Genes encoding the KDM5 family of transcriptional regulators are disrupted in individuals with intellectual disability (ID). To understand the link between KDM5 and ID, we characterized five Drosophila strains harboring missense alleles analogous to those observed in patients. These alleles disrupted neuroanatomical development, cognition and other behaviors, and displayed a transcriptional signature characterized by the downregulation of many ribosomal protein genes. A similar transcriptional profile was observed in KDM5C knockout iPSC-induced human glutamatergic neurons, suggesting an evolutionarily conserved role for KDM5 proteins in regulating this class of gene. In Drosophila, reducing KDM5 changed neuronal ribosome composition, lowered the translation efficiency of mRNAs required for mitochondrial function, and altered mitochondrial metabolism. These data highlight the cellular consequences of altered KDM5-regulated transcriptional programs that could contribute to cognitive and behavioral phenotypes. Moreover, they suggest that KDM5 may be part of a broader network of proteins that influence cognition by regulating protein synthesis.

• MeSH
• aktivace transkripce MeSH
• Drosophila melanogaster genetika   metabolismus   MeSH
• Drosophila genetika   metabolismus   MeSH
• histondemethylasy metabolismus   genetika   MeSH
• lidé MeSH
• mentální retardace genetika   metabolismus   MeSH
• mitochondrie metabolismus   genetika   MeSH
• neurony * metabolismus   MeSH
• proteiny Drosophily * genetika   metabolismus   MeSH
• proteosyntéza MeSH
• ribozomální proteiny * genetika   metabolismus   MeSH
• ribozomy metabolismus   genetika   MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH

Genetic screens have been used extensively to probe interactions between nuclear genes and their impact on phenotypes. Probing interactions between mitochondrial genes and their phenotypic outcome, however, has not been possible due to a lack of tools to map the responsible polymorphisms. Here, using a toolkit we previously established in Drosophila, we isolate over 300 recombinant mitochondrial genomes and map a naturally occurring polymorphism at the cytochrome c oxidase III residue 109 (CoIII109) that fully rescues the lethality and other defects associated with a point mutation in cytochrome c oxidase I (CoIT300I). Through lipidomics profiling, biochemical assays and phenotypic analyses, we show that the CoIII109 polymorphism modulates cardiolipin binding to prevent complex IV instability caused by the CoIT300I mutation. This study demonstrates the feasibility of genetic interaction screens in animal mitochondrial DNA. It unwraps the complex intra-genomic interplays underlying disorders linked to mitochondrial DNA and how they influence disease expression.

• MeSH
• Drosophila genetika   MeSH
• kardiolipiny * genetika   metabolismus   MeSH
• mitochondriální DNA * genetika   metabolismus   MeSH
• mitochondrie genetika   metabolismus   MeSH
• respirační komplex IV metabolismus   MeSH
• umělé letální mutace MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH

In animals and plants, Dicer enzymes collaborate with double-stranded RNA-binding domain (dsRBD) proteins to convert precursor-microRNAs (pre-miRNAs) into miRNA duplexes. We report six cryo-EM structures of Drosophila Dicer-1 that show how Dicer-1 and its partner Loqs-PB cooperate (1) before binding pre-miRNA, (2) after binding and in a catalytically competent state, (3) after nicking one arm of the pre-miRNA, and (4) following complete dicing and initial product release. Our reconstructions suggest that pre-miRNA binds a rare, open conformation of the Dicer-1⋅Loqs-PB heterodimer. The Dicer-1 dsRBD and three Loqs-PB dsRBDs form a tight belt around the pre-miRNA, distorting the RNA helix to place the scissile phosphodiester bonds in the RNase III active sites. Pre-miRNA cleavage shifts the dsRBDs and partially closes Dicer-1, which may promote product release. Our data suggest a model for how the Dicer-1⋅Loqs-PB complex affects a complete cycle of pre-miRNA recognition, stepwise endonuclease cleavage, and product release.

• MeSH
• Drosophila genetika   MeSH
• mikro RNA * genetika   metabolismus   MeSH
• proteiny Drosophily * genetika   metabolismus   MeSH
• proteiny vázající RNA metabolismus   MeSH
• ribonukleasa III genetika   metabolismus   MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Research Support, N.I.H., Extramural MeSH
• Research Support, N.I.H., Intramural MeSH

A series of carbamate-based inhibitors of glutamate carboxypeptidase II (GCPII) were designed and synthesized using ZJ-43, N-[[[(1S)-1-carboxy-3-methylbutyl]amino]carbonyl]-l-glutamic acid, as a molecular template in order to better understand the impact of replacing one of the two nitrogen atoms in the urea-based GCPII inhibitor with an oxygen atom. Compound 7 containing a C-terminal 2-oxypentanedioic acid was more potent than compound 5 containing a C-terminal glutamic acid (2-aminopentanedioic acid) despite GCPII's preference for peptides containing an N-terminal glutamate as substrates. Subsequent crystallographic analysis revealed that ZJ-43 and its two carbamate analogs 5 and 7 with the same (S,S)-stereochemical configuration adopt a nearly identical binding mode while (R,S)-carbamate analog 8 containing a d-leucine forms a less extensive hydrogen bonding network. QM and QM/MM calculations have identified no specific interactions in the GCPII active site that would distinguish ZJ-43 from compounds 5 and 7 and attributed the higher potency of ZJ-43 and compound 7 to the free energy changes associated with the transfer of the ligand from bulk solvent to the protein active site as a result of the lower ligand strain energy and solvation/desolvation energy. Our findings underscore a broader range of factors that need to be taken into account in predicting ligand-protein binding affinity. These insights should be of particular importance in future efforts to design and develop GCPII inhibitors for optimal inhibitory potency.

• MeSH
• buněčné linie MeSH
• Drosophila genetika   MeSH
• enzymatické testy MeSH
• glutamátkarboxypeptidasa II antagonisté a inhibitory   chemie   metabolismus   MeSH
• inhibitory proteas chemická syntéza   chemie   metabolismus   MeSH
• karbamáty chemická syntéza   chemie   metabolismus   MeSH
• katalytická doména MeSH
• kvantová teorie MeSH
• lidé MeSH
• močovina analogy a deriváty   chemická syntéza   chemie   metabolismus   MeSH
• molekulární modely MeSH
• stereoizomerie MeSH
• vazba proteinů MeSH
• vodíková vazba MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Research Support, N.I.H., Extramural MeSH

A large proportion of genomic information, particularly repetitive elements, is usually ignored when researchers are using next-generation sequencing. Here we demonstrate the usefulness of this repetitive fraction in phylogenetic analyses, utilizing comparative graph-based clustering of next-generation sequence reads, which results in abundance estimates of different classes of genomic repeats. Phylogenetic trees are then inferred based on the genome-wide abundance of different repeat types treated as continuously varying characters; such repeats are scattered across chromosomes and in angiosperms can constitute a majority of nuclear genomic DNA. In six diverse examples, five angiosperms and one insect, this method provides generally well-supported relationships at interspecific and intergeneric levels that agree with results from more standard phylogenetic analyses of commonly used markers. We propose that this methodology may prove especially useful in groups where there is little genetic differentiation in standard phylogenetic markers. At the same time as providing data for phylogenetic inference, this method additionally yields a wealth of data for comparative studies of genome evolution.

• MeSH
• DNA rostlinná genetika   MeSH
• Drosophila klasifikace   genetika   MeSH
• fylogeneze * MeSH
• genom genetika   MeSH
• hmyzí geny genetika   MeSH
• Magnoliopsida genetika   MeSH
• repetitivní sekvence nukleových kyselin genetika   MeSH
• shluková analýza MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

• MeSH
• Drosophila melanogaster klasifikace   genetika   MeSH
• Drosophila klasifikace   genetika   MeSH
• fylogeneze MeSH
• genom genetika   MeSH
• terminologie jako téma MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• dopisy MeSH

We examine the standard genetic code with three stop codons. Assuming that the synchronization period of length 3 in DNA or RNA is violated during the transcription or translation processes, the probability of reading a frameshifted stop codon is higher than if the code would have only one stop codon. Consequently, the synthesis of RNA or proteins will soon terminate. In this way, cells do not produce undesirable proteins and essentially save energy. This hypothesis is tested on the AT-rich Drosophila genome, where the detection of frameshifted stop codons is even higher than the theoretical value. Using the binomial theorem, we establish the probability of reading a frameshifted stop codon within n steps. Since the genetic code is largely redundant, there is still space for some hidden secondary functions of this code. In particular, because stop codons do not contain cytosine, random C → U and C → T mutations in the third position of codons increase the number of hidden frameshifted stops and simultaneously the same amino acids are coded. This evolutionary advantage is demonstrated on the genomes of several simple species, e.g. Escherichia coli.

• MeSH
• DNA genetika   MeSH
• Drosophila genetika   MeSH
• druhová specificita MeSH
• genetický kód genetika   MeSH
• genom hmyzu genetika   MeSH
• hemoglobiny genetika   MeSH
• hmyzí geny genetika   MeSH
• kodon iniciační MeSH
• lidé MeSH
• posunová mutace MeSH
• RNA genetika   MeSH
• terminační kodon MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

We are using a candidate gene approach to identify genes contributing to cancer through somatic mutation. Somatic mutations were found in breast cancer samples in the human casein kinase I epsilon (CKIepsilon) gene, a homolog of the Drosophila gene dco in which certain point mutations lead to imaginal disc overgrowth. We therefore created fly genotypes in which the dco gene carried point mutations homologous to those discovered in CKIepsilon, and tested them in vivo. The results show that the most frequent mutation discovered in breast cancer, L39Q, causes a striking overgrowth phenotype in flies. Further experiments show that this mutation affects the newly recognized Fat/Warts signaling pathway, which controls organ size and shape in both flies and mammals. Another mutation, S101R, modifies the mutant phenotype so that the affected tissue disintegrates, mimicking more aggressive forms of breast cancer. Our results thus strongly support the conclusion that CKIepsilon mutations play important roles in breast carcinogenesis.

• MeSH
• alely MeSH
• Drosophila embryologie   genetika   růst a vývoj   MeSH
• fenotyp MeSH
• kaseinkinasa Iepsilon chemie   genetika   fyziologie   MeSH
• larva genetika   MeSH
• lidé MeSH
• molekulární sekvence - údaje MeSH
• mutace MeSH
• nádory prsu genetika   MeSH
• proliferace buněk MeSH
• proteiny Drosophily chemie   genetika   fyziologie   MeSH
• sekvence aminokyselin MeSH
• signální transdukce MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• ženské pohlaví MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

• MeSH
• Caenorhabditis elegans genetika   MeSH
• databáze genetické využití   MeSH
• Drosophila genetika   MeSH
• Evropská unie MeSH
• finanční podpora výzkumu jako téma MeSH
• lidé MeSH
• svalové dystrofie epidemiologie   etiologie   genetika   MeSH
• výzkumný projekt MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• kongresy MeSH
• srovnávací studie MeSH
• Geografické názvy
• Česká republika MeSH

• MeSH
• Drosophila genetika   růst a vývoj   MeSH
• endokrinní žlázy metabolismus   růst a vývoj   MeSH
• finanční podpora výzkumu jako téma MeSH
• oogeneze genetika   MeSH
• ovarium MeSH
• proteiny Drosophily genetika   metabolismus   MeSH
• vývojová regulace genové exprese MeSH
• zvířata MeSH
• Check Tag
• ženské pohlaví MeSH
• zvířata MeSH