Structural dynamics in the C terminal domain homolog of orange carotenoid Protein reveals residues critical for carotenoid uptake

The structural features enabling carotenoid translocation between molecular entities in nature is poorly understood. Here, we present the three-dimensional X-ray structure of an expanded oligomeric state of the C-terminal domain homolog (CTDH) of the orange carotenoid protein, a key water-soluble protein in cyanobacterial photosynthetic photo-protection, at 2.9 Å resolution. This protein binds a canthaxanthin carotenoid ligand and undergoes structural reorganization at the dimeric level, which facilitates cargo uptake and delivery. The structure displays heterogeneity revealing the dynamic nature of its C-terminal tail (CTT). Molecular dynamics (MD) simulations based on the CTDH structures identified specific residues that govern the dimeric transition mechanism. Mutagenesis based on the crystal structure and these MD simulations then confirmed that these specific residues within the CTT are critical for carotenoid uptake, encapsulation and delivery processes. We present a mechanism that can be applied to other systems that require cargo uptake.     

Protein regulation of carotenoid binding; gatekeeper and locking amino acid residues in reaction centers of Rhodobacter sphaeroides

X-ray diffraction was used to determine high-resolution structures of the reaction center (RC) complex from the carotenoidless mutant, Rb. sphaeroides R-26.1, without or reconstituted with carotenoids. The results are compared with the structure of the RC from a semiaerobically grown Rb. sphaeroides strain 2.4.1. The investigation reveals the structure of the carotenoid in the different protein preparations, the nature of its binding site, and a plausible mechanism by which the carotenoid is incorporated unidirectionally in its characteristic geometric configuration. The structural data suggest that the accessibility of the carotenoid to the binding site is controlled by a specific "gatekeeper" residue which allows the carotenoid to approach the binding site from only one direction. Carotenoid binding to the protein is secured by hydrogen bonding to a separate "locking" amino acid. The study reveals the specific molecular interactions that control how the carotenoid protects the photosynthetic apparatus against photo-induced oxidative destruction.     

Mutation of a single residue, β-glutamate-20, alters protein–lipid interactions of light harvesting complex II

It is well established that assembly of the peripheral antenna complex, LH2, is required for proper photosynthetic membrane biogenesis in the purple bacterium Rhodobacter sphaeroides . The underlying interactions are, as yet, not understood. Here we examined the relationship between the morphology of the photosynthetic membrane and the lipid–protein interactions at the LH2–lipid interface. The non-bilayer lipid, phosphatidylethanolamine, is shown to be highly enriched in the boundary lipid phase of LH2. Sequence alignments indicate a putative lipid binding site, which includes β-glutamate-20 and the adjacent carotenoid end group. Replacement of β-glutamate-20 with alanine results in significant reduction of phosphatidylethanolamine and concomitant raise in phosphatidylcholine in the boundary lipid phase of LH2 without altering the lipid composition of the bulk phase. The morphology of the LH2 housing membrane is, however, unaffected by the amino acid replacement. In contrast, simultaneous modification of glutamate‐20 and exchange of the carotenoid sphaeroidenone with neurosporene results in significant enlargement of the vesicular membrane invaginations. These findings suggest that the LH2 complex, specifically β-glutamate-20 and the carotenoids' polar head group, contribute to the shaping of the photosynthetic membrane by specific interactions with surrounding lipid molecules.     

铜胁迫下链格孢菌对白车轴草生理生态的影响

通过盆栽实验研究了Cu胁迫下接种病原菌链格孢菌(Alternaria tenuis Nees)对白车轴草(Trifolium repens L.)生理生态指标的影响.结果表明:在未接种的对照组中,随着Cu浓度的增大(0~3000mg.kg-1),植株叶片失绿,生物量下降,叶绿素a、b、a b和类胡萝卜素及叶片可溶性蛋白质含量下降;植物体内丙二醛(MDA)高度积累,细胞膜结构遭到损坏,电导率增大;植株活性氧清除系统受损,不能保持原有平衡,超氧化物歧化酶(SOD)和过氧化氢酶(CAT)活性显著降低,过氧化物酶(POD)活性升高.接种链格孢菌后,植株叶片色素、膜系统及保护酶系统的损伤均加重,与不接种对照组相比,相同浓度Cu处理的叶绿素a、b、a b和类胡萝卜素、可溶性蛋白质含量、SOD和CAT活性均呈不同程度的下降,而电导率、MDA含量和POD活性则有所上升.     

Carotenoid biosynthesis in photosynthetic bacteria. Genetic characterization of the Rhodobacter capsulatus CrtI protein

Carotenoids are photoprotective pigments present in many photosynthetic and nonphotosynthetic organisms. The desaturation of phytoene into phytofluene is an early step in the biosynthetic pathway that in the photosynthetic bacterium Rhodobacter capsulatus is mediated by the product of the crtI gene. Here we report the sequence of this gene and the identification of CrtI as a membrane protein of approximate Mr 60,000. Mutant strains with 5-fold lower or 10-fold higher levels of CrtI with respect to wild type have only small differences in their carotenoid content, indicating that the cellular concentration of CrtI is not a limiting factor in carotenoid biosynthesis. However, a correlation was found between the levels of CrtI and the formation of a photosynthetic antenna system.     

Lateral organization of biological membranes

The lateral organization of biological membranes is of great importance in many biological processes, both for the formation of specific structures such as super-complexes and for function as observed in signal transduction systems. Over the last years, AFM studies, particularly of bacterial photosynthetic membranes, have revealed that certain proteins are able to segregate into functional domains with a specific organization. Furthermore, the extended non-random nature of the organization has been suggested to be important for the energy and redox transport properties of these specialized membranes. In the work reported here, using a coarse-grained Monte Carlo approach, we have investigated the nature of interaction potentials able to drive the formation and segregation of specialized membrane domains from the rest of the membrane and furthermore how the internal organization of the segregated domains can be modulated by the interaction potentials. These simulations show that long-range interactions are necessary to allow formation of membrane domains of realistic structure. We suggest that such possibly non-specific interactions may be of great importance in the lateral organization of biological membranes in general and in photosynthetic systems in particular. Finally, we consider the possible molecular origins of such interactions and suggest a fundamental role for lipid-mediated interactions in driving the formation of specialized photosynthetic membrane domains. We call these lipid-mediated interactions a ‘lipophobic effect.’     

In vitro and in vivo investigation of chlorophyll binding sites involved in non‐photochemical quenching in Chlamydomonas reinhardtii

Non‐photochemical quenching (NPQ) of the light energy absorbed is one of the main photoprotective mechanisms evolved by oxygenic photosynthetic organisms to avoid photodamage, at a cost of reduced photosynthetic efficiency. Tuning of NPQ has been reported as a promising biotechnological strategy to increase productivity in both higher plants and unicellular microalgae. Engineering of NPQ induction requires the comprehension of its molecular mechanism(s), strongly debated in the last three decades with several different models proposed. In this work, the molecular details of NPQ induction was investigated at intramolecular level by in vitro and in vitro site‐specific mutagenesis on chlorophyll binding sites of the Light‐Harvesting Complex Stress‐Related 3 (LHCSR3) protein, the pigment binding complexes identified as the quencher during NPQ induction in the model organism for green algae Chlamydomonas reinhardtii. The results obtained demonstrate a correlation between the quenching activity of LHCSR3 variants in vitro and the NPQ phenotypes observed in vivo. In particular, multiple quenching sites in LHCSR3 cooperatively dissipating the excitation energy were revealed with a peculiar role of Chl 613, a chromophore located a close distance to carotenoid binding site L1.     

Carotenoid production and change of photosynthetic functions in Scenedesmus sp. exposed to nitrogen limitation and acetate treatment

Under stress conditions, some microalgae up-regulate certain biosynthetic pathways, leading to the accumulation of specific compounds. For example, changing nutrient composition can induce stress in algae’s physiological activities, which may trigger an intense increase in carotenoid production. In this study, the change of photosynthetic functions and carotenoid production in the green microalga Scenedesmus sp. was investigated when algal cultures were exposed to conditions including limited nitrogen content with the addition of sodium acetate. Microalgal cultures were treated for 18 days under higher irradiance conditions. We observed a decrease of chlorophyll content induced concomitantly with a decline of photosystem II and I photochemistry. At the same time, an important increase in carotenoid content was detected. By using high-performance liquid chromatographic analysis, we found that the secondary carotenoids astaxanthin and canthaxanthin were accumulated compared to controls. During the process of carotenoid accumulation, chlorophyll degradation was found in addition to a strong decrease in photosynthetic electron transport. Such changes may be associated with the structural reorganization of the photosynthetic apparatus and can be a useful indicator of secondary carotenoid accumulation in algal cultures.     

General and specific lipid–protein interactions in Na,K-ATPase

The molecular activity of Na,K-ATPase and other P2 ATPases like Ca^2 +-ATPase is influenced by the lipid environment via both general (physical) and specific (chemical) interactions. Whereas the general effects of bilayer structure on membrane protein function are fairly well described and understood, the importance of the specific interactions has only been realized within the last decade due particularly to the growing field of membrane protein crystallization, which has shed new light on the molecular details of specific lipid–protein interactions. It is a remarkable observation that specific lipid–protein interactions seem to be evolutionarily conserved, and conformations of specifically bound lipids at the lipid–protein surface within the membrane are similar in crystal structures determined with different techniques and sources of the protein, despite the rather weak lipid–protein interaction energy. Studies of purified detergent-soluble recombinant αβ or αβFXYD Na,K-ATPase complexes reveal three separate functional effects of phospholipids and cholesterol with characteristic structural selectivity. The observations suggest that these three effects are exerted at separate binding sites for phophatidylserine/cholesterol (stabilizing), polyunsaturated phosphatidylethanolamine (stimulatory), and saturated PC or sphingomyelin/cholesterol (inhibitory), which may be located within three lipid-binding pockets identified in recent crystal structures of Na,K-ATPase. The findings point to a central role of direct and specific interactions of different phospholipids and cholesterol in determining both stability and molecular activity of Na,K-ATPase and possible implications for physiological regulation by membrane lipid composition. This article is part of a special issue titled “Lipid–Protein Interactions.”     

An ORF323 with homology to crtE, specifying prephytoene pyrophosphate dehydrogenase, is encoded by cyanelle DNA in the eukaryotic alga Cyanophora paradoxa.

Carotenoids are essential constituents of the light-harvesting and light-protective systems of photosynthetic organisms. The biochemistry of carotenoid biosynthesis in eukaryotes is known, whereas evidence for the genes specifying this biosynthetic pathway is scant. We report here the nucleotide sequence and expression of a gene likely encoding crtE (prephytoene pyrophosphate dehydrogenase). The reaction product of this enzyme is phytoene, a C40 carotenoid precursor common to all organisms. The gene is found in the cyanelle (plastid) DNA of an eukaryotic alga, Cyanophora paradoxa. The expression into protein of cyanelle crtE has been demonstrated in vitro. The identity and similarity scores of CrtE from cyanelles with the corresponding protein from the photosynthetic bacterium Rhodobacter capsulatus are 28.6 and 68.5%, respectively.     

Mutation of a single residue, beta-glutamate-20, alters protein-lipid interactions of light harvesting complex II.

It is well established that assembly of the peripheral antenna complex, LH2, is required for proper photosynthetic membrane biogenesis in the purple bacterium Rhodobacter sphaeroides. The underlying interactions are, as yet, not understood. Here we examined the relationship between the morphology of the photosynthetic membrane and the lipid-protein interactions at the LH2-lipid interface. The non-bilayer lipid, phosphatidylethanolamine, is shown to be highly enriched in the boundary lipid phase of LH2. Sequence alignments indicate a putative lipid binding site, which includes beta-glutamate-20 and the adjacent carotenoid end group. Replacement of beta-glutamate-20 with alanine results in significant reduction of phosphatidylethanolamine and concomitant raise in phosphatidylcholine in the boundary lipid phase of LH2 without altering the lipid composition of the bulk phase. The morphology of the LH2 housing membrane is, however, unaffected by the amino acid replacement. In contrast, simultaneous modification of glutamate-20 and exchange of the carotenoid sphaeroidenone with neurosporene results in significant enlargement of the vesicular membrane invaginations. These findings suggest that the LH2 complex, specifically beta-glutamate-20 and the carotenoids' polar head group, contribute to the shaping of the photosynthetic membrane by specific interactions with surrounding lipid molecules.     

Linear dichroism and circular dichroism in photosynthesis research

The efficiency of photosynthetic light energy conversion depends largely on the molecular architecture of the photosynthetic membranes. Linear- and circular-dichroism (LD and CD) studies have contributed significantly to our knowledge of the molecular organization of pigment systems at different levels of complexity, in pigment–protein complexes, supercomplexes, and their macroassemblies, as well as in entire membranes and membrane systems. Many examples show that LD and CD data are in good agreement with structural data; hence, these spectroscopic tools serve as the basis for linking the structure of photosynthetic pigment–protein complexes to steady-state and time-resolved spectroscopy. They are also indispensable for identifying conformations and interactions in native environments, and for monitoring reorganizations during photosynthetic functions, and are important in characterizing reconstituted and artificially constructed systems. This educational review explains, in simple terms, the basic physical principles, and theory and practice of LD and CD spectroscopies and of some related quantities in the areas of differential polarization spectroscopy and microscopy.     

Activation of zeaxanthin is an obligatory event in the regulation of photosynthetic light harvesting.

By dynamic changes in protein structure and function, the photosynthetic membranes of plants are able to regulate the partitioning of absorbed light energy between utilization in photosynthesis and photoprotective non-radiative dissipation of the excess energy. This process is controlled by features of the intact membrane, the transmembrane pH gradient, the organization of the photosystem II antenna proteins and the reversible binding of a specific carotenoid, zeaxanthin. Resonance Raman spectroscopy has been applied for the first time to wild type and mutant Arabidopsis leaves and to intact thylakoid membranes to investigate the nature of the absorption changes obligatorily associated with the energy dissipation process. The observed changes in the carotenoid Resonance Raman spectrum proved that zeaxanthin was involved and indicated a dramatic change in zeaxanthin environment that specifically alters the pigment configuration and red-shifts the absorption spectrum. This activation of zeaxanthin is a key event in the regulation of light harvesting.     

How carotenoids function in photosynthetic bacteria

Carotenoids are essential for the survival of photosynthetic organisms. They function as light-harvesting molecules and provide photoprotection. In this review, the molecular features which determine the efficiencies of the various photophysical and photochemical processes of carotenoids are discussed. The behavior of carotenoids in photosynthetic bacterial reaction centers and light-harvesting complexes is correlated with data from experiments carried out on carotenoids and model systems in vitro. The status of the carotenoid structural determinations in vivo is reviewed.     

Redox functions of carotenoids in photosynthesis

Carotenoids are well-known as light-harvesting pigments. They also play important roles in protecting the photosynthetic apparatus from damaging reactions of chlorophyll triplet states and singlet oxygen in both plant and bacterial photosynthesis. Recently, it has been found that beta-carotene functions as a redox intermediate in the secondary pathways of electron transfer within photosystem II and that carotenoid cation radicals are transiently formed after photoexcitation of bacterial light-harvesting complexes. The redox role of beta-carotene in photosystem II is unique among photosynthetic reaction centers and stems from the very strongly oxidizing intermediates that form in the process of water oxidation. Because of the extended pi-electron-conjugated system of carotenoid molecules, the cation radical is delocalized. This enables beta-carotene to function as a "molecular wire", whereby the centrally located oxidizing species is shuttled to peripheral redox centers of photosystem II where it can be dissipated without damaging the system. The physiological significance of carotenoid cation radical formation in bacterial light-harvesting complexes is not yet clear, but may provide a novel mechanism for excitation energy dissipation as a means of photoprotection. In this paper, the redox reactions of carotenoids in photosystem II and bacterial light-harvesting complexes are presented and the possible roles of carotenoid cation radicals in photoprotection are discussed.     

A Coarse Grained Model for a Lipid Membrane with Physiological Composition and Leaflet Asymmetry

The resemblance of lipid membrane models to physiological membranes determines how well molecular dynamics (MD) simulations imitate the dynamic behavior of cell membranes and membrane proteins. Physiological lipid membranes are composed of multiple types of phospholipids, and the leaflet compositions are generally asymmetric. Here we describe an approach for self-assembly of a Coarse-Grained (CG) membrane model with physiological composition and leaflet asymmetry using the MARTINI force field. An initial set-up of two boxes with different types of lipids according to the leaflet asymmetry of mammalian cell membranes stacked with 0.5 nm overlap, reliably resulted in the self-assembly of bilayer membranes with leaflet asymmetry resembling that of physiological mammalian cell membranes. Self-assembly in the presence of a fragment of the plasma membrane protein syntaxin 1A led to spontaneous specific positioning of phosphatidylionositol(4,5)bisphosphate at a positively charged stretch of syntaxin consistent with experimental data. An analogous approach choosing an initial set-up with two concentric shells filled with different lipid types results in successful assembly of a spherical vesicle with asymmetric leaflet composition. Self-assembly of the vesicle in the presence of the synaptic vesicle protein synaptobrevin 2 revealed the correct position of the synaptobrevin transmembrane domain. This is the first CG MD method to form a membrane with physiological lipid composition as well as leaflet asymmetry by self-assembly and will enable unbiased studies of the incorporation and dynamics of membrane proteins in more realistic CG membrane models.     

Mechanisms Underlying Carotenoid Absorption in Oxygenic Photosynthetic Proteins

The electronic properties of carotenoid molecules underlie their multiple functions throughout biology, and tuning of these properties by their in vivo locus is of vital importance in a number of cases. This is exemplified by photosynthetic carotenoids, which perform both light-harvesting and photoprotective roles essential to the photosynthetic process. However, despite a large number of scientific studies performed in this field, the mechanism(s) used to modulate the electronic properties of carotenoids remain elusive. We have chosen two specific cases, the two β-carotene molecules in photosystem II reaction centers and the two luteins in the major photosystem II light-harvesting complex, to investigate how such a tuning of their electronic structure may occur. Indeed, in each case, identical molecular species in the same protein are seen to exhibit different electronic properties (most notably, shifted absorption peaks). We assess which molecular parameters are responsible for this in vivo tuning process and attempt to assign it to specific molecular events imposed by their binding pockets.     

Proteomic characterization of the Rhodobacter sphaeroides 2.4.1 photosynthetic membrane: identification of new proteins

The Rhodobacter sphaeroides intracytoplasmic membrane (ICM) is an inducible membrane that is dedicated to the major events of bacterial photosynthesis, including harvesting light energy, separating primary charges, and transporting electrons. In this study, multichromatographic methods coupled with Fourier transform ion cyclotron resonance mass spectrometry, combined with subcellular fractionation, was used to test the hypothesis that the photosynthetic membrane of R. sphaeroides 2.4.1 contains a significant number of heretofore unidentified proteins in addition to the integral membrane pigment-protein complexes, including light-harvesting complexes 1 and 2, the photochemical reaction center, and the cytochrome bc(1) complex described previously. Purified ICM vesicles are shown to be enriched in several abundant, newly identified membrane proteins, including a protein of unknown function (AffyChip designation RSP1760) and a possible alkane hydroxylase (RSP1467). When the genes encoding these proteins are mutated, specific photosynthetic phenotypes are noted, illustrating the potential new insights into solar energy utilization to be gained by this proteomic blueprint of the ICM. In addition, proteins necessary for other cellular functions, such as ATP synthesis, respiration, solute transport, protein translocation, and other physiological processes, were also identified to be in association with the ICM. This study is the first to provide a more global view of the protein composition of a photosynthetic membrane from any source. This protein blueprint also provides insights into potential mechanisms for the assembly of the pigment-protein complexes of the photosynthetic apparatus, the formation of the lipid bilayer that houses these integral membrane proteins, and the possible functional interactions of ICM proteins with activities that reside in domains outside this specialized bioenergetic membrane.     

Kinetic Mechanisms of Biological Regulation in Photosynthetic Organisms

Principles of regulation on different levels of photosynthetic apparatus are discussed. Mathematical models of isolated photosynthetic reaction centers and general system of energy transduction in chloroplast are developed. A general approach to model these complex metabolic systems is suggested. Regulatory mechanisms in plant cell are correlated with the different patterns of fluorescence induction curve at different internal physiological states of the cells and external (environmental) conditions. Light regulation inside photosynthetic reaction centers, diffusion processes in thylakoid membrane, generation of transmembrane electrochemical potential, coupling with processes of CO₂ fixation in Calvin Cycle are considered as stages of control of energy transformation in chloroplasts in their connection with kinetic patterns of fluorescence induction curves and other spectrophotometric data.