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Case Studies of the Hot Dog-Fold and Acyl- Adenylate-Forming Superfamilies: Characterizing the Importance of Functional Divergence in Cellular Metabolism Lucas Zimney

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Case Studies of the Hot Dog-Fold and Acyl- Adenylate-Forming Superfamilies: Characterizing the Importance of Functional Divergence in Cellular Metabolism Lucas Zimney University of New Mexico UNM Digital Repository Chemistry ETDs Electronic Theses and Dissertations 9-1-2015 Case Studies of the Hot Dog-Fold and Acyl- Adenylate-Forming Superfamilies: Characterizing the Importance of Functional Divergence in Cellular Metabolism Lucas Zimney Follow this and additional works at: https://digitalrepository.unm.edu/chem_etds Part of the Physical Chemistry Commons Recommended Citation Zimney, Lucas. "Case Studies of the Hot Dog-Fold and Acyl-Adenylate-Forming Superfamilies: Characterizing the Importance of Functional Divergence in Cellular Metabolism." (2015). https://digitalrepository.unm.edu/chem_etds/12 This Dissertation is brought to you for free and open access by the Electronic Theses and Dissertations at UNM Digital Repository. It has been accepted for inclusion in Chemistry ETDs by an authorized administrator of UNM Digital Repository. For more information, please contact [email protected]. ! ! ! ! ! ! ! !!!!!Lucas!R.!Zimney! !!!!!!!Candidate!! !!!!!! !!!!!Chemistry!and!Chemical!Biology! !!!!!Department! !!!!!! ! !!!!!This dissertation is approved, and it is acceptable in quality and form for publication: ! !!!!!Approved!by!the!Dissertation!Committee:! ! !!!!!!!! ! ! ! ! ! ! ! !!!!!Debra!Dunaway;Mariano,!Chairperson! !! ! !!!!!Patrick!S.!Mariano! ! ! !!!!!Charles!E.!Melançon!III! ! ! !!!!!Karen!N.!Allen! ! ! !!!!!! ! ! !!!!!! ! ! !!!!!!! ! ! !!!!!!! ! ! !!!!!!! ! ! ! ! ! ! i! ! ! ! ! ! ! ! ! CASE!STUDIES!OF!THE!HOT!DOG.FOLD!AND!ACYL.! ADENYLATE.FORMING!SUPERFAMILIES:! CHARACTERIZING!THE!IMPORTANCE!OF!FUNCTIONAL! DIVERGENCE!IN!CELLULAR!METABOLISM! ! ! ! ! by! ! ! ! ! ! LUCAS!R.!ZIMNEY! ! B.S.,!Chemistry,!South!Dakota!State!University,!2009! ! ! ! ! ! ! ! ! ! ! ! DISSERTATION! ! Submitted!in!Partial!Fulfillment!of!the! ReQuirements!for!the!Degree!of! ! Doctor!of!Philosophy! Chemistry! ! The!University!of!New!Mexico! AlbuQuerQue,!New!Mexico! ! ! July,!2015! ! ! ii! DEDICATION! ! ! To!my!parents,!Barry!and!Maureen,!who!always!took!interest!in!what!I!was! doing,!even!if!they!thought!I!was!just!making!stuff!up.!Thank!you!for!the!constant! love,!support!and!the!steady!flow!of!baked!goods,!without!any!of!which!this!would! not!have!been!possible.!! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! iii! ACKNOWLEDGEMENTS! ! ! If! the! past! six! years! have! taught! me! nothing! else,! it! has! shown! me! that! success! is! seldom! achieved! alone.! Throughout! this! journey! I! have! received! many! helping!hands!from!advisors,!mentors,!colleagues!and!friends.!Those!of!you!know! who!you!are!and!deserve!more!than!just!a!small!mention!on!this!page.!Nevertheless,! here!goes.! First! and! foremost,! I! must! thank! my! advisor,! Dr.! Debra! Dunaway;Mariano,! for! her! significant! contributions! to! my! education! and! research.! Her! expertise! and! guidance! in! my! research! and! post;grad! life! has! proven! to! be! invaluable.! Also,! I! would!like!to!recognize!Dr.!Patrick!Mariano!and!my!remaining!committee!members! (Dr.!Chad!Melançon!and!Dr.!Karen!Allen),!and!thank!them!for!all!of!their!advice!and! helpful!suggestions!along!the!way.! During!my!time!in!DDM’s!lab,!I!was!fortunate!enough!to!work!with!a!truly! fantastic!group!of!people!that!I!am!proud!to!call!my!colleagues!and!friends.!I!want!to! thank! my! mentor,! Hong,! for! showing! me! the! ropes! and! teaching! me! all! of! the! molecular! biology! and! enzymology! basics.! Also,! many! thanks! to! Chunliang,! who! seemingly! had! an! unlimited! amount! of! patience! in! helping! me! with! organic! synthesis.!!To!my!two!best!friends!in!the!lab,!Tyrel!and!John!;;!thanks!for!all!of!the! intellectual!conversations,!research!discussions,!the!stupid!pranks!and!of!course,!the! dirty! jokes.! You! guys! made! life! in! and! out! of! the! lab! a! ton! of! fun.! To! my! two! undergraduate!minions,!Kaila!and!Rachel!;;!you!guys!put!in!a!lot!of!truly!spectacular! ! iv! work!on!the!ligase!project.!Without!your!hard!work!and!dedication,!we!would!not! have!accomplished!nearly!as!much!as!we!did.!! Lastly,! to! Kaila! ;;! your! love! and! support! outside! of! the! lab! was! the! only! reason! I! kept! my! sanity! during! these! last! few! months.! Thank! you! for! keeping! me! motivated!and!focused!on!the!finish!line.!It!“litrally”!means!the!world!to!me!and!I! will!be!forever!grateful.! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! v! ! ! ! ! ! ! ! ! ! CASE!STUDIES!OF!THE!HOT!DOG.FOLD!AND!ACYL.! ADENYLATE.FORMING!SUPERFAMILIES:! CHARACTERIZING!THE!IMPORTANCE!OF!FUNCTIONAL! DIVERGENCE!IN!CELLULAR!METABOLISM! ! ! ! ! by! ! ! ! ! ! LUCAS!R.!ZIMNEY! ! ! ! ! ! ! ! ! ! ! ! ABSTRACT!OF!DISSERTATION! ! ! ! Submitted!in!Partial!Fulfillment!of!the! ReQuirements!for!the!Degree!of! ! Doctor!of!Philosophy! Chemistry! ! The!University!of!New!Mexico! AlbuQuerQue,!New!Mexico! ! ! July,!2015! ! vi! Case!Studies!of!the!Hot!Dog.Fold!and!Acyl.Adenylate.Forming!Superfamilies:! Characterizing!the!Importance!of!Functional!DiVergence!in!Cellular! Metabolism! ! ! Lucas!R.!Zimney! B.S.,!Chemistry,!South!Dakota!State!University,!2009! ! ! ABSTRACT! ! ! ! Some! of! the! biggest! contributors! to! cellular! respiration! (and! cellular! metabolism!in!general)!are!acyl;CoA!derivatives,!a!subclass!of!biological!thioesters.! Known!to!function!in!a!variety!of!pathways,!the!regulation!of!their!formation!and! breakdown! are! critical,! carried! about! by! acyl;CoA! synthetases! and! thioesterases,! respectively.! The! work! reported! within! this! dissertation! will! focus! on! functional! divergence!within!two!enzyme!superfamilies!;;!the!hot!dog;fold!and!acyl;adenylate; forming!superfamilies!–!and!can!be!broken!down!into!two!main!parts.! ! Part!one!will!look!at!tracking!the!functional!divergence!within!the!hot!dog; fold!superfamily!thioesterases.!A!highly!evolved!thioesterase,!flK,!has!been!found!to! function!in!the!critical,!and!highly!specific!role!of!fluoroacetate!detoxification!within! the! fluorometabolite;producing! bacteria,! S.! cattleya.! Using! an! extensive! bioinformatics! analysis,! flK! orthologs! were! identified! and! tracked! throughout! all! ! vii! three! domains! of! life,! primarily! in! bacteria! that! make! up! the! gut! microbiome.! Additionally,! seQuence! and! structural! analyses! revealed! distinct! flK! scaffolds,! a! further! indication! of! divergent! functionality.! Various! flK! orthologs! were! then! isolated,!cloned!and!subjected!to!substrate!screening!by!measuring!their!individual! steady;state! kinetic! parameters! kcat,! Km! and! kcat/Km.! Combined! with! gene! context! analyses,! divergent! in! vivo! functionality! was! assigned! to! members! of! the! flK! subfamily,!as!they!were!proposed!to!be!involved!in!supplying!formate!for!the!one; carbon!pool.! ! Part! two! will! focus! on! the! functional! characterization! of! the! acyl;CoA! synthetases!(ligases)!in!Pseudomonas!aeruginosa,!the!dominant!pathogen!present!in! all! patients! with! cystic! fibrosis! and! the! leading! cause! of! morbidity! and! mortality! within!this!afflicted!population.!Nine!freestanding!ligases!were!cloned,!isolated!and! subjected!to!an!extensive!substrate!screening!for!acyl;CoA!synthetase!activity!using! a!novel!high;throughput!assay.!Individual!activities!were!verified!by!measuring!the! steady;state!kinetic!parameters.!Combing!these!results!with!extensive!gene!context! analyses,!in!vivo!functions!were!proposed!for!the!tested!ligases,!implicating!them!in! a!variety!of!nutrient!scavenging!pathways!as!well!as!in!virulence!factor!production.! ! ! ! ! ! ! ! ! viii! TABLE!OF!CONTENTS! ! ! LIST!OF!ABBREVIATIONS………………………………………………………………………………xii! LIST!OF!TABLES..………………………………………………………………………………………...xviii! LIST!OF!FIGURES…………………………………………………………………………………………XXVi! CHAPTER!1:!The!Biological!Thioester!–!An!OVerView!of!its!Function!in!Cellular! Metabolism!and!the!Enzymes!that!Regulate!it………………………………..…………….....1! 1.1 Overview!of!Cellular!Metabolism………………………………………………………..…1! 1.1.1!Cellular!Respiration………………………………………………………………..1! 1.1.2!Biological!Significance!of!Thioesters………………………………………..5! 1.2!Acyl;CoA!Thioesterases………………………………………………………………………..6! ! 1.2.1!The!Hot!Dog;Fold!Superfamily!and!Hot!Dog!Thioesterases……….7! ! 1.2.2!Mechanism!of!Catalysis!of!HD!Thioesterases……………………………9! ! 1.2.3!Divergence!of!Function!Within!HD!Thioesterases…………………..11! ! 1.3!The!Acyl;Adenylate;Forming!Superfamily…………………………………………..14! ! ! 1.3.1!Functional!Roles!of!Acyl;CoA!Synthetases……………………………...18! ! ! 1.3.2!Structure;Function!Relationship!of!Acyl;CoA!Synthetases……....21! ! 1.4!Summary…………………………………………………………………………………………...22! ! References……………………………………………………………………………………………....23! CHAPTER! 2:! NoVel! Thioesterase! ActiVity! from! S.#cattleya#flK! ReVeals! a! Basis! For!DiVergent!Biological!Function…………………………………………………………………30! ! 2.1!Introduction………………………………………………………………………………………30! ! ix! ! 2.2!Methods!and!Materials……………………………………………………………………….43! ! ! 2.2.1!Materials………………………………………………………………………………43! ! ! 2.2.2!Synthesis!of!Acyl;CoA!Substrates…………………………………………..44! ! ! 2.2.3!Cloning,!Expression!and!Purification!of!flK!and!Orthologs………44! ! ! 2.2.4!Determination!of!Steady;State!Kinetic!Parameters…………………46! 2.2.5! Crystallization! and! X;ray! Structure! Determination! of! MA0038! and!BVU_1957………………………………………………………………………………46! 2.2.6!Bioinformatics!Analysis………………………………………………………...47! ! 2.3!Results!and!Discussion……………………………………………………………………….48! ! ! 2.3.1!Biological!Range!of!the!Fluorinase!Cluster……………………………..48! ! ! 2.3.2!Biological!Range!and!SeQuence!Analysis!of!flK!Orthologs………..49! ! ! 2.3.3!Cloning!and!Isolation!of!flK!Orthologs……………………………………57! ! ! 2.3.4!Substrate!Specificity!of!flK!Orthologs……………………………………..57!
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