Pa42PR Structure
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REPOSITORIES: ENA
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Project description:Nucleocytoplasmic O-linked N-acetylglucosamine (O-GlcNAc) is an essential post-translational modification that is installed to thousands of protein substrates by O-GlcNAc transferase (OGT). Substrate selection by OGT and its isoforms is primarily mediated by the tetratricopeptide repeat (TPR) domain, yet the impact of truncations to the TPR domain on substrate and glycosite selection remains unresolved. Here, we report the effects of TPR truncations on the substrate and glycosite selection of OGT against the model protein GFP-JunB and the surrounding O-GlcNAc proteome in U2OS cells. Truncation of the TPR domain of OGT maintains glycosyltransferase activity but alters subcellular localization in cells. Examination of the glycoproteome across the TPR truncations revealed the broadest substrate activity from the canonical nucleocytoplasmic OGT, with the greatest changes in O-GlcNAc occurring on proteins associated with mRNA splicing processes. Glycosite analysis revealed alterations to the O-GlcNAc consensus sequence globally and differential glycosite selectivity on GFP-JunB as a function of the OGT TPR isoform. This dataset provides a foundation to analyze how perturbations to the TPR domain and expression of OGT isoforms affects the glycosylation of substrates, which will be critical for future protein engineering of OGT, the biology of OGT isoforms, and diseases associated with the TPR domain of OGT.
2021-11-01 | PXD028141 | Pride
Project description:As a member of the tetratricopeptide repeat (TPR) family, TTC7A is expected to mediate a wide range of interactions with proteins within several molecular complexes. TTC7A is expressed in hematopoietic and epithelial cells however its cellular function remains poorly understood. In this regard we performed a global transcriptional profiling by using HTA-2 microarrays on 4 healthy donors and 6 patients carrying distinct TTC7A mutations.
2018-07-19 | E-MTAB-5934 | biostudies-arrayexpress
Project description:Pentatricopeptide repeat-containing polyadenylation factor defines mitochondrial mRNA identity and stability in trypanosomes
| PRJNA376028 | ENA
Project description:Naturally-occurring catalytic RNA molecules — ribozymes — have attracted a great deal of research interest, yet very few of them have been identified in humans. Here, we developed a genome-wide approach to discover self-cleaving ribozymes and identified one naturally-occurring ribozyme in humans. The secondary structure and biochemical properties of this ribozyme indicate that it belongs to yet un-identified class of small self-cleaving ribozymes. The sequence of the ribozyme exhibits a clear evolutionary path from appearance between ~130 and ~65 million years ago (mya) to gain of self-cleavage activity very recently, ~13–10 mya, in the common ancestor of humans, chimpanzees and gorillas. The ribozyme appears to be functional in vivo and is embedded within an lncRNA belonging to the class of very long intergenic non-coding (vlinc) RNAs. The presence of a catalytic RNA enzyme in lncRNA opens a possibility that these transcripts could function by carrying catalytic RNA domains.
2020-12-19 | GSE163477 | GEO
Project description:Abstract: O-GlcNAc is an abundant post-translational modification found on nuclear and cytoplasmic proteins in all metazoans. This modification regulates a wide variety of cellular processes, and elevated O-GlcNAc levels have been implicated in cancer progression. A single essential enzyme, O-GlcNAc transferase (OGT), is responsible for all nucleocytoplasmic O-GlcNAcylation. Understanding how this enzyme chooses its substrates is critical for understanding, and potentially manipulating, its functions. Here we use protein microarray technology and proteome-wide glycosylation profiling to show that conserved aspartate residues in the tetratricopeptide repeat (TPR) lumen of OGT drive substrate selection. Changing these residues to alanines alters substrate selectivity and unexpectedly increases rates of protein glycosylation. Our findings support a model where sites of glycosylation for many OGT substrates are determined by TPR domain contacts to substrate side chains five to fifteen residues C-terminal to the glycosite. In addition to guiding design of inhibitors that target OGT's TPR domain, this information will inform efforts to engineer substrates to explore biological functions.
2019-07-24 | GSE132205 | GEO
Project description:Sequences from naturally occurring surface water viruses
| PRJNA46235 | ENA
Project description:The nuclear pore complex (NPC) has dual roles in nucleocytoplasmic transport and chromatin organisation. In many eukaryotes the coiled coil Mlp/Tpr proteins of the NPC nuclear basket have specific roles in interactions with chromatin and defining specialised regions of active transcription, while Mlp2 associates with the mitotic spindle in a cell-cycle dependent manner. We previously identified two putative Mlp-related proteins in African trypanosomes, TbNup110 and TbNup92, the latter of which associates with the spindle. We now provide evidence for independent ancestry for TbNup92/TbNup110 and Mlp/Tpr proteins. However, TbNup92 is required for correct chromosome segregation, with knockout cells exhibiting microaneuploidy and low fidelity telomere segregation. Further, TbNup92 is intimately associated with the mitotic spindle and spindle anchor site, but apparently has minimal roles in the control of gene transcription, indicating that TbNup92 lacks major barrier activity. TbNup92 therefore acts as a functional analog of Mlp/Tpr proteins, and together with the lamina analog NUP-1, represents a cohort of novel proteins operating at the nuclear periphery of trypanosomes, uncovering complex evolutionary trajectories for the NPC and nuclear lamina. Whole transcriptome comparison between parental and TbNup92? cells
2014-04-03 | E-GEOD-56436 | biostudies-arrayexpress
Project description:Environmental effects on immunity in naturally-occurring vertebrates
| PRJEB13319 | ENA