IGEM:Stanford/2009/Photosynthesis

Project Summary
Attempt to increase rate/efficiency of photosynthesis by expressing non-native photosynthetic pigments in cyanobacteria. Our theory is if we can expand the wavelengths that cyanobacteria can absorb, then it can photosynthesize faster/more efficiently.

Original Presentation: [[Media:030409-photosynthesis.ppt|Increase Absorption Range for Photosynthesis]]

You guys... I think we have it completely backwards! Check this paper out: Dunaliella salina (Chlorophyta) with small chlorophyll antenna sizes exhibit higher photosynthetic productivities and photon use efficiencies than normally pigmented cells

What We Know

 * Interesting general information sites:
 * Review of Photosynthesis
 * Overview of Photosynthetic Pigments
 * Photosynthetic Pigments: Structure and Spectroscopy
 * Stanford Lab/Potential Faculty?: Bhaya Lab - They do a bunch of stuff with cyanobacteria. Ariana said she would talk to Dr. Bhaya, but others can help too!

What We Don't Know (but need to know)

 * How do we incorporate pigments into the photosystems?
 * How do we measure photosynthesis rate or efficiency?
 * Photosynthetic Bioelectricity- I think this group/project is trying to take advantage of the hydrogen gradient created
 * A Rapid Field Method for Measuring Photosynthesis with Labelled Carbon Dioxide
 * Photosynthesis... using algae wrapped in jelly balls - uses pH?
 * Photosynthesis in Elodea - another pH measurement method
 * Field Photosynthesis Measurement Systems - measures gas exchange?
 * Thanks to Jerome for the above links!


 * How are cyanobacteria cultured?
 * What specific pigments would we try to make?
 * What enzymes are needed and are they available?

Experiment Ideas

 * Resources on Culturing Cyanobacteria
 * Harvard 2006 Cyanobacteria Protocols
 * Working with Algae and Cyanobacteria
 * Jeff Chabot's Dissertation "Genetic Noise in cyanobacterial circadian oscillator" - protocols start on page 47
 * Efficient gene transfer in Synechococcus sp. strains PCC 7942 and PCC 6301 by interspecies conjugation and chromosomal recombination.


 * Photosynthesis Protocols
 * Photosynthesis Research Protocols

Important/Interesting Papers
''' Fleming's lab -Atom
 * Chlorophyll b Expressed in Cyanobacteria Functions as a Light-harvesting Antenna in Photosystem I through Flexibility of the Proteins - This group expressed Chlorophyll B in Cyanobacteria and it incorporated itself into the photosystem!
 * Other iGEM projects
 * A BioBrick toolkit for cyanobacteria - The team from Hawaii last year built some biobrick parts that work with Cyanobacteria
 * see also Photosynthesis Links
 * BERKELEY has lots of research going on with elucidating mechanisms of photosynthesis and is one of the leaders in artificial photosynthesis, thanks to Steve Chu. An example is: "Graham Fleming, a physical chemist who holds joint appointments with the U.S. Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) and the University of California (UC) at Berkeley, is the leader of an ongoing effort to discover how plants are able to transfer energy through a network of pigment-protein complexes with '''nearly 100-percent efficiency."
 * Nano-sized Photocatalyst for Artificial Photosynthesis
 * Berkeley Researchers Identify Photosynthetic Dimmer Switch
 * Quantum Secrets of Photosynthesis Revealed!

Thylakoid Membrane Stuff

 * Chapter 11: Biogenesis and Dynamics of Thylakoid Membranes and the Photosynthetic Aparatus
 * Thylakoid Membrane Reduction Affects the Photosystem Stoichiometry in the Cyanobacterium Synechocystis sp. PCC 6803
 * Thylakoid membrane biogenesis in Chlamydomonas reinhardtii 137+. II. Cell-cycle variations in the synthesis and assembly of pigment
 * The thylakoid membranes of cyanobacteria: structure, dynamics and function

Oxidative Stress

 * A small heat-shock protein confers stress tolerance and stabilizes thylakoid membrane proteins in cyanobacteria under oxidative stress
 * Overexpression of Superoxide Dismutase Protects Plants from Oxidative Stress (Induction of Ascorbate Peroxidase in Superoxide Dismutase-Overexpressing Plants
 * Mechanism of downregulation of photosystem I content under high-light conditions in the cyanobacterium Synechocystis sp. PCC 6803

Questions/Discussion

 * Robert 01:10, 2 April 2009 (EDT): So apparently, we have competition! On my way out of our meeting, I ran into Josh (a member in the Smolke lab and previous iGEM mentor) and he mentioned to me that Chris Voigt (a UCSF professor) was working on engineering photosynthesis into E. coli. I did a little google search and saw an abstract Voigt. Ill try to find some papers that may be useful to us! Check this out too Cool Stuff it may be useful to us. It looks he does not have everything finished, or is finished and in the process of writing a paper.
 * Robert 18:22, 1 April 2009 (EDT): I agree with Anusuya - the fact that we should do a project in E. coli (or a fast replicating org.) as well, in addition to our modification in Cyano. I spoke with one of the 08 Hawaii iGEM members (the toolkit for cyano) and they mentioned a few times where they had to wait two weeks for results, in which we could be working on the other half!
 * Anusuya Ramasubramanian 12:10, 1 April 2009 (PST): I think of the three projects suggested, this one is the most widely applicable. Working off of Leon's comment, I also think we should look further into engineering E. coli to perform an enhanced photosynthesis through insertion of genes for specific protein productions.  Perhaps we can also look into boosting or modulating the expression of Carotenoids and phycobilins.  Given that these two pigments are naturally found in photosynthetic systems, they seem to be the most natural candidates to work with.
 * Leon: Before I forget about this, I remember reading somewhere that there is a protein called proteorhodopsin which can be put into E. coli so that the E. coli could potentially perform photosynthesis. This might be useful when thinking about how to design our project.
 * Jerome Bonnet: A good application for enhancing photosynthesis in cyanobacteria is increasing carbon sequestration:some folks have patented a method for "removing a carbon-containing compound from a flowing gas stream by interposing in the stream a membrane having photosynthetic microbes, such as algae and cyanobacteria, deposited thereon".
 * Ariana: In response to Jerome's comment, would it be possible to physically isolate the dark and light reactions of photosynthesis in cyanobacteria (modeled on what happens in C4 plants) in order to decrease losses due to photorespiration? Also, if we end up working with E. coli, I was wondering whether it would be useful to use the proton pumps already in its genome that are associated with the flagella and try to make these proteins co-localize with photosystems/chlorophyll that we express on a vector.
 * Mark Y. Fang 03:48, 28 March 2009 (EDT): I've been reading a chapter on Photosynthesis in the Berg Biochemistry book, and here are some of my ideas for an iGEM project in photosynthesis:
 * (Apologies beforehand; the notes aren't very coherent. They're mostly just musings at the moment.)
 * Cyanobacterial photosynthesis systems have only 4 bacteriochlorophyll b molecules bound, which is not as effective at absorbing photons and transferring the light energy carried by these photons to the reactions center (i.e. the chlorophyll a molecules in photosystem II absorb different wavelengths of light, not all of which are optimal, but as they drop back to ground state they re-emit a photon with a lower energy that may correspond to the optimal wavelength/energy; this photon would be taken up by the special pair P680). Engineer cyanobacteria to express a mutant photosynthesis system that binds more bacteriochlorophyll b?  But photosynthetic bacteria do have light harvesting complexes (LHC).
 * Or, to enable cyanobacteria to absorb more wavelengths of light, determine the proteins that reduce one of the pyrrole rings and add other small modifications to create the differences between bacteriochlorophyll b and plant chlorophyll a; can we knock out the genes for these proteins to see if the cyanobacteria produce chlorophyll a and absorb at the 680 nm wavelength?
 * Why do thylakoid membranes contain such high galactolipid contect (~40%)? Note that Glycolipids are found exclusively on the extra-cellular leaflet of lipid bilayers.  Glycolipids include the sphingolipids, which are important to lipid raft formation.  Are lipid raft analogues comprised of galactolipids present in thylakoid membranes to bring together photosystem II, cytochrom bf, and photosystem I?
 * Developing thylakoid membranes “bud off” of the inside chloroplast membrane; i.e. they are like cristae in mitochondria that have fully pinched off. Thus the lumen of the thylakoid is analogous to the intermembranous space of the mitochondria; both accumulate a high concentration of H+ during the generation of the H+ gradient needed for ATP synthesis (via F1-F0 ATP synthase in oxidative phosphorylation in mitochondria and via CF1-CF0 ATP synthase – chloroplast factor 1 and chloroplast factor 0 – in the light reactions in the thylakoid stacks/grana).  Can we identify and stimulate the genes that cause this budding off, thus creating more thylakoid?  We’d probably have to look at the genome of the chloroplast.
 * Note that bacteria, like mitochondria and chloroplasts, have two (or more) lipid bilayer membranes and that in the cyanobacteria the H+ accumulates in the periplasmic (intermembranous) space, just as in mitochondria and in the chloroplast analogue, the thylakoid lumen.
 * Cyanobacteria probably create a H+ gradient with a higher concentration of H+ in the periplasmic space because the cytoplasmic proteins are sensitive to pH.
 * The dark reactions occur in the stroma of the chloroplast.
 * Note that peak solar radiation occurs at wavelengths between 450 and 650 nm.
 * UNRELATED: Can we kill bacteria by cause the integration of bacterial ATP synthase backwards, resulting in no ATP synthesis? Or could we even cause backward integration of cytochrome bc1 so that the cytoplasm drops in pH, denaturing the cytoplasmic proteins and killing the microbe?  Antibacterial…
 * We’d probably have to generate a virus that can mutate the integration gene for ATP synthase/cytochrome bc1.