scholarly journals Post-translational modifications of Drosophila melanogaster HOX protein, Sex combs reduced

2019 ◽  
Author(s):  
Anirban Banerjee ◽  
Anthony Percival-Smith
Keyword(s):  
Dna Binding ◽  
Post Translational Modification ◽  
Hox Proteins ◽  
Sex Combs Reduced ◽  
Post Translational Modifications ◽  
Dna Binding Sites ◽  
Sex Combs ◽  
Evolutionarily Conserved ◽  
The Individual ◽  
Hox Protein

AbstractHomeotic selector (HOX) transcription factors (TFs) regulate gene expression that determines the identity of Drosophila segments along the anterior-posterior (A-P) axis. The current challenge with HOX proteins is understanding how they achieve their functional specificity while sharing a highly conserved homeodomain (HD) that recognize the same DNA binding sites. One mechanism proposed to regulate HOX activity is differential post-translational modification (PTM). As a first step in investigating this hypothesis, the sites of PTM on a Sex combs reduced protein fused to a triple tag (SCRTT) extracted from developing embryos were identified by Tandem Mass Spectrometry (MS/MS). The PTMs identified include phosphorylation at S185, S201, T315, S316, T317 and T324, acetylation at K218, S223, S227, K309, K434 and K439, formylation at K218, K309, K325, K341, K369, K434 and K439, methylation at S19, S166, K168 and T364, carboxylation at D108, K298, W307, K309, E323, K325 and K369, and hydroxylation at P22, Y87, P107, D108, D111, P269, P306, R310, N321, K325, Y334, R366, P392 and Y398. Of the 44 modifications, 18 map to functionally important regions of SCR. Besides a highly conserved DNA-binding HD, HOX proteins also have functionally important, evolutionarily conserved small motifs, which may be Short Linear Motifs (SLiMs). SLiMs are proposed to be preferential sites of phosphorylation. Although 6 of 7 phosphosites map to regions of predicted SLiMs, we find no support for the hypothesis that the individual S, T and Y residues of predicted SLiMs are phosphorylated more frequently than S, T and Y residues outside of predicted SLiMs.

scholarly journals The HOX Homeodomain Proteins Block CBP Histone Acetyltransferase Activity

2001 ◽  
Vol 21 (21) ◽  
pp. 7509-7522 ◽  
Author(s):  
Wei-fang Shen ◽  
Keerthi Krishnan ◽  
H. J. Lawrence ◽  
Corey Largman
Keyword(s):  
Dna Binding ◽  
Protein Function ◽  
Histone Acetyltransferase ◽  
Gene Activation ◽  
Homeodomain Proteins ◽  
Hox Proteins ◽  
Reporter Assays ◽  
Hox Protein

ABSTRACT Despite the identification of PBC proteins as cofactors that provide DNA affinity and binding specificity for the HOX homeodomain proteins, HOX proteins do not demonstrate robust activity in transient-transcription assays and few authentic downstream targets have been identified for these putative transcription factors. During a search for additional cofactors, we established that each of the 14 HOX proteins tested, from 11 separate paralog groups, binds to CBP or p300. All six isolated homeodomain fragments tested bind to CBP, suggesting that the homeodomain is a common site of interaction. Surprisingly, CBP-p300 does not form DNA binding complexes with the HOX proteins but instead prevents their binding to DNA. The HOX proteins are not substrates for CBP histone acetyltransferase (HAT) but instead inhibit the activity of CBP in both in vitro and in vivo systems. These mutually inhibitory interactions are reflected by the inability of CBP to potentiate the low levels of gene activation induced by HOX proteins in a range of reporter assays. We propose two models for HOX protein function: (i) HOX proteins may function without CBP HAT to regulate transcription as cooperative DNA binding molecules with PBX, MEIS, or other cofactors, and (ii) the HOX proteins may inhibit CBP HAT activity and thus function as repressors of gene transcription.

scholarly journals iProteinDB: an integrative database of Drosophila post-translational modifications

2018 ◽  
Author(s):  
Yanhui Hu ◽  
Richelle Sopko ◽  
Verena Chung ◽  
Romain A. Studer ◽  
Sean D. Landry ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Protein Function ◽  
Large Scale ◽  
Model Organisms ◽  
General Strategy ◽  
Post Translational Modification ◽  
Post Translational Modifications ◽  
Functional Sites ◽  
Evolutionarily Conserved ◽  
And Function

AbstractPost-translational modification (PTM) serves as a regulatory mechanism for protein function, influencing stability, protein interactions, activity and localization, and is critical in many signaling pathways. The best characterized PTM is phosphorylation, whereby a phosphate is added to an acceptor residue, commonly serine, threonine and tyrosine. As proteins are often phosphorylated at multiple sites, identifying those sites that are important for function is a challenging problem. Considering that many phosphorylation sites may be non-functional, prioritizing evolutionarily conserved phosphosites provides a general strategy to identify the putative functional sites with regards to regulation and function. To facilitate the identification of conserved phosphosites, we generated a large-scale phosphoproteomics dataset from Drosophila embryos collected from six closely-related species. We built iProteinDB (https://www.flyrnai.org/tools/iproteindb/), a resource integrating these data with other high-throughput PTM datasets, including vertebrates, and manually curated information for Drosophila. At iProteinDB, scientists can view the PTM landscape for any Drosophila protein and identify predicted functional phosphosites based on a comparative analysis of data from closely-related Drosophila species. Further, iProteinDB enables comparison of PTM data from Drosophila to that of orthologous proteins from other model organisms, including human, mouse, rat, Xenopus laevis, Danio rerio, and Caenorhabditis elegans.

Evolution of the insect body plan as revealed by the Sex combs reduced expression pattern

Development ◽  
1997 ◽  
Vol 124 (1) ◽  
pp. 149-157 ◽  
Author(s):  
B.T. Rogers ◽  
M.D. Peterson ◽  
T.C. Kaufman
Keyword(s):  
Morphological Evolution ◽  
Expression Patterns ◽  
Morphological Characters ◽  
Homeotic Gene ◽  
Homeotic Genes ◽  
Cell Fates ◽  
Sex Combs Reduced ◽  
Sex Combs ◽  
Evolutionarily Conserved ◽  
Epidermal Expression

The products of the HOM/Hox homeotic genes form a set of evolutionarily conserved transcription factors that control elaborate developmental processes and specify cell fates in many metazoans. We examined the expression of the ortholog of the homeotic gene Sex combs reduced (Scr) of Drosophila melanogaster in insects of three divergent orders: Hemiptera, Orthoptera and Thysanura. Our data reflect how the conservation and variation of Scr expression has affected the morphological evolution of insects. Whereas the anterior epidermal expression of Scr, in a small part of the posterior maxillary and all of the labial segment, is found to be in common among all four insect orders, the posterior (thoracic) expression domains vary. Unlike what is observed in flies, the Scr orthologs of other insects are not expressed broadly over the first thoracic segment, but are restricted to small patches. We show here that Scr is required for suppression of wings on the prothorax of Drosophila. Moreover, Scr expression at the dorsal base of the prothoracic limb in two other winged insects, crickets (Orthoptera) and milkweed bugs (Hemiptera), is consistent with Scr acting as a suppressor of prothoracic wings in these insects. Scr is also expressed in a small patch of cells near the basitarsal-tibial junction of milkweed bugs, precisely where a leg comb develops, suggesting that Scr promotes comb formation, as it does in Drosophila. Surprisingly, the dorsal prothoracic expression of Scr is also present in the primitively wingless firebrat (Thysanura) and the leg patch is seen in crickets, which have no comb. Mapping both gene expression patterns and morphological characters onto the insect phylogenetic tree demonstrates that in the cases of wing suppression and comb formation the appearance of expression of Scr in the prothorax apparently precedes these specific functions.

scholarly journals CENP-B dynamics at centromeres is regulated by a SUMOylation/ubiquitination and proteasomal-dependent degradation mechanism involving the SUMO-targeted ubiquitin E3 ligase RNF4

2018 ◽  
Author(s):  
Jhony El Maalouf ◽  
Pascale Texier ◽  
Indri Erliandri ◽  
Camille Cohen ◽  
Armelle Corpet ◽  
...  
Keyword(s):  
Dna Binding ◽  
Degradation Mechanism ◽  
E3 Ligase ◽  
Major Constituent ◽  
Post Translational Modification ◽  
Post Translational Modifications ◽  
Ubiquitin E3 Ligase ◽  
Satellite Repeats ◽  
Histone H3 Variant ◽  
Centromeric Protein

AbstractCentromeric protein B (CENP-B) is a major constituent of the centromere. It is a DNA binding protein that recognizes a specific 17-nt sequence present in the centromeric alphoid satellite repeats. CENP-B importance for centromere stability has only been revealed recently. In addition to its DNA binding properties, CENP-B interacts with the histone H3 variant CENP-A and CENP-C. These interactions confer a mechanical strength to the kinetochore that enables accurate sister chromatids segregation to avoid aneuploidy. Therefore, understanding the mechanisms that regulate CENP-B stability at the centromere is a major unresolved issue for the comprehension of centromere function. In this study, we demonstrate that lysine K402 of CENP-B is a substrate for SUMO post-translational modifications. We show that K402 regulates CENP-B stability at centromeres through a SUMOylation/ubiquitination and proteasomal-dependent degradation mechanism involving the SUMO-Targeted Ubiquitin E3 Ligase RNF4/SNURF. Our study describes SUMOylation of CENP-B as a major post-translational modification involved in centromere dynamics.

scholarly journals Structural determinants within Pbx1 that mediate cooperative DNA binding with pentapeptide-containing Hox proteins: proposal for a model of a Pbx1-Hox-DNA complex.

1996 ◽  
Vol 16 (4) ◽  
pp. 1632-1640 ◽  
Author(s):  
Q Lu ◽  
M P Kamps
Keyword(s):  
Dna Binding ◽  
Protein A ◽  
Alpha Helix ◽  
Binding Motif ◽  
Binding Studies ◽  
Structural Determinants ◽  
Hox Proteins ◽  
Core Motif ◽  
C Proteins ◽  
Hox Protein

Genetic studies have identified a family of divergent homeodomain proteins, including the human protooncoprotein Pbx1 and its drosophila homolog extradenticle (Exd), which function as cofactors with a subset of Hox and HOM-C proteins, and are essential for specific target gene expression. Pbx1/Exd binds DNA elements cooperatively with a large subset of Hox/HOM-C proteins containing a conserved pentapeptide motif, usually YPWMR, located just N terminally to their homeodomains. The pentapeptide is essential for cooperative DNA binding with Pbx1. In this study, we identify structural determinants of Pbx1 that are required for cooperative DNA binding with the pentapeptide-containing Hox protein HoxA5. We demonstrate that the homeodomain of Pbx1 contains a surface that binds the pentapeptide motif and that the Pbx1 homeodomain is sufficient for cooperative DNA binding with a Hox protein. A sequence immediately C terminal to the Pbx1 homeodomain, which is highly conserved in Pbx2 and Pbx3 and predicted to form an alpha-helix, enhances monomeric DNA binding by Pbx1 and also contributes to maximal cooperativity with Hox proteins. Binding studies with chimeric HoxA5-Pbx1 fusion proteins suggest that the homeodomains of Pbx1 and HoxA5 are docked on the representative element, TTGATTGAT, in tandem, with Pbx1 recognizing the 5' TTGAT core motif and the Hox protein recognizing the 3' TGAT core. The proposed binding orientation permits Hox proteins to exhibit further binding specificity on the basis of the identity of the four residues 3' to their core binding motif.

scholarly journals A micro-evolutionary change in target binding sites as key determinant of Ultrabithorax function in Drosophila.

2021 ◽  
Author(s):  
Soumen Khan ◽  
Saurabh J. Pradhan ◽  
Guillaume Giraud ◽  
Françoise Bleicher ◽  
Rachel Paul ◽  
...  
Keyword(s):  
Dna Binding ◽  
Binding Sites ◽  
Morphological Changes ◽  
Binding Motif ◽  
Core Sequence ◽  
Dna Binding Sites ◽  
Target Binding ◽  
Hox Protein

All Hox proteins are known to recognize, in vitro, similar DNA-binding sites containing a TAAT core sequence. This poor DNA-binding specificity is in sharp contrast with their specific functions in vivo. Here we report a new binding motif with TAAAT core sequence to which the Hox protein Ultrabithorax (Ubx) binds with higher affinity and specificity. Using transgenic and luciferase assays, we show that this new motif is critical for Ubx-mediated regulation of a target gene in Drosophila melanogaster. Interestingly, this new motif with TAAAT core sequences is not associated with the targets of Ubx in the honeybee, Apis mellifera, wherein hindwings are nearly identical to the forewings. We show that introduction of TAAAT motif in the place of TAAT motif is sufficient to bring an enhancer of a wing-promoting gene of A. mellifera under the regulation of Ubx. Our results, thus, suggest that binding motifs with a TAAAT core sequence may help identify functionally relevant direct targets of Ubx in D. melanogaster and the emergence of these binding sites may be crucial for Hox-mediated morphological changes during insect evolution.

scholarly journals Breaking the Histone Code with Two-Dimensional Partial Covariance Mass Spectrometry

2020 ◽  
Author(s):  
Taran Driver ◽  
Ruediger Pipkorn ◽  
Vitali Averbukh ◽  
Leszek Frasinski ◽  
Jon P. Marangos ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Large Body ◽  
Active Role ◽  
Repeated Measurements ◽  
Charge Ratio ◽  
Two Dimensional ◽  
Post Translational Modification ◽  
Post Translational Modifications ◽  
Single Fragment ◽  
The Individual

<div> <p>A large body of research points to the biological importance of combinatorial post-translational modifications in proteins, such as the active role played by histone modification patterns in the development of cancers, neurodevelopmental disorders, neurodegenerative and other diseases. Nonetheless, our understanding of the precise biological function of different modification patterns is limited by the difficulty of identifying and quantifying different combinatorial isomers in their mixtures as they naturally occur. Tandem mass spectrometry, which infers primary structure from the mass-to-charge ratios of biomolecular fragments, is the preferred method of analysis for proteins and their post-translational modifications. However, the information contained in the mass-to-charge ratios of the individual fragments is frequently insufficient to identify the correct set of modification patterns present in a mixture of combinatorial isomers. This is because no possible single fragment of a combinatorially modified sequence is unique to that sequence in its mass-to-charge ratio. Here we show that the combinatorial post-translational modification problem can be solved by the recently introduced technique of two-dimensional partial covariance mass spectrometry, which provides information about fragment connectivity in a biomolecule by quantifying correlations between the random intensity fluctuations of its fragments, across repeated measurements. Unique fragment-fragment correlations provide the missing link between the non-unique individual fragments to produce unambiguous fingerprints of co-occurring combinatorial isomers, enabling the discovery of biomolecular combinatorial modification patterns by mass spectrometry.</p> </div>

Ectopic expression and function of the Antp and Scr homeotic genes: the N terminus of the homeodomain is critical to functional specificity

Development ◽  
1993 ◽  
Vol 118 (2) ◽  
pp. 339-352 ◽  
Author(s):  
W. Zeng ◽  
D.J. Andrew ◽  
L.D. Mathies ◽  
M.A. Horner ◽  
M.P. Scott
Keyword(s):  
Dna Binding ◽  
Target Genes ◽  
Ectopic Expression ◽  
Homeotic Genes ◽  
Cell Fates ◽  
Nmr Studies ◽  
Sex Combs Reduced ◽  
Sex Combs ◽  
N Terminus

The transcription factors encoded by homeotic genes determine cell fates during development. Each homeotic protein causes cells to follow a distinct pathway, presumably by differentially regulating downstream ‘target’ genes. The homeodomain, the DNA-binding part of homeotic proteins, is necessary for conferring the specificity of each homeotic protein's action. The two Drosophila homeotic proteins encoded by Antennapedia and Sex combs reduced determine cell fates in the epidermis and internal tissues of the posterior head and thorax. Genes encoding chimeric Antp/Scr proteins were introduced into flies and their effects on morphology and target gene regulation observed. We find that the N terminus of the homeodomain is critical for determining the specific effects of these homeotic proteins in vivo, but other parts of the proteins have some influence as well. The N-terminal part of the homeodomain has been observed, in crystal structures and in NMR studies in solution, to contact the minor groove of the DNA. The different effects of Antennapedia and Sex combs reduced proteins in vivo may depend on differences in DNA binding, protein-protein interactions, or both.

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