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1.  Conserved properties of Drosophila and human spermatozoal mRNA repertoires 
It is now well established that mature mammalian spermatozoa carry a population of mRNA molecules, at least some of which are transferred to the oocyte at fertilization, however, their function remains largely unclear. To shed light on the evolutionary conservation of this feature of sperm biology, we analysed highly purified populations of mature sperm from the fruitfly, Drosophila melanogaster. As with mammalian sperm, we found a consistently enriched population of mRNA molecules that are unlikely to be derived from contaminating somatic cells or immature sperm. Using tagged transcripts for three of the spermatozoal mRNAs, we demonstrate that they are transferred to the oocyte at fertilization and can be detected before, and at least until, the onset of zygotic gene expression. We find a remarkable conservation in the functional annotations associated with fly and human spermatozoal mRNAs, in particular, a highly significant enrichment for transcripts encoding ribosomal proteins (RPs). The substantial functional coherence of spermatozoal transcripts in humans and the fly opens the possibility of using the power of Drosophila genetics to address the function of this enigmatic class of molecules in sperm and in the oocyte following fertilization.
doi:10.1098/rspb.2012.0153
PMCID: PMC3350705  PMID: 22378807
Drosophila; spermatogenesis; sperm; spermatozoa; transcriptome
2.  Comparison of embryonic expression within multigene families employing the FlyExpress discovery platform reveals more spatial than temporal divergence 
Overlaps in spatial patterns of gene expression are frequently an initial clue to genetic interactions during embryonic development. However, manual inspection of images requires considerable time and resources impeding the discovery of important interactions because tens of thousands of images exist. The FlyExpress discovery platform was developed to facilitate data-driven comparative analysis of expression pattern images from Drosophila embryos. An image-based search of the BDGP and Fly-FISH datasets conducted in FlyExpress yields fewer but more precise results than text-based searching when the specific goal is to find genes with overlapping expression patterns. We also provide an example of a FlyExpress contribution to scientific discovery: an analysis of gene expression patterns for multigene family members revealed that spatial divergence is far more frequent than temporal divergence, especially after the maternal to zygotic transition. This discovery provides a new clue to molecular mechanisms whereby duplicated genes acquire novel functions.
doi:10.1002/dvdy.22749
PMCID: PMC3241901  PMID: 21960044
Drosophila; FlyExpress; gene expression patterns; image analysis; multigene family
3.  FlyExpress: visual mining of spatiotemporal patterns for genes and publications in Drosophila embryogenesis 
Bioinformatics  2011;27(23):3319-3320.
Summary: Images containing spatial expression patterns illuminate the roles of different genes during embryogenesis. In order to generate initial clues to regulatory interactions, biologists frequently need to know the set of genes expressed at the same time at specific locations in a developing embryo, as well as related research publications. However, text-based mining of image annotations and research articles cannot produce all relevant results, because the primary data are images that exist as graphical objects. We have developed a unique knowledge base (FlyExpress) to facilitate visual mining of images from Drosophila melanogaster embryogenesis. By clicking on specific locations in pictures of fly embryos from different stages of development and different visual projections, users can produce a list of genes and publications instantly. In FlyExpress, each queryable embryo picture is a heat-map that captures the expression patterns of more than 4500 genes and more than 2600 published articles. In addition, one can view spatial patterns for particular genes over time as well as find other genes with similar expression patterns at a given developmental stage. Therefore, FlyExpress is a unique tool for mining spatiotemporal expression patterns in a format readily accessible to the scientific community.
Availability: http://www.flyexpress.net
Contact: s.kumar@asu.edu
doi:10.1093/bioinformatics/btr567
PMCID: PMC3223365  PMID: 21994220
4.  Segmental dataset and whole body expression data do not support the hypothesis that non-random movement is an intrinsic property of Drosophila retrogenes 
Background
Several studies in Drosophila have shown excessive movement of retrogenes from the X chromosome to autosomes, and that these genes are frequently expressed in the testis. This phenomenon has led to several hypotheses invoking natural selection as the process driving male-biased genes to the autosomes. Metta and Schlötterer (BMC Evol Biol 2010, 10:114) analyzed a set of retrogenes where the parental gene has been subsequently lost. They assumed that this class of retrogenes replaced the ancestral functions of the parental gene, and reported that these retrogenes, although mostly originating from movement out of the X chromosome, showed female-biased or unbiased expression. These observations led the authors to suggest that selective forces (such as meiotic sex chromosome inactivation and sexual antagonism) were not responsible for the observed pattern of retrogene movement out of the X chromosome.
Results
We reanalyzed the dataset published by Metta and Schlötterer and found several issues that led us to a different conclusion. In particular, Metta and Schlötterer used a dataset combined with expression data in which significant sex-biased expression is not detectable. First, the authors used a segmental dataset where the genes selected for analysis were less testis-biased in expression than those that were excluded from the study. Second, sex-biased expression was defined by comparing male and female whole-body data and not the expression of these genes in gonadal tissues. This approach significantly reduces the probability of detecting sex-biased expressed genes, which explains why the vast majority of the genes analyzed (parental and retrogenes) were equally expressed in both males and females. Third, the female-biased expression observed by Metta and Schlötterer is mostly found for parental genes located on the X chromosome, which is known to be enriched with genes with female-biased expression. Fourth, using additional gonad expression data, we found that autosomal genes analyzed by Metta and Schlötterer are less up regulated in ovaries and have higher chance to be expressed in meiotic cells of spermatogenesis when compared to X-linked genes.
Conclusions
The criteria used to select retrogenes and the sex-biased expression data based on whole adult flies generated a segmental dataset of female-biased and unbiased expressed genes that was unable to detect the higher propensity of autosomal retrogenes to be expressed in males. Thus, there is no support for the authors’ view that the movement of new retrogenes, which originated from X-linked parental genes, was not driven by selection. Therefore, selection-based genetic models remain the most parsimonious explanations for the observed chromosomal distribution of retrogenes.
doi:10.1186/1471-2148-12-169
PMCID: PMC3532075  PMID: 22950647
5.  Re-analysis of the larval testis data on meiotic sex chromosome inactivation revealed evidence for tissue-specific gene expression related to the drosophila X chromosome 
BMC Biology  2012;10:49.
Background
Meiotic sex chromosome inactivation (MSCI) during spermatogenesis has been proposed as one of the evolutionary driving forces behind both the under-representation of male-biased genes on, and the gene movement out of, the X chromosome in Drosophila. However, the relevance of MSCI in shaping sex chromosome evolution is controversial. Here we examine two aspects of a recent study on testis gene expression (Mikhaylova and Nurminsky, BMC Biol 2011, 9:29) that failed to support the MSCI in Drosophila. First, Mikhaylova and Nurminsky found no differences between X-linked and autosomal genes based on the transcriptional profiling of the early testis development, and thus concluded that MSCI does not occur in D. melanogaster. Second, they also analyzed expression data from several D. melanogaster tissues and concluded that under-representation on the X chromosome is not an exclusive property of testis-biased genes, but instead, a general property of tissue-specific genes.
Results
By re-analyzing the Mikhaylova and Nurminsky's testis data and the expression data on several D. melanogaster tissues, we made two major findings that refuted their original claims. First, the developmental testis data has generally greater experimental error than conventional analyses, which reduced significantly the power to detect chromosomal differences in expression. Nevertheless, our re-analysis observed significantly lower expression of the X chromosome in the genomic transcriptomes of later development stages of the testis, which is consistent with the MSCI hypothesis. Second, tissue-specific genes are also in general enriched with genes more expressed in testes than in ovaries, that is testis-biased genes. By completely excluding from the analyses the testis-biased genes, which are known to be under-represented in the X, we found that all the other tissue-specific genes are randomly distributed between the X chromosome and the autosomes.
Conclusions
Our findings negate the original study of Mikhaylova and Nurminsky, which concluded a lack of MSCI and generalized the pattern of paucity in the X chromosome for tissue-specific genes in Drosophila. Therefore, MSCI and other selection-based models such as sexual antagonism, dosage compensation, and meiotic-drive continue to be viable models as driving forces shaping the genomic distribution of male-related genes in Drosophila.
doi:10.1186/1741-7007-10-49
PMCID: PMC3391172  PMID: 22691264
6.  Sperm Proteomics Reveals Intensified Selection on Mouse Sperm Membrane and Acrosome Genes 
Molecular Biology and Evolution  2010;27(6):1235-1246.
Spermatozoa are a focal point for the impact of sexual selection due to sperm competition and sperm–female interactions in a wide range of sexually reproducing organisms. In-depth molecular investigation of the ramifications of these selective regimes has been limited due to a lack of information concerning the molecular composition of sperm. In this study, we utilize three previously published proteomic data sets in conjunction with our whole mouse sperm proteomic analysis to delineate cellular regions of sperm most impacted by positive selection. Interspecific analysis reveals robust evolutionary acceleration of sperm cell membrane genes (which include genes encoding acrosomal and sperm cell surface proteins) relative to other sperm genes, and evidence for positive selection in approximately 22% of sperm cell membrane components was obtained using maximum likelihood models. The selective forces driving the accelerated evolution of these membrane proteins may occur at a number of locations during sperm development, maturation, and transit through the female reproductive tract where the sperm cell membrane and eventually the acrosome are exposed to the extracellular milieu and available for direct cell–cell interactions.
doi:10.1093/molbev/msq007
PMCID: PMC2877994  PMID: 20080865
Mus; sperm; proteomics; sexual selection; acrosome
7.  Expansion and functional diversification of a leucyl aminopeptidase family that encodes the major protein constituents of Drosophila sperm 
BMC Genomics  2011;12:177.
Background
The evolutionary diversification of gene families through gene creation (and loss) is a dynamic process believed to be critical to the evolution of functional novelty. Previous identification of a closely related family of eight annotated metalloprotease genes of the M17 Merops family in the Drosophila sperm proteome (termed, Sperm-LeucylAminoPeptidases, S-LAPs 1-8) led us to hypothesize that this gene family may have experienced such a diversification during insect evolution.
Results
To assess putative functional activities of S-LAPs, we (i) demonstrated that all S-LAPs are specifically expressed in the testis, (ii) confirmed their presence in sperm by two-dimensional gel electrophoresis and mass spectrometry, (iii) determined that they represent a major portion of the total protein in sperm and (iv) identified aminopeptidase enzymatic activity in sperm extracts using LAP-specific substrates. Functionally significant divergence at the canonical M17 active site indicates that the largest phylogenetic group of S-LAPs lost catalytic activity and likely acquired novel, as yet undetermined, functions in sperm prior to the expansion of the gene family.
Conclusions
Comparative genomic and phylogenetic analyses revealed the dramatic expansion of the S-LAP gene family during Drosophila evolution and copy number heterogeneity in the genomes of related insects. This finding, in conjunction with the loss of catalytic activity and potential neofunctionalization amongst some family members, extends empirical support for pervasive "revolving door" turnover in the evolution of reproductive gene family composition and function.
doi:10.1186/1471-2164-12-177
PMCID: PMC3078892  PMID: 21466698
sperm; proteomics; gene duplication; gene family; protease; spermatogenesis; testis
8.  Relationship between gene co-expression and sharing of transcription factor binding sites in Drosophila melanogaster 
Bioinformatics  2009;25(19):2473-2477.
Motivation: In functional genomics, it is frequently useful to correlate expression levels of genes to identify transcription factor binding sites (TFBS) via the presence of common sequence motifs. The underlying assumption is that co-expressed genes are more likely to contain shared TFBS and, thus, TFBS can be identified computationally. Indeed, gene pairs with a very high expression correlation show a significant excess of shared binding sites in yeast. We have tested this assumption in a more complex organism, Drosophila melanogaster, by using experimentally determined TFBS and microarray expression data. We have also examined the reverse relationship between the expression correlation and the extent of TFBS sharing.
Results: Pairs of genes with shared TFBS show, on average, a higher degree of co-expression than those with no common TFBS in Drosophila. However, the reverse does not hold true: gene pairs with high expression correlations do not share significantly larger numbers of TFBS. Exception to this observation exists when comparing expression of genes from the earliest stages of embryonic development. Interestingly, semantic similarity between gene annotations (Biological Process) is much better associated with TFBS sharing, as compared to the expression correlation. We discuss these results in light of reverse engineering approaches to computationally predict regulatory sequences by using comparative genomics.
Contact: amarcoca@asu.edu
doi:10.1093/bioinformatics/btp462
PMCID: PMC2752616  PMID: 19633094
9.  Stage-Specific Expression Profiling of Drosophila Spermatogenesis Suggests that Meiotic Sex Chromosome Inactivation Drives Genomic Relocation of Testis-Expressed Genes 
PLoS Genetics  2009;5(11):e1000731.
In Drosophila, genes expressed in males tend to accumulate on autosomes and are underrepresented on the X chromosome. In particular, genes expressed in testis have been observed to frequently relocate from the X chromosome to the autosomes. The inactivation of X-linked genes during male meiosis (i.e., meiotic sex chromosome inactivation—MSCI) was first proposed to explain male sterility caused by X-autosomal translocation in Drosophila, and more recently it was suggested that MSCI might provide the conditions under which selection would favor the accumulation of testis-expressed genes on autosomes. In order to investigate the impact of MSCI on Drosophila testis-expressed genes, we performed a global gene expression analysis of the three major phases of D. melanogaster spermatogenesis: mitosis, meiosis, and post-meiosis. First, we found evidence supporting the existence of MSCI by comparing the expression levels of X- and autosome-linked genes, finding the former to be significantly reduced in meiosis. Second, we observed that the paucity of X-linked testis-expressed genes was restricted to those genes highly expressed in meiosis. Third, we found that autosomal genes relocated through retroposition from the X chromosome were more often highly expressed in meiosis in contrast to their X-linked parents. These results suggest MSCI as a general mechanism affecting the evolution of some testis-expressed genes.
Author Summary
During the course of Drosophila evolution, genes expressed in males have accumulated on the autosomes. Meiotic sex chromosome X inactivation in males was proposed, among other hypotheses, as a selective force favoring the accumulation of testis-expressed genes on the autosomes. Under such a model, the inactivation of X-linked genes would favor the accumulation of testis-expressed genes in autosomes, wherein these genes would still be expressed. In this study, we observed meiotic expression reduction for X-linked genes in D. melanogaster through a global gene expression analysis in different phases of spermatogenesis, in agreement with MSCI. In order to test the effects of MSCI on the chromosomal distribution of testis-expressed genes, we analyzed their expression pattern throughout spermatogenesis. First, X chromosome underrepresentation was restricted to testis-biased genes over-expressed in meiosis. Second, we observed that the autosomal genes retroposed from the X chromosome more often showed complementary expression in meiosis to their X-linked parents. These results support MSCI in Drosophila, suggesting its mechanistic role in the evolution of testis-expressed genes.
doi:10.1371/journal.pgen.1000731
PMCID: PMC2770318  PMID: 19936020
10.  Recent Origins of Sperm Genes in Drosophila 
Molecular Biology and Evolution  2008;25(10):2157-2166.
Newly created genes often acquire testis-specific or enhanced expression but neither the mechanisms responsible for this specificity nor the functional consequences of these evolutionary processes are well understood. Genomic analyses of the Drosophila melanogaster sperm proteome has identified 2 recently evolved gene families on the melanogaster lineage and 4 genes created by retrotransposition during the evolution of the melanogaster group that encode novel sperm components. The expanded Mst35B (protamine) and tektin gene families are the result of tandem duplication events with all family members displaying testis-specific expression. The Mst35B family encodes rapidly evolving protamines that display a robust signature of positive selection within the DNA-binding high-mobility group box consistent with functional diversification in genome repackaging during sperm nuclear remodeling. The Mst35B paralogs also reside in a significant regional cluster of testis-overexpressed genes. Tektins, known components of the axoneme, are encoded by 3 nearly identical X-linked genes, a finding consistent with very recent gene family expansion. In addition to localized duplication events, the evolution of the sperm proteome has also been driven by recent retrotransposition events resulting in Cdlc2, CG13340, Vha36, and CG4706. Cdlc2, CG13340, and Vha36 all display high levels of overexpression in the testis, and Cdlc2 and CG13340 reside within testis-overexpressed gene clusters. Thus, gene creation is a dynamic force in the evolution of sperm composition and possibly function, which further suggests that acquisition of molecular functionality in sperm may be an influential pathway in the fixation of new genes.
doi:10.1093/molbev/msn162
PMCID: PMC2727386  PMID: 18653731
sperm; gene duplication; retrotransposition; testis; protamines; proteomics
11.  Heads or Tails: Host-Parasite Interactions in the Drosophila-Wolbachia System 
Wolbachia strains are endosymbiotic bacteria typically found in the reproductive tracts of arthropods. These bacteria manipulate host reproduction to ensure maternal transmission. They are usually transmitted vertically, so it has been predicted that they have evolved a mechanism to target the host's germ cells during development. Through cytological analysis we found that Wolbachia strains display various affinities for the germ line of Drosophila. Different Wolbachia strains show posterior, anterior, or cortical localization in Drosophila embryos, and this localization is congruent with the classification of the organisms based on the wsp (Wolbachia surface protein) gene sequence. This embryonic distribution pattern is established during early oogenesis and does not change until late stages of embryogenesis. The posterior and anterior localization of Wolbachia resembles that of oskar and bicoid mRNAs, respectively, which define the anterior-posterior axis in the Drosophila oocyte. By comparing the properties of a single Wolbachia strain in different host backgrounds and the properties of different Wolbachia strains in the same host background, we concluded that bacterial factors determine distribution, while bacterial density seems to be limited by the host. Possible implications concerning cytoplasmic incompatibility and evolution of strains are discussed.
doi:10.1128/AEM.70.9.5366-5372.2004
PMCID: PMC520876  PMID: 15345422
12.  Hsp70 and thermal pretreatment mitigate developmental damage caused by mitotic poisons in Drosophila 
Cell Stress & Chaperones  2002;7(3):297-308.
To assess the ability of the heat-inducible molecular chaperone heat-shock protein 70 (Hsp70) to mitigate a specific developmental lesion, we administered the antimicrotubule drugs vinblastine (VB) and colchicine (COL) to larvae of Drosophila engineered to express differing levels of Hsp70 after heat pretreatment (HP). VB and COL decreased survival during metamorphosis, disrupted development of the adult eye and other structures as well as their precursor imaginal disks, and induced chromosome nondisjunction in the wing imaginal disk as indicated by the somatic mutation and recombination test (SMART) assay. Hsp70-inducing HP reduced many of these effects. For the traits viability, adult eye morphology, eye imaginal disk morphology, cell death in the eye imaginal disks, and single and total mutant clone formation in the SMART assay, HP reduced the impact of VB to a greater extent in Drosophila with 6 hsp70 transgenes than in a sister strain from which the transgenes had been excised. Because the extra-copy strain has higher levels of Hsp70 than does the excision strain but is otherwise almost identical in genetic background to the excision strain, these outcomes are attributable to Hsp70. The hsp70 copy number had a variable interaction with HP and COL administration.
PMCID: PMC514829  PMID: 12482205
13.  Wolbachia: Evolutionary novelty in a rickettsial bacteria 
Background
Although closely related, the alpha-proteobacteria Wolbachia and the Rickettsiacae (Rickettsia and Ehrlichia), employ different evolutionary life history strategies. Wolbachia are obligate endocellular symbionts that infect an extraordinary host range and, in contrast to the infectious and pathogenic Rickettsia and Ehrlichia, profoundly influence host reproductive biology.
Results
Phylogenies of the Rickettsia, Ehrlichia, and Wolbachia were independently inferred from 16S rDNA sequences and GroEL amino acid sequences. Topologies inferred from both sets of sequence data were consistent with one another, and both indicate the genus Wolbachia shared a common ancestor most recently with Ehrlichia. These two genera are a sister group to the genus Rickettsia. Mapping biological properties onto this phylogeny reveals that manipulation of host reproduction, characteristic of Wolbachia strains, is a derived characteristic. This evolutionary novelty is accompanied by the loss of the ability to infect vertebrate hosts.
Conclusions
Because of the contrasting transmission strategies employed by each, Wolbachia is expected to maximize efficiency of vertical transmission, while Ehrlichia and Rickettsia will optimize horizontal transfer of infection. Wolbachia manipulation of host reproduction could thus be viewed as strategy employed by this bacterium to foster its own propagation via vertical transmission.
doi:10.1186/1471-2148-1-10
PMCID: PMC60491  PMID: 11734058

Results 1-13 (13)