Photosynthesis | Doran Bennett

Photosystem II Light Harvesting: Literature

Excitation Energy Transfer and Charge Separation in Photosystem II

Membranes Revisited

Koen Broess, Gediminas Trinkunas, Chantal D. van der Weij-de Wit, Jan P. Dekker, Arie van Hoek, and Herbert van Amerongen

Question 1: What is a BBY preparation? How are the 'lifetime' values the authors discuss relate to TCSPC measurements and what do they tell us about the process of light harvesting in the sample?

Question 2: What model do the authors use to simulate their fluorescence lifetimes? Try to understand both the physical meaning/interpretation of their model as well as how they represent it mathematically.

Question 3: What is the relative timescale of charge separation vs exciton migration in both their samples and PSII membranes more broadly?

Question 4: To what extent is their modeling approach "bottom-up" vs "top-down" and what does that mean for how we should understand their results?

A Structure-Based Model of Energy Transfer Reveals the Principles of

Light Harvesting in Photosystem II Supercomplexes

Doran I. G. Bennett, Kapil Amarnath, and Graham R. Fleming

Question 1: What is a photosystem II super complex and what is their role in light harvesting in vivo? What structural model was used for the simulations and how was it obtained?

Question 2: What model is used for the simulations and how were the parameters determined? What is the physical meaning of 'domains of chlorophyll' and why are they convenient for calculations?

Question 3: How were the time scales for diffusion, transfer-to-trap, and charge separation determined within the simulations? What does this suggest about the process of light harvesting both in isolated PSII super complexes and in vivo?

Question 4: The authors note that the quality of fit cannot be used as a proxy for the quality of the excitation energy transfer model. How should we determine the quality of their results? To what extent are the presented simulations representative (or not) of the actual process of light harvesting in photosystem II?

Multiscale model of light harvesting by photosystem II
in plants

Kapil Amarnatha, Doran I. G. Bennett, Anna R. Schneider, and Graham R. Fleming

Question 1: What model is used for the presented simulations? Pay attention to both the structural and excitation-energy transport components of the model.

Question 2: What does it mean for excitation energy transport to be diffusive vs sub-diffusive? What is the excitation diffusion length and what does it mean for the process of light harvesting in the simulations?

Question 3: How does the formation of PSII-S crystalline arrays influence light-harvesting in the simulations? How do the authors interpret this result and how do you interpret it? (Meaning, what do you think it tells us about the real process of light harvesting in a PSII membrane?)

Question 4: What are the lake/puddle models and how have they been used previously? What do the current results suggest about the applicability of these models to PSII?

Energy-dependent quenching adjusts the excitation diffusion length to regulate photosynthetic light harvesting

Doran I. G. Bennett, Graham R. Fleming, and Kapil Amarnath

Question 1: What is NPQ and qE? How are they related to protecting photosystem II from bright light?

Question 2: How is qE modeled in these simulations and what does it mean for the diffusional picture of excitation energy transfer? How was this model parameterized?

Question 3: How does qE interact with PSII light harvesting and how is this reflected in the RC antenna size?

Question 4: What is PAM fluorescence and how does it probe qE dynamics? Why are the 'lake' and 'puddle' models problematic according to the authors and what solution do they suggest?

Introduction to Chlamy: Literature

The Natural History of Model Organisms: From molecular manipulation of domesticated Chlamydomonas reinhardtii to survival in nature

Severin Sasso, Herwig Stibor, Maria Mittag and Arthur R Grossman

This paper provides an overview of Chlamy as a model organism. We want to read it in order to give more context to the papers that will follow.

Dynamic regulation of photosynthesis in Chlamydomonas reinhardtii

Jun Minagawa and Ryutaro Tokutsu

Question 1: What is the definition of state 1 and 2 in Chlamy? How is state 2 thought to occur (the authors suggest two mechanisms)?

Question 2: What is qE and what role does LHCSR play in the qE response of Chlamy? How is LHCSR induced and what timescale does this occur on? Think about what this means for using state transitions vs qE to mitigate high light exposure.

Question 3: What is linear vs cyclic electron flow (pay attention to the two different cyclic mechanisms)? Why does a cell need to change the balance of linear and cyclic electron flow? What is the significance of the spatial organization of the protein components for cyclic electron flow?

Question 4: What is the role of membrane organization in how Chlamy acclimates to changes in the environment? Think about how different processes are all being executed by a single membrane – what does that mean for how we can model these dynamics.

Charting the native architecture of thylakoid membranes with single-molecule precision

Wojciech Wietrzynski, Miroslava Schaffer, Dimitry Tegunov, Sahradha Albert, Atsuko Kanazawa, Jürgen M. Plitzko, Wolfgang Baumeister, Benjamin D. Engel

Question 1: What are the different approaches the authors describe for measuring membrane organization? What advantages and disadvantages do the different approaches have and how does the current measurement improve on the state-of-the-art? [Remember to also think about what limitations are present in all of these methods]

Question 2: What is the difference between appressed vs non-appressed membranes and where do the different protein components (PSI, PSII, b6f, ATP-S, Ribo) appear? What are the hypothesized ‘grana margins’ and to what extent do they appear in Chlamy? What does this protein organization mean for cyclic and linear electron flow?

Question 3: How do PSII core complexes arrange within/between layers of the membrane and to what extent does this support the existence of super complexes? What conceptual picture do the authors suggest for thinking about the organization of PSII core complexes and what evidence do they offer?

Question 4: Given this data, how would you interpret the state transition measurements we discussed last week? What would long range LHCII transport require structurally and what would you expect to see in in the membrane if the hypothesized short-range LHCII reorganization + quenching occurred?

pH dependence, kinetics and light-harvesting regulation of nonphotochemical quenching

in Chlamydomonas

Lijin Tiana, Wojciech J. Nawrockia, Xin Liua, Iryna Polukhinaa, Ivo H. M. van Stokkuma, and Roberta Crocea

Question 1: We have discussed how the photosynthetic regulation occurs on multiple timescales. How does this complicate experimental studies of the dynamics? How do the authors suggest resolving this problem for their experiment?

Question 2: In order to establish a physiologically relevant model to study, the authors design a very specific experimental protocol for sample preparation. First, what samples do the authors prepare (i.e what mutants, conditions, etc)? Second, how do the authors characterize the physiological response associated with NPQ? Finally, what evidence do they offer that their specific protocol is preparing a system that is relevant to natural conditions?

Question 3: After developing the sample preparation, the authors measure the time-resolved fluorescence. What is the ‘compartment model’ they use (i.e. how is built and what does it represent physically)? What conclusions do the authors reach from their ‘compartment model’ and to what extent do you agree with these conclusions?

Question 4: In addition to a compartment model, the authors consider the role of NPQ in changing the antenna size in chlamy. What is the `NPQ parameter’ that they using in Fig. 4C and why is that a measure of NPQ? How do they quantify the antenna size of PSII and how does this compare to the definition of antenna size that we considered previously?

Chlamydomonas reinhardtii Exhibits De Facto Constitutive NPQ Capacity in Physiologically Relevant Conditions

Wojciech J. Nawrocki, Xin Liu, and Roberta Croce

Question 1: Chlamy has two different mechanisms for managing saturating light conditions: state transitions and NPQ. What are these two mechanisms (what proteins are the key players, what processes are important, etc.) and what are their relevant timescales? Why do the authors propose looking at the NPQ and state transition capacity of cells grown in sinusoidal light conditions?

Question 2: The authors look at the NPQ capacity of cells at different periods of the day night cycle. What samples are they using and how do they characterize NPQ? How does the NPQ capacity change during the day and how do the authors explain this in terms of LHCSR? Note the authors discuss Fv/Fm – how does that compare to the NPQ parameter we discussed last week? Pay attention to how the different mutants behave and what we learn from that.

Question 3: How do the authors quantify the capacity for state transitions in in cells that have been grown in sinusoidal light conditions? What conclusions do they reach about the capacity of both WT and mutant strains to perform state transitions? How did they support these conclusions?

Regulation and Dynamics of the Light-Harvesting System

Jean-David Rochaix

Question 1: Take a step back. We have read 4 different papers on light response in chalmy and now it is time to try and synthesize what we have learned. Imagine you have a dark acclimated Chlamydomonas sample that you expose to bright continuous light - describe the different responses you expect to see on the seconds, minutes, hours, and day timescales. Think about these responses both in terms of common measurable (chlorophyll fluorescence, protein expression) and the hypothetical mechanisms. Draw diagrams to present this information.

Key words: Photochemical yield, State transitions, NPQ, photo-inhibition, gene regulation

Question 2: For the different processes - articulate what evidence you have for your hypothesized responses. What measurements have people already made, how confident are you in the picture they suggest?

Question 3: If you were going to clarify one aspect of this overall problem - what question would you try to answer? What measurement or model would you want to use? Why?