Posted on Authorea 31 Oct 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.160413141.16511994/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. plcto ed fTsegneig nti eiw ebifl eiwteT-eae oeua risof traits molecular TF-related the review the briefly broaden we and TFs review, functional natural this TFs of In native shortcomings of of the engineering. strategies series for TFs new a up make of the fuse can which fields With They (ATFs) chassis application factors production. the functions. transcription of extensive industrial tools. have artificial metabolism biology and domains up, the synthetic tolerance promote springing of strains helps development TFs improving engineering, further using of genetic the direction by enable the operated and toward TFs TFs theory responsive native biology stress of synthetic Native with applications combination deal the in improve engineering markedly TFs will will have of engineering understanding (TFs) enhanced TFs factor an Simultaneously, stress-responded [11]. scales transcription tolerance by networks spatial stress that metabolic tolerance to and contribute on indicate strains temporal to stress studies the contribute specific with that improving Recent a stim- genes Therefore, tolerance in stress 10]. of transcription traits. under level [9, transcriptional gene nucleus regulating phenotype control the on to complex to focused potential the signals kinases, the improve transmit with have interact to to TFs can molecules they challenges So, metabolite and significant networks ulation. and environment still signaling and factors complex are operations of transcription there extra components of other undermines, important cost the are production pro- TFs reduce high the accumulation, relatively to pollution. Despite the (ROS) ways including oxidative 8]. species chemical process, 7, and oxygen fermentation and dysmetabolism[1, toxicities from reactive physical and product cause of destruction shock, can organic membrane use limited heat stresses cell intensive biofuels, are damage, as these yield as chromosome such are product denaturation, such issues reasons tein and the products, key rate to Some industrial growth due cell of stress[6]. processes, However, biosynthesis fermentation flavonoids[1-5]. in industrial and factory in acid cell abscisic microbial terpenoids, valuable acids a is Yeast products. Introduction economy the bio-based 1 for A discuss strategies for we Lastly, novel and engineering discussed. particular, TFs are heat, In exploiting evaluation of in quantitative transcription stresses artificial solutions cells. and of upon potential optimization applications yeast the and fluxes responses within addition, challenges metabolic adaptive In modules in yeast examined. different are fabricating of engineering (ATFs)-based into TFs mechanisms factor by stress them the yield different transcription and in classify tolerance of engineer advances both levels and to of recent enhancement transcript oxidants is the the and bottlenecks on remodeling such acid focus through resolve acetic efficiency we conditions to production Here, stress way various and effective However, genes. tolerance One resistant chemicals. strain fine enhance benefits. fermented to and make (TFs) costs to factors platform production microbial the typical restrict a severely as well-used been has Yeast Abstract 2020 31, October 3 2 1 Dong Shuxin Yeast in requirements to industrial Networks meeting Metabolic Harnesses Engineering Factor Transcription ejn nttt fTechnology of Institute Beijing University Tsinghua available not Affiliation 1 e Qin Lei , 1 hnLi Chun , 2 n u Li Jun and , 1 3 Posted on Authorea 31 Oct 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.160413141.16511994/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. inaditaellrsbtneitrcin epu nesadtemcaimo ihtmeauea the at temperature high phosphoryla- of transmission, mechanism cascade the this signal understand In as us [25-27]. such help regulator TFs interactions pathways substance of biosynthesis intracellular several functions Gal11p, or and the with coactivator tion module, interacts II directly response pol Gcn4p temperature RNA as a high such as TFs, which different Msn2/4p-regulated Pho2p, multiple between revealed Bas1p, relationships have acquisition interacting analysis independent the database Data base and SGD and AGGGG (SWATH) or genes STRING or spectra Sequen- with ion CCCCT Microarray-assisted, combined fragment Besides, a analyses can Theoretical containing (DIA) [22-24]. Msn2/4p all (STREs) genes of result, thus response elements Acquisition a stress Window Msn2/4p, response as of tial stress phosphorylate and, transcription removed, the the to activate is to cAMP (PKA) to inhibition bind high sequences A this and kinase results stress, nucleus heat protein which the Upon and active, enter via cAMP inhibition. is response are of stress protein activity interaction yeast Ras Msn2/4p the regulates temperature, mainly promotes normal Msn2/4p the and deep Under confirmed level temperature. have and pathway. high technology in signaling immunoprecipitation proteomics Msn2/4p Ras-PKA Chromatin and TFs as another (RNA-seq) damage of sequencing such irreversible function deep techniques to mRNA characterization resistance (ChIP-seq), advanced sequencing cells the correct years, of regulate with recent generation to combination 21]. In In the nucleus [20, assembly the led 1). They ribosome into has (Fig. incorrect (RASTR). enter RASTR genes by assembly, then response assembly caused ribosome and ribosome stress and r-proteins of assembly also genes orphan operation ribosome synthetic Hsf1p of Two ribosome the addition, phosphorylation pathway. production of in ribosomal In its excessive expression involve the by Hsp70, in Ifh1pare [19]. induced participating with and genes through are combined ribosomes stress-related Hsf1p the is toxic downstream TFs, better to Hsf1 of the resistance independent and When of is, level proteins degree Hsf1p transcription of certain of be. the confers level booster structure will promote phosphorylation a correct complex the also is the mediation higher phosphorylation can maintain Furthermore, the the can temperature, [18]. of high genes proteins recruitment Under transcription damaged HSPs activity. the of facilitate Hsf1p degradation genes. to to or (HSPs) II repairing phosphory- transcription- protein polymerase be recruit the RNA can shock rapidly promote and it can heat and Med15p) they state the where Med3p, natural stress, Med2p, of under heat as Hsp70 during (such with nucleus mediators binding 1). the to friendly into (Fig. due translocated inhibited [14-17] then be chaperones and to lated molecular known and TF from a proteins cells is response microbial Hsf1p stress DNA inside of metabolism and expression cell the dysfunction protein of induced shutdown mitochondrial including which and chain, process, growth of respiratory fermentation inhibitions stressors, during electronic avoid To disturbances the [11-13]. metabolic from damage and spillover growth electron cause misfolding, can stress Heat yeast. module in response networks stress metabolic different regulate Heat up and wake Among system stress mechanism oxidative effectors. stress-sensing and acid, of ultimate 2.1 acetic part to temperature, are modules high which of TFs natural response types of different These process. common types ma- productions most through selection. industrial three defense transmitted in the natural perfect are homeostasis them, of relatively maintain stresses a force on diverse evolved ability the strains Highly has under engineered yeast stresses the environment, environmental confer changing mechanisms various dynamic Yeast counteract a in to in stress chineries survive of to effect order achieving inhibitory In as gene in in invented tuning understanding regulation been TFs. fine has by the TFs to it tools Native discuss Even, biology parts 2 we synthetic as Lastly, before. of than used innovations content. pathways and better metabolic metabolites biomanufacturing be in strains evaluate either genes quantitatively control can to to which devices switch tolerance TFs, for transcription stress Artificial native or the of expression from improving applications recent in originated most pattern the (ATFs) regular summarize also factors TFs We on biomanufacturing. based in engineering efficiency TFs and and responses stress cellular HSF1 , MSN2/4 noigTsaetems omnrgltr nha tesrato (HSR), reaction stress heat in regulators common most the are TFs encoding 2 Posted on Authorea 31 Oct 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.160413141.16511994/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. ula xotsga NS shdd hsihbtteepeso fatoiatgns nadto,some addition, In genes. antioxidant of expression the the inhibit C-terminal connecting thus and it hided, N-terminal ROS, between is of (NES) bonds glycolysis concentration intramolecular-disulfide signal MDR, inhibitory forms export to resistance networks Ybp1p nuclear exposure multidrug metabolic protein key Upon system, scaffold the glutathione [56]. controls with detoxification including that cellular TF systems, and major resistant pathway a stress is oxidative Yap1p pathways, 3). of regulatory glutathione (Fig. ROS-induced and detoxification thioredoxin most ROS as In in such role system defense important [55]. overcoming molecules yeast an Innately, in nonenzymatic play networks [52-54]. or also metabolic acid enzymatic reconstruct some ferulic which causes signaling addition, and it TFs-related In or furfural different (ROS) 51], mercury, on [50, species cobalt, depend mitochondria oxygen stress as or oxidative reactive such (ER) of reticulum compounds, accumulation is pro-oxidant/antioxidant endoplasmic electrophilic the intracellular peroxisomes, by to of the due from balance it comes original mainly Sometimes, the which which disorders. in metabolic damage and of disturbed type a stress is of Stress Oxidative types module different of response state roles stress membrane key order Oxidative cell the in 2.3 and presents change regulation module can retrograde acid composition regulation, membrane channel acetic lipid the ion the and of changes. including fluidity So, change pathway, as in to stress. such TFs known acid sole status responsive process acetic membranes the a with cell encoding is cope The which OLE1 to (UFA), [49]. addition, acid yeast fatty In in unsaturated fluidity into 48]. induced (SFA) [47, be acids yeast fatty can in TF a tolerance ( as regulons acid Hog1p of stretch that a reveals of research when to metabolites Another ability other the overexpressing synthesizing [40-46]. by for confers impaired acid acid system was glutamic acetic enough activity regulation generate of mitochondrial retrograde to expression So, plastic networks the metabolic carboxylase). stimulate harness (pyruvate to PYC1 (NAD nucleus com- and the the Mks1-Bmh1/2p IDH1/2 dehydrogenase) by the enters including by induced metabolic smoothly repressed genes, is the be complex activity stress-responsive and alleviate Rtg3p-Rtg1p complex activator to an Active Rtg3p-Rtg1p as occurs serves [39]. plex. and which mitochondria complex, Mks1p) of formed Mks1p-Rtg2p and is of disturbance It activity Rtg3p the TFs- destruction. Rtg1p, by the acid Recently, (Rtg2p, caused acetic against disorders subunits [36-38]. ABC to acid comprising anion system acetic a and complex to as Pma1p the phosphorylated discovered by resistance protein When been Fps1p in channel has assist proton causes 34]. regulation also Fps1p, retrograde thus [33, Pdr18p) involved to effects and addition and toxic In Pdr12p Fps1p its aquaglyceroporin (Pdr10p, with [35]. decrease transporters closes endocytosis interacts to by and directly degraded and Fps1p Hog1p then cell divorces and serious, yeast turn the more in phosphorylated permeating becomes is which acid acidity Hog1p Rgc2p, acetic TF prevent osmoregulation factor active to regulatory decrease acid, channel the acetic to [32]. to activates membrane disrupted response then In cell is and on synthesis cell. ATP yeast. the cations into the in and disso- molecules and acetate cell effects anions drops yeast acid transporting into pH acetic specifically goes intracellular the it the transporters when ions, numbers and of are pretreatment, states biomass There different of two byproduct into abundant most ciating the is influence acid stress Acetic from recovery membrane to cell contribute the of effect, regulation 2). adaptation the retrograde the (Fig. with and transporters, cope reactions include To downstream systems Hog1p-depend 31]. facilitate response components, undermines [30, molecular furan biomass to toxic and of pretreatment TF-mediated furfural pretreatment during acid, major through fermentation asacetic and such go growth products, normal hydrolysate must strains material However, lignocellulose 29]. producing, [28, reactions bioethanol the During module response stress acid yeast. 2.2Acetic in folding protein and level transcription OLE1 CTT1 n hnsqetal hshrlt,etrn h ulu ocnrlteexpression the control to nucleus the entering phosphorylate, sequentially then and FPS1 , HSP12 oe qalcrprncanli eeal eurdfrpermeating for required generally is channel aquaglyceroporin coded and , STL1 + dpnetioirt eyrgns) L3(D-lactate DLD3 dehydrogenase), isocitrate -dependent orcntutmtblcntok n nac acetic enhance and networks metabolic reconstruct to ) 3 Δ- eauaectlzssaturated catalyzes desaturase 9 Posted on Authorea 31 Oct 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.160413141.16511994/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. fsm motn ee eedw-euain uha ncro eaoim(B1 P1adTDH2), and GPM1 (FBA1, metabolizing metabolism level carbon xylose transcription in effective the as an and such networks, down-regulation, introducing metabolic were has by native genes yeast only effect important microorganisms, can ethanol some valuable system of into to xylose lignocellulose phenotype Heterologous sensitive convert pathway[68]. of to conversion potential to protein the used enhancing is and content overexpressing acetyl-CoA to Besides [67]. and regulator flux mg/L) negative glycolysis ( production(634 a increasing enzymes squalene as in the capacity resulting for acts synthesis pathway, microenvironment MVA overexpressing Opi1p high-quality the By while a in synthesis, provide ) Ino4p. to lipid the and expanded regulate changes Ino2p been that had and of TFs acid activity are the glycyrrhetinic Ino4p inhibit and and acid, overexpressing Ino2p glycyrrhizic instance, yeast. For squalene, as rate. such conversion xylose products [64, natural such yeast vivo, of in in synthesis improved upregulated ( been genes had TFs multiple acid, xylose global leaded and acetic Prs1p ( glucose xylose, with Catalase of interacted glucose, as rate engineered Whi2p contain addition, utilization overexpressing which In the Similarly, hydrolysate g/g. and 65]. 0.32 hardwood inhibitors, to non-detoxified other g/g and in 0.26 furfural from grow yield also ethanol could the The increased strains and [63]. environment over- stress xylose After acid g/L dysfunctions. to 50 cellular response stress-induced prevent in metabolism in TFs roles ceramide other expressing important and played and have Com2p genes sphingolipid Stp4p, regulated Fkh2p, above as Nrg1p, such Msn4p, regulates expression indirectly genes example, stress-induced For controls 62]. ( overex- yeast[61, directly repeatedly in been networks only en- have metabolic traits, not inhibitors harnessing tolerance or in activators of knocked-out as understanding or functioning valuable pressed TFs providing native datasets responsive sequencing stress genome vironmental and omics many the TFs With with native arise of and modification stress various enetic to infor- conventional3.1G resistance genetic (gTME), cells of engineering of diversity generation machinery during the phenotype. the transcription important enhance desired increasing markedly global more or will recon- and be engineering modification direction expression to proper TFs genetic the shown heterologous that with into has by reveals combination flux which mation pathway In productivity, engineering and improving TFs structure modification. and and organelle strain tolerance change value strains can industrial enhancing network of strains transcription gene the of between struction correlation requirements clear meetingindustrial A in eliminate implicated to engineering help response system TFs response Conventional stress oxidation three 3 oxidative the homeostasis. mainly of strains classical branch The use maintain another the to pathways as reductases recycling. of metabolic molecules molecules reconstruction various reductive oxidizing achieve part and some state to time, And redox forms maintaining state same yeast. in Hac1p) oxidized in position the important and an an At Ire1p occupies into and (Yap1p, transform module with the molecules. TFs proteins to Besides, utilize transcriptionally oxidizing donor responsive They it electron oxidative reduce 60]. and strains. an [59, to ROS, in yeast as residues with state of NADPH redox cope acid homeostasis maintain to mitochondria amino in activates UPR and involve reductive it the growth systems protein, regulating glutaredoxin regulating unfolded TF and genes the thioredoxin a of senses as number yeast. When Hac1p a in reticulum. induces folding and introns. ROS, endoplasmic protein splicing outputting on by correct by located nuclear proteins and Hac1p endonuclease oxidized Yap1p homeostasis an with catalyzes reticulum inhibits is in endoplasmic catalytic cope which Ire1p activated maintains peroxidase to Yap1p, (UPR) is thiol And, in response which encoding protein nucleus. Yap1, bonds Hyr1p the of instance, disulfide For in residue intramolecular accumulating Cys 58]. of [57, C-terminal formation Gpx3 to the of adduct independent direct manner also a can compounds electrophilic YPC1 ,croyrt eaoim( metabolism carbohydrate ), HAA Msn2/4 CTA1 ramn,mdfidxls tan oeae niiilaiiylvlo 0Maei acid, acetic 50mM of level acidity initial an tolerated strains xylose modified treatment, 1 ,guahoeatoiatsse ( system antioxidant glutathione ), 6] ute,aie nraigsristlrne F niern a rmt the promote can engineering TFs tolerance, strains increasing asides Further, [66]. ) TOS3 ,adcl alrltdsceoygyorti ( glycoprotein secretory related wall cell and ), INO2 4 GSH1 a mrvdsuln rdcini engineered in production squalene improved had INO2 ,rdcn ua leyeezms( enzymes aldehyde furan reducing ), h rao h nolsi reticulum endoplasmic the of area the , Ire1-Hac1 ERG9 HAA1 aha funfolded of pathway , HMG1 YGP1 saT which TF a is and ,btalso but ), ADH7 PPDS ), Posted on Authorea 31 Oct 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.160413141.16511994/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. rncito rcs.Atog h AAcmlxbnst B i p3,i sese o p8 obind bonds to hydrogen Spt8p of quantity for and easier distance is force, it the Spt3p, changed Spt8p via of Mutated TBP initialization Spt3p. to the than binds TBP for and complex necessary TFIIA SAGA is to which the deacetylated Although subunits process. nucleosome Spt-Ada-Gcn5p- transcription involve and thereby and (TFIID) TBP, D with encoded factor factors associated transcription (TBP) complexes instance, protein initiation by TATA-box binding For Transcription possess Furthermore, gTME. jointly xylose [80]. which of by (SAGA) respectively rates Acetyltransferase operated utilization 97.3%, The were and glucose. TFs 90.8% and xylose to included of up medium were mixed the glucose the on in and to strains regulators amino efficiency leading The high negative two which obtained [9]. NC2 and complex, other reconstructed of regulatory networks the effect transcriptional metabolic TF of inhibited mutate the and interaction of level of synergistic impact transcription SPT3-SAGA the genes the subunit for the and results site with acid These capacity. mutant interaction amino fermentation the improved Tyr195His at and in glucose recoveredacids g/L that change Lys218Arg) 120 that Using Tyr195His, and (Phe177Ser, improvement. ethanol illustrated mutant tolerance TF 6% a showing under obtained the to building mutants normally of able growing to identify library were advantage to mutant authors selective the a screening strategy, a created this a offers researchers by PCR proof-of-strategy, followed error-prone a protein, TATA-binding by As information mutants. genetic tolerant changing on based organisms. different gTME for engineering apply TFs and TFs So, strains Modified by production. industrial 3.3 played ethanol obtain role and to critical tolerance networks of display ethanol metabolic reconstruction enhancing process harness the in gluconeogenesis can that expression or revealed glucose, heterologous glycolysis g/L analysis of and 104.8 transcriptomic TFs transport of And, glucose presence 78]. the metabolism, [77, in lipid structure respectively primitive g/L 27.2 from and different in g/L reported 27.6 been to had up 43 method production this bioethanol while the 1), led (Table plants also had in meet the expression phenotypes Transforming to heterologous the using yeast. species modify engineering different effectively TFs between to quickly. different proven barrier material been from genetic communication new genes information acquiring dominant genetic of purpose of the the expression through the breaks realizes It genes sources. TFs stress-related TFs heterogeneous native Introducing of expression Heterologous 2 3. utilizes Complex chromatin out [72-76]. facilitates Remodeling knocking which Chromatin by nucleosomes, ( production (BAF) of dehydrogenase movement ethanol SWI/SNF the of expression drive ( genes [71]. to promotes hydrolysis and strains ATP remodeling knock-out structure remodeling by chromatin released in of energy TFs ) by the played Swi3p role critical as displays (such production ethanol signaling investigating 70]. of study of [69, Another out fermentation)) initiation utilization stage(xylose knocking xylose the X Therefore, efficient controlled the an in strongly metabolism. though, xylose still fermentative Even cAMP/PKA) in 67.7%). and processes (increase Snf1p/Mig1p stage (Snf3p/Rgt2p, GX effects system the positive in had target the xylose which of metabolism, in of number energy utilization thiamine a and the vitamin synthesis of a subunits on transcription is or complex the Thi2p factor cycle-related regulates initiation and cell down-regulation. transcription Pdc2p slightly out And, and Knocking also Thi3p had with genes. co-fermentation). interacts Thi2p RPL22B that (glucose-xylose and TF (RPL22A, stage Yhp1p, biosynthetic ribosome Nrm1p, GX of TFs constituent the structural metabolic-related during (HTA2), repair RPL7A) and and respond stimulus damage DNA GAL1 ° SPT3 ,adtebs n aea4%hge hncnrl n esnwsdet N idn oanwas domain binding DNA to due was reason One control. than higher 46% a made one best the and C, THI2 and and SPT15 SUC2 SPT8 nce-u es tani iie ycro orecniin,i hc lcs responding glucose which in conditions, source carbon by limited is strain yeast knocked-out .S,reducing So, ). dutteptwy fgyoyi,rsiain lcnoeei n P nG tg [79], stage GX in PPP and gluconeogenesis respiration, glycolysis, of pathways the adjust r novdi h eetasrpinpoes[18] p3 n p8 sTscninteract can TFs as Spt8p and Spt3p [81-84]. process transcription gene the in involved are H2ecdn Thi2p) THI2(encoding lyeoye marxianus Kluyveromyces SWI3 ADH2 hc noe uui fSISFcrmtnrmdln complex remodeling chromatin SWI/SNF of subunit a encodes which xrsinmgtb n ftemjrcnrbtost ethanol to contributions major the of one be might expression eutdi h peuaino ee novdi iooeand ribosome in involved genes of upregulation the in resulted FMnpo s1 in Hsf1p or Msn2p TF 5 THI2 iga uagteam Ouyang Pingkai acaoye cerevisiae Saccharomyces intices h tlzto of utilization the increase didn’t ADH1/2 n galactokinase and ) SPT15 SPT15 favorably loused also encoding n the and Posted on Authorea 31 Oct 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.160413141.16511994/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. oan thdbe oe htdffrn obntoslae otedffrn custo ftlrneto tolerance of acquisition inhibition different or the activation to an leaded either (50 combinations to ketoconazole different coupled and that ZFs (52) noted four shock been or heat metabolic had three regulate It of by domain. combinations tolerance yeast random and enhance containing butanol, favorably ATFs (vol/vol) of can 1.5% tolerance also genes. of butanol domains environment related and different networks the heat hybridized in improving survive with in ATF to expedient strain of three were the and TFs enable CRP hybrid could truncated ( Z23) this of combination and tolerance ( the Z4, heat genes found (Z11, also of to ZFs study upregulation Further related of [94]. the negatively down-regulated polymerase) in significantly selected genes RNA were resulted Similarly, Researchers Z25 with heat-resistant. tolerance. into and (interact with with them Z2 domain linked transformed Z13, associated CRP After of usually ATFs. the combination and are of the with tolerance libraries in family them combinatorial exists strains this fused construct generally improve in to and which to TFs DBD, ZFs and common And, human-derived problems is have [93]. 40 ATFs domain these their family specific finger avoid even Several bZIP zinc cell. to and the Cys2-His2 the regulation, part network. example, within For complex reconstruction transcription network capacity. and metabolic the gene production TFs, complex elaborate of in by the more reconstruction implicated by regulated satisfy diluted to been are to be modification reticulum will fail Due genetic endoplasmic effects biology. sometimes or for original synthetic TFs cycle, part in known cell as direction the metabolism, research used However, growth, a commonly of is are pathway needs they of production serious meet a can to that cells cells chassis chassis deficiencies Constructing industrial the partconstruct supply transcriptionalreconstruction also the con- as ATFs by the ATFs biology, scope. by synthetic tolerance 4.1 application constructed for with their devices tools associated expands biosensor practical and the genes new while them predict bring addition, of to still In used DNA. system to TFs been binding ventional has structure even the switch, ATFs orthogonal of creating So, specificity bistable activity, devices. transcriptional adding bio-function enhancing and by specialized construction remodeling develop systems ATF transcription and trans- the as achieve performance in potentials integration to transcriptional certain and have the cell SRDX selection give the EAR, domains to KRAB, in function imperative (SID, components of is repressor zinc combination transcription-related and The native with Gal4) [92]. from co-interact control and TFs can are cription CRP 91]which powerful DBD VP64, [89], [90, of of (dCas9) (VP16, Effector Ume6) activator Cas9 type type into and and of The one divided form (DBD) [88]. inactive are is domain applications catalytically ED ATF (TALEs), various DNA-binding while effectors biosensor. suit as activator-like transcription to genetic such (ZFs), designed domains, in for fingers rational important use metabolism are its to strains (ED) and reconstruct tool domain TFs in a native TFs as from powerful biosynthesis and originated developed the regulate to requirements and attempted industrial tolerance have strains meet improve they to rese- TFs products, biology, native interest computational engineer of to bioinformatics, limited testing, longer high-throughput no editing, are archers gene of development the With gTME factors [87]. than mutation study transcription efficiency the future Artificial mutation stress, for Designed better ER TF Although has 4 to mutant CRISPR-Cas9 yield. resistant for that the option product recommended in other desired be phenotypes proposed may and noticeable and It any resistant 63%. with was (ER) associated efficiency reticulum been in had not Endoplasmic change tolerance had analyses improve of yeast strains genotypes enhanced to degree gene to The technology ( contributed and yeast have lead. Cas9 methylotrophic phenotypes TF g/L mutated mutated tolerance researchers 1.8 by Interestingly, the accumulation of [86]. trehalose between library environment altered relationship mutagenesis the that the under Spt3p used identified researchers and survive build Further, could expression [85]. to which gene increased technology were strain (RAISE) strains screened the Exchange and system. of Strand transfer yield charge Insertional-deletional and ethanol activity and Random its tolerance alter simultaneously ethanol to the leading Finally, structure, protein the maintained that i-o i tal et Kim Jin-Soo μ )adsapn w ieetE hwdarvre phenotype. reversed a showed ED different two swapping and M) epcieycoe 5ad4 F ocet olo multiple of pool a create to ZFs 40 and 25 chosed respectively . 6 O.thermomethanolica .coli E. ompW .coli E. marR n cenn on that found screening and 9] ec,ti strategy this Hence, [95]. , TF ) cpxP , HAC1 marA , yliH yCRISPR- by and and marB ybaT .coli E. ) ) Posted on Authorea 31 Oct 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.160413141.16511994/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. eil n ihyaatbeAF ytmi eddt aif nutilnes ugse httesyn- reesei as the Trichoderma such that from host suggested which different A (CPs) in needs. promoters industrial creating core satisfy by with Therefore, to constituted limited niger needed strains. (SES) is still engineered system system to is expression ATFs application thetic adaptable application large-scale highly the of and orthogonality, difficulty flexible the meet a increases can which to system promoter want mismatches expression matching people nucleotide above If single spacers the 1-2 and TFs. Although introducing or BSs via machinery achieved oriented [101]. be transcription the BSs can basal by the it initia- the caused intensity, into transcription and effect regulation factors, ATFs of AD hindrance influencing the number between steric fine-tune main the interaction a the to the Further, owing as affected BS. outputs considered also by transcriptional were recruited of (BS) of switch complexes spectrum ATF-related sites design tion the of binding the with causes for of various associated indispensable direction among which was and And, switch number network. ATF-related the metabolic strengths. plasticity, and small expression (P signaling a inducible by promoter regulated of target orthogonally synthetic range DNA matched wide bp the 20 a a to fied to bound guided they be from activator VP64), from derived transcription DBD derived a is RNA is TALEs production, single dCas9 and systems. activity orthogonal growth endonuclease in in the no used yield of and also states product were two target ATFs COM- TALEs-based the the or decoupled created transcription in and orthogonal also increase constructed expression researches an artificial genes library, achieving this multiple ATFs And the above transcriptional method. balanced ATFs mentioned cloning system plant-derived high-throughput the and a Employing sites was which DNA-binding PASS [99]. of this numbers suggested copy In were the output between yeast. link in yeast a constitutive together and yEGFP, strong switch ( combinations the expression output exceeded gene high which orthorhombic the with pigment) an ATFs from (violet TFs constructed some of violacein system, were whole and sites the pigment) or binding motif (red cognate period deoxyviolacein parts a the pigment), were Besides, (green which towards [98]. VioD proviolacein developed and and of reconstructed VioC instance, synthesis successfully For of pathway the expression metabolism states. the two the pathway, fine-tune between violacein domain to switched even heterologous binding suited used and of well was genes, DNA switch be regulated of thus bistable of ATFs-based corre- could types expression switch the this the more bistable with activating the paired the or So, prompter), repressing of THI4 repressors for domain. and threshold localization activation The (GAL1 VP16 nuclear NLS, promoters C-terminal SV40 switch. inducible same additional the sponding bistable and the and TetR) a and had LacI) LexA, for and activators Orf2, establish Bm3R1, (TarA, the TetR, could and PhlF, effect (NLS), (SrpR, opposite domain signal binding with DNA ATFs metabolic of two for consisted that limitations revealed to species study benefit breaks A of switch states ATF be two universal will the Additionally, switch switch decoupled expression ATF-related reconstruction. as production. network of by such and development accurately expression growth in run Variable gene the pathways interest of of and metabolic plasticity. great multilayered quantity modulation a or subsequently the fine to orthogonality the of The promote lead regulation, limitation ATFs, of properties. still of novel ability is utilization with and there range parts design, wider switches and response new in structure rarely discovering elements the native and including of tolerance quality, use stress intensive the the not switchDespite enhancing withATFs was in System It Expression role 97]. Gene positive [96, 4.2 a library ATFs play this ATFs by genes. that obtained regulated noted also were to strains difficult acid-tolerant acetic the Subsequently, Besides, and PDR5 rcoem reesei Trichoderma and and YLL053C ihakudriavzevii Pichia acaoye cerevisiae Saccharomyces tetccu pyogenes. Streptococcus Ts(eAV1 rB31NSV1)a ela S civdworking achieved BSs as well as Bm3R1-NLS-VP16) or (LexA-VP16 ATFs , eecnre opriiaei ofrigktcnzl eitnei yeast. in resistance ketoconazole conferring in participate to confirmed were n,fu taeis novn hnigtenme rtype or number the changing involving strategies, four And, . D3promoter TDH3 fe h w eersetvl ue ihA V4and (VP4 AD with fused respectively were two the After ; arwalipolytica Yarrowia acaoye cerevisiae Saccharomyces e.g., 7 Arabidopsis L-A4DJBadNLS-GAL4AD-ATAF1) NLS-GAL4AD-JUB1and Syn orglt h ee xrsinadsatis- and expression genes the regulate to ) eeietfidb eetn h teghof strength the detecting by identified were ope ohtrlgu Dadtheir and AD heterologous to coupled ; seglu niger Aspergillus 10.Mroe,dCas9-based Moreover, [100]. .crvsa,Aspergillus cerevisiae, S. atooa spp Xanthomonas ; ihapastoris; Pichia Posted on Authorea 31 Oct 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.160413141.16511994/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. hntp ol eeegtclyals otyadcnein fcetn nvra Tswihwudnot would which ATFs high-quality universal a a creating causes if which strains convenient to system, modifying and devoted actively defense costly Even, also less ”unique” 109]. but a defense a [108, network, energetically novel products build regulatory be target less to would of existing by the production phenotype TFs to efficient limited known of achieve attention factory still transform pay understanding cell to is or chassis on need TFs productivity there based only new high Although system not taped for stress-resistant [107]. by researchers chassis research traditional determined So, stress. the future the by as the mechanism, means. for showing well strain Truly necessary under metabolism as engineered function. be and strain TFs robust gene might growth the of of and a characterize study regulation genes been the target the objectively has affects to in to negatively binding effect intricacies TFs difficulty of the the of characteristics a redundancy to sometimes become functional due However, the has It then Besides, and them. it 106]. TFs, regulating circumstances, key [65, combinatorial meaningful specific effective more or changes very find determine adjusting can not proteomics, revealed These by is Transcriptomic, stress levels. tolerance to expression response strains engineering. genes yeast multiple improve TFs of and analysis of fluxes locus) metabolic application trait in (Quantitative the QTL underlying and challenges GC-MS, yeast. several engineering in ATFs- TFs directions are of various future. 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TF identified in been genes, network have of metabolic stress whole expression the the affecting of effect, regulator a As biosensors yeast. ATFs Conclusions to [105], as 5 mevalonate easy such a flavonoids, are Eukaryote acid, and monitoring biosensors in Itaconic ATF TF-based accurate creation as traditional achieved to of such Although avoided and lack bind molecules [104]. device small signaling, be populations screening detection Rho could cell in new or application mammalian that the signaling in OCRP device, MAPK signals site cAMP another reporter signaling, of operator and CRE calcium specific traditional cAMP of the intracellular interference CRP with the with single Compared combined a protein which contained promoter. ATF receptor part chimeric that contained cAMP reporter shown one of have a the Studies consisted as plasmids, cells vivo. two mammalian in into metabolites to structed biosensors respond device ATFs and from TFs, detection monitor native CRP cAMP of to ATF-based ranges strain orthogonal detection the narrow a in avoiding introduced and was sensitivity TFs system the of advantage in take 3-HP the of adjusting (LTTR), devel- tration regulator P the by transcriptional example, protein, LysR-type optimized For TF with and screening. consisted MmsR biosensors high-throughput interest (3-HP) in acid of potential 3-hydroxypropionic huge oped metabolites have evaluate biosensors were TF-based to devices Sometimes, synthetic elements. used modular functional are biology, of synthetic diversity they and of general, adaptability concept In design the by invented. drove development ATFs Upon evaluate inquantitatively expanded applicated have ATFs device Overall, ATFs-dependent pathways. [102]. 4.3 metabolic intensity switching modifying to for respective type act switch ATFs the for codons optimizing CP, of E.coli n P6tasciaindmi rmHre ipe iu.Ad hsto a con- was tool this And, virus. simplex Herpes from domain transactivation VP16 and suooa denitrificans Pseudomonas mmsA rmtradGPrpre eewr novdi h epneo h concen- the of response the in involved were gene reporter GFP and promoter hc oee iednmcrne(-0m)[0] To [103]. (0-100mM) range dynamic wide a covered which 8 Posted on Authorea 31 Oct 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.160413141.16511994/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. hc atr1 agtGenes. Target 1) Factor Shock 4 oas .SgodT,oz .BhrBe al., efficient B.et for B.,Bohar microorganisms T.,Hotzi of D.,Sigmond Kovacs, reprogramming and 14. mechanisms stresses. Resistance environmental C., multiple Li under yeast J., biorefinery Y.S.,Li rendering K.,Lee antioxidant the for Xu, on base 13. modifications yeast of and thermo-tolerance the mechanisms Improving al., system. in Z.et defense J.U.,Zhao Advances L.,Hassan K.,Gao al., Xu, 12. C.et H.,Li Y.,Sun L.,Liu thermotolerance. Gao, process. in fermentation changes bioethanol 11. metabolic the Intracellular during al., tolerance F.et ethanol 105046-105055. C.,Wang of Z.,Yi promotion Z.,Zheng and Chen, Improved for 10. Machinery Transcription Yeast Engineering Production. with al., and G.R.et Tolerance associated E.,Fink Ethanol stresses J.,Nevoigt H.,Moxley to Alper, responses 9. Yeast al., C.D.et J.P.,Powell handling. brewery S.J.,Leclaire industrial B.R.,Lawrence Gibson, encountered stresses 8. to tolerance concen- and response ethanol adaptive fermentation. yeast high ethanol the to of during mechanisms tolerant Molecular become C., Auesukaree, cells 7. yeast do How K., Voordeckers in K.J., trations? pathway T.,Verstrepen heterologous Snoek, multi-step a 6. of Integration al., F.et cerevisiae M.I.,David Saccharomyces P.G.,Vizcaino dicarboxylic M.,Teixeira to Otto, tolerance of 5. evolution laboratory Adaptive al., M.et in E.,Radi acids 64-74. Y.,Mohamed 3, R.,Wei 2020, of Pereira, engineering acids. 4. fatty Multidimensional medium-chain al., of R.et synthesis P.G.,Pereira efficient Y.,Teixeira Phosphate for Pentose Z.,Hu Ethanol the Zhu, of of Yeast. Roles in 3. Conditions Tolerance Critical Inhibitory Isobutanol-Specific al., in J.et to GLN3 Lopez Tolerance and Y.,Montano Pathway S.K.,Watanabe Yeast K.,Hammer Modifying Kuroda, J., 2. Nielsen T., Processes. L.,Castillo Production Caspeta, 1. References interest. 6 of conflict no declare (21808013) authors China The of Foundation Science Natural interest the of the Conflict by supported financially was work This networks products metabolic industrial in will advancement. of capacity it engineering improved biosynthesis Acknowledgement efforts, TFs TFs the of continuous native and research these from tolerance the With originated promotes strains ATF design Similarly, improving yeast. for in chassis. strategy engineered reconstruction tools achieves mainstream in genetic and a limitations advanced others the be as many avoid soon stress and to mutation, ability under random and networks evolution, power metabolic has laboratory networks including metabolic methods harnessed of engineering TFs conclusion, In species. by restrict acaoye cerevisiae Saccharomyces urGenet Curr hmclEgneigScience Engineering Chemical isiBioeng Biosci J 06 2 475-480. 62, 2016, rn iegBiotechnol Bioeng Front o h rdcino bcscacid. abscisic of production the for ESMcoilRev Microbiol FEMS isiBioeng Biosci J n o Sci Mol J Int . 06 2,599-606. 121, 2016, Science ea Eng Metab 06 1,1565-1568. 314, 2006, 07 2,133-142. 124, 2017, 09 0 5815. 20, 2019, 08 7,335-342. 175, 2018, 09 6 130-141. 56, 2019, 05 ,184. 3, 2015, 07 1 535-569. 31, 2007, yt ytBiotechnol Syst Synth HSF1 9 ae opeesv aaaeof Database Comprehensive A Base: irbCl Fact Cell Microb elSyst Cell 09 ,5457e535. 534-547 9, 2019, 09 ,92-98. 4, 2019, 09 8 205. 18, 2019, acaoye cerevisiae Saccharomyces acaoye cerevisiae Saccharomyces S Advances RSC HSF1 06 6, 2016, (Heat Posted on Authorea 31 Oct 2020 — The copyright holder is the author/funder. 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All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.160413141.16511994/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. 0.Dri .VjylkhiR,KrngrnD,Anvlrpre ytmfrcci M eitdgene mediated AMP cyclic system. for expression system transgene reporter synthetic novel on based A cells D., mammalian Karunagaran in R., expression L.,Vijayalakshmi Durai, Acid. 3-Hydroxypropionic 104. for Biosensor of Engineering Development Bioprocess for S., and system Park ogy J.-R., expression N.H.,Kim gene Nguyen, universal 103. A al., A.et J.,Korppoo C.P.,Kuivanen fungi. A.,Landowski Rantasalo, 102. Transcrip- in and Expression Promoters 63. Protein Synthetic 5, Heterologous 2017, K., Messerschmidt for B., Factors S.,Mueller-Roeber tion optimization F.,Balazadeh combinatorial Machens, rapid factors. transcription for 101. COMPASS artificial on B., based Mueller-Roeber pathways L., biochemical J.,Rieper of G.,Behrend Naseri, Yeast 100. the in Orthol- for Expression Factors Transcription Gene 1742-1756. Plant-Derived Circuit of al., Genetic I.et Regulation F.,Kamranfar Complex ogous S.,Machens for G.,Balazadeh Toolkit Naseri, Synthetic 99. al., acetic J.et in M.,Jantti involved in J.,Penttila Engineering genes A.,Kuivanen novel Rantasalo, of 98. identification of and tolerance factor acid randomized acetic transcription tolerance. of using artificial acid Improvement cells zinc-finger-based al., eukaryotic F.et a C.,Zhang of using X.,Sun alteration C.,Wei Phenotypic Ma, al., 97. Y.et factors. transcription H.,Lee with artificial D.K.,Lee coli of K.S.,Lee escherichia libraries in Park, butanol-tolerance Engineering 96. al., libraries. B.H.et factor S.A.,Sung transcription K.S.,Jang artificial J.Y.,Yang Lee, 95. sn oe rica rncito atr nEceihacoli. transcription Escherichia gene in reprogramming by factors engineering transcription Phenotypic artificial al., novel J.H.et regulation using B.J.,Lee gene B.H.,Yu in J.Y.,Sung applications Lee, practical 94. for development their and fingers manipulation. zinc genome of discovery and The eukaryotes. A., in Klug, factors 93. transcription synthetic of design Rule-based T.K., Biol Lu Synth J., factors. O.,Peccoud transcription Purcell, and 92. promoters synthetic plant Plant for Jr., 36-44. C.N., 37, factors Stewart 2016, transcription W., Targeting Liu, R., 91. Deshmukh paradigm. K.K., shifting J.,Tiwari tran- resistance: artificial A.,Purohit disease with Chattopadhyay, fate cell 90. Reprogramming A.Z., Ansari M.C., factors. A.,Spurgat scription E.A.,Eguchi genomics. Heiderscheit, functional and 89. therapeutics for tools as factors transcription Pharmacology Designed Biochemical E.J., Rebar F.D., Urnov, 88. thermomethanolica. Ogataea enabled yeast CRISPR-Cas9 methylotrophic Lett thermotolerant al., crobiol the L.et in S.,Eurwilaichitr mutagenesis A.,Wongwisansri targeted C.,Puseenam Phithakrotchanakoon, 87. 6 h,L,a .ZagH,un .ta. mrvmn fLa oeac of Tolerance Lead of Improvement Regulator al., Transcription of H.et Mutagenesis H.,Huang Random S.,Zhang by L.,Gao Zhu, 86. uli cd Res Acids Nucleic 04 ,737-744. 3, 2014, 08 365. 2018, acaoye cerevisiae Saccharomyces plMcoilBiotechnol Microbiol Appl ESLett FEBS 08 6 e111. 46, 2018, e Biophys Rev Q 02 4 919-923. 64, 2002, 08 9,888-900. 592, 2018, 09 4 109-118. 24, 2019, urn science Current itcnlBioeng Biotechnol . 05 9 2441-2449. 99, 2015, a Biotechnol Nat 00 3 1-21. 43, 2010, C yt Biol Synth ACS 14 SPT3 acaoye cerevisiae Saccharomyces 09 1,1598-1607. 117, 2019, acaoye cerevisiae Saccharomyces 01 0,742-749. 108, 2011, 03 1 1208-1214. 21, 2003, . 08 ,1573-1587. 7, 2018, plBohmBiotechnol Biochem Appl uli cd Res Acids Nucleic a Commun Nat . u Pharmacol J Eur 09 0 2615. 10, 2019, . 08 6 e102. 36, 2008, C yt Biol Synth ACS acaoye cerevisiae Saccharomyces acaoye cerevisiae Saccharomyces rn iegBiotechnol Bioeng Front urOi Biotechnol Opin Curr 08 8,155-167. 184, 2018, Biotechnol- ESMi- FEMS 09 855, 2019, 07 6, 2017, ACS Posted on Authorea 31 Oct 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.160413141.16511994/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. RR34 Source TaWRKY142 TaWRKY112 TaWRKY92 TaWRKY49 factor Transcription Plants in sheepgrass, applications from TFs factor stress. Heterogeneous drought transcription 1. under MYB-related Table growth A root al., and J.et germination X.,Jia seed factor S.,Guo promotes P.,Hou binding Zhao, C-repeat Arabidopsis 116. of expression L.). Heterologous melongena al., (Solanum X.et J.,Chen ( Y.,Li 3 F.,Pan cadmium reduce Wan, markgrafii Aegilops 115. from factors transcription wheat. NAC transgenic factor, al., M.et in transcription B.,Ren concentration F.,Zhu bZIP X.,He Arabidopsis. ABA-dependent Du, in 114. al., tolerance C.et freezing regulates H.,Ding negatively X.,Cao sinensis Camellia L.,Hao cinerea. Yao, Botrytis to 113. and Arabidopsis in DC3000 VqERFs tomato grapevine pv. 110421. wild syringae 293, Chinese Pseudomonas 2020, of to expression resistance Heterologous enhance Y., Wang thaliana W., L.,Liu Wang, Soybean 112. a of Expression Heterologous al., 494. N.C.et X.L.T.,Nguyen N.N.,Hoang in Gene D.H.T.,Chuong tolerance wheat stress Nghia, biotic of and 111. expression abiotic alters Heterologous strains S., necrosis Arabidopsis. hybrid Takumi transgenic in K., activated transcriptionally R.,Yoshida genes Y.,Ohno factor Kuki, 110. Stresses Industrial Multiple Relieves of (MDS) 572-582. Production System 5, Ethanol Defense 2020, Multilevel Boosting al., Economically X.Y.et W.X.,Wang for L.,Bai K.,Qin Xu, 109. enable microbes non-conventional biosynthesis. Stress-tolerant I., chemical Wheeldon next-generation functional J.W., C.,Chartron for S.,Schwartz mechanisms Thorwall, yeast. molecular 108. in the factors provide transcription modules among regulatory observed factor redundancy Transcription yeast. T.H., sugar in Yang, coordinates fermentation signaling 107. xylose cellular anaerobic Rewired for al., responses T.K.et hypoxic M.E.,Sato Strain and N.M.,MacGilvray High-Throughput K.S.,Riley for Myers, Review. Engineering 106. A Factor Transcription Bioproduction: Y.P., Acid Bai Organic H., and X.Y.,Wu Evolution J.W.,Zhang Li, 105. 56-64. AtCBF3 RR34 ofre mrvdDogtRssac fTasei Arabidopsis. Transgenic of Resistance Drought Improved Conferred n odrgltd1A( 15A cold-regulated and ) lcnmxIpoedrought Improve Heterologous Glycinemax Wheat ln hso Biochem Physiol Plant ln elRep Cell Plant ln n Soil and Plant a hmBiol Chem Nat AtCOR15A 04 3 1951-1961. 33, 2014, ehdVle References Values expression method Engineered 00 5,71-79. 150, 2020, 2020, 15 nacdciln oeac ntasei eggplant transgenic in tolerance chilling enhanced ) 00 6 113-121. 16, 2020, 449, rn iegBiotechnol Bioeng Front M Bioinformatics BMC 39–50. acaoye cerevisiae Saccharomyces LSGenet PLoS M ln Biol Plant BMC arabidopsis transgenic of resistance expression AtPR1 STZ/Zat10, promoted and tolerance stress osmotic and salinity Increased ln elRep Cell Plant 09 5 e1008037. 15, 2019, lns(Basel) Plants 00 ,98. 8, 2020, 09 0 630. 20, 2019, 09 9 564. 19, 2019, WRKY 00 9 553-565. 39, 2020, . CsbZIP18 c nryLett Energy Acs [111] [110] transcription 2020, LcMYB2 ln Sci Plant from , 9 (4), , Posted on Authorea 31 Oct 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.160413141.16511994/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. iin.We h tan xouet ctcai,Mtcodildsucinlast eraei ATP in inhibiting decrease of a function to complex Mks1-Bmh1/2p leads the dysfunction inhibit Mitochondrial to con- combined acid, normal are acetic in Rtg2p transmission to and concentration signals Mks1p exposure retrograde intracellular And, strains the maintaining content. the inhibits in and When nucleus role trans- to Fps1p ditions. important ATPase-dependent cyto- translocate stress, other an complexes to acid And Rtg1p play acetic and extracellular concentration. to with acid from seem cope acetic CH acid Pma1) To cellular of Pdr12, in acetic Rgc1p/Rgc2p. increases (Pdr10, the proteins to porters regulatory transports response with in which interact closed channel is can it aquaglyceroporin and the plasm, is Fps1p (1) stress other 2. Msn2/3p protein the leads ribosomal which Figure On expression Stress of genes (STREs) regulated phosphorylate. synthesis elements downstream genes. by the the response activate Msn2/3p homeostasis inhibits stress Hsf1p and of nucleus have protein turn activation the enters aggregate. in of the then which r-proteins influence and expression dephosphorylated, pathway r-proteins, orphan the Ras-PKA orphan the (3) new stimulate by in of activated genes. then resulting number also which match, The Ifh1p (2) not them, hand, genes do by synthesis. target rRNAs trehalose activated of and and expression is homeostasis smooth (RPs) enables protein proteins which (HSPs), prompter, ribosomal Med3p, protein of which Med2p, shock regions of promoters. protein, regulatory heat subunits the on component involving misfolded in Its recruit distribution weak. with chromatin can complex. to the is coactivation Med15p Hsp70p reconstructing Kinase) transcriptional and association conserved of and and a Tail, occupied the binding is Middle, II mediator which (Head, Pol by The mediators RNA Hsp70 released of recruiting amount nucleus to is the the binding increase into Hsf1p imported by temperature, and inhibited phosphorylates high then is to Hsf1p response circumstances, In normal Under (1) 1. Figure legends Figure Arabidopsis LcMYB2 AtCBF3 sinensis Camellia NAC2 Source CsbZIP18 VqERF072 VqERF114 VqERF112 factor Transcription 3 / COOH Aegilops 3 h oeua ehnsso es nelighg eprtr epneadthermotolerance and response temperature high underlying yeast of mechanisms molecular The eeeiu ffcso tao n ctcai nyatclsadclua dpiersos to response adaptive cellular and cells yeast on acid acetic and ethanol of effects Deleterious - /H + oesai.()HprhshrltdMspbnst m12,ihbtn h Rtg3p the inhibiting Bmh1/2p, to binds Mks1p Hyperphosphorylated (2) homeostasis. hegasIpoethe Improve Sheepgrass markgrafii quinquangularis Vitis Wild ehdVle References Values method Engineered 16 fplants of tolerance osmotic and drought grains and shoot root, the in concentration Cd Reduce bacteria pathogenic to Arabidopsis of resistance the Improve eggplant transgenic in tolerance cold Improve Arabidopsis in tolerance freezing regulates Negatively [116] [114] [112] [115] [113] Posted on Authorea 31 Oct 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.160413141.16511994/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. oeue n N-idn oan(B)cmie ihDA hc rvdsmr potnte to opportunities small more sensing provides for which (ED) DNA, domain with effector combined of content. consist (DBD) substance evaluating biosensors cognate domain quantitatively TF-based their DNA-binding (D) with and together (P ATF expression. molecules ex- (C) promoter genes gene heterologous synthetic productivity. the enhancing and and and regulate and tolerance gTME self-activity (CBS) promoting the (B) sites for to binding possibility contribute into system. a brought that provides defense level be structures transcription can stress multi-TF knockout maintain on in and based to especially overexpression pression substrate including networks, methods reducing metabolic modifying a reconstructing gene as conventional used The (A) be can It 4. proteins. Figure reductase. thiol-rich peroxidase. thioredoxin thioredoxin of with and together class thioredoxin redox a reductase, intracellular oxidizing to thioredoxin is with GSSG includes restore interact (TPX) to system antioxidant activity Thioredoxin NADPH thioredoxin reducing non-enzymatic and the reductase has the glutathione And, GSH Using of GSH. of (GSSG). (GSH) representative glutathione sulfydryl glutathione oxidized as The form reducing The to regard a system. chemicals (3) antioxidant as respectively used enzyme reductase. be be and thioredoxin can system system with It (TRX) together thioredoxin proteins. thioredoxin and thiol-rich redox reductase, of and reductase thioredoxin intracellular class includes maintain glutathione a system to is Using thioredoxin (TPX) substrate the (GSSG). Thioredoxin activity And, glutathione peroxidase. reducing GSH. thioredoxin has oxidized to and non- GSH GSSG form the of restore (3) of to sulfydryl to representative expression. chemicals The NADPH as genes oxidizing regard system. UPR antioxidant with respectively of (2) enzyme expression interact be Ire1p the and system Once nuclear. stimulate system (TRX) activity. to antioxidant from thioredoxin transcription cut enzymatic and is its and output (GSH) introns inhibit Ire1p YAP1 GSN, Hac1p glutathione will the stress, inhibit The which GSH, i.e., from ER introns regulators, can as upon contains transits two such from complex mRNA contains it releases Hac1p mainly gene Ybp1p-Gpx3p chemicals, pathway original responsive oxidizing signaling or The stress (UPR) by Hyr1p Hac1p. oxidative response caused And, protein of ROS unfolded expression on The GLR1. the not stimulate and or to dependent SOD2 nucleus is Yap1p to of cytoplasm activation in The Pbs2p (1) by stimulated is pathway 3. HOG Figure caused Finally, overexpressing destruction by stress. Pbs2p. activated membrane ethanol and is cell to Ssk2/22p regulator activated with response activates intermediate be deal phosphorelay sequentially will To it Cytoplasmic then acetate, is (4) Ole1p, regulate form which to toxicity. (3) to Ssk1p cell the anionic ethanol, nucleus in PYC1. by avoiding cell dissociated DLD3, thus acid the acetic IDH12, dephosphorylation, much entering by too IDH1, After complex as Rtg3p-Rtg1p acid. such acetic activated intracellular expression the genes in nuclear RTG-dependent resulting pathway, RTG the rncito atrEgneigue oipoesrisidsra au n raenwtools new create and value industrial strains improve to used Engineering Factor Transcription signals stress molecule Toxic and oxidant to reaction Functional Syn osrc notohmi eeepeso ytmto system expression gene orthorhombic an construct ) 17 HAA1 ssniieto sensitive is Posted on Authorea 31 Oct 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.160413141.16511994/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. 18 Posted on Authorea 31 Oct 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.160413141.16511994/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. 19