Control of membrane barrier during bacterial type-III protein secretion

Type-III secretion systems (T3SSs) of the bacterial flagellum and the evolutionarily related injectisome are capable of translocating proteins with a remarkable speed of several thousand amino acids per second. Here, we investigate how T3SSs are able to transport proteins at such a high rate while preventing the leakage of small molecules. Our mutational and evolutionary analyses demonstrate that an ensemble of conserved methionine residues at the cytoplasmic side of the T3SS channel create a deformable gasket (M-gasket) around fast-moving substrates undergoing export. The unique physicochemical features of the M-gasket are crucial to preserve the membrane barrier, to accommodate local conformational changes during active secretion, and to maintain stability of the secretion pore in cooperation with a plug domain (R-plug) and a network of salt-bridges. The conservation of the M-gasket, R-plug, and salt-bridge network suggests a universal mechanism by which the membrane integrity is maintained during high-speed protein translocation in all T3SSs.Peer Reviewe

Controlling membrane barrier during bacterial type-III protein secretion

Type-III secretion systems (T3SSs) of the bacterial flagellum and the evolutionarily related injectisome are capable of translocating proteins with a remarkable speed of several thousand amino acids per second. Here, we investigated how T3SSs are able to transport proteins at such a high rate while preventing the leakage of small molecules. Our mutational and evolutionary analyses demonstrate that an ensemble of conserved methionine residues at the cytoplasmic side of the T3SS channel create a deformable gasket (M-gasket) around fast-moving substrates undergoing export. The unique physicochemical features of the M-gasket are crucial to preserve the membrane barrier, to accommodate local conformational changes during active secretion, and to maintain stability of the secretion pore in cooperation with a plug domain (R-plug) and a network of salt-bridges. The conservation of the M-gasket, R-plug, and salt-bridge network suggests a universal mechanism by which the membrane integrity is maintained during high-speed protein translocation in all T3SSs

Regulations of proapoptotic protein Bax : role of Akt and GSK-3β kinases and of antiapoptotic protein Bcl-xL

La protéine proapoptotique Bax joue un rôle fondamental au cours de la voie intrinsèque de l’apoptose. Elle participe au déclenchement de la mort en permettant la libération de facteurs apoptogéniques mitochondriaux vers le cytosol. Un des points-clé de la fonction de Bax est son activation, caractérisée par la transition entre une forme cytosolique, globulaire et inactive de la protéine et une conformation mitochondriale, membranaire et active. Les différentes étapes de l’activation de Bax sont relativement bien connues, toutefois un grand nombre de questions reste en suspens quant-à leur régulation.Ce travail s’est focalisé sur la régulation de l’activation de Bax par les kinases Akt et GSK-3β ainsi que par la protéine antiapoptotique Bcl-xL . Ces régulations ont été caractérisées en exprimant la protéine Bax humaine chez la levure Saccharomyces cerevisiae, un paradigme d’étude simplifié qui permet d’accéder aux composantes individuelles des mécanismes d’activation de Bax.Les données obtenues suggèrent qu’il existe deux étapes régulées indépendamment au cours de l’activation de Bax. Nous avons montré que la protéine kinase GSK-3β favorise l’adressage de Bax vers la mitochondrie mais qu’elle n’entraîne pas un changement de conformation suffisant à son activation complète et à la perméabilisation de la membrane mitochondriale externe. Des changements de conformations complémentaires de Bax sont requis pour conduire à une forme capable d’entraîner la libération des facteurs apoptogéniques mitochondriaux. La protéine kinase Akt est impliquée dans le contrôle de Bax via la phosphorylation de la sérine 184 et participe à l’inhibition de l’apoptose. Nous avons mis en évidence qu’une mutation phosphomimétique de la sérine 184 ou l’expression d’Akt, en l’absence de partenaires antiapoptotiques, stimulent un changement de conformation de Bax vers une forme active. Akt semble donc plus jouer un rôle sur la conformation de Bax qu’entraîner une inhibition directe. La présence de protéines antiapoptotiques serait ainsi requise pour l’inhibition de Bax en présence d’Akt.D’autre part, nous nous sommmes intéressés aux mécanismes d’action de la protéine antiapoptotique Bcl-xL . Nous avons déterminé que Bcl-xL pouvait favoriser l’adressage de Bax vers la membrane mitochondriale tout en exerçant un rôle antiapoptotique. Ceci suggère que Bcl-xL intervienne dans le contrôle des étapes tardives de l’activation de Bax. Ce contrôle est dépendant d’une interaction stable entre les deux protéines. Inversement, un variant de Bcl-xL n’interagissant que de façon transitoire avec Bax (Bcl-xL ∆C) entraîne l’activation de Bax. Cette observation est en faveur d’un modèle d’activation indirecte de Bax consécutive à la rupture de l’interaction avec Bcl-xL et dans lequel les protéines à BH3-seulement telles que Bad joueraient un rôle crucial.Proapoptotic protein Bax plays a major role during apoptosis intrinsic pathway. Bax promotes cell death by inducing the release of apoptogenic factors from mitochondria to cytosol. Bax activation is a key step of its function which involves a change from a globular, cytosolic and inactive conformation to an active mitochondrial, membrane inserted conformation. Bax activation substeps are rather well known, however their regulation remains to be characterized.This work focuses on the study of the regulation of Bax activation by kinases Akt and GSK-3β and by antiapoptotic protein Bcl-xL . Human Bax regulations have been studied by expressing the protein in yeast Saccharomyces cerevisiae which represents a simplified paradigm for the understanding of the individual components of Bax activation mecha- nisms.Our data suggest that there are two independently regulated steps during Bax activation. We showed that GSK-3β expression led to Bax addressing to mitochondria but was not sufficent to promote a complete activation and mitochondrial outer membrane premeabilization. Further conformational changes are required to promote Bax full activation and the release of mitochondrial apoptotic factors. Protein kinase Akt is involved in Bax activation control through the phosphorylation of serine 184 and contributes to apoptosis inhibition. We observed that either a phosphomimetic mutation of serine 184 or coexpression of Akt, in the absence of antiapoptotic partners, were responsible of Bax conformational change into an active form. By itself Akt did not inhibit Bax but appeared more likely to control its conformational change. Thus, implication of antiapoptotic proteins seems to be critical in a model of Bax inhibition by Akt.Furthermore, we tried to understand the molecular mechanisms of antiapoptotic protein Bcl-xL inhibition on Bax. We determined that Bcl-xL could increase Bax mitochondrial localization while leading to its inhibition suggesting that Bcl-xL controled Bax late activation steps. Bax inhibition was dependent on a stable interaction with Bcl-xL . Conversely, a variant of Bcl-xL having a transitory interaction with Bax (Bcl-xL ∆C) was able to promote Bax activation. This supports a model of Bax indirect activation following the rupture of interaction with Bcl-xL in which BH3-only proteins like Bad would play an important role

Regulations of proapoptotic protein Bax : role of Akt and GSK-3β kinases and of antiapoptotic protein Bcl-xL

La protéine proapoptotique Bax joue un rôle fondamental au cours de la voie intrinsèque de l’apoptose. Elle participe au déclenchement de la mort en permettant la libération de facteurs apoptogéniques mitochondriaux vers le cytosol. Un des points-clé de la fonction de Bax est son activation, caractérisée par la transition entre une forme cytosolique, globulaire et inactive de la protéine et une conformation mitochondriale, membranaire et active. Les différentes étapes de l’activation de Bax sont relativement bien connues, toutefois un grand nombre de questions reste en suspens quant-à leur régulation.Ce travail s’est focalisé sur la régulation de l’activation de Bax par les kinases Akt et GSK-3β ainsi que par la protéine antiapoptotique Bcl-xL . Ces régulations ont été caractérisées en exprimant la protéine Bax humaine chez la levure Saccharomyces cerevisiae, un paradigme d’étude simplifié qui permet d’accéder aux composantes individuelles des mécanismes d’activation de Bax.Les données obtenues suggèrent qu’il existe deux étapes régulées indépendamment au cours de l’activation de Bax. Nous avons montré que la protéine kinase GSK-3β favorise l’adressage de Bax vers la mitochondrie mais qu’elle n’entraîne pas un changement de conformation suffisant à son activation complète et à la perméabilisation de la membrane mitochondriale externe. Des changements de conformations complémentaires de Bax sont requis pour conduire à une forme capable d’entraîner la libération des facteurs apoptogéniques mitochondriaux. La protéine kinase Akt est impliquée dans le contrôle de Bax via la phosphorylation de la sérine 184 et participe à l’inhibition de l’apoptose. Nous avons mis en évidence qu’une mutation phosphomimétique de la sérine 184 ou l’expression d’Akt, en l’absence de partenaires antiapoptotiques, stimulent un changement de conformation de Bax vers une forme active. Akt semble donc plus jouer un rôle sur la conformation de Bax qu’entraîner une inhibition directe. La présence de protéines antiapoptotiques serait ainsi requise pour l’inhibition de Bax en présence d’Akt.D’autre part, nous nous sommmes intéressés aux mécanismes d’action de la protéine antiapoptotique Bcl-xL . Nous avons déterminé que Bcl-xL pouvait favoriser l’adressage de Bax vers la membrane mitochondriale tout en exerçant un rôle antiapoptotique. Ceci suggère que Bcl-xL intervienne dans le contrôle des étapes tardives de l’activation de Bax. Ce contrôle est dépendant d’une interaction stable entre les deux protéines. Inversement, un variant de Bcl-xL n’interagissant que de façon transitoire avec Bax (Bcl-xL ∆C) entraîne l’activation de Bax. Cette observation est en faveur d’un modèle d’activation indirecte de Bax consécutive à la rupture de l’interaction avec Bcl-xL et dans lequel les protéines à BH3-seulement telles que Bad joueraient un rôle crucial.Proapoptotic protein Bax plays a major role during apoptosis intrinsic pathway. Bax promotes cell death by inducing the release of apoptogenic factors from mitochondria to cytosol. Bax activation is a key step of its function which involves a change from a globular, cytosolic and inactive conformation to an active mitochondrial, membrane inserted conformation. Bax activation substeps are rather well known, however their regulation remains to be characterized.This work focuses on the study of the regulation of Bax activation by kinases Akt and GSK-3β and by antiapoptotic protein Bcl-xL . Human Bax regulations have been studied by expressing the protein in yeast Saccharomyces cerevisiae which represents a simplified paradigm for the understanding of the individual components of Bax activation mecha- nisms.Our data suggest that there are two independently regulated steps during Bax activation. We showed that GSK-3β expression led to Bax addressing to mitochondria but was not sufficent to promote a complete activation and mitochondrial outer membrane premeabilization. Further conformational changes are required to promote Bax full activation and the release of mitochondrial apoptotic factors. Protein kinase Akt is involved in Bax activation control through the phosphorylation of serine 184 and contributes to apoptosis inhibition. We observed that either a phosphomimetic mutation of serine 184 or coexpression of Akt, in the absence of antiapoptotic partners, were responsible of Bax conformational change into an active form. By itself Akt did not inhibit Bax but appeared more likely to control its conformational change. Thus, implication of antiapoptotic proteins seems to be critical in a model of Bax inhibition by Akt.Furthermore, we tried to understand the molecular mechanisms of antiapoptotic protein Bcl-xL inhibition on Bax. We determined that Bcl-xL could increase Bax mitochondrial localization while leading to its inhibition suggesting that Bcl-xL controled Bax late activation steps. Bax inhibition was dependent on a stable interaction with Bcl-xL . Conversely, a variant of Bcl-xL having a transitory interaction with Bax (Bcl-xL ∆C) was able to promote Bax activation. This supports a model of Bax indirect activation following the rupture of interaction with Bcl-xL in which BH3-only proteins like Bad would play an important role

Régulations de la protéine proapoptotique Bax (rôle des kinases Akt et GSK-3b et de la protéine antiapoptotique Bcl-xL)

La protéine proapoptotique Bax joue un rôle fondamental au cours de la voie intrinsèque de l apoptose. Elle participe au déclenchement de la mort en permettant la libération de facteurs apoptogéniques mitochondriaux vers le cytosol. Un des points-clé de la fonction de Bax est son activation, caractérisée par la transition entre une forme cytosolique, globulaire et inactive de la protéine et une conformation mitochondriale, membranaire et active. Les différentes étapes de l activation de Bax sont relativement bien connues, toutefois un grand nombre de questions reste en suspens quant-à leur régulation.Ce travail s est focalisé sur la régulation de l activation de Bax par les kinases Akt et GSK-3b ainsi que par la protéine antiapoptotique Bcl-xL . Ces régulations ont été caractérisées en exprimant la protéine Bax humaine chez la levure Saccharomyces cerevisiae, un paradigme d étude simplifié qui permet d accéder aux composantes individuelles des mécanismes d activation de Bax.Les données obtenues suggèrent qu il existe deux étapes régulées indépendamment au cours de l activation de Bax. Nous avons montré que la protéine kinase GSK-3b favorise l adressage de Bax vers la mitochondrie mais qu elle n entraîne pas un changement de conformation suffisant à son activation complète et à la perméabilisation de la membrane mitochondriale externe. Des changements de conformations complémentaires de Bax sont requis pour conduire à une forme capable d entraîner la libération des facteurs apoptogéniques mitochondriaux. La protéine kinase Akt est impliquée dans le contrôle de Bax via la phosphorylation de la sérine 184 et participe à l inhibition de l apoptose. Nous avons mis en évidence qu une mutation phosphomimétique de la sérine 184 ou l expression d Akt, en l absence de partenaires antiapoptotiques, stimulent un changement de conformation de Bax vers une forme active. Akt semble donc plus jouer un rôle sur la conformation de Bax qu entraîner une inhibition directe. La présence de protéines antiapoptotiques serait ainsi requise pour l inhibition de Bax en présence d Akt.D autre part, nous nous sommmes intéressés aux mécanismes d action de la protéine antiapoptotique Bcl-xL . Nous avons déterminé que Bcl-xL pouvait favoriser l adressage de Bax vers la membrane mitochondriale tout en exerçant un rôle antiapoptotique. Ceci suggère que Bcl-xL intervienne dans le contrôle des étapes tardives de l activation de Bax. Ce contrôle est dépendant d une interaction stable entre les deux protéines. Inversement, un variant de Bcl-xL n interagissant que de façon transitoire avec Bax (Bcl-xL C) entraîne l activation de Bax. Cette observation est en faveur d un modèle d activation indirecte de Bax consécutive à la rupture de l interaction avec Bcl-xL et dans lequel les protéines à BH3-seulement telles que Bad joueraient un rôle crucial.Proapoptotic protein Bax plays a major role during apoptosis intrinsic pathway. Bax promotes cell death by inducing the release of apoptogenic factors from mitochondria to cytosol. Bax activation is a key step of its function which involves a change from a globular, cytosolic and inactive conformation to an active mitochondrial, membrane inserted conformation. Bax activation substeps are rather well known, however their regulation remains to be characterized.This work focuses on the study of the regulation of Bax activation by kinases Akt and GSK-3b and by antiapoptotic protein Bcl-xL . Human Bax regulations have been studied by expressing the protein in yeast Saccharomyces cerevisiae which represents a simplified paradigm for the understanding of the individual components of Bax activation mecha- nisms.Our data suggest that there are two independently regulated steps during Bax activation. We showed that GSK-3b expression led to Bax addressing to mitochondria but was not sufficent to promote a complete activation and mitochondrial outer membrane premeabilization. Further conformational changes are required to promote Bax full activation and the release of mitochondrial apoptotic factors. Protein kinase Akt is involved in Bax activation control through the phosphorylation of serine 184 and contributes to apoptosis inhibition. We observed that either a phosphomimetic mutation of serine 184 or coexpression of Akt, in the absence of antiapoptotic partners, were responsible of Bax conformational change into an active form. By itself Akt did not inhibit Bax but appeared more likely to control its conformational change. Thus, implication of antiapoptotic proteins seems to be critical in a model of Bax inhibition by Akt.Furthermore, we tried to understand the molecular mechanisms of antiapoptotic protein Bcl-xL inhibition on Bax. We determined that Bcl-xL could increase Bax mitochondrial localization while leading to its inhibition suggesting that Bcl-xL controled Bax late activation steps. Bax inhibition was dependent on a stable interaction with Bcl-xL . Conversely, a variant of Bcl-xL having a transitory interaction with Bax (Bcl-xL C) was able to promote Bax activation. This supports a model of Bax indirect activation following the rupture of interaction with Bcl-xL in which BH3-only proteins like Bad would play an important role.BORDEAUX2-Bib. électronique (335229905) / SudocSudocFranceF

Bax mitochondrial relocation is linked to its phosphorylation and its interaction with Bcl-xL

The heterologous expression of Bax, and other Bcl-2 family members, in the yeast Saccharomyces cerevisiae, has proved to be a valuable reporter system to investigate the molecular mechanisms underlying their interaction with mitochondria. By combining the co-expression of Bax and Bcl-xL mutants with analyzes of their localization and interaction in mitochondria and post-mitochondrial supernatants, we showed that the ability of Bax and Bcl-xL to interact is dependent both on Bax phosphorylation - mimicked by a substitution S184D - and by Bax and Bcl-xL localization. This, and previous data, provide the molecular basis for a model of dynamic equilibrium for Bax localization and activation, regulated both by phosphorylation and Bcl-xL

Tetracenomycin X sequesters peptidyl-tRNA during translation of QK motifs

With antibiotic-resistant bacteria threatening our ability to treat common infections, new lead compounds with distinct target binding sites and limited cross-resistance are urgently needed. Natural products that inhibit the bacterial ribosome – a target for more than half of the antibiotics in use today – are a promising source of such leads and have the potential to be developed into potent drugs through structure-guided design. However, because the mechanisms of action of many of these compounds are not well understood, they are often poor candidates for a structure-based approach. Here, we use inverse toeprinting coupled to next-generation sequencing to show that the aromatic polyketide tetracenomycin X (TcmX) primarily inhibits the formation of a peptide bond between an incoming aminoacyl-tRNA and a terminal Gln-Lys (QK) motif in the nascent polypeptide. Using cryogenic electron microscopy, we reveal that translation inhibition at QK motifs occurs via an unusual mechanism involving sequestration of the 3’ adenosine of peptidyl-tRNA Lys in the drug-occupied nascent polypeptide exit tunnel of the ribosome. Our study provides mechanistic insights into the mode of action of TcmX on the bacterial ribosome and paves the path for the development of novel antibiotics based on a common aromatic polyketide scaffold

In vivo 3′-to-5′ exoribonuclease targetomes of Streptococcus pyogenes

mRNA decay plays an essential role in the control of gene expression in bacteria. Exoribonucleases (exoRNases), which trim transcripts starting from the 5′ or 3′ end, are particularly important to fully degrade unwanted transcripts and renew the pool of nucleotides available in the cell. While recent techniques have allowed genome-wide identification of ribonuclease (RNase) targets in bacteria in vivo, none of the 3′-to-5′ exoRNase targetomes (i.e., global processing sites) have been studied so far. Here, we report the targetomes of YhaM, polynucleotide phosphorylase (PNPase), and RNase R of the human pathogen Streptococcus pyogenes. We determined that YhaM is an unspecific enzyme that trims a few nucleotides and targets the majority of transcript ends, generated either by transcription termination or by endonucleolytic activity. The molecular determinants for YhaM-limited processivity are yet to be deciphered. We showed that PNPase clears the cell from mRNA decay fragments produced by endoribonucleases (endoRNases) and is the major 3′-to-5′ exoRNase for RNA turnover in S. pyogenes. In particular, PNPase is responsible for the degradation of regulatory elements from 5′ untranslated regions. However, we observed little RNase R activity in standard culture conditions. Overall, our study sheds light on the very distinct features of S. pyogenes 3′-to-5′ exoRNases

Variability in bacterial flagella re-growth patterns after breakage.

Many bacteria swim through liquids or crawl on surfaces by rotating long appendages called flagella. Flagellar filaments are assembled from thousands of subunits that are exported through a narrow secretion channel and polymerize beneath a capping scaffold at the tip of the growing filament. The assembly of a flagellum uses a significant proportion of the biosynthetic capacities of the cell with each filament constituting ~1% of the total cell protein. Here, we addressed a significant question whether a flagellar filament can form a new cap and resume growth after breakage. Re-growth of broken filaments was visualized using sequential 3-color fluorescent labeling of filaments after mechanical shearing. Differential electron microscopy revealed the formation of new cap structures on broken filaments that re-grew. Flagellar filaments are therefore able to re-grow if broken by mechanical shearing forces, which are expected to occur frequently in nature. In contrast, no re-growth was observed on filaments that had been broken using ultrashort laser pulses, a technique allowing for very local damage to individual filaments. We thus conclude that assembly of a new cap at the tip of a broken filament depends on how the filament was broken

An RNA-seq based comparative approach reveals the transcriptome-wide interplay between 3 '-to-5 ' exoRNases and RNase Y

RNA degradation is an essential process that allows bacteria to control gene expression and adapt to various environmental conditions. It is usually initiated by endoribonucleases (endoRNases), which produce intermediate fragments that are subsequently degraded by exoribonucleases (exoRNases). However, global studies of the coordinated action of these enzymes are lacking. Here, we compare the targetome of endoRNase Y with the targetomes of 3-to-5 ' exoRNases from Streptococcus pyogenes, namely, PNPase, YhaM, and RNase R. We observe that RNase Y preferentially cleaves after guanosine, generating substrate RNAs for the 3 '-to-5 ' exoRNases. We demonstrate that RNase Y processing is followed by trimming of the newly generated 3 ' ends by PNPase and YhaM. Conversely, the RNA 5 ' ends produced by RNase Y are rarely further trimmed. Our strategy enables the identification of processing events that are otherwise undetectable. Importantly, this approach allows investigation of the intricate interplay between endo- and exoRNases on a genome-wide scale