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Microbial Ecology

by: Kyler Ondricka

Microbial Ecology BIOL 6410

Kyler Ondricka

GPA 3.84

Samantha Parks

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About this Document

Samantha Parks
Class Notes
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This 0 page Class Notes was uploaded by Kyler Ondricka on Monday November 2, 2015. The Class Notes belongs to BIOL 6410 at Georgia Institute of Technology - Main Campus taught by Samantha Parks in Fall. Since its upload, it has received 25 views. For similar materials see /class/233991/biol-6410-georgia-institute-of-technology-main-campus in Biology at Georgia Institute of Technology - Main Campus.


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Date Created: 11/02/15
Microbes and transformation degradation Why microbially mediated processes Toxicity a All synthesized O orgamccompounds handle chemicals Varied metabolism Biosorption Biodcgl39adation data organic compounds All lheorelically possible organic compounds 1018 10200 Biotransformation Biodegradation Biomineralization Modified from Wackett Why so many compounds Coordination Symbiosis Defense Antibiotics Toxins Microbial Metabolic Diversity Diverse metabolic pathways allow bacteria to degrade both natural and 1 R 39 f Synthetlc compounds ecru1tmento genes from preestablished pathways Microbes are very good at responding to the challenge of a 2 Evolution of gene new compound properties to bene t metabolism Tremendous undertaking to H identify diverse and novel enzymes 239 EVOMO Of regulat1onorgan1zatlon Pathway predICtion genespathways Functional annotation Abundance of aromatic on Ammzrwammn and megmms mama awedomm o Qm nwe w mlya megwm mama r immethMetibu es mm Fuchset 52011 Aromatic degradation oar o Not very reactive Activate ring with oxygen Successive monooxvgenation Dioxvgena ion Form catechols gentisate homogentisate or protorcatechuates for further i n degradat o Ring rearrangement with epoxidat Useful with low uctuating oz leve Fumarate addition anaerobic toiuene degradation Oxygenrindependent hydroxyiation anaerobic ethyibenzene degradation denitrifyers u i u i ion benzoate phenyiacetates IS F 1 39h no biochem evidence Few central pathways for degradation Many substra es Deai separateiy with shared ring and varied side chains Fuchset 52011 H3 V V xquot H 7 Plants 5439 D i H M quotf 7quot quotIii 3 NC NlH lIydmxy J nJLmpheuyljethyl 0 3 11ltm 4 l1ydrmyplmnelhylamina 3 melhyl butanmnide mu f ML U rquot PIN f HO r rm 11 1 J a 0 1 T a quot0 quot 1 I4hydmxy3nitmphenyl WK J I acetic acid 11 U l39l ester Phldolnpm 4hydrmyJmtmbemmc and 39 o Bryozoa Bacterla M O Am DA 7 cm L m x w x x V4 x on W a k v N 0W f I 0H J r Y Pyriculaunid D M Fungl 4 ydmxy 3nitrubenzampneacelit acid HD fl Jun s mquot no f T 1 V OH SNitmtyro ne N ZMl lydaxyBniuopl39lenyljethyl fl muIhylprc39xpzummj EEC D O 03 quot xquot m GEN t fa f H f 1 Dr H N aquot hJK 0H m if HQ 1 r ZlnydmxyB 4hydmxy3nilrophenyl 4 hydra Humphmyn quota r39I quot 5 0H d I 1 I pn ap1umc and 4 Eyckmylrmmphenetlmylulccatml 39Fmpmmquot 4 me 1339 I 4Hydrox ulammbenzyl ulcuhnl HQ 0 DIMEquot ffax MO 0 Qxbt39 In1 l INC I A E KH f HY J f KNC 339 139 DH 0 xx 31 mm 4 4 mlmclhmyllplwnul Sluitmgenislejn 11M NZHhy dru iyEl mm nitmpl nenymethleucetamidu Unifying pathways 0 Funnels for central metabolism unique periphery pathways or enzymes Centrallower pathways for generalized intermediates Acetyl CoA SuccinylCoA Pyruvate Benzyl CoA most common for anaerobic degradation pathways 8 E 6 2 Emug 232 A Imam 33 5015 SEE qu 333 Eu i m 3 ti m k 9 335310 fx 333m 20 m 53 ME W 330 0 x z U boo m o amusing 331555 n rOOMUJ Ema A IU E SHEEP forquot 35 wumc cegmwlt Emu bum w O fo ga m f m 1124 E ci i1 boo n 0 98 L80 gg agan d i HBEEiO a N a KM i E f mgwgiznv 08 ay um mama we Mum T a Y on 0H Cxxml CI v f1 Vega Liz my 1 W mm muznm My mm D mumde quotm mama Gmnxy39 mm gmmama 1 up 1 9 Hcon chn a D 4o pm K v muckyk mm we smmm w W mam mm o BkemadwylCDA 8 sum Q 3 9 E as MuyicoA ortho meta para Fuchs er 12011 Phylogeny of Rieske nonheme iron oxygenases ZChlomllcnmaln NAPHTHALENE S Ilicvlm BENZOATE Nuphllmlenc l llenamhrenc uHal the 10 e TriclIlornphennxyacelale lsupmpylhenzome Anlhmnilale Phenamhrcne Naphtlmlen a I mhydmahietic acid Carlmznle Ox0 12 dihydrmuinolin Dihenzodioxiu L Carbuzule Bipheuyl 1 3l henyll7mpiunzlle 3Chkrohenmate PHTHALATE Plnhulale Aniline l llenoxybenwnte TOLUENEBIPHENBYL Vanillntc pTnluenc sulfonale LP Wockett Enzyme and Microbial Technology 31 2002 577 587 Epoxidation strategies 3 IE J VIM Ha I rx gt 40 Fuchs et 02011 Oxygenindependent reactions aamucb mm Reduce the ring Water free systems enzyme pockets Couple ring reduction to ATP hydrolysis Akin to sodium as reducing agent Birch reduction Alternating electron transfer and protonation steps Typically forms cyclhexael rdienes Dearomatizing reductases ATPdependent facultative anaerobes ATPindependent obligate anaerobes fermenters Electron bifurcation Fuchs at 122011 Fuchset 52011 womb Emy bemenz Strategies for degradation of nitro aromatic compounds R R Ill HydrideIleisenheimer IV Reduction Io Formation Amine 24 Dinitrophlnol 245 T nnrophonol HO N02 NH T i R NH R 02 R E R R J R L H i I 2 A J H no N 02 H OH OH N93 N20 N OH OH ll Dioxygenau39un log H i V Hydroxylamlno Nitmbonunc lyase 2Niuoiotuano Hquot M 24mnmmlum R R mnbu 26Odnlu oznlmno awnmphmol 3Nilrobonzoall 1 3Dinitrobnnnnl 260iniU39ophnnol VIA Mum 0 H0 Nth NIU39DbII39IlInI NH 3Nitmphanol A limmzlgenauon 2Chioro5n39mophmnl Humphmol NO LChIoronikoblnuno i 4Chloro2nmophcnnl R R dNltrnanlsoh OHC HOD Different key strategies benefit per climate Table 1 DiHront trlitwgio fur thl dogrndll un of Iramath compauntie Strater Dzdependent ring cleavage of dihydrox y39lated aromatic compounds Elldependent ring epnxidation elf CoA thieesters ATPdependent ring reduction 0f CUA thices ers ATPindependent ring reduction cf CoA thioes ers Conditions Ox Oxic but with uctuating or low Clz concentrations Anoxic diuring anaerobic respiraticrn with a high v39i39LTF yield in facultetive anaerobea and during annxygeinic photosynthesis Anoxic diuring anaembic reapiratian with a luwATF yield in etriczt anaerubes and during femamnion Key enzymes Ringcleaving dimygenazes Ring epaxidases of the diiron protein family A39I39Fdepenclent benznyl CQA reductaae ATPindependent benznylCGA raductese Fuchs et a 2011


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