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Physiological Effects of Heterologous Expression of Proteorhodopsin Photosystems

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Physiological Effects of Heterologous Expression of Proteorhodopsin Photosystems Physiological Effects of Heterologous Expression of Proteorhodopsin Photosystems by MASSACHUSETTS NSTITUTE Justin David Buck Bachelor of Science, Chemical Engineering Colorado School of Mines, 2004 Submitted to the Department of Biological Engineering ARCHIVES in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biological Engineering at the Massachusetts Institute of Technology February, 2012 0 2012 Massachusetts Institute of Technology. All Rights Reserved. S i g n a tu r e o f A u th o r : J u st inD ._Bu ck Justin D. Buck Department of Biological Engineering January 6, 2012 Certified by: -j / Edward F. Delong Professor of Civil and Environmen ngi ering, and Biological Engineering Thesis Advisor z/ 7 0 Accepted by: Forest White Associate Professor of Biological Engineering Course 20 Graduate Program Committee Chairperson This doctoral thesis has been examined by a committee of the Biological Engineering Department as follows: Chairperson, Graduate Thesis Committee: John M. Essigmann Professor of Chemistry, Toxicology and Biological Engineering Thesis Advisor, Committee Member: ard F. DeL ng Department of Civil and Environmental, and B' logical Engine ing Thesis Committee Member: Y/ Kristala Jones Prather Associate Professor of Chemical Engineering Thesis Committee Member: Michael Laub Associate Professor of Biology Physiological Effects of Heterologous Expression of Proteorhodopsin Photosystems by Justin David Buck Submitted to the Department of Biological Engineering in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biological Engineering Abstract Proteorhodopsin (PR) phototrophy plays an important role in the marine ecosystem, harvesting energy from sunlight for a diverse community of hetertrophic organisms. The simple proteorhodopsin photosystem (PRPS) composed of six to seven genes is sufficient for producing a functional light-driven proton pump, capable of powering cellular processes. This thesis describes the functional characterization of a subcloned PRPS previously identified from a large insert metagenomic library (Martinez et al., 2007). Incorporation of the PRPS into a strain of Pseudomonasputida resulted in a light-dependent increase in viable cell yield of cultures grown in low carbon media. The light-dependent effect demonstrates a dependence on carbon, reducing at increasing carbon concentrations until no differential effect is observed. A survey of six PR- containing vectors from metagenomic libraries revealed PR transcription in two hosts, P. putida and Pseudoalteromonas atlantica, and of the three additional vectors with PRPS tested, two demonstrated the same qualitative light-dependent yield increase. This work illustrates the utility of a simple rhodopsin photosystem for supplementing the cellular energy system of a heterologous host, paving the way for future engineering applications in photoheterotrophy. Advisor: Ed DeLong 6 Table of Contents Chapter 1: Light Energy Harvesting and the Ecological Significance of Proteorhodopsin Significance of Light Energy............................................................................................... 11 Biological Light Capturing M echanisms............................................................................. 11 Retinylidene Proteins (Rhodopsins)................................................................................. 12 Type I Rhodopsins............................................................................................................ 14 Sensory Rhodopsins .................................................................................................. 17 Halorhodopsin............................................................................................................ 17 Bacteriorhodopsin ..................................................................................................... 18 Proteorhodopsin ....................................................................................................... 19 Xanthorhodopsin and Actinorhodopsin ................................................................... 20 Biophysical Characterization of Proteorhodopsin Structure, Photocycle, and Key Residues of the Proton Pumping M echanism ................................................................................. 20 Protorhodopsin Diversity................................................................................................ 26 The Proteorhodopsin Photosystem ................................................................................. 26 Evidence for Ecological Significance of Proteorhodopsin .. ...... ...... ................... 28 Diversity of Strains Harboring Proteorhodopsin ............................................................ 29 Physiological Effects Associated with Proteorhodopsin ................................................ 32 Physiological Effects of Proton-Pumping Rhodopsins in Native Hosts.......................... 34 Proteorhodopsin Effects in Heterologous Hosts.............................................................. 37 Biotechnology applications of PR .................................................................................... 38 Thesis Overview .................................................................................................................. 39 Chapter 2: Functional Characterization of a Subcloned Proteorhodopsin Photosystem in Escherichiacoli Abstract................................................................................................................................ 43 Introduction & Background............... ................................... ......................................... 44 Functional Arrangement of Proteorhodopsin Photosystems...................................... 44 Phylogenetic Origin of the HF10_19P19 PRPS....................................................... 50 M ethods............................................................................................................................... 54 Cloning and Constructs M ade.................................................................................... 54 Production of Retinal................................................................................................ 61 Absorbance Spectrum of Protorhodopsin in Membrane Preparations ...................... 63 Verification of Proton Pumping Behavior ................................................................ 64 Photophosphorylation with the Photosystem ............................................................ 65 R esu lts ................................................................................................................................. 6 7 Subcloning the Proteorhodopsin Photosystem......................................................... 67 Production of Photosystem Components .................................................................. 77 Functionality of the Photosystem ........ .... .................... ...................... 82 Discussion & Conclusion ............................................................................................... 86 Chapter 3: Physiological Effects of a Proteorhodopsin Photosystem in Pseudomonasputida Ab stract................................................................................................................................ 89 Introduction & Background Information........................................................................ 90 A Conjugative and Integrative Vector-Host System for Functional Screening of Large- Insert Environmental Libraries in M ultiple Hosts..................................................... 91 Psedumonasputida.................................................................................................. 92 M ethods ............................................................................................................................... 97 Construction of retrofit fosmid vectors pSJ2B6 and pSCCFOS.............................. 97 Conjugation from E. coli DH1OB/pUB307 to Pseudomonasputida ......................... 97 Transcription of the PR through RT-PCR..... ............................ ............................. 99 Growth effect in low carbon defined media................................................................ 102 Results ............................................................................................................................... 107 Conjugation of Modified Fosmid (pCC1FOS) Vectors pSJ2B6 and pSCCFOS into P. putida M BD1 .............................................................................................................. 107 Expression of the PRPS from pSJ2B6 in P. putida M BD1......................................... 112 Growth Effects at Low Dissolved Organic Carbon Imparted by the PRPS................ 115 Effect of Glucose Concentration on PRPS-Associated Light-Related Yield Increase 119 Discussion.......................................................................................................................... 122 Conclusion......................................................................................................................... 128 Chapter 4: Survey of Heterologous Expression of Various PRPS-Containing Constructs Abstract.............................................................................................................................. 129 Introduction & Background..............................................................................................
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