A comprehensive Drosophila resource to identify key functional interactions between SARS-CoV-2 factors and host proteins.

Development of effective therapies against SARS-CoV-2 infections relies on mechanistic knowledge of virus-host interface. Abundant physical interactions between viral and host proteins have been identified, but few have been functionally characterized. Harnessing the power of fly genetics, we develop a comprehensive Drosophila COVID-19 resource (DCR) consisting of publicly available strains for conditional tissue-specific expression of all SARS-CoV-2 encoded proteins, UAS-human cDNA transgenic lines encoding established host-viral interacting factors, and GAL4 insertion lines disrupting fly homologs of SARS-CoV-2 human interacting proteins. We demonstrate the utility of the DCR to functionally assess SARS-CoV-2 genes and candidate human binding partners. We show that NSP8 engages in strong genetic interactions with several human candidates, most prominently with the ATE1 arginyltransferase to induce actin arginylation and cytoskeletal disorganization, and that two ATE1 inhibitors can reverse NSP8 phenotypes. The DCR enables parallel global-scale functional analysis of SARS-CoV-2 components in a prime genetic model system.

A cross-species approach for the identification of Drosophila male sterility genes.

Male reproduction encompasses many essential cellular processes and interactions. As a focal point for these events, sperm offer opportunities for advancing our understanding of sexual reproduction at multiple levels during development. Using male sterility genes identified in human, mouse, and fruit fly databases as a starting point, 103 Drosophila melanogaster genes were screened for their association with male sterility by tissue-specific RNAi knockdown and CRISPR/Cas9-mediated mutagenesis. This list included 56 genes associated with male infertility in the human databases, but not found in the Drosophila database, resulting in the discovery of 63 new genes associated with male fertility in Drosophila. The phenotypes identified were categorized into six distinct classes affecting sperm development. Interestingly, the second largest class (Class VI) caused sterility despite apparently normal testis and sperm morphology suggesting that these proteins may have functions in the mature sperm following spermatogenesis. We focused on one such gene, Rack 1, and found that it plays an important role in two developmental periods, in early germline cells or germline stem cells and in spermatogenic cells or sperm. Taken together, many genes are yet to be identified and their role in male reproduction, especially after ejaculation, remains to be elucidated in Drosophila, where a wealth of data from human and other model organisms would be useful.

The Drosophila Neprilysin 4 gene is essential for sperm function following sperm transfer to females.

Sperm are modified substantially in passing through both the male and the female reproductive tracts, only thereafter becoming functionally competent to fertilize eggs. Drosophila sperm become motile in the seminal vesicle; after ejaculation, they interact with seminal fluid proteins and undergo biochemical changes on their surface while they are stored in the female sperm storage organs. However, the molecular mechanisms underlying these maturation processes remain largely unknown. Here, we focused on Drosophila Neprilysin genes, which are the fly orthologs of the mouse Membrane metallo-endopeptidase-like 1 (Mmel1) gene. While Mmel1 knockout male mice have reduced fertility without abnormality in either testis morphology or sperm motility, there are inconsistent results regarding the association of any Neprilysin gene with male fertility in Drosophila. We examined the association of the Nep1-5 genes with male fertility by RNAi and found that Nep4 gene function is specifically required in germline cells. To investigate this in more detail, we induced mutations in the Nep4 gene by the CRISPR/Cas9 system and isolated two mutants, both of which were viable and female fertile, but male sterile. The mutant males had normal-looking testes and sperm; during copulation, sperm were transferred to females and stored in the seminal receptacle and paired spermathecae. However, following sperm transfer and storage, three defects were observed for Nep4 mutant sperm. First, sperm were quickly discarded by the females; second, the proportion of eggs fertilized was significantly lower for mutant sperm than for control sperm; and third, most eggs laid did not initiate development after sperm entry. Taking these observations together, we conclude that the Nep4 gene is essential for sperm function following sperm transfer to females.

Humanized Flies and Resources for Cross-Species Study.

The completion of whole-genome sequences has greatly broadened our understanding of genes and genomes. The availability of model organism databases facilitates the sharing of information. However, it is still challenging to predict the pathogenicity of missense mutations, and it is more difficult to evaluate the functional impact of noncoding variants. What is more, it is a primary question to understand what variants interact to express phenotypes. Powerful genetic tools and resources available in Drosophila now make it much easier to replace endogenous genes with exogenous DNA. This allows us to directly investigate and compare the functions of orthologs, variants, and fragments in a single genetic background, the value of which should be widely appreciated. To take one example, we are currently studying so-called ultra-conserved elements, which have been conserved over hundreds of millions of years of vertebrate evolution. Many highly conserved elements are in noncoding regions and are thought to play a pivotal role in gene regulation. We generated transgenic fly lines carrying human ultra-conserved elements for enhancer reporter assay and indeed observed the reporter expression in one or more tissues of embryos and larvae in all elements tested. Currently, transgenic human-ORF lines expressing human genes under the control of GAL4/UAS system are also been developed, which will greatly facilitate the cross-species in Drosophila. In this chapter, I introduce useful tools and resources available in Drosophila to nonspecialists, encouraging their further use in many applications.

Severe Fertility Effects of sheepish Sperm Caused by Failure To Enter Female Sperm Storage Organs in Drosophila melanogaster.

In Drosophila, mature sperm are transferred from males to females during copulation, stored in the sperm storage organs of females, and then utilized for fertilization. Here, we report a gene named sheepish (shps) of Drosophila melanogaster that is essential for sperm storage in females. shps mutant males, although producing morphologically normal and motile sperm that are effectively transferred to females, produce very few offspring. Direct counts of sperm indicated that the primary defect was correlated to failure of shps sperm to migrate into the female sperm storage organs. Increased sperm motion parameters were seen in the control after transfer to females, whereas sperm from shps males have characteristics of the motion parameters different from the control. The few sperm that occasionally entered the female sperm storage organs showed no obvious defects in fertilization and early embryo development. The female postmating responses after copulation with shps males appeared normal, at least with respect to conformational changes of uterus, mating plug formation, and female remating rates. The shps gene encodes a protein with homology to amine oxidases, including as observed in mammals, with a transmembrane region at the C-terminal end. The shps mutation was characterized by a nonsense replacement in the third exon of CG13611, and shps was rescued by transformants of the wild-type copy of CG13611 Thus, shps may define a new class of gene responsible for sperm storage.

Sperm of the wasted mutant are wasted when females utilize the stored sperm in Drosophila melanogaster.

Females of many animal species store sperm after copulation for use in fertilization, but the mechanisms controlling sperm storage and utilization are largely unknown. Here we describe a novel male sterile mutation of Drosophila melanogaster, wasted (wst), which shows defects in various processes of sperm utilization. The sperm of wst mutant males are stored like those of wild-type males in the female sperm storage organs, the spermathecae and seminal receptacles, after copulation and are released at each ovulation. However, an average of thirteen times more wst sperm than wild type sperm are released at each ovulation, resulting in rapid loss of sperm stored in seminal receptacles within a few days after copulation. wst sperm can enter eggs efficiently at 5 hr after copulation, but the efficiency of sperm entry decreases significantly by 24 hr after copulation, suggesting that wst sperm lose their ability to enter eggs during storage. Furthermore, wst sperm fail to undergo nuclear decondensation, which prevents the process of fertilization even when sperm enter eggs. Our results indicate that the wst gene is essential for independent processes in the utilization of stored sperm; namely, regulation of sperm release from female storage organs, maintenance of sperm efficiency for entry into eggs, and formation of the male pronucleus in the egg at fertilization.

A rapid decrease in number of the complete ninja element and concomitant increase of the defective element in a strain of Drosophila simulans.

The ninja element, originally isolated from an unstable white mutant strain white-milky (w(mky)) of Drosophila simulans, is a member of the retrotransposon family with long terminal repeats (LTRs). We show that ninja is present in high copy numbers in the w(mky)-derivative sublines white-chocolate (w(cho)) and white-persimmonl (w(psm1)), in a low copy number in another derivative subline white-milky 3 (w(mky3)), and in only a few copies in a wild type strain. We have cloned the ninja elements from these sublines and examined their structures. Most of the elements cloned (38 out of 41 independent clones) from w(cho) were full length. In contrast, only 9 of 23 independent clones from w(mky3) were full length. We hypothesize that ninja elements were integrated and lost frequently in the w(mky) strain and its derivative genomes, and that a rapid decrease in numbers of the ninja element was caused not by an increased rate of loss but by a reduction of integration of full length ninja elements in w(mky3). Each defective element had a unique deletion and/or an insertion except for the three from w(mky3), which had exactly the same 81-bp deletion in each of the 5' and 3' LTRs. The 5' and 3' ends of the deletion appeared to represent sequences similar to those of Drosophila consensussplicing sites. Ectopic splicing may have produced these defective ninja elements.

Isolation and cytogenetic characterization of male meiotic mutants of Drosophila melanogaster.

Proper segregation of homologous chromosomes in meiosis I is ensured by pairing of homologs and maintenance of sister chromatid cohesion. In male Drosophila melanogaster, meiosis is achiasmatic and homologs pair at limited chromosome regions called pairing sites. We screened for male meiotic mutants to identify genes required for normal pairing and disjunction of homologs. Nondisjunction of the sex and the fourth chromosomes in male meiosis was scored as a mutant phenotype. We screened 2306 mutagenized and 226 natural population-derived second and third chromosomes and obtained seven mutants representing different loci on the second chromosome and one on the third. Five mutants showed relatively mild effects (<10% nondisjunction). mei(2)yh149 and mei(2)yoh7134 affected both the sex and the fourth chromosomes, mei(2)yh217 produced possible sex chromosome-specific nondisjunction, and mei(2)yh15 and mei(2)yh137 produced fourth chromosome-specific nondisjunction. mei(2)yh137 was allelic to the teflon gene required for autosomal pairing. Three mutants exhibited severe defects, producing >10% nondisjunction of the sex and/or the fourth chromosomes. mei(2)ys91 (a new allele of the orientation disruptor gene) and mei(3)M20 induced precocious separation of sister chromatids as early as prometa-phase I. mei(2)yh92 predominantly induced nondisjunction at meiosis I that appeared to be the consequence of failure of the separation of paired homologous chromosomes.

The Drosophila misfire gene has an essential role in sperm activation during fertilization.

The male sterile mutation, misfire (mfr), of Drosophila melanogaster is a novel paternal effect, fertilization defective mutant that effects sperm head decondensation. mfr sperm were motile, appeared normal morphologically and were transferred to the female during copulation. However, less than 0.1% of eggs laid by females mated to mfr males hatched. Although mfr sperm entered eggs at a high frequency (93%), 99% of the inseminated eggs did not initiate the first nuclear division. Unlike wild type fertilizing sperm, the position and shape of mfr sperm tails within the egg were not constant, but varied in a seemingly random manner. The heads of inseminating mutant sperm were always located near the surface of eggs just underlying the egg plasma membrane, and maintained their needle-like shape indicating the failure of nuclear decondensation. Further observations revealed that plasma membrane of inseminating sperm appeared intact, including the head region. These phenotypes were equivalent to those of sneaky (snky), another fertilization defective male sterile mutation. Our observations strongly suggest that mfr mutant males are sterile because their inseminating sperm fail to form a male pronucleus due to the inability of the sperm to properly respond to egg factors responsible for the breakdown of the plasma membrane. Although mfr and snky mutations were phenotypically identical, they mapped to cytologically distinct genetic loci and no genetic interactions were observed, suggesting that at least two distinct paternal gene products are involved in the early stages of pronuclear formation.

Drosophila lola encodes a family of BTB-transcription regulators with highly variable C-terminal domains containing zinc finger motifs.

Alternative splicing is an important mechanism contributing to the increased proteome diversity in higher eukaryotes. We have explored the alternative splicing events in the Drosophila longitudinals lacking (lola) gene by means of 5' RACE, 3' RACE, genome sequence searches, and EST sequencing. We demonstrated that the lola locus is comprised of 32 exons spanning over 60 kb, and encodes a total of 80 alternatively spliced variants consisting of 5' and 3' variable sequences and constitutive common exons. All the variants shared a common sequence (exons 5-8) encoding the N-terminal region containing the BTB domain, but both the 5' and 3' ends were variable. There were four promoters responsible for the variation in the 5' end (exons 1-4). Alternative splicing was involved in the variation in the 3' end corresponding to the C-terminal variable region, which was encoded by one or two exons that were selected from 20 groups of exons in a mutually exclusive manner (exons 9-32). Seventeen of the 20 isoforms contained C(2)H(2)-like zinc finger motifs in the C-terminal variable region. Analyses of the 3' variant-specific cDNA pools revealed that all combinations of 5' and 3' variable sequences were expressed in both the embryonic and third instar larval stages. Since the BTB domain mediates dimerization, lola encodes a family of transcription regulators with a large variety of DNA- or protein-binding specificities, and could be involved in various developmental processes, including the embryonic neural pathfindings. We also showed that the structures of Lola isoforms were highly conserved in Drosophila pseudoobscura.