells during stage 10B, and these defective nurse cells are unable to transport their cytoplasm to the oocyte, as normally happens between stages 10B and 12. In addition to its role in the actin-mediated transport of nurse cell cytoplasm, OGP also appears to alter the morphology of giant polytene chromosomes, which form as the nurse cells undergo endocycles of DNA replication. Genetic evidence suggests that otu also encodes a second product (SP) that is utilized late in oogenesis. SP is required for the synthesis in the ooplasm of glycogen-rich, beta yolk spheres. Products of the otu gene also play a vital but unknown role in embryogenesis.

Fertile heteroallelic combinations of mutant alleles of the otu locus of Drosophila melanogaster.

This paper describes the ovarian pathologies observed when 108 different heteroallelic combinations were made involving 17 independent mutations at the ovarian tumor (otu) locus. Most of the mutant phenotypes can be explained as graded responses by individual germ cells to different levels of functionally active otu gene product (OGP) synthesized by the mutant cells themselves. The lowest and highest levels of OGP appear to be produced by otu 10 and otu 14, respectively. In most heteroallelic ovaries the alleles have additive effects, and hybrid germ cells reach a developmental stage more advanced than the "weaker" homozygote but less advanced than the "stronger" homozygote. However, examples of both positive and negative complementation also have been found, and these suggest that the products encoded by different mutant alleles can combine to form dimers or multimers which may be superior or inferior to the homodimers. In flies homozygous for otu 11 most ovarioles contain tumors, but some germ cells are able to develop further than those in otu 14 homozygotes. This suggests that, while otu 11 produces intermediate levels of OGP, it also produces a second product (which otu 14 cannot make) that is utilized at the period in oogenesis when development in cells homozygous for otu 14 is blocked. When otu 11 is combined with any one of eight specific alleles, it allows oocyte/nurse cell syncytia to differentiate that can complete development and undergo embryogenesis, if fertilized. The endopolyploid nurse cells of these hybrids have giant polytene chromosomes, and the presence of GPCs in functionally active, germ-line derived cells provides an interesting new system for experimental study. Analysis of the characteristic ovarian pathologies produced by flies of different genotypes leads to the conclusion that the products of the otu + gene are utilized during at least six different periods in Drosophila oogenesis.

Complementation between alleles at the ovarian tumor locus of Drosophila melanogaster.

The (ovarian tumor) otu gene resides at 23.2 on the genetic map of the X chromosome and near 7F1 on the cytological map. This germ line-expressed locus behaves as if it encodes a gene product which is required during certain steps in the transformation of oogonia into functional oocytes. On the basis of their ovarian morphologies 17 ethyl methane sulfonate (EMS)-induced mutants have been distributed among three developmental classes as follows: quiescent (eight), oncogenic (four), and differentiated (five). The otu13 and otu14 alleles interact to yield fertile females, and many other heteroallelic combinations show partial complementation. Since many mutant alleles interact beneficially, the functional product of the otu gene may be a multimer. We conclude, from an analysis of heteroallelic interactions and dosage effects, that the abnormal phenotypes observed are graded consequences of reduced levels of functional gene product and that the minimum concentration required for development increases as oogenesis proceeds.