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Authors: Aureliano Bombarely, Boyce Thompson Institute LycoCyc: Solanum lycopersicum Cellular Overview Lukas Mueller, Boyce Thompson Institute a xenobiotic a xenobiotic a xenobiotic a xenobiotic + a xenobiotic a xenobiotic H phosphonate 2+ an a xenobiotic a xenobiotic ABC a xenobiotic a xenobiotic a xenobiotic ABC a xenobiotic Cd a xenobiotic a xenobiotic a xenobiotic ABC a xenobiotic ABC a xenobiotic a xenobiotic a xenobiotic oligopeptide a xenobiotic a xenobiotic Cd 2+ a xenobiotic sucrose a xenobiotic transporter transporter transporter transporter sucrose H + a xenobiotic a xenobiotic C family C family C family C family a xenobiotic a xenobiotic ABC a xenobiotic a xenobiotic a xenobiotic a xenobiotic a xenobiotic Macrolide ABC a xenobiotic sucrose H(+)-ATPase H + member 4/ member 8/ a xenobiotic member 10/ member 10/ Cu 2+ H + transporter ABC export ATP- ABC transporter 4//H(\+)- ABC /Multidrug ABC ABC ABC /Multidrug ABC Cadmium- ABC ABC ABC /Multidrug ABC /Multidrug ABC ABC ABC Sucrose C family transporter ABC binding/ transporter B family Sucrose transporting transporter ABC resistance transporter transporter transporter resistance transporter transporting Cadmium/zinc- ABC transporter transporter transporter resistance transporter resistance transporter transporter transporter transport ABC transporter member 2/ I family transporter permease B family member transport Sucrose ATP synthase atpase plant/ MATE efflux ABC C family transporter protein ABC C family C family C family protein ABC C family ATPase// transporting transporter C family B family C family protein ABC C family protein ABC C family ABC C family C family protein ABC C family member /Multidrug ABC ABC ABC member 11, ABC ABC family protein/ protein member 9//Lipid A ABC protein// transport epsilon chain, fungi plasma ATP synthase family protein/ transporter member 12/ B family transporter member 10/ member 10/ member 8/ transporter member 10/ Probable ATPase 3// G family member 10/ member ABC member 14/ transporter member 3/ transporter member 3/ transporter member 12/ member 10/ Copper SUC3// ATP synthase transporter 12//Cystic fibrosis resistance transporter transporter transporter chloroplastic// transporter transporter /Lipid A MacB//RNA- 19//ABC export ATP- transporter Sucrose protein mitochondrial// membrane subunit beta /multidrug C family /Multidrug member 1// family// /Multidrug /Multidrug /Multidrug family// /multidrug cadmium/zinc- Potassium- member 14// /Multidrug 15//Lipid A transporter /Multidrug family// /multidrug family// /Multidrug C family /Multidrug /multidrug transporting sucrose subunit beta C family transmembrane ABC C family C family B family Cobalt import C family C family export ATP- directed DNA transporter- binding/ B family transporter/ SUC4// ATP synthase type, putative/ chloroplastic resistance member 14/ resistance ATP binding multidrug resistance resistance resistance multidrug resistance transporting transporting ABC-2 type resistance export ATP- family protein resistance multidrug resistance multidrug resistance member 12/ resistance resistance ATPase 2 transporter member 9 conductance transporter member 9 member 5 member 6 ATP-binding member 14 member 14 binding/ polymerase like protein// permease member 2 /sucrose- sucrose epsilon subunit 1 /Plasma pump, putative /ATMRP10 protein ABC cassette resistance- protein ABC protein ABC protein ABC resistance- protein ABC ATPase ATPase transporter protein ABC binding/ protein ABC resistance- protein ABC resistance- protein ABC /ATMRP13 protein ABC protein ABC 2//sucrose regulator ATP- protein CbiO 2/ permease (reverse ATP binding protein proton transporter membrane transporter subfamily B1 associated transporter transporter transporter associated transporter HMA1, B chain family protein transporter permease transporter associated transporter associated transporter transporter transporter transporter- H + binding and /non-intrinsic protein msbA transcriptase) cassette msbA//MDR- symporter 2 ATPase 2 H + family protein 2, family family family protein 1, family chloroplastic family protein msbA a xenobiotic family protein 1, family protein 1, family family family Cu 2+ like protein a xenobiotic permease a xenobiotic a xenobiotic a xenobiotic ABC protein 14 a xenobiotic a xenobiotic -related subfamily B19 like ABC a xenobiotic H + (Fragment) a xenobiotic a xenobiotic 6 (mrp2, 3 (mrp1, 3 (mrp1, 3 (mrp1, a xenobiotic a xenobiotic protein family protein transporter sucrose-6- a xenobiotic 6), abc- 3), abc- Cd 2+ a xenobiotic 3), abc- 3), abc- transoprter, transoprter, 2+ a xenobiotic transoprter, transoprter, sucrose-6- phosphate a xenobiotic a xenobiotic a xenobiotic a xenobiotic a xenobiotic Cd a xenobiotic a xenobiotic a xenobiotic a xenobiotic a xenobiotic a xenobiotic a xenobiotic sucrose-6- putative putative a xenobiotic putative putative phosphate H + an phosphate a xenobiotic oligopeptide a xenobiotic phosphonate AMINO ACIDS DEGRADATION FATTY ACID AND LIPID BIOSYNTHESIS AROMATIC COMPOUNDS DEGRADATION a xenobiotic a xenobiotic a xenobiotic a xenobiotic xyloglucan SECONDARY METABOLITES BIOSYNTHESIS valine degradation I dCMP dCMP β dTDP α a monocarboxylic a [protein]- uridine all-t actinorhodin biosynthesis methylthiopropionate chlorogenic acid biosynthesis I α-amyrin lipid-independent phytate biosynthesis cinnamate esters apigenin glycosides biosynthesis phenylpropanoid betaxanthin β-carotene avenacin biosynthesis superpathway of fatty acid biosynthesis II (plant) superpathway of glycolysis, pyruvate GLYCOLYSIS lysine degradation II leucine methionine degradation isoleucine phenylalanine degradation III L-cysteine superpathway of purines degradation in plants -D-glucose lactose oligosaccharide oxalate an aryl aldehyde m7G(5')pppAm -glucan a phenyl acetate hypoglycin biosynthesis sanguinarine and simple coumarins biosynthesis superpathway of lipid-dependent phytate biosynthesis superpathway of anthocyanin biosynthesis (from delphinidin 3-O-glucoside) calystegine canavanine biosynthesis antheraxanthin and flavonoid biosynthesis chlorogenic acid biosynthesis II hyperforin biosynthesis geraniol methylquercetin biosynthesis volatile cinnamoic ester biosynthesis cholesterol biosynthesis sphingomyelin metabolism stearate biosynthesis cis-vaccenate triacylglycerol biosynthesis ACETYL-COA BIOSYNTHESIS leucine degradation I threonine acid amide L-histidine dip biosynthesis biosynthesis biosynthesis biosynthesis, biosynthesis biosynthesis phospholipid biosynthesis II dehydrogenase, TCA, and glyoxylate bypass degradation III I (to homocysteine) degradation II degradation II Deoxycytidylate Uridylate kinase: Nucleoside macarpine biosynthesis biosynthesis violaxanthin biosynthesis and geranial III (via desmosterol) I (animals) biosynthesis glycolysis III degradation III uridine cytidine malonyl-CoA β-D-glucose- delphinidin-3-O initial reactions (via dopamine) (S)-2,3- deaminase: Solyc08g077300.2 Beta-galactosidase: diphosphate kinase: oxalate oxidase: aldehyde oxidase: mRNAadenosine glucan water amidase: Histidine kinase: arylesterase: D-myo-inositol D-myo-inositol 1 3,7-di- acetyl-CoA β L-valine (to methylglyoxal) xylose isomerase: Alpha-xylosidase: kinase I, putative: 4-coumarate 1,2-dihydroxy-3-keto- 4-coumaroyl-CoA (S)-2,3- N-methyl-∆ - 4-coumarate 4-coumaroyl-CoA H + biosynthesis apigenin dihydroxyacetone sn-glycerol- -D-glucose- superpathway of acetyl-CoA biosynthesis L-lysine Solyc03g093750.1 Solyc11g068600.1 dikinase: Solyc12g039070.1 L-threonine (S)-reticuline 6-phosphate (1,3,4)-trisphosphate (1,4,5)-trisphosphate -β-D-glucoside homoserine zeaxanthin trans-cinnamate a quercetin trans-cinnamate methylcinnamate trans-lycopene epoxysqualene all-trans-farnesyl a ceramide palmitate L-leucine L-leucine L-methionine L-isoleucine L-phenylalanine adenosine- Solyc03g111350.2 [+ 2 isozymes] Solyc07g006650.2 Solyc12g049370.1 Solyc04g007160.1 Solyc01g088210.2 methylase: Solyc03g118690.2 Solyc12g099670.1 Solyc10g005880.2 5-methylthiopentene epoxysqualene Inositol-3-phosphate pyrrolinium cation methylquercetagetin phosphate a palmitoleoyl-[acp] 3-phosphate 6-phosphate β-D-glucose L-cysteine [+ 3 isozymes] [+ 14 isozymes] Solyc05g005020.2 [+ 16 isozymes] geranyl-diphosphate L-phenylalanine L-dopa Acetyl-coenzyme diphosphate a [pyruvate L-threonine tryptophan 5'-phosphate [+ 7 isozymes] [+ 9 isozymes] Solyc08g066730.2 [+ 8 isozymes] [+ 13 isozymes] Reticuline oxidase precursor, Acireductone beta-amyrin synthase: myo-inositol polyphosphate 5- 4-coumarate-coa ligase: UDP-glucose Lycopene beta-cyclase Glycerol-3- Glycerol-3- glucose-6- Branched-chain- lysine-ketoglutarate dUMP dCDP [+ 9 isozymes] threonine 4-coumarate-coa ligase: Hydroxycinnamoyl- Hydroxycinnamoyl- anthocyanin 5-O- Zeaxanthin lupeol synthase: Cycloartenol A carboxylase long-chain-fatty- Hexokinase: dehydrogenase Branched-chain- Methionine aminotransferase: hyoscyamine dioxygenase: synthase: Solyc05g051850.2 Inositol- Inositol- kinase||polyphosphate Solyc03g005090.2 Hydroxycinnamoyl- Hydroxycinnamoyl- quercetin 3-O- O-methyltransferase: 1: Solyc04g040190.1 farnesyl-diphosphate sphingomyelin phosphate citrate amino-acid reductase||saccharopine L-threonine 3- Branched-chain- Branched-chain- tyrosine transaminase: Cystathionine AMP deaminase: D-fructose allolactose D-xylose H O CO [phospho-α-glucan] acetate a phenol deaminase: putative: Solyc02g069690.1 Solyc03g005090.2 CoA shikimate/quinate CoA shikimate/quinate kinase: glucosyltransferase: epoxidase, glucosyltransferase: phenylalanine Aromatic L-amino Solyc07g042630.2 Synthase: carboxyl
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  • Summary & Conclusions

    Summary & Conclusions

    Enzymatic functionalization and degradation of natural and synthetic polymers Von der Fakultät für Mathematik, Informatik und Naturwissenschaften der RWTH Aachen University zur Erlangung des akademischen Grades einer Doktorin der Naturwissenschaften genehmigte Dissertation vorgelegt von Shohana Subrin Islam M. Sc. Biotechnologie aus Dhaka, Bangladesch Berichter: Univ. -Prof. Dr. Ulrich Schwaneberg Univ. -Prof. Dr. Lothar Elling Tag der mündlichen Prüfung: 23.01.2019 Diese Dissertation ist auf den Internetseiten der Universitätsbibliothek verfügbar. To my mom & my sister-the two persons in the world who always stand by me Table of content Table of content Table of content _______________________________________________________________ v Publications and patents ________________________________________________________ ix Abstract _____________________________________________________________________ xi 1. General introduction _______________________________________________________ 1 1.1 Enzymatic functionalization of (bio)polymers _______________________________________ 1 1.2 Enzymatic degradation of polymers _______________________________________________ 3 1.3 Protein engineering ____________________________________________________________ 5 1.3.1 Directed evolution of enzymes _________________________________________________________ 6 1.3.2 KnowVolution – Directed Evolution 2.0 __________________________________________________ 9 1.4 Aims of the dissertation _______________________________________________________ 11 2. Engineering of