A fragmented alignment method detects a putative phosphorylation site and a putative BRC repeat in the Drosophila melanogaster BRCA2 protein

Mutations in the BRCA2 tumor suppressor protein leave individuals susceptible to breast, ovarian and other cancers. The BRCA2 protein is a critical component of the DNA repair pathways in eukaryotes, and also plays an integral role in fostering genomic variability through meiotic recombination. Although present in many eukaryotes, as a whole the BRCA2 gene is weakly conserved. Conserved fragments of 30 amino acids (BRC repeats), which mediate interactions with the recombinase RAD51, helped detect orthologs of this protein in other organisms. The carboxy-terminal of the human BRCA2 has been shown to be phosphorylated by checkpoint kinases (Chk1/Chk2) at T3387, which regulate the sequestration of RAD51 on DNA damage. However, apart from three BRC repeats, the Drosophila melanogaster gene has not been annotated and associated with other functionally relevant sequence fragments in human BRCA2. In the current work, the carboxy-terminal phosphorylation threonine site (E=9.1e-4) and a new BRC repeat (E=17e-4) in D. melanogaster has been identified, using a fragmented alignment methodology (FRAGAL). In a similar study, FRAGAL has also identified a novel half-a- tetratricopeptide (HAT) motif (E=11e-4), a helical repeat motif implicated in various aspects of RNA metabolism, in Utp6 from yeast. The characteristic three aromatic residues with conserved spacing are observed in this new HAT repeat, further strengthening my claim. The reference and target sequences are sliced into overlapping fragments of equal parameterized lengths. All pairs of fragments in the reference and target proteins are aligned, and the gap penalties are adjusted to discourage gaps in the middle of the alignment. The results of the best matches are sorted based on differing criteria to aid the detection of known and putative sequences. The source code for FRAGAL results on these sequences is available at https://github.com/sanchak/FragalCode, while the database can be accessed at www.sanchak.com/fragal.html.

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Knock-down gene Ubiquitin Carboxy-Terminal Hydrolase (duch) resulted in reducing tyrosine hydroxylase in dopaminergic cells and inducing apoptosis in Drosophila melanogaster

TAP CHI SINH HOC ◽

10.15625/0866-7160/v37n1se.6121 ◽

2015 ◽

Vol 37 (1se) ◽

Author(s):

Dang Ngoc Anh Suong ◽

Tran Hoang Hiep ◽

Nguyen Thi Thanh ◽

Dang Thi Phuong Thao

Keyword(s):

Drosophila Melanogaster ◽

Tyrosine Hydroxylase ◽

Dopaminergic Cells ◽

Knock Down ◽

Carboxy Terminal

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Expression of a gene duplication encoding conserved sperm tail proteins is translationally regulated in Drosophila melanogaster.

Molecular and Cellular Biology ◽

10.1128/mcb.13.3.1708 ◽

1993 ◽

Vol 13 (3) ◽

pp. 1708-1718 ◽

Cited By ~ 36

Author(s):

M Schäfer ◽

D Börsch ◽

A Hülster ◽

U Schäfer

Keyword(s):

Drosophila Melanogaster ◽

Gene Family ◽

Translational Control ◽

Germ Line ◽

Gene Families ◽

Homologous Gene ◽

Male Sterile ◽

Sperm Tail ◽

Repetitive Motif ◽

Carboxy Terminal

We have analyzed a locus of Drosophila melanogaster located at 98C on chromosome 3, which contains two tandemly arranged genes, named Mst98Ca and Mst98Cb. They are two additional members of the Mst(3)CGP gene family by three criteria. (i) Both genes are exclusively transcribed in the male germ line. (ii) Both transcripts encode a protein with a high proportion of the repetitive motif Cys-Gly-Pro. (iii) Their expression is translationally controlled; while transcripts can be detected in diploid stages of spermatogenesis, association with polysomes can be shown only in haploid stages of sperm development. The genes differ markedly from the other members of the gene family in structure; they do not contain introns, they are of much larger size, and they have the Cys-Gly-Pro motifs clustered at the carboxy-terminal end of the encoded proteins. An antibody generated against the Mst98Ca protein recognizes both Mst98C proteins in D. melanogaster. In a male-sterile mutation in which spermiogenesis is blocked before individualization of sperm, both of these proteins are no longer synthesized. This finding provides proof of late translation for the Mst98C proteins and thereby independent proof of translational control of expression. Northern (RNA) and Western immunoblot analyses indicate the presence of homologous gene families in many other Drosophila species. The Mst98C proteins share sequence homology with proteins of the outer dense fibers in mammalian spermatozoa and can be localized to the sperm tail by immunofluorescence with an anti-Mst98Ca antibody.

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Molecular Characterization and Phylogenetic Analysis of MADS-Box Gene VroAGL11 Associated with Stenospermocarpic Seedlessness in Muscadine Grapes

Genes ◽

10.3390/genes12020232 ◽

2021 ◽

Vol 12 (2) ◽

pp. 232

Author(s):

M Atikur Rahman ◽

Subramani P Balasubramani ◽

Sheikh M Basha

Keyword(s):

Phylogenetic Analysis ◽

Phosphorylation Site ◽

Orthologous Gene ◽

Mads Box ◽

Vitis Species ◽

Vitis Rotundifolia ◽

Seed Content ◽

Putative Phosphorylation Site ◽

Mads Box Gene ◽

Muscadine Grapes

Reduced expression of MADS-box gene AGAMOUS-LIKE11 (VviAGL11) is responsible for stenospermocarpic seedlessness in bunch grapes. This study is aimed to characterize the VviAGL11 orthologous gene (VroAGL11) in native muscadine grapes (Vitis rotundifolia) at the molecular level and analyze its divergence from other plants. The VroAGL11 transcripts were found in all muscadine cultivars tested and highly expressed in berries while barely detectable in leaves. RT-PCR and sequencing of predicted ORFs from diverse grape species showed that AGL11 transcripts were conservatively spliced. The encoded VroAGL11 protein contains highly conserved MADS-MEF2-like domain, MADS domain, K box, putative phosphorylation site and two sumoylation motifs. The muscadine VroAGL11 proteins are almost identical (99%) to that of seeded bunch cultivar, Chardonnay, except in one amino acid (A79G), but differs from mutant protein of seedless bunch grape, Sultanina, in two amino acids, R197L and T210A. Phylogenetic analysis showed that AGL11 gene of muscadine and other Vitis species formed a separate clade than that of other eudicots and monocots. Muscadine grape cultivar “Jane Bell” containing the highest percentage of seed content in berry (7.2% of berry weight) had the highest VroAGL11 expression, but almost none to nominal expression in seedless cultivars Fry Seedless (muscadine) and Reliance Seedless (bunch). These findings suggest that VroAGL11 gene controls the seed morphogenesis in muscadine grapes like in bunch grape and can be manipulated to induce stenospermocarpic seedlessness using gene editing technology.

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Drosophila melanogaster H1 histone is phosphorylated stably

Molecular and Cellular Biology ◽

10.1128/mcb.7.11.4118-4121.1987 ◽

1987 ◽

Vol 7 (11) ◽

pp. 4118-4121

Author(s):

D A Talmage ◽

M Blumenfeld

Keyword(s):

Drosophila Melanogaster ◽

Salivary Gland ◽

Dna Replication ◽

Cultured Cells ◽

Phosphorylation Site ◽

Developmentally Regulated ◽

Central Domain ◽

Salivary Gland Cells ◽

Adult Head ◽

The Relationship

Phosphorylation of histone H1 is developmentally regulated in Drosophila spp. It cannot be detected in preblastoderm embryos or polytene salivary gland cells, but in cellular blastoderm, postblastoderm embryo, and amitotic adult head nuclei, it occurs with a frequency of roughly 4 x 10(5) molecules per nucleus. We used pulse-labeling to study the relationship between H1 synthesis and modification in cultured cells. These results reveal that the H1-associated phosphate is stable and suggest that Drosophila H1 is synthesized, translocated to the nucleus, associated with chromatin, and then phosphorylated. Partial tryptic digestion of Drosophila H1 revealed that the phosphorylation site is located within the globular, central domain of the protein. Thus, the developmentally regulated phosphorylation of Drosophila H1 presents two contrasts with previously studied H1 phosphorylation. It is not correlated with DNA replication, and it is located in the central domain of the protein.

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Characterization and Expression Analysis of Genes Encoding Phosphoenolpyruvate Carboxylase and Phosphoenolpyruvate Carboxylase Kinase of Lotus japonicus, a Model Legume

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi.2003.16.4.281 ◽

2003 ◽

Vol 16 (4) ◽

pp. 281-288 ◽

Cited By ~ 19

Author(s):

Tomomi Nakagawa ◽

Tomoko Izumi ◽

Mari Banba ◽

Yosuke Umehara ◽

Hiroshi Kouchi ◽

...

Keyword(s):

Phosphoenolpyruvate Carboxylase ◽

Root Nodules ◽

Expression Patterns ◽

Phosphorylation Site ◽

Lotus Japonicus ◽

Specific Protein ◽

Mrna Levels ◽

Model Legume ◽

Putative Phosphorylation Site

Phosphoenolpyruvate carboxylases (PEPCs), one form of which in each legume species plays a central role in the carbon metabolism in symbiotic root nodules, are activated through phosphorylation of a conserved residue by a specific protein kinase (PEPC-PK). We characterized the cDNAs for two PEPC isoforms of Lotus japonicus, an amide-translocating legume that forms determinate nodules. One gene encodes a nodule-enhanced form, which is more closely related to the PEPCs in amide-type indeterminate nodules than those in ureide-type determinate nodules. The other gene is expressed in shoots and roots at a low level. Both forms have the putative phosphorylation site, Ser11. We also isolated a cDNA and the corresponding genomic DNA for PEPC-PK of L. japonicus. The recombinant PEPC-PK protein expressed in Escherichia coli phosphorylated recombinant maize C4-form PEPC efficiently in vitro. The level of mRNA for PEPC-PK was high in root nodules, and those in shoots and roots were also significant. In situ hybridization revealed that the expression patterns of the transcripts for PEPC and PEPC-PK were similar in mature root nodules, but were different in emerging nodules. When L. japonicus seedlings were subjected to prolonged darkness and subsequent illumination, the activity of PEPC-PK and the mRNA levels of both PEPC and PEPC-PK in nodules decreased and then recovered, suggesting that they are regulated according to the amounts of photosynthates transported from shoots.

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Metal ion mediated reduction in surface entropy and a putative phosphorylation site of the IRAK‐4 death domain

The FASEB Journal ◽

10.1096/fasebj.20.4.a498-c ◽

2006 ◽

Vol 20 (4) ◽

Author(s):

Michael V. Lasker ◽

S Kuruvilla ◽

M Gajjar ◽

Satish K. Nair

Keyword(s):

Metal Ion ◽

Phosphorylation Site ◽

Death Domain ◽

Surface Entropy ◽

Putative Phosphorylation Site ◽

Mediated Reduction

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Expression of a gene duplication encoding conserved sperm tail proteins is translationally regulated in Drosophila melanogaster

Molecular and Cellular Biology ◽

10.1128/mcb.13.3.1708-1718.1993 ◽

1993 ◽

Vol 13 (3) ◽

pp. 1708-1718

Author(s):

M Schäfer ◽

D Börsch ◽

A Hülster ◽

U Schäfer

Keyword(s):

Drosophila Melanogaster ◽

Gene Family ◽

Translational Control ◽

Germ Line ◽

Gene Families ◽

Homologous Gene ◽

Male Sterile ◽

Sperm Tail ◽

Repetitive Motif ◽

Carboxy Terminal

We have analyzed a locus of Drosophila melanogaster located at 98C on chromosome 3, which contains two tandemly arranged genes, named Mst98Ca and Mst98Cb. They are two additional members of the Mst(3)CGP gene family by three criteria. (i) Both genes are exclusively transcribed in the male germ line. (ii) Both transcripts encode a protein with a high proportion of the repetitive motif Cys-Gly-Pro. (iii) Their expression is translationally controlled; while transcripts can be detected in diploid stages of spermatogenesis, association with polysomes can be shown only in haploid stages of sperm development. The genes differ markedly from the other members of the gene family in structure; they do not contain introns, they are of much larger size, and they have the Cys-Gly-Pro motifs clustered at the carboxy-terminal end of the encoded proteins. An antibody generated against the Mst98Ca protein recognizes both Mst98C proteins in D. melanogaster. In a male-sterile mutation in which spermiogenesis is blocked before individualization of sperm, both of these proteins are no longer synthesized. This finding provides proof of late translation for the Mst98C proteins and thereby independent proof of translational control of expression. Northern (RNA) and Western immunoblot analyses indicate the presence of homologous gene families in many other Drosophila species. The Mst98C proteins share sequence homology with proteins of the outer dense fibers in mammalian spermatozoa and can be localized to the sperm tail by immunofluorescence with an anti-Mst98Ca antibody.

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Evidence That Runt Acts as a Counter-Repressor of Groucho During Drosophila melanogaster Primary Sex Determination

G3 Genes|Genome|Genetics ◽

10.1534/g3.120.401384 ◽

2020 ◽

Vol 10 (7) ◽

pp. 2487-2496

Author(s):

Sharvani Mahadeveraju ◽

Young-Ho Jung ◽

James W. Erickson

Keyword(s):

Drosophila Melanogaster ◽

Sex Determination ◽

Transcriptional Repression ◽

Biological Effects ◽

Regulatory Gene ◽

Animal Cells ◽

Interaction Domain ◽

Link Type ◽

High Level ◽

Runx Proteins

Runx proteins are bifunctional transcription factors that both repress and activate transcription in animal cells. Typically, Runx proteins work in concert with other transcriptional regulators, including co-activators and co-repressors to mediate their biological effects. In Drosophila melanogaster the archetypal Runx protein, Runt, functions in numerous processes including segmentation, neurogenesis and sex determination. During primary sex determination Runt acts as one of four X-linked signal element (XSE) proteins that direct female-specific activation of the establishment promoter (Pe) of the master regulatory gene Sex-lethal (Sxl). Successful activation of SxlPe requires that the XSE proteins overcome the repressive effects of maternally deposited Groucho (Gro), a potent co-repressor of the Gro/TLE family. Runx proteins, including Runt, contain a C-terminal peptide, VWRPY, known to bind to Gro/TLE proteins to mediate transcriptional repression. We show that Runt’s VWRPY co-repressor-interaction domain is needed for Runt to activate SxlPe. Deletion of the Gro-interaction domain eliminates Runt-ability to activate SxlPe, whereas replacement with a higher affinity, VWRPW, sequence promotes Runt-mediated transcription. This suggests that Runt may activate SxlPe by antagonizing Gro function, a conclusion consistent with earlier findings that Runt is needed for Sxl expression only in embryonic regions with high Gro activity. Surprisingly we found that Runt is not required for the initial activation of SxlPe. Instead, Runt is needed to keep SxlPe active during the subsequent period of high-level Sxl transcription suggesting that Runt helps amplify the difference between female and male XSE signals by counter-repressing Gro in female, but not in male, embryos.

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CDK and Mec1/Tel1-catalyzed phosphorylation of Sae2 regulate different responses to DNA damage

Nucleic Acids Research ◽

10.1093/nar/gkz814 ◽

2019 ◽

Vol 47 (21) ◽

pp. 11238-11249 ◽

Cited By ~ 4

Author(s):

Tai-Yuan Yu ◽

Valerie E Garcia ◽

Lorraine S Symington

Keyword(s):

Dna Damage ◽

Dna Damage Response ◽

Phosphorylation Site ◽

Physiological Role ◽

Checkpoint Signaling ◽

Strand Breaks ◽

Checkpoint Kinases ◽

Damage Response ◽

End Resection

Abstract Sae2 functions in the DNA damage response by controlling Mre11-Rad50-Xrs2 (MRX)-catalyzed end resection, an essential step for homology-dependent repair of double-strand breaks (DSBs), and by attenuating DNA damage checkpoint signaling. Phosphorylation of Sae2 by cyclin-dependent kinase (CDK1/Cdc28) activates the Mre11 endonuclease, while the physiological role of Sae2 phosphorylation by Mec1 and Tel1 checkpoint kinases is not fully understood. Here, we compare the phenotype of sae2 mutants lacking the main CDK (sae2-S267A) or Mec1 and Tel1 phosphorylation sites (sae2-5A) with sae2Δ and Mre11 nuclease defective (mre11-nd) mutants. The phosphorylation-site mutations confer DNA damage sensitivity, but not to the same extent as sae2Δ. The sae2-S267A mutation is epistatic to mre11-nd for camptothecin (CPT) sensitivity and synergizes with sgs1Δ, whereas sae2-5A synergizes with mre11-nd and exhibits epistasis with sgs1Δ. We find that attenuation of checkpoint signaling by Sae2 is mostly independent of Mre11 endonuclease activation but requires Mec1 and Tel1-dependent phosphorylation of Sae2. These results support a model whereby CDK-catalyzed phosphorylation of Sae2 activates resection via Mre11 endonuclease, whereas Sae2 phosphorylation by Mec1 and Tel1 promotes resection by the Dna2-Sgs1 and Exo1 pathways indirectly by dampening the DNA damage response.

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