Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Chemical proteomics reveals protein tyrosination extends beyond the alpha-tubulins in human cells.

ABSTRACT: Tubulin detyrosination-tyrosination cycle regulates the stability of microtubules. Thus far described on α-tubulins, the tyrosination level is maintained by a single tubulin-tyrosine ligase (TTL). However, the precise dynamics and tubulin isoforms which undergo (de)tyrosination in neurons are unknown. Here, we exploit the substrate promiscuity of the TTL to introduce an O-propargyl-L-tyrosine in cancer cell lines and neurons. Mass spectrometry-based chemical proteomics in neuroblastoma cells using the O-propargyl-L-tyrosine probe revealed previously discussed tyrosination of TUBA4A, MAPRE1, and other non-tubulin proteins. This finding was further corroborated in differentiating neurons. We present the method for tubulin tyrosination profiling in living cells. Our results show that detyrosination-tyrosination is not restricted to α-tubulins with coded C-terminal tyrosine and is thus involved in fine-tuning of the tubulin and non-tubulin proteins during neuronal differentiation.

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Dmytro Makarov

LAB HEAD: Dr. Pavel Kielkowski

PROVIDER: PXD037402 | Pride | 2022-10-20

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	2022-05-23-decoys-contam-Human_20200401_can-iso.fasta	Fasta
	SH-SY5Y_dia_enrichment_raw.zip	Other
	SH-SY5Y_dia_enrichment_results.zip	Other
	SH-SY5Y_msfragger_whole_prot_raw.zip	Other
	SH-SY5Y_msfragger_whole_prot_results.zip	Other

Items per page:

1 - 5 of 11

Similar Datasets

Autoregulation of tubulin mRNA via reversible TTC5 sequestration by soluble ab-tubulins

Project description:Microtubule cytoskeleton, built from heterodimers of α and β-tubulins, is critically important to physically organize cells, mediate intracellular transport and power cell division. The availability of soluble αβ-tubulins influences the biomechanical properties and functions of microtubules. When present in excess, soluble αβ-tubulins induce degradation of their encoding mRNAs. This process involves the activation of a specificity factor TTC5, which recognizes nascent tubulins and recruits effectors that degrade the mRNA. But how TTC5 activity is regulated is unknown. Our biochemical and structural proteomic approaches reveal that soluble αβ-tubulins at steady-state levels sequester TTC5, repressing its activity. The carboxy-terminal domain of TTC5 acts as a molecular switch, toggling between soluble αβ-tubulin-bound and nascent tubulin-bound states. Loss of sequestration by soluble αβ-tubulins constitutively activates TTC5, leading to diminished tubulin mRNA levels and compromised microtubule-dependent chromosome segregation during cell division. Our findings provide a paradigm for how cells regulate the activity of a specificity factor to adapt posttranscriptional regulation of gene expression to cellular needs.

2024-10-18 | PXD050483 | Pride

Autoregulation of tubulin mRNA via reversible TTC5 sequestration by soluble αβ-tubulins

Project description:The microtubule cytoskeleton, built from heterodimers of α and β-tubulins, is critically important to physically organize cells, mediate intracellular transport and power cell division. The availability of soluble αβ-tubulins influences the biomechanical properties and dynamic functions of microtubules. When present in excess, soluble αβ-tubulins induce degradation of their encoding mRNAs. This process involves the specificity factor TTC5, which recognizes nascent tubulins and recruits effectors that degrade the mRNA. But how TTC5 activity is regulated is unknown. Our biochemical and structural proteomic approaches reveal that soluble αβ-tubulins sequester TTC5 at steady-state, repressing its activity. The carboxy-terminal domain of TTC5 acts as a molecular switch, toggling between soluble αβ-tubulin-bound and nascent tubulin-bound states. Loss-of-function mutantions that abolish sequestration by soluble αβ-tubulins constitutively activate TTC5, leading to diminished tubulin mRNA levels and compromised microtubule-dependent chromosome segregation during cell division. Our findings provide a paradigm for how cells regulate the activity of a specificity factor to adapt posttranscriptional regulation of gene expression to cellular needs.

2024-10-18 | PXD050557 | Pride

AMpylation is a hallmark of human neuronal differentiation

Project description:The AMPylation is novel protein post-translation modification. In consist of attachment of the adenosine monophosphate onto the serine, threonine or tyrosine amino acid residues of the protein. This process is catalysed by bacterial effectors or in human by protein FICD (also called HYPE) which contain conserved fic domain. In our study we have focused on identification of the unknown AMPylated proteins and their function in human cells (HeLa, A549, SH-SY5Y, iPSCs, NPCs and neurons) and cerebral organoids (COs). For this purpose we designed and synthesized the small molecule N6-propargyl phosphoramidate adenosine (PAK-76) which was used for in situ labelling of the AMPylation in cells and COs. Subsequnetly the the propargyl tag was employed for preparation of chemical-proteomic samples which were measured by LC-MS/MS. This approach confirmed the known AMPylation of heat shock protein HSPA5 and found diverse group of novel AMPylation targets. Several cathepsins found as AMPylation targets were further characterized by identification of AMP binding site. Based on our chemical proteomic data we found out that neurons and neuronal like cells contain distinct AMPylatino pattern from other studied cell types. This also suggested the importance of the AMPylation in these cell types which were then studied in cerebral organoids by overexpressing the FICD wt and E234G highly active mutant. This led to the accelerated differentiation of progenitors into the neurons. Overall our approach is suitable for identification of the AMPylated proteins in living cells and led to characterization of FICD function.

2024-05-21 | PXD008394 | Pride

FICD activity and AMPylation remodelling modulate human neurogenesis

Project description:The AMPylation is novel protein post-translation modification. In consist of attachment of the adenosine monophosphate onto the serine, threonine or tyrosine amino acid residues of the protein. This process is catalysed by bacterial effectors or in human by protein FICD (also called HYPE) which contain conserved fic domain. In our study we have focused on identification of the unknown AMPylated proteins and their function in human cells (HeLa, A549, SH-SY5Y, iPSCs, NPCs and neurons) and cerebral organoids (COs). For this purpose we designed and synthesized the small molecule N6-propargyl phosphoramidate adenosine (pro-N6pA) which was used for in situ labelling of the AMPylation in cells and COs. Subsequnetly the the propargyl tag was employed for preparation of chemical-proteomic samples which were measured by LC-MS/MS. This approach confirmed the known AMPylation of heat shock protein HSPA5 and found diverse group of novel AMPylation targets. Several cathepsins found as AMPylation targets were further characterized by identification of AMP binding site. Based on our chemical proteomic data we found out that neurons and neuronal like cells contain distinct AMPylatino pattern from other studied cell types. This also suggested the importance of the AMPylation in these cell types which were then studied in cerebral organoids by overexpressing the FICD wt and E234G highly active mutant. This led to the accelerated differentiation of progenitors into the neurons. Overall our approach is suitable for identification of the AMPylated proteins in living cells and led to characterization of FICD function.

2019-12-04 | PXD015062 | Pride

Differential modifications of the C-terminal tails of alpha-tubulin isoforms and their importance for kinesin-based microtubule transport in vivo

Project description:Microtubules (MTs) are built from alpha/beta-tubulin dimers and used as tracks by kinesin and dynein motors to transport a variety of cargos, such as mRNAs, proteins, and organelles, within the cell. Tubulins are subjected to several post-translational modifications (PTMs). Glutamylation is one of them, and it is responsible for adding one or more glutamic acid residues as branched peptide chains to the C-terminal tails of both alpha- and beta-tubulin. However, very little is known about the specific modifications found on the different tubulin isoforms in vivo and the role of these PTMs in cargo transport along MTs in vivo. In this study, we found that in Drosophila, glutamylation of the alpha-tubulin isoforms occurs specifically on the C-terminal ends of TBA1 and TBA3 in the ovaries. In contrast, the ovarian isoform TBA4 is not glutamylated. The C-terminal ends of TBA1 and TBA3 are glutamylated at several glutamyl side chains in various combinations. Drosophila TTLL5 is required for the mono- and polyglutamylation of ovarian TBA1 and 3. Furthermore, glutamylation of the alpha-tubulin is essential for the efficient localization of Staufen/osk mRNA and to give directionality to the fast ooplasmic streaming, two processes known to depend on kinesin mediated processes during oogenesis. In the nervous system, the kinesin-dependent neuronal transport of mitochondria also depends on TTLL5. Additionally, alpha-tubulin glutamylation affects the pausing of the transport of individual mitochondria in the axons. Our results demonstrate the in vivo role of TTLL5 in differential glutamylation of alpha-tubulin isoforms and point to the in vivo importance of alpha-tubulin glutamylation for kinesin-dependent processes.

2023-07-11 | PXD035270 | Pride

Enzymatic or in vivo installation of propargyl groups in combination with click chemistry enables enrichment and detection of methyltransferase target sites in RNA

Project description:m6A is the most abundant internal modification in eukaryotic mRNA. It is introduced by METTL3-METTL14 and tunes mRNA metabolism, impacting cell differentiation and development. Precise transcriptome-wide assignment of m6A sites is of utmost importance. However, m6A does not interfere with Watson-Crick base pairing making polymerase-based detection challenging. We developed a chemical biology approach for the precise mapping of methyltransferase (MTase) target sites based on the introduction of a bioorthogonal propargyl group in vitro and in cells. We show that propargyl can be introduced enzymatically by wild-type METTL3-METTL14. Reverse transcription terminated up to 65 % at m6A sites after bioconjugation and purification, hence enabling detection of METTL3-METTL14 target sites by next generation sequencing. Importantly, we implemented metabolic propargyl labeling of RNA MTase target sites in vivo based on propargyl-L-selenohomocysteine and validated different types of known rRNA methylation sites.

2018-02-21 | GSE109298 | GEO

Project description:clodinafop-propargyl-degrading

| PRJNA1067419 | ENA

Differential expression between mature zone of the olfactory organ and the dactyl of the walking legs, a taste organ

Project description:A cDNA microarray was constructed and used to assess mRNA abundance differences between two of the lobster’s major chemosensory structures, the mature zone of the olfactory organ and the dactyl of the walking legs, a taste organ. The 115 differences detected again emphasized the abundance of neurons in the olfactory organ, especially a cluster of mRNAs encoding cytoskeletal-associated proteins and cell adhesion molecules such as 14-3-3zeta, actins, tubulins, trophonin, Fax, Yel077cp, Suppressor of profilin 2, and gelsolin. Keywords: Differential expression

2005-12-26 | GSE3785 | GEO

Bulk RNA-sequencing from whole heart lysates of a mouse model of hypertrophic cardiomyopathy after TTL overexpression.

Project description:Reducing microtubule detyrosination has been shown to inprove contractility in heart failure cardiomyocytes. To evaluate the feasibility of targeting the detyrosinated microtubule network for treatment of cardiomyopathy in an in-vivo context we overexpressed tubulin tyrosine ligase (TTL) by AAV9 delivery in a mouse model of HCM (Mybpc3-/-) and an empty vector as control in HCM and WT mice.

2024-08-27 | GSE233851 | GEO

Cu-Catalyzed Azide-Alkyne-Thiol Reaction Forms Ubiquitous Background in Chemical Proteomics Studies

Project description:We report here a Cu-catalyzed azide-alkyne-thiol reaction forming thiotriazoles as the major by-product under widely used bioorthogonal protein labelling “click” conditions. The development of Cu(I)-catalyzed azide-alkyne cycloaddition (CuAAC) had tremendous impact on many biological discoveries. However, the considered chemoselectivity of CuAAC is hampered by high reactivity of cysteine free thiols yielding thiotriazole protein conjugates. The reaction by-products generate false positive protein hits in “functional” proteomic studies. The reported detail investigation of conjugates between chemical probes containing terminal alkynes, azide-tags and cell lysates reveals formation of thiotriazoles, which can be readily detected by in-gel fluorescence scanning or after peptide and protein enrichment by MS-based proteomics. The produced fluorescent bands or enriched proteins may not result from the important enzymatically driven reaction and can be falsely assigned as hits. This study provides a complete list of the most common background proteins. The knowledge of this previously overlooked reactivity now leads to improved experimental design. Here, we present modified CuAAC conditions, which avoids the undesired product formation and diminishes the background.

2024-01-12 | PXD043402 | Pride