Stress-induced metabolic exchanges between complementary bacterial types underly a dynamic mechanism of inter-species stress resistance.

Metabolic cross-feeding plays vital roles in promoting ecological diversity. While some microbes depend on exchanges of essential nutrients for growth, the forces driving the extensive cross-feeding needed to support the coexistence of free-living microbes are poorly understood. Here we characterize bacterial physiology under self-acidification and establish that extensive excretion of key metabolites following growth arrest provides a collaborative, inter-species mechanism of stress resistance. This collaboration occurs not only between species isolated from the same community, but also between unrelated species with complementary (glycolytic vs. gluconeogenic) modes of metabolism. Cultures of such communities progress through distinct phases of growth-dilution cycles, comprising of exponential growth, acidification-triggered growth arrest, collaborative deacidification, and growth recovery, with each phase involving different combinations of physiological states of individual species. Our findings challenge the steady-state view of ecosystems commonly portrayed in ecological models, offering an alternative dynamical view based on growth advantages of complementary species in different phases.

A Genome-Scale Metabolic Model of Marine Heterotroph Vibrio splendidus Strain 1A01.

While Vibrio splendidus is best known as an opportunistic pathogen in oysters, Vibrio splendidus strain 1A01 was first identified as an early colonizer of synthetic chitin particles incubated in seawater. To gain a better understanding of its metabolism, a genome-scale metabolic model (GSMM) of V. splendidus 1A01 was reconstructed. GSMMs enable us to simulate all metabolic reactions in a bacterial cell using flux balance analysis. A draft model was built using an automated pipeline from BioCyc. Manual curation was then performed based on experimental data, in part by gap-filling metabolic pathways and tailoring the model's biomass reaction to V. splendidus 1A01. The challenges of building a metabolic model for a marine microorganism like V. splendidus 1A01 are described. IMPORTANCE A genome-scale metabolic model of V. splendidus 1A01 was reconstructed in this work. We offer solutions to the technical problems associated with model reconstruction for a marine bacterial strain like V. splendidus 1A01, which arise largely from the high salt concentration found in both seawater and culture media that simulate seawater.

Microbes contribute to setting the ocean carbon flux by altering the fate of sinking particulates.

Sinking particulate organic carbon out of the surface ocean sequesters carbon on decadal to millennial timescales. Predicting the particulate carbon flux is therefore critical for understanding both global carbon cycling and the future climate. Microbes play a crucial role in particulate organic carbon degradation, but the impact of depth-dependent microbial dynamics on ocean-scale particulate carbon fluxes is poorly understood. Here we scale-up essential features of particle-associated microbial dynamics to understand the large-scale vertical carbon flux in the ocean. Our model provides mechanistic insight into the microbial contribution to the particulate organic carbon flux profile. We show that the enhanced transfer of carbon to depth can result from populations struggling to establish colonies on sinking particles due to diffusive nutrient loss, cell detachment, and mortality. These dynamics are controlled by the interaction between multiple biotic and abiotic factors. Accurately capturing particle-microbe interactions is essential for predicting variability in large-scale carbon cycling.

Models and mechanisms of the rapidly reversible regulation of photosynthetic light harvesting.

The rapid response of photosynthetic organisms to fluctuations in ambient light intensity is incompletely understood at both the molecular and membrane levels. In this review, we describe research from our group over a 10-year period aimed at identifying the photophysical mechanisms used by plants, algae and mosses to control the efficiency of light harvesting by photosystem II on the seconds-to-minutes time scale. To complement the spectroscopic data, we describe three models capable of describing the measured response at a quantitative level. The review attempts to provide an integrated view that has emerged from our work, and briefly looks forward to future experimental and modelling efforts that will refine and expand our understanding of a process that significantly influences crop yields.

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

An important determinant of crop yields is the regulation of photosystem II (PSII) light harvesting by energy-dependent quenching (qE). However, the molecular details of excitation quenching have not been quantitatively connected to the fraction of excitations converted to chemical energy by PSII reaction centers (PSII yield), which determines flux to downstream metabolism. Here, we incorporate excitation dissipation by qE into a pigment-scale model of excitation transfer and trapping for a 200 × 200-nm patch of the grana membrane. We show that excitation transport can be rigorously coarse grained to a 2D random walk with an excitation diffusion length determined by the extent of quenching. We present an alternative method for analyzing pulse amplitude-modulated chlorophyll fluorescence measurements that incorporates the effects of a variable excitation diffusion length during qE activation.

Natural changes in light interact with circadian regulation at promoters to control gene expression in cyanobacteria.

The circadian clock interacts with other regulatory pathways to tune physiology to predictable daily changes and unexpected environmental fluctuations. However, the complexity of circadian clocks in higher organisms has prevented a clear understanding of how natural environmental conditions affect circadian clocks and their physiological outputs. Here, we dissect the interaction between circadian regulation and responses to fluctuating light in the cyanobacterium Synechococcus elongatus. We demonstrate that natural changes in light intensity substantially affect the expression of hundreds of circadian-clock-controlled genes, many of which are involved in key steps of metabolism. These changes in expression arise from circadian and light-responsive control of RNA polymerase recruitment to promoters by a network of transcription factors including RpaA and RpaB. Using phenomenological modeling constrained by our data, we reveal simple principles that underlie the small number of stereotyped responses of dusk circadian genes to changes in light.

Multiscale model of light harvesting by photosystem II in plants.

The first step of photosynthesis in plants is the absorption of sunlight by pigments in the antenna complexes of photosystem II (PSII), followed by transfer of the nascent excitation energy to the reaction centers, where long-term storage as chemical energy is initiated. Quantum mechanical mechanisms must be invoked to explain the transport of excitation within individual antenna. However, it is unclear how these mechanisms influence transfer across assemblies of antenna and thus the photochemical yield at reaction centers in the functional thylakoid membrane. Here, we model light harvesting at the several-hundred-nanometer scale of the PSII membrane, while preserving the dominant quantum effects previously observed in individual complexes. We show that excitation moves diffusively through the antenna with a diffusion length of 50 nm until it reaches a reaction center, where charge separation serves as an energetic trap. The diffusion length is a single parameter that incorporates the enhancing effect of excited state delocalization on individual rates of energy transfer as well as the complex kinetics that arise due to energy transfer and loss by decay to the ground state. The diffusion length determines PSII's high quantum efficiency in ideal conditions, as well as how it is altered by the membrane morphology and the closure of reaction centers. We anticipate that the model will be useful in resolving the nonphotochemical quenching mechanisms that PSII employs in conditions of high light stress.

Characterizing non-photochemical quenching in leaves through fluorescence lifetime snapshots.

We describe a technique to measure the fluorescence decay profiles of intact leaves during adaptation to high light and subsequent relaxation to dark conditions. We show how to ensure that photosystem II reaction centers are closed and compare data for wild type Arabidopsis thaliana with conventional pulse-amplitude modulated (PAM) fluorescence measurements. Unlike PAM measurements, the lifetime measurements are not sensitive to photobleaching or chloroplast shielding, and the form of the fluorescence decay provides additional information to test quantitative models of excitation dynamics in intact leaves.

Models and measurements of energy-dependent quenching.

Energy-dependent quenching (qE) in photosystem II (PSII) is a pH-dependent response that enables plants to regulate light harvesting in response to rapid fluctuations in light intensity. In this review, we aim to provide a physical picture for understanding the interplay between the triggering of qE by a pH gradient across the thylakoid membrane and subsequent changes in PSII. We discuss how these changes alter the energy transfer network of chlorophyll in the grana membrane and allow it to switch between an unquenched and quenched state. Within this conceptual framework, we describe the biochemical and spectroscopic measurements and models that have been used to understand the mechanism of qE in plants with a focus on measurements of samples that perform qE in response to light. In addition, we address the outstanding questions and challenges in the field. One of the current challenges in gaining a full understanding of qE is the difficulty in simultaneously measuring both the photophysical mechanism of quenching and the physiological state of the thylakoid membrane. We suggest that new experimental and modeling efforts that can monitor the many processes that occur on multiple timescales and length scales will be important for elucidating the quantitative details of the mechanism of qE.

A structure-based model of energy transfer reveals the principles of light harvesting in photosystem II supercomplexes.

Photosystem II (PSII) initiates photosynthesis in plants through the absorption of light and subsequent conversion of excitation energy to chemical energy via charge separation. The pigment binding proteins associated with PSII assemble in the grana membrane into PSII supercomplexes and surrounding light harvesting complex II trimers. To understand the high efficiency of light harvesting in PSII requires quantitative insight into energy transfer and charge separation in PSII supercomplexes. We have constructed the first structure-based model of energy transfer in PSII supercomplexes. This model shows that the kinetics of light harvesting cannot be simplified to a single rate limiting step. Instead, substantial contributions arise from both excitation diffusion through the antenna pigments and transfer from the antenna to the reaction center (RC), where charge separation occurs. Because of the lack of a rate-limiting step, fitting kinetic models to fluorescence lifetime data cannot be used to derive mechanistic insight on light harvesting in PSII. This model will clarify the interpretation of chlorophyll fluorescence data from PSII supercomplexes, grana membranes, and leaves.

A kinetic model of rapidly reversible nonphotochemical quenching.

Oxygen-evolving photosynthetic organisms possess nonphotochemical quenching (NPQ) pathways that protect against photo-induced damage. The majority of NPQ in plants is regulated on a rapid timescale by changes in the pH of the thylakoid lumen. In order to quantify the rapidly reversible component of NPQ, called qE, we developed a mathematical model of pH-dependent quenching of chlorophyll excitations in Photosystem II. Our expression for qE depends on the protonation of PsbS and the deepoxidation of violaxanthin by violaxanthin deepoxidase. The model is able to simulate the kinetics of qE at low and high light intensities. The simulations suggest that the pH of the lumen, which activates qE, is not itself affected by qE. Our model provides a framework for testing hypothesized qE mechanisms and for assessing the role of qE in improving plant fitness in variable light intensity.

Fluorescence lifetime snapshots reveal two rapidly reversible mechanisms of photoprotection in live cells of Chlamydomonas reinhardtii.

Photosynthetic organisms avoid photodamage to photosystem II (PSII) in variable light conditions via a suite of photoprotective mechanisms called nonphotochemical quenching (NPQ), in which excess absorbed light is dissipated harmlessly. To quantify the contributions of different quenching mechanisms to NPQ, we have devised a technique to measure the changes in chlorophyll fluorescence lifetime as photosynthetic organisms adapt to varying light conditions. We applied this technique to measure the fluorescence lifetimes responsible for the predominant, rapidly reversible component of NPQ, qE, in living cells of Chlamydomonas reinhardtii. Application of high light to dark-adapted cells of C. reinhardtii led to an increase in the amplitudes of 65 ps and 305 ps chlorophyll fluorescence lifetime components that was reversed after the high light was turned off. Removal of the pH gradient across the thylakoid membrane linked the changes in the amplitudes of the two components to qE quenching. The rise times of the amplitudes of the two components were significantly different, suggesting that the changes are due to two different qE mechanisms. We tentatively suggest that the changes in the 65 ps component are due to charge-transfer quenching in the minor light-harvesting complexes and that the changes in the 305 ps component are due to aggregated light-harvesting complex II trimers that have detached from PSII. We anticipate that this technique will be useful for resolving the various mechanisms of NPQ and for quantifying the timescales associated with these mechanisms.

Design principles of photosynthetic light-harvesting.

Photosynthetic organisms are capable of harvesting solar energy with near unity quantum efficiency. Even more impressively, this efficiency can be regulated in response to the demands of photosynthetic reactions and the fluctuating light-levels of natural environments. We discuss the distinctive design principles through which photosynthetic light-harvesting functions. These emergent properties of photosynthesis appear both within individual pigment-protein complexes and in how these complexes integrate to produce a functional, regulated apparatus that drives downstream photochemistry. One important property is how the strong interactions and resultant quantum coherence, produced by the dense packing of photosynthetic pigments, provide a tool to optimize for ultrafast, directed energy transfer. We also describe how excess energy is quenched to prevent photodamage under high-light conditions, which we investigate through theory and experiment. We conclude with comments on the potential of using these features to improve solar energy devices.

Pyridoxamine: an extremely potent scavenger of 1,4-dicarbonyls.

1,4-Dicarbonyl compounds, which include 2,5-hexanedione and recently discovered endogenous 4-ketoaldehydes (levuglandins, isoketals, and neuroketals), exhibit severe toxicity. The key step in the toxicity of these compounds is their reaction with the lysyl residues of proteins to form pyrrole adducts. To screen for effective scavengers of these toxic compounds, we determined the reaction rates of pyrrole formation for a series of primary amines with a model 4-ketoaldehyde, 4-oxopentanal (OPA). We found pyridoxamine (PM) to react extremely rapidly, with a second-order rate constant at physiological pH being approximately 2300 times faster than that of Nalpha-acetyllysine. The extreme reactivity of PM was unique to 1,4-dicarbonyls, as its reactions with methylglyoxal and 4-hydroxy-2(E)-nonenal were much slower and only slightly faster than with Nalpha-acetyllysine. The phenolic group of PM was found to be essential to its high reactivity, and the rate constant for pyrrole formation with OPA exhibited a maximum at pH 7.5, close to the second pKa of PM. We therefore propose a mechanism involving transfer of the phenolic proton to the carbonyl of the initially formed hemiacetal, which facilitates subsequent nucleophilic attack and ring closure. Only 1,4-dicarbonyls are likely to participate in the proposed mechanism, thereby conferring unique sensitivity of this class of compounds to scavenging by PM.

A specific HPLC-UV method for the determination of cysteine and related aminothiols in biological samples.

We present a highly selective and sensitive method for the determination of cysteine (Cys) and related aminothiols that play important roles in health and disease. The key step in the analysis is treatment with 1,1'-thiocarbonyldiimidazole (TCDI) that rapidly and quantitatively reacts with both the amino and thiol groups to form stable cyclic dithiocarbamates with intense UV absorption. Cys, homocysteine (hCys), and cysteinylglycine in plasma (75 microl), urine (100 microl), or cerebrospinal fluid (100-500 microl) were determined by separating and measuring their cyclic derivatives by a high performance liquid chromatograph (HPLC) connected to a UV detector. The chromatograms obtained using TCDI contained fewer and better-resolved peaks than those produced by less selective reagents used previously. Using chemically similar 2-methylcysteine as the internal standard, high repeatability (variation of less than 5%) and adequate sensitivity to detect small increments (10-20%) in the concentrations of cysteinylglycine and hCys were achieved. The HPLC method can also be modified to measure d-penicillamine (greater than 0.8 muM) in plasma (50 microl) providing a potential method to monitor plasma levels of this drug in patients.

Specific determination of cysteine and penicillamine through cyclization to 2-thioxothiazolidine-4-carboxylic acids.

A very simple and highly specific method for the determination of cysteine and penicillamine is presented. Treatment with 1,1'-thiocarbonyldiimidazole in slightly basic solutions converts cysteine rapidly and quantitatively to a very stable derivative, 2-thioxothiazolidine-4-carboxylic acid, which is not formed by thiols or amines. The cyclic derivative has a characteristic UV spectrum with a maximum at 272 nm and it can be quantified by one of two ways. (1) When only inorganic ions and common additives are present, a spectrophotometer or a plate reader capable of handling multiple samples is sufficient to estimate cysteine in the concentration range of 2-150 muM. Penicillamine is determined similarly by cyclization to 5,5-dimethyl-2-thioxothiazolidine-4-carboxylic acid. The method is also applicable to derivatives of cysteine modified only at the carboxyl group. (2) To determine cysteine in complex mixtures, a liquid chromatograph connected to a UV detector is used. The elution is rapid with well-separated peaks for the thiazolidine derivatives. The detection limit is 2 pmole of cysteine or penicillamine per injection and the detector response is linear up to 1 nmole. The usefulness of the method is demonstrated by determining cysteine and penicillamine in capsules and by measuring cysteine in a dietary supplement.