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  1. MicroRNA regulation of CTP synthase and cytoophidium in Drosophila melanogaster
    Dzaki N, Woo WK, Thangadurai S, Azzam G
    Exp Cell Res, 2019 12 15;385(2):111688.
    PMID: 31678212 DOI: 10.1016/j.yexcr.2019.111688
    CTPsyn is a crucial metabolic enzyme which synthesizes CTP nucleotides. It has the extraordinary ability to compartmentalize into filaments termed cytoophidia. Though the structure is evolutionarily conserved across kingdoms, the mechanisms behind their formation remain unknown. MicroRNAs (miRNAs) are short single-stranded RNA capable of directing mRNA silencing and degradation. D. melanogaster has a high total gene count to miRNA gene number ratio, alluding to the possibility that CTPsyn too may come under their regulation. A thorough miRNA overexpression involving 123 miRNAs was conducted, followed by CTPsyn-specific staining upon cytoophidia-rich egg chambers. This revealed a small group of candidates which confer either a lengthening or truncating effect on cytoophidia, suggesting they may play a role in regulating CTPsyn. MiR-975 and miR-1014 are both cytoophidia-elongating, whereas miR-190 and miR-932 are cytoophidia-shortening. Though target prediction shows that miR-975 and miR-932 do indeed have binding sites on CTPsyn mRNA, in vitro assays instead revealed a low probability of this being true, instead indicating that the effects asserted by overexpressed miRNAs indirectly reach CTPsyn and its cytoophidia through the actions of middling elements. In silico target prediction and qPCR quantification indicated that, at least for miR-932 and miR-1014, these undetermined elements may be players in fat metabolism. This is the first study to thoroughly investigate miRNAs in connection to CTPsyn expression and activity in any species. The findings presented could serve as a basis for further queries into not only the fundamental aspects of the enzyme's regulation, but may uncover new facets of closely related pathways as well.
    Matched MeSH terms: Drosophila Proteins/genetics; Drosophila Proteins/metabolism*
  2. Fulltext A multiplexable TALE-based binary expression system for in vivo cellular interaction studies
    Toegel M, Azzam G, Lee EY, Knapp DJHF, Tan Y, Fa M, et al.
    Nat Commun, 2017 11 21;8(1):1663.
    PMID: 29162808 DOI: 10.1038/s41467-017-01592-3
    Binary expression systems have revolutionised genetic research by enabling delivery of loss-of-function and gain-of-function transgenes with precise spatial-temporal resolution in vivo. However, at present, each existing platform relies on a defined exogenous transcription activator capable of binding a unique recognition sequence. Consequently, none of these technologies alone can be used to simultaneously target different tissues or cell types in the same organism. Here, we report a modular system based on programmable transcription activator-like effector (TALE) proteins, which enables parallel expression of multiple transgenes in spatially distinct tissues in vivo. Using endogenous enhancers coupled to TALE drivers, we demonstrate multiplexed orthogonal activation of several transgenes carrying cognate variable activating sequences (VAS) in distinct neighbouring cell types of the Drosophila central nervous system. Since the number of combinatorial TALE-VAS pairs is virtually unlimited, this platform provides an experimental framework for highly complex genetic manipulation studies in vivo.
    Matched MeSH terms: Drosophila Proteins/genetics*; Drosophila Proteins/metabolism
  3. Fulltext Cloning and mutagenetic modification of the firefly luciferase gene and its use for bioluminescence microscopy of engrailed expression during Drosophila metamorphosis
    Ogoh K, Akiyoshi R, Suzuki H
    Biochem Biophys Rep, 2020 Sep;23:100771.
    PMID: 32490216 DOI: 10.1016/j.bbrep.2020.100771
    Bioluminescence microscopy is an area attracting considerable interest in the field of cell biology because it offers several advantages over fluorescence microscopy, including no requirement for excitation light and being phototoxicity free. This method requires brighter luciferase for imaging; however, suitable genetic resource material for this purpose is not available at present. To achieve brighter bioluminescence microscopy, we developed a new firefly luciferase. Using the brighter luciferase, a reporter strain of Drosophila Gal4-UAS (Upstream Activating Sequence) system was constructed. This system demonstrated the expression pattern of engrailed, which is a segment polarity gene, during Drosophila metamorphosis by bioluminescence microscopy, and revealed drastic spatiotemporal change in the engrailed expression pattern during head eversion in the early stage of pupation.
    Matched MeSH terms: Drosophila Proteins
  4. Fulltext Regions of very low H3K27me3 partition the Drosophila genome into topological domains
    El-Sharnouby S, Fischer B, Magbanua JP, Umans B, Flower R, Choo SW, et al.
    PLoS One, 2017;12(3):e0172725.
    PMID: 28282436 DOI: 10.1371/journal.pone.0172725
    It is now well established that eukaryote genomes have a common architectural organization into topologically associated domains (TADs) and evidence is accumulating that this organization plays an important role in gene regulation. However, the mechanisms that partition the genome into TADs and the nature of domain boundaries are still poorly understood. We have investigated boundary regions in the Drosophila genome and find that they can be identified as domains of very low H3K27me3. The genome-wide H3K27me3 profile partitions into two states; very low H3K27me3 identifies Depleted (D) domains that contain housekeeping genes and their regulators such as the histone acetyltransferase-containing NSL complex, whereas domains containing moderate-to-high levels of H3K27me3 (Enriched or E domains) are associated with regulated genes, irrespective of whether they are active or inactive. The D domains correlate with the boundaries of TADs and are enriched in a subset of architectural proteins, particularly Chromator, BEAF-32, and Z4/Putzig. However, rather than being clustered at the borders of these domains, these proteins bind throughout the H3K27me3-depleted regions and are much more strongly associated with the transcription start sites of housekeeping genes than with the H3K27me3 domain boundaries. While we have not demonstrated causality, we suggest that the D domain chromatin state, characterised by very low or absent H3K27me3 and established by housekeeping gene regulators, acts to separate topological domains thereby setting up the domain architecture of the genome.
    Matched MeSH terms: Drosophila Proteins/genetics; Drosophila Proteins/metabolism*; Drosophila Proteins/chemistry
  5. Hesperidin modulates the rhythmic proteomic profiling in Drosophila melanogaster under oxidative stress
    Jayapalan JJ, Subramanian P, Kani A, Hiji J, Najjar SG, Abdul-Rahman PS, et al.
    Arch Insect Biochem Physiol, 2020 Nov;105(3):e21738.
    PMID: 32924199 DOI: 10.1002/arch.21738
    The circadian clock regulates vital aspects of physiology including protein synthesis and oxidative stress response. In this investigation, we performed a proteome-wide scrutiny of rhythmic protein accrual in Drosophila melanogaster on exposure to rotenone, rotenone + hesperidin and hesperidin in D. melanogaster. Total protein from fly samples collected at 6 h intervals over the 24 h period was subjected to two-dimensional gel electrophoresis and mass spectrometry. Bioinformatics tool, Protein ANalysis THrough Evolutionary Relationships classification system was used to the determine the biological processes of the proteins of altered abundance. Conspicuous variations in the proteome (151 proteins) of the flies exposed to oxidative stress (by rotenone treatment) and after alleviating oxidative stress (by hesperidin treatment) were observed during the 24 h cycle. Significantly altered levels of abundance of a wide variety of proteins under oxidative stress (rotenone treatment) and under alleviation of oxidative stress (rotenone + hesperidin treatment) and hesperidin (alone) treatment were observed. These proteins are involved in metabolism, muscle activity, heat shock response, redox homeostasis, protein synthesis/folding/degradation, development, ion-channel/cellular transport, and gustatory and olfactory function of the flies. Our data indicates that numerous cellular processes are involved in the temporal regulation of proteins and widespread modulations happen under rotenone treatment and, action of hesperidin could also be seen on these categories of proteins.
    Matched MeSH terms: Drosophila Proteins/metabolism
  6. Atypical Myosin Tunes Dendrite Arbor Subdivision
    Yoong LF, Lim HK, Tran H, Lackner S, Zheng Z, Hong P, et al.
    Neuron, 2020 05 06;106(3):452-467.e8.
    PMID: 32155441 DOI: 10.1016/j.neuron.2020.02.002
    Dendrite arbor pattern determines the functional characteristics of a neuron. It is founded on primary branch structure, defined through cell intrinsic and transcription-factor-encoded mechanisms. Developing arbors have extensive acentrosomal microtubule dynamics, and here, we report an unexpected role for the atypical actin motor Myo6 in creating primary branch structure by specifying the position, polarity, and targeting of these events. We carried out in vivo time-lapse imaging of Drosophila adult sensory neuron differentiation, integrating machine-learning-based quantification of arbor patterning with molecular-level tracking of cytoskeletal remodeling. This revealed that Myo6 and the transcription factor Knot regulate transient surges of microtubule polymerization at dendrite tips; they drive retrograde extension of an actin filament array that specifies anterograde microtubule polymerization and guides these microtubules to subdivide the tip into multiple branches. Primary branches delineate functional compartments; this tunable branching mechanism is key to define and diversify dendrite arbor compartmentalization.
    Matched MeSH terms: Drosophila Proteins/metabolism
  7. Fulltext Ectopic miR-975 induces CTP synthase directed cell proliferation and differentiation in Drosophila melanogaster
    Woo WK, Dzaki N, Thangadurai S, Azzam G
    Sci Rep, 2019 Apr 15;9(1):6096.
    PMID: 30988367 DOI: 10.1038/s41598-019-42369-6
    CTP synthase (CTPSyn) is an essential metabolic enzyme, synthesizing precursors required for nucleotides and phospholipids production. Previous studies have also shown that CTPSyn is elevated in various cancers. In many organisms, CTPSyn compartmentalizes into filaments called cytoophidia. In Drosophila melanogaster, only its isoform C (CTPSynIsoC) forms cytoophidia. In the fruit fly's testis, cytoophidia are normally seen in the transit amplification regions close to its apical tip, where the stem-cell niche is located, and development is at its most rapid. Here, we report that CTPSynIsoC overexpression causes the lengthening of cytoophidia throughout the entirety of the testicular body. A bulging apical tip is found in approximately 34% of males overexpressing CTPSynIsoC. Immunostaining shows that this bulged phenotype is most likely due to increased numbers of both germline cells and spermatocytes. Through a microRNA (miRNA) overexpression screen, we found that ectopic miR-975 concurrently increases both the expression levels of CTPSyn and the length of its cytoophidia. The bulging testes phenotype was also recovered at a penetration of approximately 20%. However, qPCR assays reveal that CTPSynIsoC and miR-975 overexpression each provokes a differential response in expression of a number of cancer-related genes, indicating that the shared CTPSyn upregulation seen in either case is likely the cause of observed testicular overgrowth. This study presents the first instance of consequences of miRNA-asserted regulation upon CTPSyn in D. melanogaster, and further reaffirms the enzyme's close ties to germline cells overgrowth.
    Matched MeSH terms: Drosophila Proteins/metabolism
  8. Fulltext Characterisation of Drosophila Ubx CPTI000601 and hth CPTI000378 protein trap lines
    Choo SW, Beh CY, Russell S, White R
    ScientificWorldJournal, 2014;2014:191535.
    PMID: 25389534 DOI: 10.1155/2014/191535
    In Drosophila, protein trap strategies provide powerful approaches for the generation of tagged proteins expressed under endogenous control. Here, we describe expression and functional analysis to evaluate new Ubx and hth protein trap lines generated by the Cambridge Protein Trap project. Both protein traps exhibit spatial and temporal expression patterns consistent with the reported endogenous pattern in the embryo. In imaginal discs, Ubx-YFP is expressed throughout the haltere and 3rd leg imaginal discs, while Hth-YFP is expressed in the proximal regions of haltere and wing discs but not in the pouch region. The Ubx (CPTI000601) line is semilethal as a homozygote. No T3/A1 to T2 transformations were observed in the embryonic cuticle or the developing midgut. The homozygous survivors, however, exhibit a weak haltere phenotype with a few wing-like marginal bristles on the haltere capitellum. Although hth (CPTI000378) is completely lethal as a homozygote, the hth (CPTI000378) /hth (C1) genotype is viable. Using a hth deletion (Df(3R)BSC479) we show that hth (CPTI000378) /Df(3R)BSC479 adults are phenotypically normal. No transformations were observed in hth (CPTI000378), hth (CPTI000378) /hth (C1), or hth (CPTI000378) /Df(3R)BSC479 embryonic cuticles. We have successfully characterised the Ubx-YFP and Hth-YFP protein trap lines demonstrating that the tagged proteins show appropriate expression patterns and produce at least partially functional proteins.
    Matched MeSH terms: Drosophila Proteins/deficiency; Drosophila Proteins/genetics*; Drosophila Proteins/metabolism
  9. Melatonin improves cognitive behavior, oxidative stress, and metabolism in tumor-prone lethal giant larvae mutant of Drosophila melanogaster
    Wong KC, Sankaran S, Jayapalan JJ, Subramanian P, Abdul-Rahman PS
    Arch Insect Biochem Physiol, 2021 May;107(1):e21785.
    PMID: 33818826 DOI: 10.1002/arch.21785
    Mutant lethal giant larvae (lgl) flies (Drosophila melanogaster) are known to develop epithelial tumors with invasive characteristics. The present study has been conducted to investigate the influence of melatonin (0.025 mM) on behavioral responses of lgl mutant flies as well as on biochemical indices (redox homeostasis, carbohydrate and lipid metabolism, transaminases, and minerals) in hemolymph, and head and intestinal tissues. Behavioral abnormalities were quantitatively observed in lgl flies but were found normalized among melatonin-treated lgl flies. Significantly decreased levels of lipid peroxidation products and antioxidants involved in redox homeostasis were observed in hemolymph and tissues of lgl flies, but had restored close to normalcy in melatonin-treated flies. Carbohydrates including glucose, trehalose, and glycogen were decreased and increased in the hemolymph and tissues of lgl and melatonin-treated lgl flies, respectively. Key enzymes of carbohydrate metabolism showed a significant increment in their levels in lgl mutants but had restored close to wild-type baseline levels in melatonin-treated flies. Variables of lipid metabolism showed significantly inverse levels in hemolymph and tissues of lgl flies, while normalization of most of these variables was observed in melatonin-treated mutants. Lipase, chitinase, transaminases, and alkaline phosphatase showed an increment in their activities and minerals exhibited decrement in lgl flies; reversal of changes was observed under melatonin treatment. The impairment of cognition, disturbance of redox homeostasis and metabolic reprogramming in lgl flies, and restoration of normalcy in all these cellular and behavioral processes indicate that melatonin could act as oncostatic and cytoprotective agents in Drosophila.
    Matched MeSH terms: Drosophila Proteins/drug effects; Drosophila Proteins/genetics; Drosophila Proteins/metabolism
  10. Fulltext Reduced Expression of Glycerol-3-phosphate dehydrogenase (Gpdh) in Drosophila melanogaster pasha mutants Suggests A miRNA-dependency in Its Regulation
    Najat Dzaki, Ghows Azzam
    Trop Life Sci Res, 2019;30(2):191-200.
    MyJurnal
    In Drosophila, the Glycerol-3-phosphate dehydrogenase (Gpdh) enzyme plays an active role in many pathways, including the glycerol metabolic pathway and the alphaglycerophosphate cycle. It is also important for ethanol metabolism, as well as flight muscle development. Recent years have exposed small RNAs as a major posttranscriptional regulator of multiple metabolic-pathway genes. Of the many kinds of these RNAs at work, micro RNAs (miRNAs) are the most widely implicated and well understood. However, the roles they may play in regulating Gpdh has never been shown in any model organism. In this study, a pasha-mutant D. melanogaster strain was found to express only 25% of the Gpdh levels typical of their wild type counterparts. Such mutants lack the ability to produce pasha, a protein integral during miRNA-processing, and as a consequence do not produce mature miRNAs. As miRNA-centric regulation often culminates in the depletion of their targets, the concurrent downregulation of Gpdh observed in their absence here therefore alludes to two possibilities: one, that rather than being explicitly bound and repressed by miRNAs, Gpdh expression relies on their action upon an upstream Gpdh-antagonist; or two, that Gpdh may come under the regulation of another class of miRNA-like elements called mirtrons, which do not require pasha to be processed into their functional form. The preliminary findings in this study further highlights the imperative nature of miRNAs in regulating metabolic processes and subsequently, ensuring proper organismal development and its continued survival.
    Matched MeSH terms: Drosophila Proteins
  11. Utilizing shared interacting domain patterns and Gene Ontology information to improve protein-protein interaction prediction
    Roslan R, Othman RM, Shah ZA, Kasim S, Asmuni H, Taliba J, et al.
    Comput Biol Med, 2010 Jun;40(6):555-64.
    PMID: 20417930 DOI: 10.1016/j.compbiomed.2010.03.009
    Protein-protein interactions (PPIs) play a significant role in many crucial cellular operations such as metabolism, signaling and regulations. The computational methods for predicting PPIs have shown tremendous growth in recent years, but problem such as huge false positive rates has contributed to the lack of solid PPI information. We aimed at enhancing the overlap between computational predictions and experimental results in an effort to partially remove PPIs falsely predicted. The use of protein function predictor named PFP() that are based on shared interacting domain patterns is introduced in this study with the purpose of aiding the Gene Ontology Annotations (GOA). We used GOA and PFP() as agents in a filtering process to reduce false positive pairs in the computationally predicted PPI datasets. The functions predicted by PFP() were extracted from cross-species PPI data in order to assign novel functional annotations for the uncharacterized proteins and also as additional functions for those that are already characterized by the GO (Gene Ontology). The implementation of PFP() managed to increase the chances of finding matching function annotation for the first rule in the filtration process as much as 20%. To assess the capability of the proposed framework in filtering false PPIs, we applied it on the available S. cerevisiae PPIs and measured the performance in two aspects, the improvement made indicated as Signal-to-Noise Ratio (SNR) and the strength of improvement, respectively. The proposed filtering framework significantly achieved better performance than without it in both metrics.
    Matched MeSH terms: Drosophila Proteins
  12. Expression of DDR1 and DVL1 in invasive ductal and lobular breast carcinoma does not correlate with histological type, grade and hormone receptor status
    Ameli F, Rose IM, Masir N
    Asian Pac J Cancer Prev, 2015;16(6):2385-90.
    PMID: 25824769
    BACKGROUND: Invasive ductal (IDC) and lobular (ILC) carcinomas are the common histological types of breast carcinoma which are difficult to distinguish when poorly differentiated. Discoidin domain receptor (DDR1) and Drosophila dishevelled protein (DVL1) were recently suggested to differentiate IDC from ILC.

    OBJECTIVES: To assess the expression of DDR1 and DVL1 and their association with histological type, grading and hormonal status of IDC and ILC.

    MATERIALS AND METHODS: This cross sectional study was conducted on IDC and ILC breast tumours. Tumours were immunohistochemically stained for (DDR1) and (DVL1) as well as estrogen receptor (ER), progesterone receptor (PR) and C-erbB2 receptor. Demographic data including age and ethnicity were obtained from patient records.

    RESULTS: A total of 51 cases (30 IDCs and 21 ILCs) were assessed. DDR1 and DVL1 expression was not significantly associated with histological type (p=0.57 and p=0.66 respectively). There was no association between DDR1 and DVL1 expression and tumour grade (p=0.32 and p=1.00 respectively), ER (p=0.62 and 0.50 respectively), PR (p=0.38 and p=0.63 respectively) and C-erbB2 expression (p=0.19 and p=0.33 respectively) in IDC. There was no association between DDR1 and DVL1 expression and tumour grade (p=0.52 and p=0.33 respectively), ER (p=0.06 and p=0.76 respectively), PR (p=0.61 and p=0.43 respectively) and C-erbB2 expression (p=0.58 and p=0.76 respectively) in ILC.

    CONCLUSIONS: This study revealed that DDR1 and DVL1 are present in both IDC and ILC regardless of the tumour differentiation. More studies are needed to assess the potential of these two proteins in distinguishing IDC from ILC in breast tumours.

    Matched MeSH terms: Drosophila Proteins
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