Prideapplication/xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/08/PXD010607/SearchEngineResultsStreptomycesspM7.xlsxftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/08/PXD010607/Glucose04_StreptomycesM7.7zftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/08/PXD010607/Glucose05_Streptomyces_M7.7zftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/08/PXD010607/Lindane02_StreptomycesM7.7zftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/08/PXD010607/Glucose05StreptomycesM7.7zftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/08/PXD010607/Glucose06_Streptomyces_M7.7zftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/08/PXD010607/Lindane01StreptomycesM7.7zftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/08/PXD010607/Lindane02StreptomycesM7.7zftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/08/PXD010607/Glucose04StreptomycesM7.7zftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/08/PXD010607/Lindane03_StreptomycesM7.7zftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/08/PXD010607/Glucose06StreptomycesM7.7zftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/08/PXD010607/AminoacidssequenceStreptomycesM7.faaftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/08/PXD010607/Lindane03StreptomycesM7.7zftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/08/PXD010607/Lindane01_StreptomycesM7.7zprimaryOK200002100jsdavilacosta@gmail.comJose Davila CostaMass SpectrometryShotgun proteomicsNot availableDegradationLindaneStreptomyces sp. m7http://www.ebi.ac.uk/pride/archive/projects/PXD010607Protein extracts for label-free quantitative proteomic analysis. Cells were washed with washing buffer (25 mM Tris buffer pH 7, 2 mM EDTA), resuspended in the same buffer and crushed with liquid nitrogen. After centrifugation (16,100 g, 30 min, 4 °C) concentration of proteins was measured and 50 µg of proteins were treated with 20 µl of reducing solution (200 mM DTT, 100 mM Tris, pH 7.8) and alkylation solution (200 mM iodoacetamide, 100 mM Tris, pH 7.8). Samples were incubated 1 h at RT with each solution and proteins were then precipitated with TCA 10%. After centrifugation (16,100 g, 30 min, 4 °C), protein pellet was washed three times by rinsing with pre-chilled (-20 °C) acetone. Protein pellet was then resuspended with 50 mM ammonium bicarbonate up to a concentration of 10 µg µl-1 and 50 µg of proteins were digested with trypsin. Finally, digested proteins were purified with a Zip-Tip C18 column stored at -80 °C until subjected to MS analysis. LC-MS/MS analysis of protein extracts. Samples were dissolved in trifluoroacetic acid and LC of the peptide samples were performed using a Thermo Scientific-EASY-nLC 1000 equipped with an Easy-Spray Column PepMap RSLC (C18, 2 µm, 100A, 50 µm x 150 mm). A gradient with two solutions was used (Solution A, 0.1% formic acid (v/v); Solution B, ACN with 0.1% formic acid). Peptides were eluted with a gradient of 7% B to 95% B over 135 min at flow rate of 0.300 µl min-1. Mass spectra were obtained by a Q-Exactive Orbitrap instrument (Thermo Fisher Scientific). Instrument configuration allowed the identification of peptides to be carried out at the same time that they were separated by chromatography, obtaining Full MS and MS/MS. The 20 most intense peaks in each MS spectrum were selected for MS/MS fragmentation. LC-MS/MS of protein extract was performed in CEQUIBIEM-University of Buenos Aires-Argentina.PrideNot availablecarbamoylated residueData analysis – protein quantification. Data analysis was performed using the softwares Proteome Discoverer 2.1 and Perseus. Samples obtained from Lindane were compared to the corresponding Glucose samples. Protein database of Streptomyces sp. M7 was used for peptide identification. Proteins were considered significantly regulated when: (1) they showed on average an increase ˃2-fold in their abundance; (2) t-test showed a ρ-value below 0.05. ρ-value and statistical parameters were calculated by Perseus software. To estimate the limit of detection of our instrument on the protein level, we considered the ninety-ninth percentile of the area of all proteins identified by Proteome Discoverer passing the identification score threshold with a false discovery rate of 0.01. This value was 590898. We then used this value to impute missing area values in our label-free quantitation.ProteomicsJose Sebastian Davila CostaQ ExactiveActinobacteria Laboratory, PROIMI-CONICET, Tucuman-ArgentinaPARTIALStreptomyces Coelicolor A3(2)jsdavilacosta@gmail.comNot availableBiologicalPROIMI-CONICETArgentinaliquid chromatography tandem mass spectroscopy, sodium salt, Nup32D, CPD photolyase activity, ammonium formate, PLIP, 13C-labeled, cadmium salt, PhrB photolyase activity, MHC, determination, GPATCH6, Ethylenediaminetetraacetic acid, instrument configuration, zinc formate, lead salt, protein, magnesium formate, pigmented epithelium, zinc salt, Type 2A-interacting protein, (ethylenedinitrilo)tetraacetic acid, Long Term, Alkylations, 2-Propanone, Myo, Trifluoroacetate, peptide, Polypeptides, protein polypeptide chains, ammonium tetraformate, ClvPrd, peptido, BANF, cobalt(II) formate dihydrate, dJ69E11.3, B1, 2, Min, 3, 2', NUP96, outer pigmented layer of retina, protein aggregate, epithelium, Effect, WMS, DmelCG42273, HTATIP, Edetic acid, nup154, 2-diyldinitrilo)tetraacetate, DmelCG3533, Divorced, LCMSMS, C79325, ion(4-), peptides, Myo2, N, 2610036I19Rik, 2610510L13Rik, pigmented retina, min, HardwareType, mAPC, DROMHC, proteins, Divorces, copper, free, DNA cyclobutane dipyrimidine photolyase activity, SUPPRESSOR OF AUXIN RESISTANCE 3, AI047805, NMMII, fSAP152, pigment epithelium of retina, lithium salt, cPLA2, column, ACN, D1, trifluoro-, Acn, NMM, pigmented retina epithelium, (ethane-1, GPHYSD2, TIP, ammonium (2:1) salt, Long-Term Effects, Myo II, acidum edeticum, nickel salt, SGS, LC-MS2, PRE, ethylenediaminetetraacetate, cobalt (+2) salt, ZC2HC5, deoxyribonucleic cyclobutane dipyrimidine photolyase activity, LC-MS/MS, 2'', Dmel_CG7826, Longterm Effect, Mhc-c[1], {[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL]-CARBOXYMETHYL-AMINO}-ACETIC ACID, HTATIP1, pigmented retinal epithelium, tip, myoII, ANAC091, Thermo Scientific, ACMICD, Putative MAPK-activating protein PM10, sodium (4:1:1) salt, Stickstoff, Dm1, retinal pigment, magnesium salt, dipyrimidine photolyase (photosensitive), University, TIP60, nickel (+2) salt, retinal pigment layer, Dmel_CG7835, Acetic acid, Mnb, MNB, DLK, Acid, ammonium salt, instrument, retinal pigmented epithelium, Trifluoroacetic, formate, cobaltous formate, cromium (+3), MASS, N'-1, AW124434, beta Trypsin, KIAA1847, Argentina <bony fishes>., phr A photolyase activity, Osi, nitrogen, DNA-photoreactivating enzyme, Cesium, Acetamide, liquid chromatography-tandem mass spectroscopy, copper salt, ammonium (4:1) salt, CG3533, Polypeptide, MyoII, 7N, tlp, lead (+2) salt, TIP41, time, ZIP, Zip, nickel formate dihydrate, lead formate, Effects, aluminum salt, cesium salt, number, FBN, Gene, Myo-II HC, ethylenediaminetetraacetic acid, ACINUS, photoreactivating enzyme activity, protein-containing complex, presence, EDTA tetraanion, CG7826, deoxyribodipyrimidine photolyase activity, ESA1, stratum pigmentosum retinae, LC-MS-MS, hardware, Buffer, zip, formic acid, period, potassium salt, Dm nmII, polypeptide chain, ECTOL1, 14C-labeled, Acide ethylenediaminetetracetique, Arabidopsis NAC domain containing protein 91, LC-MSMS, CG7835, Gene Products, CG42273, zk, stratum pigmentosa retinae, Separated, acide edetique, CG15792, ZIPK, Cesium Trifluoroacetate, l(2)10432, MOS3, 2'''-(ethane-1, deoxyribocyclobutadipyrimidine pyrimidine-lyase activity, 2-Ethane diylbis-(N-(carboxymethyl)glycine), ZC3HDC9, PRECOCIOUS, Acinus, Myo-II, thallium (+1) salt, Longterm, ethylenediamine tetraacetic acid tetraanion, zip/MyoII, beta-Trypsin, rubidium salt, F23A5.3, Long-Term, calcium formate, methanoic acid, Solution, acinusL, OCTD, edta, 2-diyldinitrilo)tetraacetic acid, DmelCG4579, ms(2)zk, acinusS, EDTA, peptidos, liquid, cromium (+3) salt, Long-Term Effect, DmnmII, l(2)01501, ZIP3, Chromatographies, 2-iodo-, F23A5_3, sodium formate, PTHB1, l(2)02957, GPATC6, DYRK1, ZC3H9, nickel formate, protein complex, BcDNA:LD21772, Proteins, strontium formate, E(br), potassium formate, copper (+2) salt, strontium salt, buffer, Cell, Peptide, mKIAA0670, acido edetico, polypeptide, count in organism, stratum pigmentosum (retina), MODIFIER OF SNC1, LC/MS/MS, native protein, natural protein, nmMHC, C18, cupric formate, Protein, chemical analysis, Long Term Effects, proteomic analysis, deoxyribonucleic photolyase activity, Mhc-c, MFS1, Dyrk1, aluminum formate, WMS2, DmelCG15792, nzip, AU020952, Separation, nup32D, RPE, lithium formate, photolyase activity, Separations, CC1, H4edta, Tripcellim, CG4579, azote, retinal pigment epithelium, chromic formate, Longterm Effects, nitrogeno, ME-IV, p. pigmentosa retinae, Protein Gene Products, Gene Proteins, Trypure, concentration, SSKS, TCV-interacting protein, calcium salt, Dronm-MII, anon-WO0140519.37, liquid chromatography tandem mass spectrometry, Peptid, edetic acid, deoxyribonucleate pyrimidine dimer lyase (photosensitive), assay, quantitative, SCH, zpr, nmy-2, presence or absence in organism, ethylenediaminetetraacetate tetraaniongluco-hexose, Glucose, False, Ass-1, Glukose, instrument configuration, Monohydrate, Gene, protein, (DL)-Isomer, Computer, protein-containing complex, peptide, Polypeptides, protein polypeptide chains, ClvPrd, peptido, polypeptide chain, AA408052, Dextrose, Gene Products, fold, Software Engineering, Analysis, protein aggregate, Computer Program, Application, Normalities, average, Open Source Softwares, proportion, F, peptides, Analyses, Software Application, Open, Open Source Software, Computer Programs and Programming, proteins, DL-glucose, Computer Software Application, ASS, glucose, Tools, peptidos, Anhydrous, ratio, Applications Software, Open Source, Detection Limits, Computer Software, (beta-D)-Isomer, protein complex, Proteins, free., Normalcy, Peptide, Source Softwares, Software Tools, Tool, Programs, polypeptide, Program, Computer Applications, Software Tool, native protein, natural protein, Protein, Computer Applications Software, Computer Applications Softwares, Detection Limit, Softwares, (alpha-D)-Isomer, Software, Data Base, D-Glucose, Software Applications, instrument, Normality, Source Software, Engineering, proportionality, rate, Anhydrous Dextrose, Protein Gene Products, Computer Programs, Gene Proteins, Applications, Health, Applications Softwares, Data, D Glucose, Limits of Detection, quotient, Peptid, Polypeptide, Glucose Monohydrate, Data Analyses, Glc, Computer Software Applicationsprojections, multicellular organismal catabolic process, single-organism catabolic process, Forms, anatomical protrusion, "Microstreptospora" Yan et al., degradation, Actinobacteriota, lamellae, anatomical process, Proteins, number, lamina, flanges, Gene, organ process., presence, process of organ, results, Culture, Kitasatoa Matsumae and Hata 1968 (Approved Lists 1980), SDR18C1, biomineral formation, actinobacteria, protrusion, lamella, count in organism, Actinosporangium Krasil'nikov and Yuan 1961, Actinopycnidium Krasil'nikov 1962, Media, Streptoverticillium Baldacci 1958, Elytrosporangium Falcao de Morais et al. 1966, Protein, DECR, shelf, Gene Products, pseudoplasmodial stream, mineralization, Chainia, flange, NADPH, study, Actinobacteraeota, breakdown, catabolism, High G+C Gram-Positive Bacteria, shelves, Nadph, 1200012F07Rik, proteins, ridges, Actinobacteria, projection, free, ridge, Protein Gene Products, Gene Proteins, processes, process, Actinomycete, spine, Gram-Positive Bacteria, papilla, High G+C, Decr, processus, quantitative, mineralisation, laminae, Actinomycetes, biomineralisation, presence or absence in organismMedia, Culture.2100trueStreptomyces sp. M7 LC-MS - Streptomyces sp. M7 has demonstrated ability to remove lindane from culture media and soilsStreptomyces sp. M7 has demonstrated ability to remove lindane from culture media and soils. In this study, we used MS-based label-free quantitative proteomic to understand lindane degradation and its metabolic context in Streptomyces sp. M7. We identified the proteins involved in the up-stream degradation pathway. Our results demonstrated that mineralization of lindane is feasible since proteins from an unusual down-stream degradation pathway were also identified. Degradative steps were supported by an active catabolism that supplied energy and reducing equivalents in the form of NADPH. This is the first study in which degradation steps of an organochlorine compound and metabolic context are elucidate in a biotechnological genus as Streptomyces. These results serve as basement to study other degradative actinobacteria and to improve the degradation processes of Streptomyces sp. M7.2018-08-102018-07-30PXD0106072806551646099180498511145422492156843544071284218327042363336351198343006636362758385696363121766668888111430155571145263145262364934613126957366649239161936413645106656889511363647627236611123294422295558326813042323122586365434607925193659106321432059712938655819125023254537111957748186619682158672256807617554373592536685862740816918045427877512010892250583674147956410039236942049433445974142001258641935293NCBITaxon:77643671567593643867716054048313152826930456271639162429204277944762376369612181003296292211376394863948840479NCBITaxon:215713152731051067125027820596875497792016516368407173630969893610478214836432042929410106132049138169374327732046640707453511110310780621745921612928867128867641006945694101676341021076127735113165821358430141729817463367541287356756840301350621813019411192943936711041136445913949843202530127032022149875110475941204788613474951537211097165299827905135551398031758543980126086639808137575551832019644719821118503114155421932555211383439119318198139818102697026635311069955529NCBITaxon:47518502983354764146547798251021691572739823897648407413735186287054824153NCBITaxon:50557984467525100036433414754802103597413708115466547812159149835322159983810677103481985234878042253148841422286322663479461571871259399159919157295292921175271986014884063342495186912342352381523359858985988655974649987039202111072639903635272159874190828743942324182350241451139692931902593907190174636012374746361722625360013197221191585310588596989511051989972379897720002634196102642667227588581568996287375626907244202371720199985707240747679274596153335543193118734961671833554184005136861505968666211961748666134751536329NCBITaxon:17632862871103411033348837670580271848186536859598607575527472036105135294296110098402321000734882412336363071047005187878945556449447NCBITaxon:13356262664955419591399878168119011478281055524NCBITaxon:96063181781358584690081366848197915351930728593008526411409005118499526225412133759139014381113944235084370416744312044143708351581990119519532590841370137023943222774862615835583715371633376057267998086371137121906503714759172073127262981274575727090309031637910372814243371421044792491108239412NCBITaxon:96156588581478026926610065813735275045413566381647520375064422366950212934979054632245552536519976499081438992374537472647323760264731288705595536141691525274032716029385114978647943637552938247943722511775299120447416738721750919384413765939343473932715910022637674234442345467001287689591198467041464792936528034280382803510803483307791793921126212295027113118037386819112652699710286225273910760159736114324250711409810871355477436581424507229533796982042321242233218033698221300803470816457331858897165467599287770203829314125295508114817448886437452649997283035718308550717629970767892683704151562887651388563924561152932020865955516551811354914321371597495350261432138587817076831949634016142800531646862751104660381518454744850097476974771180512401748418556015554792042743815135535201488711053253297261005941289093164351211604990013894382835423242331082934122058560416299131122731701879915429131267818187104931640729946714423683033373304852646383011306413992530642369923121162065261610337286129940207340115357652611114716133865431201725323712552329935316317NCBITaxon:11084993841063267872862321933486208621160791392227681196125522814953932132232334774121827532917573129948861814084341033519963139248913924881153381153393304393755699286265599339112094886241571839975864442374864353324442606653324134390976821271786371979856863999839986865535291486541042986357358257632884019864982380111911028688999586652203411508599632138119380625631886571303443112130886581144889198466645463NCBITaxon:11072NCBITaxon:11071142800628835374375116597145943116598854331116781077854314408043933434NCBITaxon:11082693977381382189931824431935128387145953116885311213278695berry8694100333586972443664701501114286921504751499105484204714722354025120847014649744497431170089306218644193061107632330805660396016217974825853946055396513212790568813377512981766378876017112147861050236694657349632051124501897441739412450128853183889198679488531911137910371647351660152943631631198573896939343237956026087121346334323223544314275241433611334565560291699636436802790105603140818838185733703401881274414936530437552196969716203871398558408172405598609183827275921274423408170275981274420127442623545513656531762793821176275943286303902474801199150956481882291690255120455148167238473848190695148498101510693731263753405203860186497405224052141856451804NCBITaxon:813478009152275484793870333849387191722617561094616143512032581205505235259447320549386411257226512165125388037668612067811220223074322011867051186705738733486938070312193879186802398007186801215451468351408186150847120677769183885160861138886915216778672127901008704351231719692812392948677133154845422612621981318826824112292657163295769381247124614854513283883483929491139036312041626658907715148800369426941694369451879010150808170539420654210556873174471270153292428141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