The proteolysis adaptor, NblA, binds to the N-terminus of β-phycocyanin: Implications for the mechanism of phycobilisome degradation

Tailoring regulatory components for metabolic engineering in cyanobacteria

The looming climate crisis has prompted an ever-growing interest in cyanobacteria due to their potential as sustainable production platforms for the synthesis of energy carriers and value-added chemicals from CO2 and sunlight. Nonetheless, cyanobacteria are yet to compete with heterotrophic systems in terms of space-time yields and consequently production costs. One major drawback leading to the low production performance observed in cyanobacteria is the limited ability to utilize the full capacity of the photosynthetic apparatus and its associated systems, i.e. CO2 fixation and the directly connected metabolism. In this review, novel insights into various levels of metabolic regulation of cyanobacteria are discussed, including the potential of targeting these regulatory mechanisms to create a chassis with a phenotype favorable for photoautotrophic production. Compared to conventional metabolic engineering approaches, minor perturbations of regulatory mechanisms can have wide-ranging effects.

Interactome Analysis of ClpX Reveals Its Regulatory Role in Metabolism and Photosynthesis in Cyanobacteria

Protein homeostasis is essential for cyanobacteria to maintain proper cellular function under adverse and fluctuating conditions. The AAA+ superfamily of proteolytic complexes in cyanobacteria plays a critical role in this process, including ClpXP, which comprises a hexameric ATPase ClpX and a tetradecameric peptidase ClpP. Despite the physiological effects of ClpX on growth and photosynthesis, its potential substrates and underlying mechanisms in cyanobacteria remain unknown. In this study, we employed a streptavidin-biotin affinity pull-down assay coupled with label-free proteome quantitation to analyze the interactome of ClpX in the model cyanobacterium Synechocystis sp. PCC 6803 (hereafter Synechocystis). We identified 503 proteins as potential ClpX-binding targets, many of which had novel interactions. These ClpX-binding targets were found to be involved in various biological processes, with particular enrichment in metabolic processes and photosynthesis. Using protein-protein docking, GST pull-down, and biolayer interferometry assays, we confirmed the direct association of ClpX with the photosynthetic proteins, ferredoxin-NADP+ oxidoreductase (FNR) and phycocyanin subunit (CpcA). Subsequent functional investigations revealed that ClpX participates in the maintenance of FNR homeostasis and functionality in Synechocystis grown under different light conditions. Overall, our study provides a comprehensive understanding of the extensive functions regulated by ClpX in cyanobacteria to maintain protein homeostasis and adapt to environmental challenges.

The increasing role of structural proteomics in cyanobacteria

Cyanobacteria, also known as blue–green algae, are ubiquitous organisms on the planet. They contain tremendous protein machineries that are of interest to the biotechnology industry and beyond. Recently, the number of annotated cyanobacterial genomes has expanded, enabling structural studies on known gene-coded proteins to accelerate. This review focuses on the advances in mass spectrometry (MS) that have enabled structural proteomics studies to be performed on the proteins and protein complexes within cyanobacteria. The review also showcases examples whereby MS has revealed critical mechanistic information behind how these remarkable machines within cyanobacteria function.

A Unique Set of Auxiliary Metabolic Genes Found in an Isolated Cyanophage Sheds New Light on Marine Phage-Host Interactions

Cyanophages, viruses that infect cyanobacteria, are abundant and widely distributed in aquatic ecosystems, playing important roles in regulating the abundance, activity, diversity, and evolution of cyanobacteria. A T4-like cyanophage, S-SCSM1, infecting Synechococcus and Prochlorococcus strains of different ecotypes, was isolated from the South China Sea in this study. For the first time, a mannose-6-phosphate isomerase (MPI) gene was identified in the cultured cyanophage. At least 11 phylogenetic clusters of cyanophage MPIs were retrieved and identified from the marine metagenomic data sets, indicating that cyanophage MPIs in the marine environment are extremely diverse. The existence of 24 genes encoding 2-oxoglutarate (2OG)-Fe(II) oxygenase superfamily proteins in the S-SCSM1 genome emphasizes their potential importance and diverse functions in reprogramming host metabolism during phage infection. Novel cell wall synthesis and modification genes found in the S-SCSM1 genome indicate that diverse phenotypic modifications imposed by phages on cyanobacterial hosts remain to be discovered. Two noncoding RNAs of cis-regulatory elements in the S-SCSM1 genome were predicted to be associated with host exopolysaccharide metabolism and photosynthesis. The isolation and genomic characterization of cyanophage S-SCSM1 provide more information on the genetic diversity of cyanophages and phage-host interactions in the marine environment. IMPORTANCE Cyanophages play important ecological roles in aquatic ecosystems. Genomic and proteomic characterizations of the T4-like cyanophage S-SCSM1 indicate that novel and diverse viral genes and phage-host interactions in the marine environment remain unexplored. The first identified mannose-6-phosphate isomerase (MPI) gene from a cultured cyanophage was found in the S-SCSM1 genome, although MPIs were previously found in viral metagenomes at high frequencies similar to those of the cyanophage photosynthetic gene psbA. The presence of 24 genes encoding 2-oxoglutarate (2OG)-Fe(II) oxygenase superfamily proteins, novel cell wall synthesis and modification genes, a nonbleaching protein A gene, and 2 noncoding RNAs of cis-regulatory elements in the S-SCSM1 genome as well as the presence of a virion-associated regulatory protein indicate the diverse functions that cyanophages have in reprogramming the metabolism and modifying the phenotypes of hosts during infection.

The Self-Bleaching Process of Microcystis aeruginosa is Delayed by a Symbiotic Bacterium Pseudomonas sp. MAE1-K and Promoted by Methionine Deficiency

Various interactions between marine cyanobacteria and heterotrophic bacteria have been known, but the symbiotic relationships between Microcystis and heterotrophic bacteria remain unclear. An axenic M. aeruginosa culture (NIES-298) was quickly bleached after exponential growth, whereas a xenic M. aeruginosa culture (KW) showed a normal growth curve, suggesting that some symbiotic bacteria may delay this bleaching. The bleaching process of M. aeruginosa was distinguished from the phenomena of previously proposed chlorosis and programmed cell death in various characteristics. Bleached cultures of NIES-298 quickly bleached actively growing M. aeruginosa cultures, suggesting that M. aeruginosa itself produces bleach-causing compounds. Pseudomonas sp. MAE1-K delaying the bleaching of NIES-298 cultures was isolated from the KW culture. Bleached cultures of NIES-298 treated with strain MAE1-K lost their bleaching ability, suggesting that strain MAE1-K rescues M. aeruginosa from bleaching via inactivation of bleaching compounds. From Tn5 transposon mutant screening, a metZ mutant of strain MAE1-K (F-D3) unable to synthesize methionine, promoting the bleaching of NIES-298 cultures but capable of inactivating bleaching compounds, was obtained. The bleaching process of NIES-298 cultures was promoted with the coculture of mutant F-D3 and delayed by methionine supplementation, suggesting that the bleaching process of M. aeruginosa is promoted by methionine deficiency.

IMPORTANCE Cyanobacterial blooms in freshwaters represent serious global concerns for the ecosystem and human health. In this study, we found that one of the major species in cyanobacterial blooms, Microcystis aeruginosa, was quickly collapsed after exponential growth by producing self-bleaching compounds and that a symbiotic bacterium, Pseudomonas sp. MAE1-K delayed the bleaching process via the inactivation of bleaching compounds. In addition, we found that a metZ mutant of strain MAE1-K (F-D3) causing methionine deficiency promoted the bleaching process of M. aeruginosa, suggesting that methionine deficiency may induce the production of bleaching compounds. These results will provide insights into the symbiotic relationships between M. aeruginosa and heterotrophic bacteria that will contribute to developing novel strategies to control cyanobacterial blooms.

Degron-mediated proteolysis of CrhR-like DEAD-box RNA helicases in cyanobacteria

Conditional proteolytic degradation is an irreversible and highly regulated process that fulfills crucial regulatory functions in all organisms. As proteolytic targets tend to be critical metabolic or regulatory proteins, substrates are targeted for degradation only under appropriate conditions through the recognition of an amino acid sequence referred to as a “degron”. DEAD-box RNA helicases mediate all aspects of RNA metabolism, contributing to cellular fitness. However, the mechanism by which abiotic-stress modulation of protein stability regulates bacterial helicase abundance has not been extensively characterized. Here, we provide in vivo evidence that proteolytic degradation of the cyanobacterial DEAD-box RNA helicase CrhR is conditional, being initiated by a temperature upshift from 20 to 30 °C in the model cyanobacterium, Synechocystis sp. PCC 6803. We show degradation requires a unique, highly conserved, inherently bipartite degron located in the C-terminal extension found only in CrhR-related RNA helicases in the phylum Cyanobacteria. However, although necessary, the degron is not sufficient for proteolysis, as disruption of RNA helicase activity and/or translation inhibits degradation. These results suggest a positive feedback mechanism involving a role for CrhR in expression of a crucial factor required for degradation. Furthermore, AlphaFold structural prediction indicated the C-terminal extension is a homodimerization domain with homology to other bacterial RNA helicases, and mass photometry data confirmed that CrhR exists as a dimer in solution at 22 °C. These structural data suggest a model wherein the CrhR degron is occluded at the dimerization interface but could be exposed if dimerization was disrupted by nonpermissive conditions.

Photosynthesis and Cell Growth Trigger Degradation of Phycobilisomes during Nitrogen Limitation

Under nitrogen (N)-limited conditions, the non-N2-fixing cyanobacterium Synechocystis sp. PCC 6803 (Synechocystis 6803) actively grows during early stages of starvation by performing photosynthesis but gradually stops the growth and eventually enters dormancy to withstand long-term N limitation. During N limitation, Synechocystis 6803 cells degrade the large light-harvesting antenna complex phycobilisomes (PBSs) presumably to avoid excess light absorption and to reallocate available N to essential functions for growth and survival. These two requirements may be driving forces for PBS degradation during N limitation, but how photosynthesis and cell growth affect PBS degradation remains unclear. To address this question, we examined involvements of photosynthesis and cell growth in PBS degradation during N limitation. Treatment of photosynthesis inhibitors and shading suppressed PBS degradation and caused non-bleaching of cells during N limitation. Limitations of photosynthesis after initial gene responses to N limitation suppressed PBS degradation, implying that photosynthesis affects PBS degradation in a post-translational manner. In addition, limitations of cell growth by inhibition of peptidoglycan and fatty acid biosynthesis, low growth temperature and phosphorous starvation suppressed PBS degradation during N limitation. Because decreased photosynthetic activity led to decreased cell growth, and vice versa, photosynthesis and cell growth would inseparably intertwine each other and affect PBS degradation during N limitation in a complex manner. Our data shed light on the coordination mechanisms among photosynthesis, cell growth and PBS degradation during N limitation.

Hostile Takeover: How Viruses Reprogram Prokaryotic Metabolism

To reproduce, prokaryotic viruses must hijack the cellular machinery of their hosts and redirect it toward the production of viral particles. While takeover of the host replication and protein synthesis apparatus has long been considered an essential feature of infection, recent studies indicate that extensive reprogramming of host primary metabolism is a widespread phenomenon among prokaryotic viruses that is required to fulfill the biosynthetic needs of virion production. In this review we provide an overview of the most significant recent findings regarding virus-induced reprogramming of prokaryotic metabolism and suggest how quantitative systems biology approaches may be used to provide a holistic understanding of metabolic remodeling during lytic viral infection. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Discovery of a small protein factor involved in the coordinated degradation of phycobilisomes in cyanobacteria

During genome analysis, genes encoding small proteins are frequently neglected. Accordingly, small proteins have remained underinvestigated in all domains of life. Based on a previous systematic search for such genes, we present the functional analysis of the 66 amino acids protein NblD in a photosynthetic cyanobacterium. We show that NblD plays a crucial role during the coordinated dismantling of phycobilisome light-harvesting complexes. This disassembly is triggered when the cells become starved for nitrogen, a condition that frequently occurs in nature. Similar to NblA that tags phycobiliproteins for proteolysis, NblD binds to phycocyanin polypeptides but has a different function. The results show that, even in a well-investigated process, crucial new players can be discovered if small proteins are taken into consideration.

Phycobilisomes are the major pigment–protein antenna complexes that perform photosynthetic light harvesting in cyanobacteria, rhodophyte, and glaucophyte algae. Up to 50% of the cellular nitrogen can be stored in their giant structures. Accordingly, upon nitrogen depletion, phycobilisomes are rapidly degraded following an intricate genetic program. Here, we describe the role of NblD, a cysteine-rich, small protein in this process in cyanobacteria. Deletion of the nblD gene in the cyanobacterium Synechocystis sp. PCC 6803 prevented the degradation of phycobilisomes, leading to a nonbleaching (nbl) phenotype, which could be complemented by a plasmid-localized gene copy. Competitive growth experiments between the ΔnblD and the wild-type strain provided direct evidence for the physiological importance of NblD under nitrogen-limited conditions. Ectopic expression of NblD under nitrogen-replete conditions showed no effect, in contrast to the unrelated proteolysis adaptors NblA1 and NblA2, which can trigger phycobilisome degradation. Transcriptome analysis indicated increased nblA1/2 transcript levels in the ΔnblD strain during nitrogen starvation, implying that NblD does not act as a transcriptional (co)regulator. However, immunoprecipitation and far-western experiments identified the chromophorylated (holo form) of the phycocyanin β-subunit (CpcB) as its target, while apo-CpcB was not bound. The addition of recombinant NblD to isolated phycobilisomes caused a reduction in phycocyanin absorbance and a broadening and shifting of the peak to lower wavelengths, indicating the occurrence of structural changes. These data demonstrate that NblD plays a crucial role in the coordinated dismantling of phycobilisomes and add it as a factor to the genetically programmed response to nitrogen starvation.

Light Harvesting in Fluctuating Environments: Evolution and Function of Antenna Proteins across Photosynthetic Lineage

Photosynthesis is the major natural process that can harvest and harness solar energy into chemical energy. Photosynthesis is performed by a vast number of organisms from single cellular bacteria to higher plants and to make the process efficient, all photosynthetic organisms possess a special type of pigment protein complex(es) that is (are) capable of trapping light energy, known as photosynthetic light-harvesting antennae. From an evolutionary point of view, simpler (unicellular) organisms typically have a simple antenna, whereas higher plants possess complex antenna systems. The higher complexity of the antenna systems provides efficient fine tuning of photosynthesis. This relationship between the complexity of the antenna and the increasing complexity of the organism is mainly related to the remarkable acclimation capability of complex organisms under fluctuating environmental conditions. These antenna complexes not only harvest light, but also provide photoprotection under fluctuating light conditions. In this review, the evolution, structure, and function of different antenna complexes, from single cellular organisms to higher plants, are discussed in the context of the ability to acclimate and adapt to cope under fluctuating environmental conditions.

Structure, function, and substrates of Clp AAA+ protease systems in cyanobacteria, plastids, and apicoplasts: A comparative analysis

ATPases Associated with diverse cellular Activities (AAA+) are a superfamily of proteins that typically assemble into hexameric rings. These proteins contain AAA+ domains with two canonical motifs (Walker A and B) that bind and hydrolyze ATP, allowing them to perform a wide variety of different functions. For example, AAA+ proteins play a prominent role in cellular proteostasis by controlling biogenesis, folding, trafficking, and degradation of proteins present within the cell. Several central proteolytic systems (e.g., Clp, Deg, FtsH, Lon, 26S proteasome) use AAA+ domains or AAA+ proteins to unfold protein substrates (using energy from ATP hydrolysis) to make them accessible for degradation. This allows AAA+ protease systems to degrade aggregates and large proteins, as well as smaller proteins, and feed them as linearized molecules into a protease chamber. This review provides an up-to-date and a comparative overview of the essential Clp AAA+ protease systems in Cyanobacteria (e.g., Synechocystis spp), plastids of photosynthetic eukaryotes (e.g., Arabidopsis, Chlamydomonas), and apicoplasts in the nonphotosynthetic apicomplexan pathogen Plasmodium falciparum. Recent progress and breakthroughs in identifying Clp protease structures, substrates, substrate adaptors (e.g., NblA/B, ClpS, ClpF), and degrons are highlighted. We comment on the physiological importance of Clp activity, including plastid biogenesis, proteostasis, the chloroplast Protein Unfolding Response, and metabolism, across these diverse lineages. Outstanding questions as well as research opportunities and priorities to better understand the essential role of Clp systems in cellular proteostasis are discussed.

Phycobilisome breakdown effector NblD is required to maintain the cellular amino acid composition during nitrogen starvation

Small proteins are critically involved in the acclimation response of photosynthetic cyanobacteria to nitrogen starvation. NblD is the 66-amino-acid effector of nitrogen-limitation-induced phycobilisome breakdown, which is believed to replenish the cellular amino acid pools. To address the physiological functions of NblD, the concentrations of amino acids, intermediates of the arginine catabolism pathway and several organic acids were measured during the response to nitrogen starvation in the cyanobacterium Synechocystis sp. PCC 6803 wild type and in an nblD deletion strain. A characteristic signature of metabolite pool composition was identified, which shows that NblD-mediated phycobilisome degradation is required to maintain the cellular amino acid and organic acid pools during nitrogen starvation. Specific deviations from the wild type suggest wider-reaching effects that also affect such processes as redox homeostasis via glutathione and tetrapyrrole biosynthesis, both of which are linked to the strongly decreased glutamate pool, and transcriptional reprogramming via an enhanced concentration of 2-oxoglutarate, the metabolite co-regulator of the NtcA transcription factor. The essential role played by NblD in metabolic homeostasis is consistent with the widespread occurrence of NblD throughout the cyanobacterial radiation and the previously observed strong positive selection for the nblD gene under fluctuating nitrogen supply. Importance Cyanobacteria play important roles in the global carbon and nitrogen cycles. In their natural environment, these organisms are exposed to fluctuating nutrient conditions. Nitrogen starvation induces a coordinated nitrogen-saving program that includes the breakdown of nitrogen-rich photosynthetic pigments, particularly phycobiliproteins. The small protein NblD was recently identified as an effector of phycobilisome breakdown in cyanobacteria. In this study, we demonstrate that the NblD-mediated degradation of phycobiliproteins is needed to sustain cellular pools of soluble amino acids and other crucial metabolites. The essential role played by NblD in metabolic homeostasis explains why genes encoding this small protein are conserved in almost all members of cyanobacterial radiation.

Assessment of Protein Content and Phosphorylation Level in Synechocystis sp. PCC 6803 under Various Growth Conditions Using Quantitative Phosphoproteomic Analysis

The photosynthetic apparatus and metabolic enzymes of cyanobacteria are subject to various controls, such as transcriptional regulation and post-translational modifications, to ensure that the entire cellular system functions optimally. In particular, phosphorylation plays key roles in many cellular controls such as enzyme activity, signal transduction, and photosynthetic apparatus restructuring. Therefore, elucidating the governing functions of phosphorylation is crucial to understanding the regulatory mechanisms underlying metabolism and photosynthesis. In this study, we determined protein content and phosphorylation levels to reveal the regulation of intracellular metabolism and photosynthesis in Synechocystis sp. PCC 6803; for this, we obtained quantitative data of proteins and their phosphorylated forms involved in photosynthesis and metabolism under various growth conditions (photoautotrophic, mixotrophic, heterotrophic, dark, and nitrogen-deprived conditions) using targeted proteomic and phosphoproteomic analyses with nano-liquid chromatography-triple quadrupole mass spectrometry. The results indicated that in addition to the regulation of protein expression, the regulation of phosphorylation levels of cyanobacterial photosynthetic apparatus and metabolic enzymes was pivotal for adapting to changing environmental conditions. Furthermore, reduced protein levels of CpcC and altered phosphorylation levels of CpcB, ApcA, OCP, and PsbV contributed to the cellular response of the photosynthesis apparatus to nitrogen deficiency.

The role of lyases, NblA and NblB proteins and bilin chromophore transfer in restructuring the cyanobacterial light-harvesting complex‡

Phycobilisomes are large light-harvesting complexes attached to the stromal side of thylakoids in cyanobacteria and red algae. They can be remodeled or degraded in response to changing light and nutritional status. Both the core and the peripheral rods of phycobilisomes contain biliproteins. During biliprotein biosynthesis, open-chain tetrapyrrole chromophores are attached covalently to the apoproteins by dedicated lyases. Another set of non-bleaching (Nb) proteins has been implicated in phycobilisome degradation, among them NblA and NblB. We report in vitro experiments with lyases, biliproteins and NblA/B which imply that the situation is more complex than currently discussed: lyases can also detach the chromophores and NblA and NblB can modulate lyase-catalyzed binding and detachment of chromophores in a complex fashion. We show: (i) NblA and NblB can interfere with chromophorylation as well as chromophore detachment of phycobiliprotein, they are generally inhibitors but in some cases enhance the reaction; (ii) NblA and NblB promote dissociation of whole phycobilisomes, cores and, in particular, allophycocyanin trimers; (iii) while NblA and NblB do not interact with each other, both interact with lyases, apo- and holo-biliproteins; (iv) they promote synergistically the lyase-catalyzed chromophorylation of the β-subunit of the major rod component, CPC; and (v) they modulate lyase-catalyzed and lyase-independent chromophore transfers among biliproteins, with the core protein, ApcF, the rod protein, CpcA, and sensory biliproteins (phytochromes, cyanobacteriochromes) acting as potential traps. The results indicate that NblA/B can cooperate with lyases in remodeling the phycobilisomes to balance the metabolic requirements of acclimating their light-harvesting capacity without straining the overall metabolic economy of the cell.

A minimum set of regulators to thrive in the ocean

Marine cyanobacteria of the genus Prochlorococcus thrive in high cell numbers throughout the euphotic zones of the world's subtropical and tropical oligotrophic oceans, making them some of the most ecologically relevant photosynthetic microorganisms on Earth. The ecological success of these free-living phototrophs suggests that they are equipped with a regulatory system competent to address many different stress situations. However, Prochlorococcus genomes are compact and streamlined, with the majority encoding only five different sigma factors, five to six two-component systems and eight types of other transcriptional regulators. Here, we summarize the existing information about the functions of these protein regulators, about transcriptomic responses to defined stress conditions, and discuss the current knowledge about riboswitches, RNA-based regulation and the roles of certain metabolites as co-regulators. We focus on the best-studied isolate, Prochlorococcus MED4, but extend to other strains and ecotypes when appropriate, and we include some information gained from metagenomic and metatranscriptomic analyses.

An uncultured marine cyanophage encodes an active phycobilisome proteolysis adaptor protein NblA

Phycobilisomes (PBS) are large water-soluble membrane-associated complexes in cyanobacteria and some chloroplasts that serve as light-harvesting antennae for the photosynthetic apparatus. When deplete of nitrogen or sulphur, cyanobacteria readily degrade their phycobilisomes allowing the cell to replenish these vanishing nutrients. The key regulator in the degradation process is NblA, a small protein (∼6 kDa), which recruits proteases to the PBS. It was discovered previously that not only do cyanobacteria possess nblA genes but also that they are encoded by genomes of some freshwater cyanophages. A recent study, using assemblies from oceanic metagenomes, revealed genomes of a novel uncultured marine cyanophage lineage, representatives of which contain genes coding for the PBS degradation protein. Here, we examined the functionality of nblA-like genes from these marine cyanophages by testing them in a freshwater model cyanobacterial nblA knockout. One of the viral NblA variants could complement the non-bleaching phenotype and restore PBS degradation. Our findings reveal a functional NblA from a novel marine cyanophage lineage. Furthermore, we shed new light on the distribution of nblA genes in cyanobacteria and cyanophages.

Proteomic Insights into Phycobilisome Degradation, A Selective and Tightly Controlled Process in The Fast-Growing Cyanobacterium Synechococcus elongatus UTEX 2973

Phycobilisomes (PBSs) are large (3-5 megadalton) pigment-protein complexes in cyanobacteria that associate with thylakoid membranes and harvest light primarily for photosystem II. PBSs consist of highly ordered assemblies of pigmented phycobiliproteins (PBPs) and linker proteins that can account for up to half of the soluble protein in cells. Cyanobacteria adjust to changing environmental conditions by modulating PBS size and number. In response to nutrient depletion such as nitrogen (N) deprivation, PBSs are degraded in an extensive, tightly controlled, and reversible process. In Synechococcus elongatus UTEX 2973, a fast-growing cyanobacterium with a doubling time of two hours, the process of PBS degradation is very rapid, with 80% of PBSs per cell degraded in six hours under optimal light and CO₂ conditions. Proteomic analysis during PBS degradation and re-synthesis revealed multiple proteoforms of PBPs with partially degraded phycocyanobilin (PCB) pigments. NblA, a small proteolysis adaptor essential for PBS degradation, was characterized and validated with targeted mass spectrometry. NblA levels rose from essentially 0 to 25,000 copies per cell within 30 min of N depletion, and correlated with the rate of decrease in phycocyanin (PC). Implications of this correlation on the overall mechanism of PBS degradation during N deprivation are discussed.

Distinct molecular signatures in dissolved organic matter produced by viral lysis of marine cyanobacteria

Dissolved organic matter (DOM) plays a central role in the microbial ecology and biogeochemistry of aquatic environments, yet little is known about how the mechanism of DOM release from its ultimate source, primary producer biomass, affects the molecular composition of the inputs to the dissolved pool. Here we used a model marine phytoplankton, the picocyanobacterium Synechococcus WH7803, to compare the composition of DOM released by three mechanisms: exudation, mechanical cell lysis and infection by the lytic phage S-SM1. A broad, untargeted analytical approach reveals the complexity of this freshly sourced DOM, and comparative analysis between DOM produced by the different mechanisms suggests that exudation and viral lysis are sources of unsaturated, oxygen-rich and possibly novel biomolecules. Furthermore, viral lysis of WH7803 by S-SM1 releases abundant peptides derived from specific proteolysis of the major light-harvesting protein phycoerythrin, raising the possibility that phage infection of these abundant cyanobacteria could be a significant source of high molecular weight dissolved organic nitrogen compounds.

Decomposition of cyanobacterial light harvesting complexes: NblA-dependent role of the bilin lyase homolog NblB

Phycobilisomes, the macromolecular light harvesting complexes of cyanobacteria are degraded under nutrient-limiting conditions. This crucial response is required to adjust light excitation to the metabolic status and avoid damage by excess excitation. Phycobilisomes are comprised of phycobiliproteins, apo-proteins that covalently bind bilin chromophores. In the cyanobacterium Synechococcus elongatus, the phycobiliproteins allophycocyanin and phycocyanin comprise the core and the rods of the phycobilisome, respectively. Previously, NblB was identified as an essential component required for phycocyanin degradation under nutrient starvation. This protein is homologous to bilin-lyases, enzymes that catalyze the covalent attachment of bilins to apo-proteins. However, the nblB-inactivated strain is not impaired in phycobiliprotein synthesis, but rather is characterized by aberrant phycocyanin degradation. Here, using a phycocyanin-deficient strain, we demonstrate that NblB is required for degradation of the core pigment, allophycocyanin. Furthermore, we show that the protein NblB is expressed under nutrient sufficient conditions, but during nitrogen starvation its level decreases about two-fold. This finding is in contrast to an additional component essential for degradation, NblA, the expression of which is highly induced under starvation. We further identified NblB residues required for phycocyanin degradation in vivo. Finally, we demonstrate phycocyanin degradation in a cell-free system, thereby providing support for the suggestion that NblB directly mediates pigment degradation by chromophore detachment. The dependence of NblB function on NblA revealed using this system, together with the results indicating presence of NblB under nutrient sufficient conditions, suggests a rapid mechanism for induction of pigment degradation, which requires only the expression of NblA.

Chlorosis as a Developmental Program in Cyanobacteria: The Proteomic Fundament for Survival and Awakening

Cyanobacteria that do not fix atmospheric nitrogen gas survive prolonged periods of nitrogen starvation in a chlorotic, dormant state where cell growth and metabolism are arrested. Upon nutrient availability, these dormant cells return to vegetative growth within 2-3 days. This resuscitation process is highly orchestrated and relies on the stepwise reinstallation and activation of essential cellular structures and functions. We have been investigating the transition to chlorosis and the return to vegetative growth as a simple model of a cellular developmental process and a fundamental survival strategy in biology. In the present study, we used quantitative proteomics and phosphoproteomics to describe the proteomic landscape of a dormant cyanobacterium and its dynamics during the transition to vegetative growth. We identified intriguing alterations in the set of ribosomal proteins, in RuBisCO components, in the abundance of central regulators and predicted metabolic enzymes. We found O-phosphorylation as an abundant protein modification in the chlorotic state, specifically of metabolic enzymes and proteins involved in photosynthesis. Nondegraded phycobiliproteins were hyperphosphorylated in the chlorotic state. We provide evidence that hyperphosphorylation of the terminal rod linker CpcD increases the lifespan of phycobiliproteins during chlorosis.

Structures and enzymatic mechanisms of phycobiliprotein lyases CpcE/F and PecE/F

The light-harvesting phycobilisome in cyanobacteria and red algae requires the lyase-catalyzed chromophorylation of phycobiliproteins. There are three functionally distinct lyase families known. The heterodimeric E/F type is specific for attaching bilins covalently to α-subunits of phycocyanins and phycoerythrins. Unlike other lyases, the lyase also has chromophore-detaching activity. A subclass of the E/F-type lyases is, furthermore, capable of chemically modifying the chromophore. Although these enzymes were characterized >25 y ago, their structures remained unknown. We determined the crystal structure of the heterodimer of CpcE/F from Nostoc sp. PCC7120 at 1.89-Å resolution. Both subunits are twisted, crescent-shaped α-solenoid structures. CpcE has 15 and CpcF 10 helices. The inner (concave) layer of CpcE (helices h2, 4, 6, 8, 10, 12, and 14) and the outer (convex) layer of CpcF (h16, 18, 20, 22, and 24) form a cavity into which the phycocyanobilin chromophore can be modeled. This location of the chromophore is supported by mutations at the interface between the subunits and within the cavity. The structure of a structurally related, isomerizing lyase, PecE/F, that converts phycocyanobilin into phycoviolobilin, was modeled using the CpcE/F structure as template. A H₈₇C₈₈ motif critical for the isomerase activity of PecE/F is located at the loop between h20 and h21, supporting the proposal that the nucleophilic addition of Cys-88 to C10 of phycocyanobilin induces the isomerization of phycocyanobilin into phycoviolobilin. Also, the structure of NblB, involved in phycobilisome degradation could be modeled using CpcE as template. Combined with CpcF, NblB shows a low chromophore-detaching activity.

Population-level coordination of pigment response in individual cyanobacterial cells under altered nitrogen levels

Cyanobacterial phycobilisome (PBS) pigment-protein complexes harvest light and transfer the energy to reaction centers. Previous ensemble studies have shown that cyanobacteria respond to changes in nutrient availability by modifying the structure of PBS complexes, but this process has not been visualized for individual pigments at the single-cell level due to spectral overlap. We characterized the response of four key photosynthetic pigments to nitrogen depletion and repletion at the subcellular level in individual, live Synechocystis sp. PCC 6803 cells using hyperspectral confocal fluorescence microscopy and multivariate image analysis. Our results revealed that PBS degradation and re-synthesis comprise a rapid response to nitrogen fluctuations, with coordinated populations of cells undergoing pigment modifications. Chlorophyll fluorescence originating from photosystem I and II decreased during nitrogen starvation, but no alteration in subcellular chlorophyll localization was found. We observed differential rod and core pigment responses to nitrogen deprivation, suggesting that PBS complexes undergo a stepwise degradation process.

Light harvesting in phototrophic bacteria: structure and function

This review serves as an introduction to the variety of light-harvesting (LH) structures present in phototrophic prokaryotes. It provides an overview of the LH complexes of purple bacteria, green sulfur bacteria (GSB), acidobacteria, filamentous anoxygenic phototrophs (FAP), and cyanobacteria. Bacteria have adapted their LH systems for efficient operation under a multitude of different habitats and light qualities, performing both oxygenic (oxygen-evolving) and anoxygenic (non-oxygen-evolving) photosynthesis. For each LH system, emphasis is placed on the overall architecture of the pigment–protein complex, as well as any relevant information on energy transfer rates and pathways. This review addresses also some of the more recent findings in the field, such as the structure of the CsmA chlorosome baseplate and the whole-cell kinetics of energy transfer in GSB, while also pointing out some areas in need of further investigation.

Phycobilisome truncation causes widespread proteome changes in Synechocystis sp. PCC 6803

In cyanobacteria such as Synechocystis sp. PCC 6803, large antenna complexes called phycobilisomes (PBS) harvest light and transfer the energy to the photosynthetic reaction centers. Modification of the light harvesting machinery in cyanobacteria has widespread consequences, causing changes in cell morphology and physiology. In the current study, we investigated the effects of PBS truncation on the proteomes of three Synechocystis 6803 PBS antenna mutants. These range from the progressive truncation of phycocyanin rods in the CB and CK strains, to full removal of PBS in the PAL mutant. Comparative quantitative protein results revealed surprising changes in protein abundances in the mutant strains. Our results showed that PBS truncation in Synechocystis 6803 broadly impacted core cellular mechanisms beyond light harvesting and photosynthesis. Specifically, we observed dramatic alterations in membrane transport mechanisms, where the most severe PBS truncation in the PAL strain appeared to suppress the cellular utilization and regulation of bicarbonate and iron. These changes point to the role of PBS as a component critical to cell function, and demonstrate the continuing need to assess systems-wide protein based abundances to understand potential indirect phenotypic effects.