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Identification of the protein targets of a small molecule

ABSTRACT: Mass spectrometry-based chemical proteomic approaches using limited proteolysis for analysis of the interactions between a small molecule and its protein target(s). DARTS (Drug Affinity Responsive Target Stability) has been used in this study on Hela cell lysate. Ubiquitin carboxyl-terminal hydrolase 5 (USP5) was identified as one of the targets of the studied small molecule.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Culture, Uterine Cervix

SUBMITTER: Gilda D'Urso

LAB HEAD: Agostino Casapullo

PROVIDER: PXD048098 | Pride | 2024-01-15

REPOSITORIES: Pride

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Project description:miRNA levels depend on both biogenesis and turnover. The methyltransferase HEN1 stabilizes plant miRNAs, animal piRNAs, and siRNAs in both kingdoms via 3' terminal methylation. Loss of HEN1 in plants results in non-templated oligo-uridylation and accelerated degradation of miRNAs. In hen1 mutants from Arabidopsis and rice, we found that the patterns of miRNA truncation and uridylation differ substantially among miRNA families, but such patterns for the same miRNA are conserved between species. miR166 and miR163 are truncated predominantly to ~17 and ~16 nt, and subsequently recover via uridylation to approximately their original sizes, 21 and 24 nt, suggesting that in these cases miRNA truncation triggers uridylation. miR171 is untruncated but uridylated to 22 nt in hen1 mutants, gaining the ability to trigger production of phased, secondary siRNAs. Truncated and tailed variants were bound by ARGONAUTE1 (AGO1) in hen1, implying that these events occur while miRNAs are still bound by AGO1. Unexpectedly, a portion of miR158 in wildtype remains unmethylated and thus subject to uridylation and destabilization, suggesting that plants naturally utilize miRNA methylation to modulate miRNA accumulation. Our results suggest that the AGO1-containing RISC complex may undergo programming to reflect each bound miRNA, determining a defined, distinct decay destiny. In this analysis, we sequenced sRNAs from two hen1 mutant alleles in Arabidopsis and three hen1 alleles in rice. In Arabidopsis, the strong hen1-1 allele in the Landsberg erecta (Ler) ecotype is the first hen1 mutant and emerged from an enhancer screen in the hua1-1/hua2-1 background, and hen1-8 in the Columbia (Col) background is a weak allele. In rice, WAVY LEAF1 (WAF1) is the ortholog of Arabidopsis HEN1, and two mutant alleles waf1-1 and waf1-2 each bear a single-base substitution leading to a premature stop codon in the second exon and a non-functional splicing site of the fourth intron, respectively. We identified a third mutant allele of the rice HEN1 gene (Oshen1-3 from the Korean (POSTEC) rice T-DNA mutant population).

			Action	DRS
	GE_D4_B1_1a500_100um.raw	Raw
	GE_D4_B1_1a500_10uM.raw	Raw
	GE_D4_B1_1a500_1uM.msf	Msf
	GE_D4_B1_1a500_1uM.msfView	Msf
	GE_D4_B1_1a500_1uM.raw	Raw

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Identification of the protein targets of a small molecule

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