The ancestral symbiont sensor kinase CSK links photosynthesis with gene expression in chloroplasts

Does mRNA targeting explain gene retention in chloroplasts?

During their evolution from cyanobacteria, plastids have relinquished most of their genes to the host cell nucleus, but have retained a core set of genes that are transcribed and translated within the organelle. Previous explanations have included incompatible codon or base composition, problems importing certain proteins across the double membrane, or the need for tight regulation in concert with the redox status of the electron transport chain. In this opinion article we propose the 'mRNA targeting hypothesis'. Studies in cyanobacteria suggest that mRNAs encoding core photosynthetic proteins have features that are crucial for membrane targeting and coordination of early steps in complex assembly. We propose that the requirement for intimate involvement of mRNA molecules at the thylakoid surface explains the retention of core photosynthetic genes in chloroplasts.

Freezing treatment under light conditions leads to a dramatic enhancement of freezing tolerance in cold-acclimated Arabidopsis

Overwintering plants survive subzero temperatures by cold acclimation (CA), wherein they acquire freezing tolerance through short-term exposure to low temperatures above 0°C. The freezing tolerance of CA plants increases when they are subsequently exposed to mild subzero temperatures, a phenomenon known as second-phase cold hardening (2PH). Here, we explored the molecular mechanism and physiological conditions of 2PH. The results show that, compared with supercooling, a freezing treatment during 2PH after CA enhanced the freezing tolerance of Arabidopsis. This required CA as a pretreatment, and was designated as second-phase freezing acclimation (2PFA). Light increased the effect of 2PFA to enhance freezing tolerance after CA. C-repeat binding factor and cold-regulated genes were downregulated by light during the 2PFA treatment, a different transcription profile from that during CA. The freezing tolerance of 2PFA plants was decreased by the presence of the photosynthetic electron transfer inhibitor 3-(3,4-dichlorophenyl)-1,1-dimethylurea during the 2PFA treatment. Compared with wild-type plants, phototropin1,2 and phyb mutants showed lower freezing tolerance after 2PFA treatment. These results show that exposure to freezing after CA increases freezing tolerance as a secondary process, and that freezing under light conditions further increases freezing tolerance via pathways involving photoreceptors and photosynthetic electron transfer.

Reversible protein phosphorylation in higher plants: focus on state transitions

Reversible protein phosphorylation is one of the comprehensive mechanisms of cell metabolism regulation in eukaryotic organisms. The review describes the impact of the reversible protein phosphorylation on the regulation of growth and development as well as in adaptation pathways and signaling network in higher plant cells. The main part of the review is devoted to the role of the reversible phosphorylation of light-harvesting proteins of photosystem II and the state transition process in fine-tuning the photosynthetic activity of chloroplasts. A separate section of the review is dedicated to comparing the mechanisms and functional significance of state transitions in higher plants, algae, and cyanobacteria that allows the evolution aspects of state transitions meaning in various organisms to be discussed. Environmental factors affecting the state transitions are also considered. Additionally, we gain insight into the possible influence of STN7-dependent phosphorylation of the target proteins on the global network of reversible protein phosphorylation in plant cells as well as into the probable effect of the STN7 kinase inhibition on long-term acclimation pathways in higher plants.

Low-temperature and circadian signals are integrated by the sigma factor SIG5

Chloroplasts are a common feature of plant cells and aspects of their metabolism, including photosynthesis, are influenced by low-temperature conditions. Chloroplasts contain a small circular genome that encodes essential components of the photosynthetic apparatus and chloroplast transcription/translation machinery. Here, we show that in Arabidopsis, a nuclear-encoded sigma factor that controls chloroplast transcription (SIGMA FACTOR5) contributes to adaptation to low-temperature conditions. This process involves the regulation of SIGMA FACTOR5 expression in response to cold by the bZIP transcription factors ELONGATED HYPOCOTYL5 and ELONGATED HYPOCOTYL5 HOMOLOG. The response of this pathway to cold is gated by the circadian clock, and it enhances photosynthetic efficiency during long-term cold and freezing exposure. We identify a process that integrates low-temperature and circadian signals, and modulates the response of chloroplasts to low-temperature conditions.

Characterization of the preferred cation cofactors of chloroplast protein kinases in Arabidopsis thaliana

Chloroplasts sense a variety of stimuli triggering several acclimation responses. One prominent response is the mechanism of state transitions, which enables rapid adaption to changes in illumination. Here, we investigated the link between divalent cations (calcium, magnesium, and manganese) and protein kinase activity in Arabidopsis chloroplasts. Our results show that manganese ions are the strongest activator of kinase activity in chloroplasts followed by magnesium ions, whereas calcium ions are not able to induce kinase activity. Additionally, the phosphorylation of specific protein bands is strongly reduced in chloroplasts of a cmt1 mutant, which is impaired in manganese import into chloroplasts, as compared to the wild-type. These findings provide insights for the future characterization of chloroplast protein kinase activity and potential target proteins.

Plastoquinone pool redox state and control of state transitions in Chlamydomonas reinhardtii in darkness and under illumination

Movement of LHCII between two photosystems has been assumed to be similarly controlled by the redox state of the plastoquinone pool (PQ-pool) in plants and green algae. Here we show that the redox state of the PQ-pool of Chlamydomonas reinhardtii can be determined with HPLC and use this method to compare the light state in C. reinhardtii with the PQ-pool redox state in a number of conditions. The PQ-pool was at least moderately reduced under illumination with all tested types of visible light and oxidation was achieved only with aerobic dark treatment or with far-red light. Although dark incubations and white light forms with spectral distribution favoring one photosystem affected the redox state of PQ-pool differently, they induced similar Stt7-dependent state transitions. Thus, under illumination the dynamics of the PQ-pool and its connection with light state appears more complicated in C. reinhardtii than in plants. We suggest this to stem from the larger number of LHC-units and from less different absorption profiles of the photosystems in C. reinhardtii than in plants. The data demonstrate that the two different control mechanisms required to fulfill the dual function of state transitions in C. reinhardtii in photoprotection and in balancing light utilization are activated via different means.

Regulation of photosynthetic light reaction proteins via reversible phosphorylation

The regulation of photosynthesis occurs at different levels including the control of nuclear and plastid genes transcription, RNA processing and translation, protein translocation, assemblies and their post translational modifications. Out of all these, post translational modification enables rapid response of plants towards changing environmental conditions. Among all post-translational modifications, reversible phosphorylation is known to play a crucial role in the regulation of light reaction of photosynthesis. Although, phosphorylation of PS II subunits has been extensively studied but not much attention is given to other photosynthetic complexes such as PS I, Cytochrome b6f complex and ATP synthase. Phosphorylation reaction is known to protect photosynthetic apparatus in challenging environment conditions such as high light, elevated temperature, high salinity and drought. Recent studies have explored the role of photosynthetic protein phosphorylation in conferring plant immunity against the rice blast disease. The evolution of phosphorylation of different subunits of photosynthetic proteins occurred along with the evolution of plant lineage for their better adaptation to the changing environment conditions. In this review, we summarize the progress made in the research field of phosphorylation of photosynthetic proteins and highlights the missing links that need immediate attention.

Photosystem stoichiometry adjustment is a photoreceptor-mediated process in Arabidopsis

Plant growth under spectrally-enriched low light conditions leads to adjustment in the relative abundance of the two photosystems in an acclimatory response known as photosystem stoichiometry adjustment. Adjustment of photosystem stoichiometry improves the quantum efficiency of photosynthesis but how this process perceives light quality changes and how photosystem amount is regulated remain largely unknown. By using a label-free quantitative mass spectrometry approach in Arabidopsis here we show that photosystem stoichiometry adjustment is primarily driven by the regulation of photosystem I content and that this forms the major thylakoid proteomic response under light quality. Using light and redox signaling mutants, we further show that the light quality-responsive accumulation of photosystem I gene transcripts and proteins requires phytochrome B photoreceptor but not plastoquinone redox signaling as previously suggested. In far-red light, the increased acceptor side limitation might deplete active photosystem I pool, further contributing to the adjustment of photosystem stoichiometry.

Thiol redox switches regulate the oligomeric state of cyanobacterial Rre1, RpaA, and RpaB response regulators

Cyanobacteria employ two‐component sensor‐response regulator systems to monitor and respond to environmental challenges. The response regulators RpaA, RpaB, Rre1 and RppA are integral to circadian clock function and abiotic stress acclimation in cyanobacteria. RpaA, RpaB and Rre1 are known to interact with ferredoxin or thioredoxin, raising the possibility of their thiol regulation. Here, we report that Synechocystis sp. PCC 6803 Rre1, RpaA and RpaB exist as higher‐order oligomers under oxidising conditions and that reduced thioredoxin A converts them to monomers. We further show that these response regulators contain redox‐responsive cysteine residues with an E_m7 around −300 mV. These findings suggest a direct thiol modulation of the activity of these response regulators, independent of their cognate sensor kinases.

The plastoglobule-localized protein AtABC1K6 is a Mn2+-dependent kinase necessary for timely transition to reproductive growth

The Absence of bc₁ Complex (ABC1) is an ancient, atypical protein kinase family that emerged prior to the archaeal-eubacterial divergence. Loss-of-function mutants in ABC1 genes are linked to respiratory defects in microbes and humans and to compromised photosynthetic performance and stress tolerance in plants. However, demonstration of protein kinase activity remains elusive, hampering their study. Here, we investigate a homolog from Arabidopsis thaliana, AtABC1K6, and demonstrate in vitro autophosphorylation activity, which we replicate with a human ABC1 ortholog. We also show that AtABC1K6 protein kinase activity requires an atypical buffer composition, including Mn²⁺ as a divalent cation cofactor and a low salt concentration. AtABC1K6 associates with plastoglobule lipid droplets of A. thaliana chloroplasts, along with five paralogs. We show that the protein kinase activity associated with isolated A. thaliana plastoglobules was inhibited at higher salt concentrations, but could accommodate Mg²⁺ as well as Mn²⁺, indicating salt sensitivity, but not the requirement for Mn²⁺, may be a general characteristic of ABC1 proteins. Finally, loss of functional AtABC1K6 impairs the developmental transition from vegetative to reproductive growth. This phenotype was complemented by the wild-type sequence of AtABC1K6, but not by a kinase-dead point mutant in the unique Ala-triad of the ATP-binding pocket, demonstrating the physiological relevance of the protein's kinase activity. We suggest that ABC1s are bona fide protein kinases with a unique regulatory mechanism. Our results open the door to detailed functional and mechanistic studies of ABC1 proteins and plastoglobules.

Inhibition of Arabidopsis stomatal development by plastoquinone oxidation

Stomata are the pores in the epidermal surface of plant leaves that regulate the exchange of water and CO₂ with the environment thus controlling leaf gas exchange.¹ In the model dicot plant Arabidopsis thaliana, the transcription factors SPEECHLESS (SPCH) and MUTE sequentially control formative divisions in the stomatal lineage by forming heterodimers with ICE1.² SPCH regulates entry into the stomatal lineage and its stability or activity is regulated by a mitogen-activated protein kinase (MAPK) signaling cascade, mediated by its interaction with ICE1.^3-6 This MAPK pathway is regulated by extracellular epidermal patterning factor (EPFs) peptides, which bind a transmembrane receptor complex to inhibit (EPF1 and EPF2) or promote (STOMAGEN/EPFL9) stomatal development.^7-9 MUTE controls the transition to guard mother cell identity and is regulated by the HD-ZIP transcription factor HDG2, which is expressed exclusively in stomatal lineage cells.^10,11 Light signals acting through phytochrome and cryptochrome photoreceptors positively regulate stomatal development in response to increased irradiance.^12,13 Here we report that stomatal development is also regulated by the redox state of the photosynthetic electron transport chain (PETC). Oxidation of the plastoquinone (PQ) pool inhibits stomatal development by negatively regulating SPCH and MUTE expression. This mechanism is dependent on MPK6 and forms part of the response to lowering irradiance, which is distinct to the photoreceptor dependent response to increasing irradiance. Our results show that environmental signals can act through the PETC, demonstrating that photosynthetic signals regulate the development of the pores through which CO2 enters the leaf.

Stringent Response in Bacteria and Plants with Infection

Stringent response (SR), a primary stress reaction in bacteria and plant chloroplasts, is a molecular switch that provides operational stress-induced reprogramming of transcription under conditions of abiotic and biotic stress. Because the infection is a stressful situation for both partners (the host plant and the pathogen), we analyzed the expression of bacterial and plastid SR-related genes during plant-microbial interaction. In the phytopathogenic bacterium Pectobacterium atrosepticum, SpoT-dependent SR was induced after contact with potato or tobacco plants. In plants, two different scenarios of molecular events developed under bacterial infection. Plastid SR was not induced in the host plant potato Solanum tuberosum, which co-evolved with the pathogen for a long time. In this case, the salicylic acid defense pathway was activated and plants were more resistant to bacterial infection. SR was activated in the tobacco Nicotiana tabacum (experimental host) along with activation of jasmonic acid-related genes, resulting in plant death. These results are important to more fully understand the evolutionary interactions between plants and symbionts/pathogens.

A Holistic Approach to Study Photosynthetic Acclimation Responses of Plants to Fluctuating Light

Plants in natural environments receive light through sunflecks, the duration and distribution of these being highly variable across the day. Consequently, plants need to adjust their photosynthetic processes to avoid photoinhibition and maximize yield. Changes in the composition of the photosynthetic apparatus in response to sustained changes in the environment are referred to as photosynthetic acclimation, a process that involves changes in protein content and composition. Considering this definition, acclimation differs from regulation, which involves processes that alter the activity of individual proteins over short-time periods, without changing the abundance of those proteins. The interconnection and overlapping of the short- and long-term photosynthetic responses, which can occur simultaneously or/and sequentially over time, make the study of long-term acclimation to fluctuating light in plants challenging. In this review we identify short-term responses of plants to fluctuating light that could act as sensors and signals for acclimation responses, with the aim of understanding how plants integrate environmental fluctuations over time and tailor their responses accordingly. Mathematical modeling has the potential to integrate physiological processes over different timescales and to help disentangle short-term regulatory responses from long-term acclimation responses. We review existing mathematical modeling techniques for studying photosynthetic responses to fluctuating light and propose new methods for addressing the topic from a holistic point of view.

Regulation of Phaeodactylum plastid gene transcription by redox, light, and circadian signals

Diatoms are a diverse group of photosynthetic unicellular algae with a plastid of red-algal origin. As prolific primary producers in the ocean, diatoms fix as much carbon as all rainforests combined. The molecular mechanisms that contribute to the high photosynthetic productivity and ecological success of diatoms are however not yet fully understood. Using the model diatom Phaeodactylum tricornutum, here we show rhythmic transcript accumulation of plastid psaA, psbA, petB, and atpB genes as driven by a free running circadian clock. Treatment with the electron transport inhibitor 3-(3,4-dichlorophenyl)-1,1-dimethylurea overrides the circadian signal by markedly downregulating transcription of psaA, petB, and atpB genes but not the psbA gene. Changes in light quantity produce little change in plastid gene transcription while the effect of light quality seems modest with only the psaA gene responding in a pattern that is dependent on the redox state of the plastoquinone pool. The significance of these plastid transcriptional responses and the identity of the underlying genetic control systems are discussed with relevance to diatom photosynthetic acclimation.

The intracellular ROS accumulation in elicitor-induced immunity requires the multiple organelle-targeted Arabidopsis NPK1-related protein kinases

Recognition at the plasma membrane of danger signals (elicitors) belonging to the classes of the microbe/pathogen- and damage-associated molecular patterns is a key event in pathogen sensing by plants and is associated with a rapid activation of immune responses. Different cellular compartments, including plasma membrane, chloroplasts, nuclei and mitochondria, are involved in the immune cellular program. However, how pathogen sensing is transmitted throughout the cell remains largely to be uncovered. Arabidopsis NPK1-related Proteins (ANPs) are mitogen-activated protein kinase kinase kinases previously shown to have a role in immunity. In this article, we studied the in vivo intracellular dynamics of ANP1- and ANP3-GFP fusions and found that under basal physiological conditions both proteins are present in the cytosol, while ANP3 is also localized in mitochondria. After elicitor perception, both proteins are present also in the plastids and nuclei, revealing a localization pattern that is so far unique. The N-terminal region of the protein kinases is responsible for their localization in mitochondria and plastids. Moreover, we found that the localization of ANPs coincides with the sites of elicitor-induced ROS accumulation and that plants lacking ANP function do not accumulate intracellular ROS.

Transcription initiation as a control point in plastid gene expression

The extensive processing and protein-assisted stabilization of transcripts have been taken as evidence for a viewpoint that the control of gene expression had shifted entirely in evolution from transcriptional in the bacterial endosymbiont to posttranscriptional in the plastid. This suggestion is however at odds with many observations on plastid gene transcription. Chloroplasts of flowering plants and mosses contain two or more RNA polymerases with distinct promoter preference and division of labor for the coordinated synthesis of plastid RNAs. Plant and algal plastids further possess multiple nonredundant sigma factors that function as transcription initiation factors. The controlled accumulation of plastid sigma factors and modification of their activity by sigma-binding proteins and phosphorylation constitute additional transcriptional regulatory strategies. Plant and algal plastids also contain dedicated one- or two-component transcriptional regulators. Transcription initiation thus continues to form a critical control point at which varied developmental and environmental signals intersect with plastid gene expression.

Cytochrome b6f - Orchestrator of photosynthetic electron transfer

Cytochrome b₆f (cytb₆f) lies at the heart of the light-dependent reactions of oxygenic photosynthesis, where it serves as a link between photosystem II (PSII) and photosystem I (PSI) through the oxidation and reduction of the electron carriers plastoquinol (PQH₂) and plastocyanin (Pc). A mechanism of electron bifurcation, known as the Q-cycle, couples electron transfer to the generation of a transmembrane proton gradient for ATP synthesis. Cytb₆f catalyses the rate-limiting step in linear electron transfer (LET), is pivotal for cyclic electron transfer (CET) and plays a key role as a redox-sensing hub involved in the regulation of light-harvesting, electron transfer and photosynthetic gene expression. Together, these characteristics make cytb₆f a judicious target for genetic manipulation to enhance photosynthetic yield, a strategy which already shows promise. In this review we will outline the structure and function of cytb₆f with a particular focus on new insights provided by the recent high-resolution map of the complex from Spinach.

Sigma factor 1 in chloroplast gene transcription and photosynthetic light acclimation

Sigma factors are dissociable subunits of bacterial RNA polymerase that ensure efficient transcription initiation from gene promoters. Owing to their prokaryotic origin, chloroplasts possess a typical bacterial RNA polymerase together with its sigma factor subunit. The higher plant Arabidopsis thaliana contain as many as six sigma factors for the hundred or so of its chloroplast genes. The role of this relatively large number of transcription initiation factors for the miniature chloroplast genome, however, is not fully understood. Using two Arabidopsis T-DNA insertion mutants, we show that sigma factor 1 (SIG1) initiates transcription of a specific subset of chloroplast genes. We further show that the photosynthetic control of PSI reaction center gene transcription requires complementary regulation of the nuclear SIG1 gene at the transcriptional level. This SIG1 gene regulation is dependent on both a plastid redox signal and a light signal transduced by the phytochrome photoreceptor.

An evolutionarily conserved iron-sulfur cluster underlies redox sensory function of the Chloroplast Sensor Kinase

Photosynthetic efficiency depends on equal light energy conversion by two spectrally distinct, serially-connected photosystems. The redox state of the plastoquinone pool, located between the two photosystems, is a key regulatory signal that initiates acclimatory changes in the relative abundance of photosystems. The Chloroplast Sensor Kinase (CSK) links the plastoquinone redox signal with photosystem gene expression but the mechanism by which it monitors the plastoquinone redox state is unclear. Here we show that the purified Arabidopsis and Phaeodactylum CSK and the cyanobacterial CSK homologue, Histidine kinase 2 (Hik2), are iron-sulfur proteins. The Fe-S cluster of CSK is further revealed to be a high potential redox-responsive [3Fe-4S] center. CSK responds to redox agents with reduced plastoquinone suppressing its autokinase activity. Redox changes within the CSK iron-sulfur cluster translate into conformational changes in the protein fold. These results provide key insights into redox signal perception and propagation by the CSK-based chloroplast two-component system.

RSH enzyme diversity for (p)ppGpp metabolism in Phaeodactylum tricornutum and other diatoms

The nucleotides guanosine tetraphosphate and pentaphosphate (together known as (p)ppGpp or magic spot) are produced in plant plastids from GDP/GTP and ATP by RelA-SpoT homologue (RSH) enzymes. In the model plant Arabidopsis (p)ppGpp regulates chloroplast transcription and translation to affect growth, and is also implicated in acclimation to stress. However, little is known about (p)ppGpp metabolism or its evolution in other photosynthetic eukaryotes. Here we studied (p)ppGpp metabolism in the marine diatom Phaeodactylum tricornutum. We identified three expressed RSH genes in the P. tricornutum genome, and determined the enzymatic activity of the corresponding enzymes by heterologous expression in bacteria. We showed that two P. tricornutum RSH are (p)ppGpp synthetases, despite substitution of a residue within the active site believed critical for activity, and that the third RSH is a bifunctional (p)ppGpp synthetase and hydrolase, the first of its kind demonstrated in a photosynthetic eukaryote. A broad phylogenetic analysis then showed that diatom RSH belong to novel algal RSH clades. Together our work significantly expands the horizons of (p)ppGpp signalling in the photosynthetic eukaryotes by demonstrating an unexpected functional, structural and evolutionary diversity in RSH enzymes from organisms with plastids derived from red algae.

Evidence for convergent sensing of multiple abiotic stresses in cyanobacteria

BACKGROUND

Bacteria routinely utilize two-component signal transduction pathways to sense and alter gene expression in response to environmental cues. While cyanobacteria express numerous two-component systems, these pathways do not regulate all of the genes within many of the identified abiotic stress-induced regulons.

METHODS

Electron transport inhibitors combined with western analysis and measurement of chlorophyll a fluorescent yield, using pulse amplitude modulation fluorometry, were used to detect the effect of a diverse range of abiotic stresses on the redox status of the photosynthetic electron transport chain and the accumulation and degradation of the Synechocystis sp. PCC 6803 DEAD box RNA helicase, CrhR.

RESULTS

Alterations in CrhR abundance were tightly correlated with the redox poise of the electron transport chain between Q_A and cytochrome b₆f, with reduction favoring CrhR accumulation.

CONCLUSIONS

The results provide evidence for an alternative, convergent sensing mechanism mediated through the redox poise of Q_B/PQH₂ that senses multiple, divergent forms of abiotic stress and regulates accumulation of CrhR. The RNA helicase activity of CrhR could then function as a post-translational effector to regulate downstream gene expression.

GENERAL SIGNIFICANCE

The potential for a related system in Staphylococcus aureus and higher plant chloroplasts suggest convergent sensing mechanisms may be evolutionarily conserved and occur more widely than anticipated.

Antioxidant and signaling functions of the plastoquinone pool in higher plants

The review covers data representing the plastoquinone pool as the component integrated in plant antioxidant defense and plant signaling. The main goal of the review is to discuss the evidence describing the plastoquinone-involved biochemical reactions, which are incorporated in maintaining the sustainability of higher plants to stress conditions. In this context, the analysis of the reactions of various redox forms of plastoquinone with oxygen species is presented. The review describes how these reactions can constitute both the antioxidant and signaling functions of the pool. Special attention is paid to the reaction of superoxide anion radicals with plastohydroquinone molecules, producing hydrogen peroxide as signal molecules. Attention is also given to the processes affecting the redox state of the plastoquinone pool because the redox state of the pool is of special importance for antioxidant defense and signaling.

Diversity and Evolution of Sensor Histidine Kinases in Eukaryotes

Histidine kinases (HKs) are primary sensor proteins that act in cell signaling pathways generically referred to as "two-component systems" (TCSs). TCSs are among the most widely distributed transduction systems used by both prokaryotic and eukaryotic organisms to detect and respond to a broad range of environmental cues. The structure and distribution of HK proteins are now well documented in prokaryotes, but information is still fragmentary for eukaryotes. Here, we have taken advantage of recent genomic resources to explore the structural diversity and the phylogenetic distribution of HKs in the prominent eukaryotic supergroups. Searches of the genomes of 67 eukaryotic species spread evenly throughout the phylogenetic tree of life identified 748 predicted HK proteins. Independent phylogenetic analyses of predicted HK proteins were carried out for each of the major eukaryotic supergroups. This allowed most of the compiled sequences to be categorized into previously described HK groups. Beyond the phylogenetic analysis of eukaryotic HKs, this study revealed some interesting findings: 1) characterization of some previously undescribed eukaryotic HK groups with predicted functions putatively related to physiological traits; 2) discovery of HK groups that were previously believed to be restricted to a single kingdom in additional supergroups, and 3) indications that some evolutionary paths have led to the appearance, transfer, duplication, and loss of HK genes in some phylogenetic lineages. This study provides an unprecedented overview of the structure and distribution of HKs in the Eukaryota and represents a first step toward deciphering the evolution of TCS signaling in living organisms.

Oligomeric states in sodium ion-dependent regulation of cyanobacterial histidine kinase-2

Two-component signal transduction systems (TCSs) consist of sensor histidine kinases and response regulators. TCSs mediate adaptation to environmental changes in bacteria, plants, fungi and protists. Histidine kinase 2 (Hik2) is a sensor histidine kinase found in all known cyanobacteria and as chloroplast sensor kinase in eukaryotic algae and plants. Sodium ions have been shown to inhibit the autophosphorylation activity of Hik2 that precedes phosphoryl transfer to response regulators, but the mechanism of inhibition has not been determined. We report on the mechanism of Hik2 activation and inactivation probed by chemical cross-linking and size exclusion chromatography together with direct visualisation of the kinase using negative-stain transmission electron microscopy of single particles. We show that the functional form of Hik2 is a higher-order oligomer such as a hexamer or octamer. Increased NaCl concentration converts the active hexamer into an inactive tetramer. The action of NaCl appears to be confined to the Hik2 kinase domain.

Guanosine tetraphosphate modulates salicylic acid signalling and the resistance of Arabidopsis thaliana to Turnip mosaic virus

Chloroplasts can act as key players in the perception and acclimatization of plants to incoming environmental signals. A growing body of evidence indicates that chloroplasts play a critical role in plant immunity. Chloroplast function can be regulated by the nucleotides guanosine tetraphosphate and pentaphosphate [(p)ppGpp]. In plants, (p)ppGpp levels increase in response to abiotic stress and to plant hormones which are involved in abiotic and biotic stress signalling. In this study, we analysed the transcriptome of Arabidopsis plants that over-accumulate (p)ppGpp, and unexpectedly found a decrease in the levels of a broad range of transcripts for plant defence and immunity. To determine whether (p)ppGpp is involved in the modulation of plant immunity, we analysed the susceptibility of plants with different levels of (p)ppGpp to Turnip mosaic virus (TuMV) carrying a green fluorescent protein (GFP) reporter. We found that (p)ppGpp accumulation was associated with increased susceptibility to TuMV and reduced levels of the defence hormone salicylic acid (SA). In contrast, plants with lower (p)ppGpp levels showed reduced susceptibility to TuMV, and this was associated with the precocious up-regulation of defence-related genes and increased SA content. We have therefore demonstrated a new link between (p)ppGpp metabolism and plant immunity in Arabidopsis.

ABA signalling manipulation suppresses senescence of a leafy vegetable stored at room temperature

Postharvest senescence and associated stresses limit the shelf life and nutritional value of vegetables. Improved understanding of these processes creates options for better management. After harvest, controlled exposure to abiotic stresses and/or exogenous phytohormones can enhance nutraceutical, organoleptic and commercial longevity traits. With leaf senescence, abscisic acid (ABA) contents progressively rise, but the actual biological functions of this hormone through senescence still need to be clarified. Postharvest senescence of detached green cabbage leaves (Brassica oleracea var. capitata) was characterized under cold (4 °C) and room temperature (25 °C) storage conditions. Hormonal profiling of regions of the leaf blade (apical, medial, basal) revealed a decrease in cytokinins contents during the first days under both conditions, while ABA only increased at 25 °C. Treatments with ABA and a partial agonist of ABA (pyrabactin) for 8 days did not lead to significant effects on water and pigment contents, but increased cell integrity and altered 1-aminocyclopropane-1-carboxylic acid (ACC) and cytokinins contents. Transcriptome analysis showed transcriptional regulation of ABA, cytokinin and ethylene metabolism and signalling; proteasome components; senescence regulation; protection of chloroplast functionality and cell homeostasis; and suppression of defence responses (including glucosinolates and phenylpropanoids metabolism). It is concluded that increasing the concentration of ABA (or its partial agonist pyrabactin) from the start of postharvest suppresses senescence of stored leaves, changes the transcriptional regulation of glucosinolates metabolism and down-regulates biotic stress defence mechanisms. These results suggest a potential for manipulating ABA signalling for improving postharvest quality of leafy vegetables stored at ambient temperature.

Redox regulation of PEP activity during seedling establishment in Arabidopsis thaliana

Activation of the plastid-encoded RNA polymerase is tightly controlled and involves a network of phosphorylation and, as yet unidentified, thiol-mediated events. Here, we characterize PLASTID REDOX INSENSITIVE2, a redox-regulated protein required for full PEP-driven transcription. PRIN2 dimers can be reduced into the active monomeric form by thioredoxins through reduction of a disulfide bond. Exposure to light increases the ratio between the monomeric and dimeric forms of PRIN2. Complementation of prin2-2 with different PRIN2 protein variants demonstrates that the monomer is required for light-activated PEP-dependent transcription and that expression of the nuclear-encoded photosynthesis genes is linked to the activity of PEP. Activation of PEP during chloroplast development likely is the source of a retrograde signal that promotes nuclear LHCB expression. Thus, regulation of PRIN2 is the thiol-mediated mechanism required for full PEP activity, with PRIN2 monomerization via reduction by TRXs providing a mechanistic link between photosynthetic electron transport and activation of photosynthetic gene expression.

The plastid-encoded RNA polymerase PEP is regulated according to plastid redox state. Here, the authors show that the redox-regulated PRIN2 protein is reduced to monomeric form in a thiol-dependent manner in response to light and that PRIN2 monomers are required for PEP activity and retrograde signaling.

Photosynthetic fuel for heterologous enzymes: the role of electron carrier proteins

Plants, cyanobacteria, and algae generate a surplus of redox power through photosynthesis, which makes them attractive for biotechnological exploitations. While central metabolism consumes most of the energy, pathways introduced through metabolic engineering can also tap into this source of reducing power. Recent work on the metabolic engineering of photosynthetic organisms has shown that the electron carriers such as ferredoxin and flavodoxin can be used to couple heterologous enzymes to photosynthetic reducing power. Because these proteins have a plethora of interaction partners and rely on electrostatically steered complex formation, they form productive electron transfer complexes with non-native enzymes. A handful of examples demonstrate channeling of photosynthetic electrons to drive the activity of heterologous enzymes, and these focus mainly on hydrogenases and cytochrome P450s. However, competition from native pathways and inefficient electron transfer rates present major obstacles, which limit the productivity of heterologous reactions coupled to photosynthesis. We discuss specific approaches to address these bottlenecks and ensure high productivity of such enzymes in a photosynthetic context.

Integration of light and circadian signals that regulate chloroplast transcription by a nuclear-encoded sigma factor

We investigated the signalling pathways that regulate chloroplast transcription in response to environmental signals. One mechanism controlling plastid transcription involves nuclear-encoded sigma subunits of plastid-encoded plastid RNA polymerase. Transcripts encoding the sigma factor SIG5 are regulated by light and the circadian clock. However, the extent to which a chloroplast target of SIG5 is regulated by light-induced changes in SIG5 expression is unknown. Moreover, the photoreceptor signalling pathways underlying the circadian regulation of chloroplast transcription by SIG5 are unidentified. We monitored the regulation of chloroplast transcription in photoreceptor and sigma factor mutants under controlled light regimes in Arabidopsis thaliana. We established that a chloroplast transcriptional response to light intensity was mediated by SIG5; a chloroplast transcriptional response to the relative proportions of red and far red light was regulated by SIG5 through phytochrome and photosynthetic signals; and the circadian regulation of chloroplast transcription by SIG5 was predominantly dependent on blue light and cryptochrome. Our experiments reveal the extensive integration of signals concerning the light environment by a single sigma factor to regulate chloroplast transcription. This may originate from an evolutionarily ancient mechanism that protects photosynthetic bacteria from high light stress, which subsequently became integrated with higher plant phototransduction networks.

Probing the nucleotide-binding activity of a redox sensor: two-component regulatory control in chloroplasts

Two-component signal transduction systems mediate adaptation to environmental changes in bacteria, plants, fungi, and protists. Each two-component system consists of a sensor histidine kinase and a response regulator. Chloroplast sensor kinase (CSK) is a modified sensor histidine kinase found in chloroplasts-photosynthetic organelles of plants and algae. CSK regulates the transcription of chloroplast genes in response to changes in photosynthetic electron transport. In this study, the full-length and truncated forms of Arabidopsis CSK proteins were overexpressed and purified in order to characterise their kinase and redox sensing activities. Our results show that CSK contains a modified kinase catalytic domain that binds ATP with high affinity and forms a quinone adduct that may confer redox sensing activity.

A Proposal for Formation of Archaean Stromatolites before the Advent of Oxygenic Photosynthesis

Stromatolites are solid, laminar structures of biological origin. Living examples are sparsely distributed and formed by cyanobacteria, which are oxygenic phototrophs. However, stromatolites were abundant between 3.4 and 2.4 Gyr, prior to the advent of cyanobacteria and oxygenic photosynthesis. Here I propose that many Archaean stromatolites were seeded at points of efflux of hydrogen sulfide from hydrothermal fields into shallow water, while their laminar composition arose from alternating modes of strictly anoxygenic photosynthetic metabolism. These changes were a redox regulatory response of gene expression to changing hydrogen sulfide concentration, which fluctuated with intermittent dilution by tidal action or by rainfall into surface waters. The proposed redox switch between modes of metabolism deposited sequential microbial mats. These mats gave rise to alternating carbonate sediments predicted to retain evidence of their origin in differing ratios of isotopes of carbon and sulfur and in organic content. The mats may have arisen either by replacement of microbial populations or by continuous lineages of protocyanobacteria in which a redox genetic switch selected between Types I and II photosynthetic reaction centers, and thus between photolithoautotrophic and photoorganoheterotrophic metabolism. In the latter case, and by 2.4 Gyr at the latest, a mutation had disabled the redox genetic switch to give simultaneous constitutive expression of both Types I and II reaction centers, and thus to the ability to extract electrons from manganese and then water. By this simple step, the first cyanobacterium had the dramatic advantage of emancipation from limiting supplies of inorganic electron donors, produced free molecular oxygen as a waste product, and initiated the Great Oxidation Event in Earth's history at the transition from the Archaean to the Paleoproterozoic.

Phosphorylation of GENOMES UNCOUPLED 4 Alters Stimulation of Mg Chelatase Activity in Angiosperms

GENOMES UNCOUPLED 4 (GUN4) is a positive regulator of light-dependent chlorophyll biosynthesis. GUN4 activates Mg chelatase (MgCh) that catalyzes the insertion of an Mg²⁺ ion into protoporphyrin IX. We show that Arabidopsis (Arabidopsis thaliana) GUN4 is phosphorylated at Ser 264 (S264), the penultimate amino acid residue at the C terminus. While GUN4 is preferentially phosphorylated in darkness, phosphorylation is reduced upon accumulation of Mg porphyrins. Expression of a phosphomimicking GUN4(S264D) results in an incomplete complementation of the white gun4-2 null mutant and a chlorotic phenotype comparable to gun4 knockdown mutants. Phosphorylated GUN4 has a reduced stimulatory effect on MgCh in vitro and in vivo but retains its protein stability and tetrapyrrole binding capacity. Analysis of GUN4 found in oxygenic photosynthetic organisms reveals the evolution of a C-terminal extension, which harbors the phosphorylation site of GUN4 expressed in angiosperms. Homologs of GUN4 from Synechocystis and Chlamydomonas lack the conserved phosphorylation site found in a C-terminal extension of angiosperm GUN4. Biochemical studies proved the importance of the C-terminal extension for MgCh stimulation and inactivation of GUN4 by phosphorylation in angiosperms. An additional mechanism regulating MgCh activity is proposed. In conjunction with the dark repression of 5-aminolevulinic acid synthesis, GUN4 phosphorylation minimizes the flow of intermediates into the Mg branch of the tetrapyrrole metabolic pathway for chlorophyll biosynthesis.

Map-based cloning and functional analysis of YGL8, which controls leaf colour in rice (Oryza sativa)

BACKGROUND

As the indispensable part of plant, leaf blade mainly functions as the production workshops where organic substance is produced by photosynthesis. Leaf colour mutation is a genetic phenomenon that has a high frequency and is easily identified. The mutations always exhibit negative impact on the development of plants in any of the different stages of growth. Up to now, numerous genes involved in leaf colour mutations have been cloned.

RESULTS

In this study, a yellow-green leaf mutant, yellow-green leaf 8 (ygl8), with stable genetic phenotype, has been screened out in the progeny of an excellent indica restorer line Jinhui 10 with seeds treated by EMS. The levels of Chl a, Chl b and total chlorophyll were significantly lower in ygl8 than those in the WT throughout the whole growth period, while no clear change was noted in the Chl a/b ratio. Transmission electron microscopy demonstrated that the lamellae were clearly intumescent and intricately stacked in ygl8. Furthermore, compared with those of the WT, the stomatal conductance, intercellular CO2 concentration, photosynthetic rate and transpiration rate of ylg8 were all significantly lower. Map-based cloning results showed that Loc_Os01g73450, encoding a chloroplast-targeted UMP kinase, corresponded to Ygl8 and played an important role in regulating leaf colour in rice (Oryza sativa). Complementation of ygl8 with the WT DNA sequence of Loc_Os01g73450 led to restoration of the normal phenotype, and transgenic RNA interference plants showed a yellow-green colour. Analysis of the spatial and temporal expression of Ygl8 indicated that it was highly expressed in leaf blades and weakly expressed in other tissues. qRT-PCR also showed that the expression levels of the major Photosystem I core subunits plastome-encoded PsaA, PsaB and PsbC were significantly reduced in ygl8. The expression levels of nuclear-encoded gene involved in Chl biosynthesis HEMC, HEME, and PORA were also decreased when compared with the wild-type.

CONCLUSIONS

Independent of Chl biosynthesis and photosystem, YGL8 may affect the structure and function of chloroplasts grana lamellae by regulating plastid genome encoded thylakoid membrane constitutive gene expression and indirectly influences Chl biosynthesis.

Protein phosphorylation in chloroplasts - a survey of phosphorylation targets

The development of new software tools, improved mass spectrometry equipment, a suite of optimized scan types, and better-quality phosphopeptide affinity capture have paved the way for an explosion of mass spectrometry data on phosphopeptides. Because phosphoproteomics achieves good sensitivity, most studies use complete cell extracts for phosphopeptide enrichment and identification without prior enrichment of proteins or subcellular compartments. As a consequence, the phosphoproteome of cell organelles often comes as a by-product from large-scale studies and is commonly assembled from these in meta-analyses. This review aims at providing some guidance on the limitations of meta-analyses that combine data from analyses with different scopes, reports on the current status of knowledge on chloroplast phosphorylation targets, provides initial insights into phosphorylation site conservation in different plant species, and highlights emerging information on the integration of gene expression with metabolism and photosynthesis by means of protein phosphorylation.

A Nucleus-Encoded Chloroplast Phosphoprotein Governs Expression of the Photosystem I Subunit PsaC in Chlamydomonas reinhardtii

The nucleo-cytoplasmic compartment exerts anterograde control on chloroplast gene expression through numerous proteins that intervene at posttranscriptional steps. Here, we show that the maturation of psaC mutant (mac1) of Chlamydomonas reinhardtii is defective in photosystem I and fails to accumulate psaC mRNA. The MAC1 locus encodes a member of the Half-A-Tetratricopeptide (HAT) family of super-helical repeat proteins, some of which are involved in RNA transactions. The Mac1 protein localizes to the chloroplast in the soluble fraction. MAC1 acts through the 5' untranslated region of psaC transcripts and is required for their stability. Small RNAs that map to the 5'end of psaC RNA in the wild type but not in the mac1 mutant are inferred to represent footprints of MAC1-dependent protein binding, and Mac1 expressed in bacteria binds RNA in vitro. A coordinate response to iron deficiency, which leads to dismantling of the photosynthetic electron transfer chain and in particular of photosystem I, also causes a decrease of Mac1. Overexpression of Mac1 leads to a parallel increase in psaC mRNA but not in PsaC protein, suggesting that Mac1 may be limiting for psaC mRNA accumulation but that other processes regulate protein accumulation. Furthermore, Mac 1 is differentially phosphorylated in response to iron availability and to conditions that alter the redox balance of the electron transfer chain.

An Ancient Bacterial Signaling Pathway Regulates Chloroplast Function to Influence Growth and Development in Arabidopsis

The chloroplast originated from the endosymbiosis of an ancient photosynthetic bacterium by a eukaryotic cell. Remarkably, the chloroplast has retained elements of a bacterial stress response pathway that is mediated by the signaling nucleotides guanosine penta- and tetraphosphate (ppGpp). However, an understanding of the mechanism and outcomes of ppGpp signaling in the photosynthetic eukaryotes has remained elusive. Using the model plant Arabidopsis thaliana, we show that ppGpp is a potent regulator of chloroplast gene expression in vivo that directly reduces the quantity of chloroplast transcripts and chloroplast-encoded proteins. We then go on to demonstrate that the antagonistic functions of different plant RelA SpoT homologs together modulate ppGpp levels to regulate chloroplast function and show that they are required for optimal plant growth, chloroplast volume, and chloroplast breakdown during dark-induced and developmental senescence. Therefore, our results show that ppGpp signaling is not only linked to stress responses in plants but is also an important mediator of cooperation between the chloroplast and the nucleocytoplasmic compartment during plant growth and development.

A Two-Component Regulatory System in Transcriptional Control of Photosystem Stoichiometry: Redox-Dependent and Sodium Ion-Dependent Phosphoryl Transfer from Cyanobacterial Histidine Kinase Hik2 to Response Regulators Rre1 and RppA

Two-component systems (TCSs) are ubiquitous signaling units found in prokaryotes. A TCS consists of a sensor histidine kinase and a response regulator protein as signal transducers. These regulatory systems mediate acclimation to various environmental changes by coupling environmental cues to gene expression. Hik2 is a sensor histidine kinase and its gene is found in all cyanobacteria. Hik2 is the homolog of Chloroplast Sensor Kinase (CSK), a protein involved in redox regulation of chloroplast gene expression during changes in light quality in plants and algae. Here we describe biochemical characterization of the signaling mechanism of Hik2 and its phosphotransferase activity. Results presented here indicate that Hik2 undergoes autophosphorylation on a conserved histidine residue, and becomes rapidly dephosphorylated by the action of response regulators Rre1 and RppA. We also show that the autophosphorylation of Hik2 is specifically inhibited by sodium ions.

On the Extent of Tyrosine Phosphorylation in Chloroplasts

Reanalysis of published mass spectrometry data on Tyr-phosphorylated chloroplast proteins indicates that the majority of peptide spectrum matches reporting Tyr phosphorylation are ambiguous.

Integration of plastids with their hosts: Lessons learned from dinoflagellates

After their endosymbiotic acquisition, plastids become intimately connected with the biology of their host. For example, genes essential for plastid function may be relocated from the genomes of plastids to the host nucleus, and pathways may evolve within the host to support the plastid. In this review, we consider the different degrees of integration observed in dinoflagellates and their associated plastids, which have been acquired through multiple different endosymbiotic events. Most dinoflagellate species possess plastids that contain the pigment peridinin and show extreme reduction and integration with the host biology. In some species, these plastids have been replaced through serial endosymbiosis with plastids derived from a different phylogenetic derivation, of which some have become intimately connected with the biology of the host whereas others have not. We discuss in particular the evolution of the fucoxanthin-containing dinoflagellates, which have adapted pathways retained from the ancestral peridinin plastid symbiosis for transcript processing in their current, serially acquired plastids. Finally, we consider why such a diversity of different degrees of integration between host and plastid is observed in different dinoflagellates and how dinoflagellates may thus inform our broader understanding of plastid evolution and function.

Identification of Early Nuclear Target Genes of Plastidial Redox Signals that Trigger the Long-Term Response of Arabidopsis to Light Quality Shifts

Natural illumination conditions are highly variable and because of their sessile life style, plants are forced to acclimate to them at the cellular and molecular level. Changes in light intensity or quality induce changes in the reduction/oxidation (redox) state of the photosynthetic electron chain that acts as a trigger for compensatory acclimation responses comprising functional and structural adjustments of photosynthesis and metabolism. Such responses include redox-controlled changes in plant gene expression in the nucleus and organelles. Here we describe a strategy for the identification of early redox-regulated genes (ERGs) in the nucleus of the model organism Arabidopsis thaliana that respond significantly 30 or 60 min after the generation of a reduction signal in the photosynthetic electron transport chain. By comparing the response of wild-type plants with that of the acclimation mutant stn7, we could specifically identify ERGs. The results reveal a significant impact of chloroplast redox signals on distinct nuclear gene groups including genes for the mitochondrial electron transport chain, tetrapyrrole biosynthesis, carbohydrate metabolism, and signaling lipid synthesis. These expression profiles are clearly different from those observed in response to the reduction of photosynthetic electron transport by high light treatments. Thus, the ERGs identified are unique to redox imbalances in photosynthetic electron transport and were then used for analyzing potential redox-responsive cis-elements, trans-factors, and chromosomal regulatory hot spots. The data identify a novel redox-responsive element and indicate extensive redox control at transcriptional and chromosomal levels that point to an unprecedented impact of redox signals on epigenetic processes.

Rapid transient expression of human granulocyte-macrophage colony-stimulating factor in two industrial cultivars of tobacco (Nicotiana tabacum L.) by agroinfiltration

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Successful expression of human cytokine GM-CSF in two industrial tobacco cultivars is achieved.

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Rapid cloning in two binary destination vectors is accomplished by using Gateway approach.

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Agrobacterial infiltration procedure is optimized and shown to require the surface tension lowering agent Silwet L-77.

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Accumulation of recombinant protein was confirmed by using high affinity monoclonal hemagglutinin tag antibodies.

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Production of hGM-CSF has been achieved without plant codon usage optimization.

We report the production of hGM-CSF cytokine in leaves of industrial tobacco cultivars DH-17 and DH-27 by using Agrobacterium-mediated transient expression. We prove the concept that very high biomass industrial tobacco plants are suitable platforms for rapid, low cost production of foreign proteins. Successful transient expression of the GM-CSF was achieved in less than three months, opening the possibility for future applications of this approach in rapid response production of various proteins of non-plant origin in industrial tobacco.

Why chloroplasts and mitochondria retain their own genomes and genetic systems: Colocation for redox regulation of gene expression

Chloroplasts and mitochondria are subcellular bioenergetic organelles with their own genomes and genetic systems. DNA replication and transmission to daughter organelles produces cytoplasmic inheritance of characters associated with primary events in photosynthesis and respiration. The prokaryotic ancestors of chloroplasts and mitochondria were endosymbionts whose genes became copied to the genomes of their cellular hosts. These copies gave rise to nuclear chromosomal genes that encode cytosolic proteins and precursor proteins that are synthesized in the cytosol for import into the organelle into which the endosymbiont evolved. What accounts for the retention of genes for the complete synthesis within chloroplasts and mitochondria of a tiny minority of their protein subunits? One hypothesis is that expression of genes for protein subunits of energy-transducing enzymes must respond to physical environmental change by means of a direct and unconditional regulatory control--control exerted by change in the redox state of the corresponding gene product. This hypothesis proposes that, to preserve function, an entire redox regulatory system has to be retained within its original membrane-bound compartment. Colocation of gene and gene product for redox regulation of gene expression (CoRR) is a hypothesis in agreement with the results of a variety of experiments designed to test it and which seem to have no other satisfactory explanation. Here, I review evidence relating to CoRR and discuss its development, conclusions, and implications. This overview also identifies predictions concerning the results of experiments that may yet prove the hypothesis to be incorrect.

Employing aromatic tuning to modulate output from two-component signaling circuits

Two-component signaling circuits (TCSs) govern the majority of environmental, pathogenic and industrial processes undertaken by bacteria. Therefore, controlling signal output from these circuits in a stimulus-independent manner is of central importance to synthetic microbiologists. Aromatic tuning, or repositioning the aromatic residues commonly found at the cytoplasmic end of the final TM helix has been shown to modulate signal output from the aspartate chemoreceptor (Tar) and the major osmosensor (EnvZ) of Escherichia coli. Aromatic residues are found in a similar location within other bacterial membrane-spanning receptors, suggesting that aromatic tuning could be harnessed for a wide-range of applications. Here, a brief synopsis of the data underpinning aromatic tuning, the initial successes with the method and the inherent advantages over those previously employed for modulating TCS signal output are presented.

Forcing the issue: aromatic tuning facilitates stimulus-independent modulation of a two-component signaling circuit

Two-component signaling circuits allow bacteria to detect and respond to external stimuli. Unfortunately, the input stimulus remains unidentified for the majority of these circuits. Therefore, development of a synthetic method for stimulus-independent modulation of these circuits is highly desirable because particular physiological or developmental processes could be controlled for biotechnological purposes without the need to identify the stimulus itself. Here, we demonstrate that aromatic tuning, i.e., repositioning the aromatic residues commonly found at the cytoplasmic end of the receptor (EnvZ) transmembrane domain, facilitates stimulus-independent modulation of signal output from the EnvZ/OmpR osmosensing circuit of Escherichia coli. We found that these osmosensing circuits retained the ability to respond appropriately to increased external osmolarity, suggesting that the tuned receptors were not locked in a single conformation. We also noted that circuits containing aromatically tuned variants became more sensitive to changes in the receptor concentration than their wild-type counterpart, suggesting a new way to study mechanisms underpinning receptor concentration-dependent robustness. We believe that aromatic tuning has several advantages compared to previous methods aimed at stimulus-independent modulation of receptors and that it will be generally applicable to a wide-range of two-component circuits.

Two-component phosphorelays in fungal mitochondria and beyond

Prokaryotes, eukaryotic microorganisms and plants utilize two-component signal transduction pathways to detect and respond to various environmental cues. These signaling cascades were acquired by eukaryotes via horizontal gene transfer events from ancestral bacteria. Recent exciting discoveries have identified two-component signaling systems in mitochondria and chloroplasts of several eukaryotic microorganisms and plants, therefore providing important clues to the evolutionary transition of these signaling cascades from prokaryotes to eukaryotes. This review will focus on the role of two-component signal transduction pathways in fungal pathogenesis and also discuss key new discoveries of presence of proteins participating in these signaling pathways in mitochondrion. Before addressing these issues, I first briefly describe the magnitude and the economic impact of the healthcare problems caused by fungal pathogens.

Plastid sigma factors: Their individual functions and regulation in transcription

Sigma factors are the predominant factors involved in transcription regulation in bacteria. These factors can recruit the core RNA polymerase to promoters with specific DNA sequences and initiate gene transcription. The plastids of higher plants originating from an ancestral cyanobacterial endosymbiont also contain sigma factors that are encoded by a small family of nuclear genes. Although all plastid sigma factors contain sequences conserved in bacterial sigma factors, a considerable number of distinct traits have been acquired during evolution. The present review summarises recent advances concerning the regulation of the structure, function and activity of plastid sigma factors since their discovery nearly 40 years ago. We highlight the specialised roles and overlapping redundant functions of plastid sigma factors according to their promoter selectivity. We also focus on the mechanisms that modulate the activity of sigma factors to optimise plastid function in response to developmental cues and environmental signals. This article is part of a Special Issue entitled: Chloroplast Biogenesis.