MINDY-1 is a recently discovered new family of deubiquitinating enzymes(DUB),but one of its yeast homologs,YGL082 W,does not show any DUB activity in vitro.Sequence alignment shows that YGL082 W possesses the correct ...MINDY-1 is a recently discovered new family of deubiquitinating enzymes(DUB),but one of its yeast homologs,YGL082 W,does not show any DUB activity in vitro.Sequence alignment shows that YGL082 W possesses the correct catalytic triad,and yet did not catalyze either the hydrolysis of di-ubiquitin,crosslinking with C-terminally propargylated ubiquitin,or hydrolysis of ubiquitin-7-amino-4-methylcoumarin.After obtaining a crystal structure of the catalytic domain of YGL082 W,we identified an interesting difference between the catalytic center loop of YGL082 W and that of its human homolog MINDY-1.Because the conformation of the catalytic center loop was previously reported to be important for the deubiquitination activity of MINDY-1,we hypothesized that Glu27(instead of the corresponding Pro136 in MINDY-1) of the catalytic center loop of YGL082 W may impair the conformational change and account for the lack of activity.This hypothesis was supported by homology modeling and molecular dynamics simulations,which showed that the Pro-to-Glu mutation(P136 E mutation for MINDY-1) creates a hydrogen bond that inhibits the conformation change of the catalytic center loop of MINDY-1.Further experiments through site-directed mutation validated this hypothesis,showing that the P27 E mutation caused MIY1(a homologous active DUB from yeast) to lose activity.展开更多
Insertion sequences(ISs)exist widely in bacterial genomes,but their roles in the evolution of bacterial antiphage defense remain to be clarified.Here,we report that,under the pressure of phage infection,the IS1o96 tra...Insertion sequences(ISs)exist widely in bacterial genomes,but their roles in the evolution of bacterial antiphage defense remain to be clarified.Here,we report that,under the pressure of phage infection,the IS1o96 transposition of Mycobacterium smegmatis into the Isr2 gene can occur at high frequencies,which endows the mutant mycobacterium with a broad-spectrum antiphage ability.Lsr2 functions as a negative regulator and directly silences expression of a gene island composed of 11 lipid metabolism-related genes.The complete or partial loss of the gene island leads to a significant decrease of bacteriophage adsorption to the mycobacterium,thus defending against phage infection.Strikingly,a phage that has evolved mutations in two tail-filament genes can re-escape from the Isr2 inactivation-triggered host defense.This study uncovered a new signaling pathway for activating antimycobacteriophage immunity by Is transposition and provided insight into the natural evolution of bacterial antiphage defense.展开更多
基金supported by the National Key Research and Development Program of China(2017YFA0505200)the National Natural Science Foundation of China(21532004,91753205,81621002,21621003)Shanghai Tech University
文摘MINDY-1 is a recently discovered new family of deubiquitinating enzymes(DUB),but one of its yeast homologs,YGL082 W,does not show any DUB activity in vitro.Sequence alignment shows that YGL082 W possesses the correct catalytic triad,and yet did not catalyze either the hydrolysis of di-ubiquitin,crosslinking with C-terminally propargylated ubiquitin,or hydrolysis of ubiquitin-7-amino-4-methylcoumarin.After obtaining a crystal structure of the catalytic domain of YGL082 W,we identified an interesting difference between the catalytic center loop of YGL082 W and that of its human homolog MINDY-1.Because the conformation of the catalytic center loop was previously reported to be important for the deubiquitination activity of MINDY-1,we hypothesized that Glu27(instead of the corresponding Pro136 in MINDY-1) of the catalytic center loop of YGL082 W may impair the conformational change and account for the lack of activity.This hypothesis was supported by homology modeling and molecular dynamics simulations,which showed that the Pro-to-Glu mutation(P136 E mutation for MINDY-1) creates a hydrogen bond that inhibits the conformation change of the catalytic center loop of MINDY-1.Further experiments through site-directed mutation validated this hypothesis,showing that the P27 E mutation caused MIY1(a homologous active DUB from yeast) to lose activity.
基金supported by the National Natural Science Foundation of China(32230002)the National Key R&D Program of China(2020YFA0907200),and the Ba-Gui Scholar Program of Guangxi(To Z.G.H).
文摘Insertion sequences(ISs)exist widely in bacterial genomes,but their roles in the evolution of bacterial antiphage defense remain to be clarified.Here,we report that,under the pressure of phage infection,the IS1o96 transposition of Mycobacterium smegmatis into the Isr2 gene can occur at high frequencies,which endows the mutant mycobacterium with a broad-spectrum antiphage ability.Lsr2 functions as a negative regulator and directly silences expression of a gene island composed of 11 lipid metabolism-related genes.The complete or partial loss of the gene island leads to a significant decrease of bacteriophage adsorption to the mycobacterium,thus defending against phage infection.Strikingly,a phage that has evolved mutations in two tail-filament genes can re-escape from the Isr2 inactivation-triggered host defense.This study uncovered a new signaling pathway for activating antimycobacteriophage immunity by Is transposition and provided insight into the natural evolution of bacterial antiphage defense.
基金We thank the National Key R&D Program of China(2017YFA0505200,2016YFA0400903,and 2015CB910103)National Science Foundation of China(91753205,21532004,21761142008,81621002,21621003,91849129,and 21708036)for their financial support.
文摘Mutations in genes encoding PINK1(PTEN-induced kinase 1)and Parkin(E3 ubiquitin ligase)are identified in familial Parkinson’s disease.However,it remains unclear whether the phosphorylated Ub chains activate wild-type Parkin(w-Parkin)or phosphorylated Parkin(p-Parkin),with the consequent expulsion of the damaged mitochondria.
