Maintaining a Healthy Proteome during Oxidative Stress.pdf

Molecular CellReviewMaintaining a Healthy Proteomeduring Oxidative StressDana Reichmann,1,*Wilhelm Voth,2and Ursula Jakob2,*1Department of BiologicalChemistry,TheAlexander Silberman InstituteofLife Sciences,SafraCampusGivatRam,TheHebrewUniversity ofJerusalem,Jerusalem 91904,Israel2Department of Molecular,Cellular,and Developmental Biology and Department of Biological Chemistry,University of Michigan,Ann Arbor,MI 48109-1048,USA*Correspondence:danaremail.huji.ac.il(D.R.),ujakobumich.edu(U.J.)https:/doi.org/10.1016/j.molcel.2017.12.021Some of the most challenging stress conditions that organisms encounter during their lifetime involve thetransient accumulation of reactive oxygen and chlorine species.Extremely reactive to amino acid sidechains,these oxidants cause widespread protein unfolding and aggregation.It is therefore not surprisingthat cells draw on avariety ofdifferent strategies to counteractthe damage and maintain ahealthy proteome.Orchestrated largely by direct changes in the thiol oxidation status of key proteins,the response strategiesinvolve all layers of protein protection.Reprogramming of basic biological functions helps decrease nascentprotein synthesis and restore redox homeostasis.Mobilization of oxidative stress-activated chaperones andproduction of stress-resistant non-proteinaceous chaperones prevent irreversible protein aggregation.Finally,redox-controlled increase in proteasome activity removes any irreversibly damaged proteins.Together,thesesystemspavethewaytorestoreproteinhomeostasisandenableorganismstosurvivestressconditions that are inevitable when living an aerobic lifestyle.IntroductionProteins are the most diverse and structurally complex macro-molecules in the cell.Considered natures workhorses,theyare involved in almost every known aspect of biological function.The function of proteins is defined by their specific three-dimen-sional structure,making it a top priority for every cell and organ-ism to ensure that nascent polypeptide chains adopt and nativeproteins preserve theirproperly foldedconformation evenduringstressful situations(Balchin et al.,2016).Control over a healthyproteome(i.e.,proteostasis)beginswiththe birthof the polypep-tide chain on the ribosome and ends with the coordinated deathof the mature protein by degradation.Each step in between iscarefully orchestrated and involves a complex and highly dy-namic network of proteostasis factors(Hartl et al.,2011;Taipaleet al.,2014).Failure of this network to do its job not only renderstheentire process of costly proteinsynthesis futile butmight alsolead to the toxic accumulation of misfolded proteins(i.e.,aggre-gation)(Brehme et al.,2014;Kaushik and Cuervo,2015).At theheart of the proteostasis network is a fleet of molecular chaper-ones that assist in the folding of client proteins,promote proteinassembly and disassembly,mediate protein trafficking andsignaling,and protect unfolding proteins against the formationof irreversible protein aggregates during non-stress and stressconditions(Hartl et al.,2011;Taipale et al.,2014).Chaperonesare assisted by co-chaperones,which fine-tune the activity ofchaperones and work in concert with catalytic folding factors,proteases and non-proteinaceous chaperones.Over the pastfewyears,itbecameevidentthatnotallmembers ofthisnetworkare equally capable of protecting the proteome under all condi-tions that organisms might encounter over their lifetime.Oneparticular stressful situation that most aerobically living organ-isms have to eventually deal with is the accumulation of reactiveoxygen species(ROS)or reactive chlorine species(RCS).Highlyreactive toward all cellular macromolecules,ROS and RCScause major metabolic,transcriptomic,and proteomic changesand greatly challenge the cellular proteastasis network.In thisreview,we will examine the sources of ROS and RCS,discusstheir cellular effects,and summarize the various strategies thatorganisms developed to maintain a healthy proteome during alife with oxygen.Cellular Oxidants:Where Do They Come From and WhatDo They Do?Aerobic organisms regularly encounter ROS(Murphy,2009)orRCS(Ezraty et al.,2017;Kettle et al.,2014).The physiologicallymost relevant ROS are superoxide anions(O2?)and peroxide(H2O2).They are constantly produced as byproducts of respira-tion,during oxidative protein folding in the ER,and by membersof the NADPH oxidase(Nox)and cytochrome p450 family(Holmstro m and Finkel,2014;Hrycay and Bandiera,2015;Tuand Weissman,2002).Superoxide gets readily dismuted intoperoxide by superoxide dismutase,thereby indirectly contrib-uting to the cellular H2O2reservoir.Peroxide is subsequentlydetoxified by catalases and peroxidases,reacts with proteinsinvolvedinredox-sensitivesignaltransductionprocesses(Holm-stro m and Finkel,2014),or converts into hydroxyl radicals(dOH)upon reaction with transition metals,particularly Fe2+and Cu2+ions(i.e.,Fenton reaction)(Halliwell and Gutteridge,2007;Jo-mova and Valko,2011).Hydroxyl radicals are considered to beone of the most reactive ROS and are responsible for muchof the oxidative damage that proteins,lipids,and DNA experi-ence once ROS levels increase.Some of these oxidation prod-ucts,particularly lipid peroxides,such as the electrophile 4-hy-droxynonenol(4-HNE),can then further perpetuate the cellularMolecular Cell 69,January 18,2018 2017 Elsevier Inc.203damage(Forman et al.,2008;Gaschler and Stockwell,2017).Another fate of peroxide is the formation of hypochlorous acid(HOCl),a reactive chlorine species(RCS)that is well known forits microbicidal effects and widely used as the active ingredientof household bleach(Winterbourn et al.,2016).Formation ofHOCl,which is catalyzed by enzymes such as myeloperoxidaseorlactoperoxidase,occursprimarilyaspartoftheinnateimmuneresponse in activated neutrophils as well as in milk and othermucosal secretions,and serves as a first line of antibacterial de-fense(Winterbourn and Kettle,2013).Not surprisingly,organ-isms have developed a host of oxidative defense systems tocounteract ROS and RCS production and to repair the oxidativedamage.Inaddition to ROS-detoxifying enzymesand smallnon-protein antioxidants(e.g.,glutathione;vitamins)that quench theoxidants(Marengo et al.,2016),cells use various repair systems(e.g.,methionine sulfoxide reductase,thioredoxin,and glutare-doxin)to reverse the oxidative modifications and restore redoxhomeostasis(Lu and Holmgren,2014).Oxidative Stress:A Constant Threat when Living anAerobic LifestyleCells constantly generate oxidants and produce antioxidants(Holmstro m and Finkel,2014;Miki and Funato,2012).Despitetheir attempts to strike a healthy balance,organisms encounternumerous situations in which oxidant levels are no longer insync with the cells detoxification systems,generating a poten-tially lethal condition termed oxidative stress.One classicalexample is during inflammation,when activated macrophagesand neutrophils produce large amounts of peroxide and HOClduring the so-called oxidative burst(Winterbourn et al.,2016).Although much of the ROS and RCS are produced within phag-osomes in an attempt to kill off invading pathogens,some arealso released into the environment,where they contribute tothe tissuedamage frequentlyobserved atsitesof chronicinflam-mations(Holmstro m and Finkel,2014).Accumulation of ROShas also long been considered to be a major contributor to agingand age-related diseases(Labunskyy and Gladyshev,2013).Although scientists are still debating why aging organisms accu-mulateROS,andwhetherROSaffect lifespan,thefactthatagingtissues show increased oxidative damage remains undisputable(Stadtman,2001).Proteins are one of the major cellular targets of ROS and RCS.This is in large part due to the sheer number of oxidation-sensi-tive amino acid side chains present in proteins(Winterbourn andKettle,2013).The most frequently observed oxidative modifica-tions involve cysteine and methionine,which have very high re-action rates with hydroxyl radicals or HOCl(?106108M?1s?1)(Winterbourn and Kettle,2013).Peroxide is generally lessreactive(?10 M?1s?1),except for proteins with exquisitelyperoxide-sensitive thiols(e.g.,peroxiredoxins).In addition tothe mostly reversible thiol and methionine oxidation reactions,which are often used to redox regulate protein activity(Lo Conteand Carroll,2013),proteins tend to undergo a number of irre-versible side-chain modifications,including thiol overoxidation,carbonylation,and di-tyrosine formation(Heinecke et al.,1993;Miki and Funato,2012).Newly synthesized polypeptide chainsare particularly vulnerable,presumably because side-chainmodifications directly impact nascent protein folding(Medi-cherla and Goldberg,2008).Nonetheless,mature proteins aresensitive as well.However,whereas slow-acting oxidants(e.g.,peroxide)do not cause substantial protein unfolding,oxidantssuch as HOCl cause widespread aggregation(Winter et al.,2008).This is likely due to the ability of HOCl to rapidly reactwith residues during local unfolding events,shifting the equilib-rium of proteins toward unfolding and aggregation.Redox Regulation:Controlling Protein Function duringOxidative StressWith the development of quantitative redox proteomic studies,itis now clear that nearly every physiological process in the cell iseither directly or indirectly affected by the cellular redox state(Yang et al.,2016).This level of control is achieved by employingredox-sensitive proteins at crucial checkpoints.Redox-sensitiveproteins are typically characterized by the presence of one ormorehighlyconserved(i.e.,structurallyorfunctionallyimportant)cysteines,whose thiol groups show high reactivity towardeven slow-acting oxidants such as peroxide(Roos and Mes-sens,2011).Oxidation of these protein thiols leads to the forma-tion of either intramolecular or intermolecular disulfide bonds or,inrarercases,tosulfenic acid,sulfonicacid,orsulfenylamide(LoConte and Carroll,2013).In response,proteins undergo local orglobal conformational rearrangements,which directly contributeto a loss or gain of function,depending on the protein.Membersof the glutaredoxin and thioredoxin family then reverse the thiolmodifications and return the proteins and hence the pathwaysto their original redox and functional states.While some proteinsusereversible thiolmodificationasamechanism toregulatetheiractivity,others undergo reversible oxidation of critical methio-nine residues(Mantaand Gladyshev,2017).However,since pre-cise quantification of the extent of in vivo methionine oxidation inproteins is still challenging,it is unclear how many proteins andpathways use reversible methionine oxidation as their mode ofredox control(Pe terfiet al.,2016).Metabolic Adaptations to Oxidative StressBoth newly synthesized and mature proteins undergo irreversibleoxidative side-chain modifications,which can cause protein un-folding and potentially irreversible aggregation.Since damageoften cannot be avoided,organisms face the challenge of howto cut their losses.One central metabolic event appears to guidemany of the cellular adaptations that are invoked.Organisms,ranging from E.coli to mammalian cells,appear to respond tothe accumulation of ROS,RSC,or both,with an up to 50%decrease in cellular ATP concentrations(Colussi et al.,2000;Kumsta et al.,2011;Winter et al.,2005,2008).This substantialdecrease in the energy levels of the cell has long been attributedto the oxidative inactivation of redox-regulated metabolic en-zymes involved in ATP-generating pathways(e.g.,GAPDH,F0F1-ATP-synthase)(Hildebrandt et al.,2015;Janero et al.,1994).In fact,oxidative inactivation of key glycolytic enzymes isknown to be responsible for the active re-routing of glucosefrom glycolysis to the pentose phosphate pathway,effectivelyreducing ATP synthesis at the expense of generating NADPH(Ralser et al.,2007).NADPH is necessary to fuel the thioredoxinand glutaredoxin systems,which are essential for restoringcellular redox homeostasis(Birben et al.,2012).In addition,204Molecular Cell 69,January 18,2018Molecular CellReviewmore recent data from our lab suggest that in some bacteria(and maybe other organisms as well),much of the cellular ATP isactivelyconvertedintolongchainsofpolyP,whoseprotein-stabi-lizing features contribute to decreased protein aggregation andincreasedoxidativestressresistance(Grayetal.,2014).The tran-sientdepletionofthecellsATPcontentaffectsmostcellularactiv-ities and appears to put cells into a quasi-dormant state,helpingthemto rideout the storm.However,itmight also affect the ac-tivity of ATP-dependent canonical chaperones and proteases,which would explain the need for alternative proteostasis factorsthat deal with protein homeostasis during oxidative stress.How Cells Deal with Nascent Protein Folding duringOxidative StressDownregulation of global protein synthesis(Figure 1)is commonto different pathophysiological conditions associated withFigure 1.Protein Homeostasis duringOxidative Stress:A Multilayer ApproachUndernon-stressconditions,proteinfoldingoccurs both cotranslationally and posttransla-tionally and is supported by ATP-dependent ca-nonical chaperones.Once natively folded,theproteinsfulfilltheirexpectedfunctionsuntildegradation signals trigger ubiquitination andsubsequent degradation by the ATP-dependent26S proteasome.Redox-regulated chaperonesare inactive but might exert non-stress-relatedenzymatic functions.Under oxidative stress con-ditions,cellular ATP levels drop,reducing theactivity of ATP-dependent processes.To protectcells against the accumulation of irreversibledamaged protein aggregates,a number of ROS-orRCS-mediatedchangesoccurthateitherdirectly or indirectly contribute to(1)reduction ofnew protein synthesis;(2)activation of ATP-inde-pendent chaperones;(3)conversion of ATP intopolyphosphate,an effective inorganic chaperone;and(4)increase in ATP-independent 20S protea-some activity.Please see text for more details.increasedlevelsofcellularROS,includingstarvation,exposure to antibiotics(Mor-ano et al.,2012),inflammation(Ravishan-kar et al.,2015),and aging(Ferraz et al.,2016;Luo et al.,2017).This strategy notonly directly reduces protein aggregationby decreasing the concentration of ag-gregation-pronenascentpolypeptidesbut also leads to global repression ofgene expression during potentially error-prone conditions(Morano et al.,2012;Shenton et al.,2006).Global gene repres-sion is mediated by eIF2a kinases,whichphosphorylate the translational initiationfactor 2 alpha(elF2a).Phosphorylationof elF2a causes a general decrease incap-dependentmRNAtranslation.Atthe same time,translation of cap-inde-pendentmRNAsisinitiated,leadingto the synthesis of proteins involvedinadaptationandstressresponse(Morano et al.,2012;Taniuchi et al.,2016).Although someeIF2a kinases have been shown to be directly activated byperoxide(e.g.,yeast GCN2)or arsenite-induced oxidative stress(e.g.,heme-regulated eIF2a kinase,HRI),involvement of one ormore additional redox-regulated steps in the oxidative elF2aphosphorylation processislikelyto c