Distinct responses to warming within picoplankton communities across an environmental gradient

Picophytoplankton are a ubiquitous component of marine plankton communities and are expected to be favored by global increases in seawater temperature and stratification associated with climate change. Eukaryotic and prokaryotic picophytoplankton have distinct ecology, and global models predict that the two groups will respond differently to future climate scenarios. At a nearshore observatory on the Northeast US Shelf, however, decades of year-round monitoring have shown these two groups to be highly synchronized in their responses to environmental variability. To reconcile the differences between regional and global predictions for picophytoplankton dynamics, we here investigate the picophytoplankton community across the continental shelf gradient from the nearshore observatory to the continental slope. We analyze flow cytometry data from 22 research cruises, comparing the response of picoeukaryote and Synechococcus communities to environmental variability across time and space. We find that the mechanisms controlling picophytoplankton abundance differ across taxa, season, and distance from shore. Like the prokaryote, Synechococcus, picoeukaryote division rates are limited nearshore by low temperatures in winter and spring, and higher temperatures offshore lead to an earlier spring bloom. Unlike Synechococcus, picoeukaryote concentration in summer decreases dramatically in offshore surface waters and exhibits deeper subsurface maxima. The offshore picoeukaryote community appears to be nutrient limited in the summer and subject to much greater loss rates than Synechococcus. This work both produces and demonstrates the necessity of taxon- and site-specific knowledge for accurately predicting the responses of picophytoplankton to ongoing environmental change.

Present and future potential role of toxin-producing Synechococcus in the tropical region

As anthropogenic induced temperature rises and nutrient loadings increase in fresh and brackish environments, the ecological function of the phytoplankton community is expected to favour the picocyanobacteria, of the genus Synechococcus. Synechococcus is already a ubiquitous cyanobacterium found in both freshwater and marine environments, notwithstanding that the toxigenic species still remains unexplored in many freshwaters. Their fast growth rate and their ability to produce toxins make Synechococcus a potential dominant player in harmful algal blooms under climate change scenarios. This study examines the responses of a novel toxin-producing Synechococcus (i.e., one belonging to a freshwater clade; the other belonging to a brackish clade) to environmental changes that reflect climate change effects. We conducted a series of controlled experiments under present and predicted future temperatures, as well as under various N and P nutrients loadings. Our findings highlight how Synechococcus can be altered by the differing reactions to increasing temperature and nutrients, which resulted in considerable variations in cell abundance, growth rate, death rate, cellular stoichiometry and toxin production. Synechococcus had the highest growth observed at 28 °C, and further increases in temperature resulted in a decline for both fresh and brackish waters. Cellular stoichiometry was also altered, where more nitrogen (N) per cell was required, and the plasticity of N:P was more severe for the brackish clade. However, Synechococcus become more toxic under future scenario. Anatoxin-a (ATX) saw the greatest spike when temperature was at 34 °C especially under P-enrichment conditions. In contrast, Cylindrospermopsin (CYN) was promoted at the lowest tested temperature (25 °C) and under N-limitation. Overall, both temperature and external nutrients are the dominant control over Synechococcus toxins production. A model was also created to assess Synechococcus toxicity to zooplankton grazing. Zooplankton grazing was reduced by two folds under nutrient limitation, but temperature accounted for very insignificant change.

KidA, a multi-PAS domain protein, tunes the period of the cyanobacterial circadian oscillator

The cyanobacterial clock presents a unique opportunity to understand the biochemical basis of circadian rhythms. The core oscillator, composed of the KaiA, KaiB, and KaiC proteins, has been extensively studied, but a complete picture of its connection to the physiology of the cell is lacking. To identify previously unknown components of the clock, we used KaiB locked in its active fold as bait in an immunoprecipitation/mass spectrometry approach. We found that the most abundant interactor, other than KaiC, was a putative diguanylate cyclase protein predicted to contain multiple Per-Arnt-Sim (PAS) domains, which we propose to name KidA. Here we show that KidA directly binds to the fold-switched active form of KaiB through its N-terminal PAS domains. We found that KidA shortens the period of the circadian clock both in vivo and in vitro and alters the ability of the clock to entrain to light-dark cycles. The dose-dependent effect of KidA on the clock period could be quantitatively recapitulated by a mathematical model in which KidA stabilizes the fold-switched form of KaiB, favoring rebinding to KaiC. Put together, our results show that the period and amplitude of the clock can be modulated by regulating the access of KaiB to the fold-switched form.

Acclimation of the photosynthetic apparatus to low light in a thermophilic Synechococcus sp. strain

Depending upon their growth responses to high and low irradiance, respectively, thermophilic Synechococcus sp. isolates from microbial mats associated with the effluent channels of Mushroom Spring, an alkaline siliceous hot spring in Yellowstone National Park, can be described as either high-light (HL) or low-light (LL) ecotypes. Strains isolated from the bottom of the photic zone grow more rapidly at low irradiance compared to strains isolated from the uppermost layer of the mat, which conversely grow better at high irradiance. The LL-ecotypes develop far-red absorbance and fluorescence emission features after growth in LL. These isolates have a unique gene cluster that encodes a putative cyanobacteriochrome denoted LcyA, a putative sensor histidine kinase; an allophycocyanin (FRL-AP; ApcD4-ApcB3) that absorbs far-red light; and a putative chlorophyll a-binding protein, denoted IsiX, which is homologous to IsiA. The emergence of FRL absorbance in LL-adapted cells of Synechococcus sp. strain A1463 was analyzed in cultures responding to differences in light intensity. The far-red absorbance phenotype arises from expression of a novel antenna complex containing the FRL-AP, ApcD4-ApcB3, which is produced when cells were grown at very low irradiance. Additionally, the two GAF domains of LcyA were shown to bind phycocyanobilin and a [4Fe-4S] cluster, respectively. These ligands potentially enable this photoreceptor to respond to a variety of environmental factors including irradiance, redox potential, and/or oxygen concentration. The products of the gene clusters specific to LL-ecotypes likely facilitate growth in low-light environments through a process called Low-Light Photoacclimation.

Marine Synechococcus picocyanobacteria: Light utilization across latitudes

The most ubiquitous cyanobacteria, Synechococcus, have colonized different marine thermal niches through the evolutionary specialization of lineages adapted to different ranges of temperature seawater. We used the strains of Synechococcus temperature ecotypes to study how light utilization has evolved in the function of temperature. The tropical Synechococcus (clade II) was unable to grow under 16 °C but, at temperatures >25 °C, induced very high growth rates that relied on a strong synthesis of the components of the photosynthetic machinery, leading to a large increase in photosystem cross-section and electron flux. By contrast, the Synechococcus adapted to subpolar habitats (clade I) grew more slowly but was able to cope with temperatures <10 °C. We show that growth at such temperatures was accompanied by a large increase of the photoprotection capacities using the orange carotenoid protein (OCP). Metagenomic analyzes revealed that Synechococcus natural communities show the highest prevalence of the ocp genes in low-temperature niches, whereas most tropical clade II Synechococcus have lost the gene. Moreover, bioinformatic analyzes suggested that the OCP variants of the two cold-adapted Synechococcus clades I and IV have undergone evolutionary convergence through the adaptation of the molecular flexibility. Our study points to an important role of temperature in the evolution of the OCP. We, furthermore, discuss the implications of the different metabolic cost of these physiological strategies on the competitiveness of Synechococcus in a warming ocean. This study can help improve the current hypotheses and models aimed at predicting the changes in ocean carbon fluxes in response to global warming.

A Cyanobacterial Component Required for Pilus Biogenesis Affects the Exoproteome

Protein secretion as well as the assembly of bacterial motility appendages are central processes that substantially contribute to fitness and survival. This study highlights distinctive features of the mechanism that serves these functions in cyanobacteria, which are globally prevalent photosynthetic prokaryotes that significantly contribute to primary production. Our studies of biofilm development in the cyanobacterium Synechococcus elongatus uncovered a novel component required for the biofilm self-suppression mechanism that operates in this organism. This protein, which is annotated as "hypothetical," is denoted EbsA (essential for biofilm self-suppression A) here. EbsA homologs are highly conserved and widespread in diverse cyanobacteria but are not found outside this clade. We revealed a tripartite complex of EbsA, Hfq, and the ATPase homolog PilB (formerly called T2SE) and demonstrated that each of these components is required for the assembly of the hairlike type IV pili (T4P) appendages, for DNA competence, and affects the exoproteome in addition to its role in biofilm self-suppression. These data are consistent with bioinformatics analyses that reveal only a single set of genes in S. elongatus to serve pilus assembly or protein secretion; we suggest that a single complex is involved in both processes. A phenotype resulting from the impairment of the EbsA homolog in the cyanobacterium Synechocystis sp. strain PCC 6803 implies that this feature is a general cyanobacterial trait. Moreover, comparative exoproteome analyses of wild-type and mutant strains of S. elongatus suggest that EbsA and Hfq affect the exoproteome via a process that is independent of PilB, in addition to their involvement in a T4P/secretion machinery.IMPORTANCE Cyanobacteria, environmentally prevalent photosynthetic prokaryotes, contribute ∼25% of global primary production. Cyanobacterial biofilms elicit biofouling, thus leading to substantial economic losses; however, these microbial assemblages can also be beneficial, e.g., in wastewater purification processes and for biofuel production. Mechanistic aspects of cyanobacterial biofilm development were long overlooked, and genetic and molecular information emerged only in recent years. The importance of this study is 2-fold. First, it identifies novel components of cyanobacterial biofilm regulation, thus contributing to the knowledge of these processes and paving the way for inhibiting detrimental biofilms or promoting beneficial ones. Second, the data suggest that cyanobacteria may employ the same complex for the assembly of the motility appendages, type 4 pili, and protein secretion. A shared pathway was previously shown in only a few cases of heterotrophic bacteria, whereas numerous studies demonstrated distinct systems for these functions. Thus, our study broadens the understanding of pilus assembly/secretion in diverse bacteria and furthers the aim of controlling the formation of cyanobacterial biofilms.

Proximity-based proteomics reveals the thylakoid lumen proteome in the cyanobacterium Synechococcus sp. PCC 7002

Cyanobacteria possess unique intracellular organization. Many proteomic studies have examined different features of cyanobacteria to learn about the intracellular structures and their respective functions. While these studies have made great progress in understanding cyanobacterial physiology, the conventional fractionation methods used to purify cellular structures have limitations; specifically, certain regions of cells cannot be purified with existing fractionation methods. Proximity-based proteomics techniques were developed to overcome the limitations of biochemical fractionation for proteomics. Proximity-based proteomics relies on spatiotemporal protein labeling followed by mass spectrometry of the labeled proteins to determine the proteome of the region of interest. We performed proximity-based proteomics in the cyanobacterium Synechococcus sp. PCC 7002 with the APEX2 enzyme, an engineered ascorbate peroxidase. We determined the proteome of the thylakoid lumen, a region of the cell that has remained challenging to study with existing methods, using a translational fusion between APEX2 and PsbU, a lumenal subunit of photosystem II. Our results demonstrate the power of APEX2 as a tool to study the cell biology of intracellular features and processes, including photosystem II assembly in cyanobacteria, with enhanced spatiotemporal resolution.

The structural basis of far-red light absorbance by allophycocyanins

Phycobilisomes (PBS), the major light-harvesting antenna in cyanobacteria, are supramolecular complexes of colorless linkers and heterodimeric, pigment-binding phycobiliproteins. Phycocyanin and phycoerythrin commonly comprise peripheral rods, and a multi-cylindrical core is principally assembled from allophycocyanin (AP). Each AP subunit binds one phycocyanobilin (PCB) chromophore, a linear tetrapyrrole that predominantly absorbs in the orange-red region of the visible spectrum (600-700 nm). AP facilitates excitation energy transfer from PBS peripheral rods or from directly absorbed red light to accessory chlorophylls in the photosystems. Paralogous forms of AP that bind PCB and are capable of absorbing far-red light (FRL; 700-800 nm) have recently been identified in organisms performing two types of photoacclimation: FRL photoacclimation (FaRLiP) and low-light photoacclimation (LoLiP). The FRL-absorbing AP (FRL-AP) from the thermophilic LoLiP strain Synechococcus sp. A1463 was chosen as a platform for site-specific mutagenesis to probe the structural differences between APs that absorb in the visible region and FRL-APs and to identify residues essential for the FRL absorbance phenotype. Conversely, red light-absorbing allophycocyanin-B (AP-B; ~ 670 nm) from the same organism was used as a platform for creating a FRL-AP. We demonstrate that the protein environment immediately surrounding pyrrole ring A of PCB on the alpha subunit is mostly responsible for the FRL absorbance of FRL-APs. We also show that interactions between PCBs bound to alpha and beta subunits of adjacent protomers in trimeric AP complexes are responsible for a large bathochromic shift of about ~ 20 nm and notable sharpening of the long-wavelength absorbance band.

Synechococcus elongatus PCC7942: a cyanobacterium cell factory for producing useful chemicals and fuels under abiotic stress conditions

Sucrose, a compatible osmolyte in cyanobacteria, functions both as an energy reserve and as osmoprotectant. Sugars are the most common substrates used by microorganisms to produce hydrogen (H₂) by means of anaerobic dark fermentation. Cells of the unicellular, non-nitrogen fixing, freshwater cyanobacterium Synechococcus elongatus PCC7942 accumulate sucrose under salt stress. In the present work, we used this cyanobacterium and a genetically engineered strain of it (known as PAMCOD) to investigate the optimal conditions for (a) photosynthetic activity, (b) cell proliferation and (c) sucrose accumulation, which are necessary for H₂ production via anaerobic dark fermentation of the accumulated sucrose. PAMCOD (Deshnium et al. in Plant Mol Biol 29:897-902, 1995) contains the gene codA that codes for choline oxidase, the enzyme which converts choline to the zwitterion glycine betaine. Glycine betaine is a compatible osmolyte which increases the salt tolerance of Synechococcus elongatus PCC7942. Furthermore, glycine betaine maintains cell proliferation under salt stress and results in increased sucrose accumulation. In the present study, we examine the environmental factors, such as the NaCl concentration, the culture medium pH, and the carbon dioxide content of the air bubbled through it. At optimal conditions, sucrose accumulated in the cyanobacteria cells up to 13.5 mol per mole Chl a. Overall, genetically engineered Synechococcus elongatus PCC7942 produces sucrose in sufficient quantities such that it may be a viable alternative (a) to sucrose synthesis, and (b) to H₂ formation via anaerobic dark fermentation.

Solution NMR structure of Se0862, a highly conserved cyanobacterial protein involved in biofilm formation

Biofilms are accumulations of microorganisms embedded in extracellular matrices that protect against external factors and stressful environments. Cyanobacterial biofilms are ubiquitous and have potential for treatment of wastewater and sustainable production of biofuels. But the underlying mechanisms regulating cyanobacterial biofilm formation are unclear. Here, we report the solution NMR structure of a protein, Se0862, conserved across diverse cyanobacterial species and involved in regulation of biofilm formation in the cyanobacterium Synechococcus elongatus PCC 7942. Se0862 is a class α+β protein with ααββββαα topology and roll architecture, consisting of a four-stranded β-sheet that is flanked by four α-helices on one side. Conserved surface residues constitute a hydrophobic pocket and charged regions that are likely also present in Se0862 orthologs.

The response of Synechococcus sp. PCC 7002 to micro-/nano polyethylene particles - Investigation of a key anthropogenic stressor

Microplastics or plastic particles less than 5 mm in size are a ubiquitous and damaging pollutant in the marine environment. However, the interactions between these plastic particles and marine microorganisms are just starting to be understood. The objective of this study was to measure the responses of a characteristic marine organism (Synechococcus sp. PCC 7002) to an anthropogenic stressor (polyethelene nanoparticles and microparticles) using molecular techniques. This investigation showed that polyethylene microparticles and nanoparticles have genetic, enzymatic and morphological effects on Synechococcus sp. PCC 7002. An RT-PCR analysis showed increases in the expression of esterase and hydrolase genes at 5 days of exposure to polyethylene nanoparticles and at 10 days of exposure to polyethylene microparticles. A qualitative enzymatic assay also showed esterase activity in nanoparticle exposed samples. Cryo-scanning electron microscopy was used to assess morphological changes in exopolymer formation resulting from exposure to polyethylene microparticles and nanoparticles. The data from this paper suggests that microplastic and nanoplastics could be key microbial stressors and should be investigated in further detail.

Structural variability, coordination and adaptation of a native photosynthetic machinery

Cyanobacterial thylakoid membranes represent the active sites for both photosynthetic and respiratory electron transport. We used high-resolution atomic force microscopy to visualize the native organization and interactions of photosynthetic complexes within the thylakoid membranes from the model cyanobacterium Synechococcus elongatus PCC 7942. The thylakoid membranes are heterogeneous and assemble photosynthetic complexes into functional domains to enhance their coordination and regulation. Under high light, the chlorophyll-binding proteins IsiA are strongly expressed and associate with Photosystem I (PSI), forming highly variable IsiA-PSI supercomplexes to increase the absorption cross-section of PSI. There are also tight interactions of PSI with Photosystem II (PSII), cytochrome b₆f, ATP synthase and NAD(P)H dehydrogenase complexes. The organizational variability of these photosynthetic supercomplexes permits efficient linear and cyclic electron transport as well as bioenergetic regulation. Understanding the organizational landscape and environmental adaptation of cyanobacterial thylakoid membranes may help inform strategies for engineering efficient photosynthetic systems and photo-biofactories.

Phytoplankton transcriptomic and physiological responses to fixed nitrogen in the California current system

Marine phytoplankton are responsible for approximately half of photosynthesis on Earth. However, their ability to drive ocean productivity depends on critical nutrients, especially bioavailable nitrogen (N) which is scarce over vast areas of the ocean. Phytoplankton differ in their preferences for N substrates as well as uptake efficiencies and minimal N requirements relative to other critical nutrients, including iron (Fe) and phosphorus. In this study, we used the MicroTOOLs high-resolution environmental microarray to examine transcriptomic responses of phytoplankton communities in the California Current System (CCS) transition zone to added urea, ammonium, nitrate, and also Fe in the late summer when N depletion is common. Transcript level changes of photosynthetic, carbon fixation, and nutrient stress genes indicated relief of N limitation in many strains of Prochlorococcus, Synechococcus, and eukaryotic phytoplankton. The transcriptomic responses helped explain shifts in physiological and growth responses observed later. All three phytoplankton groups had increased transcript levels of photosynthesis and/or carbon fixation genes in response to all N substrates. However, only Prochlorococcus had decreased transcript levels of N stress genes and grew substantially, specifically after urea and ammonium additions, suggesting that Prochlorococcus outcompeted other community members in these treatments. Diatom transcript levels of carbon fixation genes increased in response to Fe but not to Fe with N which might have favored phytoplankton that were co-limited by N and Fe. Moreover, transcription patterns of closely related strains indicated variability in N utilization, including nitrate utilization by some high-light adapted Prochlorococcus. Finally, up-regulation of urea transporter genes by both Prochlorococcus and Synechococcus in response to filtered deep water suggested a regulatory mechanism other than classic control via the global N regulator NtcA. This study indicated that co-existing phytoplankton strains experience distinct nutrient stresses in the transition zone of the CCS, an understudied region where oligotrophic and coastal communities naturally mix.

Assessment of the Allelochemical Activity and Biochemical Profile of Different Phenotypes of Picocyanobacteria from the Genus Synechococcus

Organisms belonging to Synechococcus sp. genera are observed in all freshwater, brackish, and marine waters of the world. They play a relevant role in these ecosystems, since they are one of the main primary producers, especially in open ocean. Eventually, they form mass blooms in coastal areas, which are potentially dangerous for the functioning of marine ecosystems. Allelopathy could be an important factor promoting the proliferation of these organisms. According to the authors’ best knowledge, there is no information on the allelopathic activity and allelopathic compounds exhibited by different Synechococcus sp. phenotypes. Therefore, the research conducted here aimed to study the bioactivity of compounds produced by three phenotypes of Synechococcus sp. by studying their influence on the growth, chlorophyll fluorescence, and photosynthetic pigments of eighteen cyanobacteria and microalgae species. We demonstrated that three different Synechococcus sp. phenotypes, including a phycocyanin (PC)-rich strain (Type 1; green strain) and phycoerythrin (PE)-rich strains containing phycoerythrobilin (PEB) and phycocyanobilin (PCB) (Type 2; red strain and Type 3a; brown strain), had a significant allelopathic effect on the selected species of cyanobacteria, diatoms, and green algae. For all green algae, a decrease in cell abundance under the influence of phenotypes of donor cyanobacteria was shown, whereas, among some target cyanobacteria and diatom species, the cell-free filtrate was observed to have a stimulatory effect. Our estimates of the stress on photosystem II (F_v/F_m) showed a similar pattern, although for some diatoms, there was an effect of stress on photosynthesis, while a stimulatory effect on growth was also displayed. The pigment content was affected by allelopathy in most cases, particularly for chlorophyll a, whilst it was a bit less significant for carotenoids. Our results showed that Synechococcus sp. Type 3a had the strongest effect on target species, while Synechococcus sp. Type 1 had the weakest allelopathic effect. Furthermore, GC-MS analysis produced different biochemical profiles for the Synechococcus strains. For every phenotype, the most abundant compound was different, with oxime-, methoxy-phenyl- being the most abundant substance for Synechococcus Type 1, eicosane for Synechococcus Type 2, and silanediol for Synechococcus Type 3a.

Structural basis for energy and electron transfer of the photosystem I-IsiA-flavodoxin supercomplex

Under iron-deficiency stress, which occurs frequently in natural aquatic environments, cyanobacteria reduce the amount of iron-enriched proteins, including photosystem I (PSI) and ferredoxin (Fd), and upregulate the expression of iron-stress-induced proteins A and B (IsiA and flavodoxin (Fld)). Multiple IsiAs function as the peripheral antennae that encircle the PSI core, whereas Fld replaces Fd as the electron receptor of PSI. Here, we report the structures of the PSI₃-IsiA₁₈-Fld₃ and PSI₃-IsiA₁₈ supercomplexes from Synechococcus sp. PCC 7942, revealing features that are different from the previously reported PSI structures, and a sophisticated pigment network that involves previously unobserved pigment molecules. Spectroscopic results demonstrated that IsiAs are efficient light harvesters for PSI. Three Flds bind symmetrically to the trimeric PSI core-we reveal the detailed interaction and the electron transport path between PSI and Fld. Our results provide a structural basis for understanding the mechanisms of light harvesting, energy transfer and electron transport of cyanobacterial PSI under stressed conditions.

Synechococcus bloom in the Pearl River Estuary and adjacent coastal area-With special focus on flooding during wet seasons

Based on the field surveys aimed at understanding the variations of Synechococcus (Syn) abundance in the Pearl River Estuary during different seasons. We found that heavy terrestrial precipitation result in significant riverine runoffs and promote Syn growth, extension and blooms during warm and wet seasons. To understand the ecological role of Syn play in this estuary during wet seasons, we combined flow cytometry and high throughput sequencing (HTS) of 16S rDNA to investigate the phytoplankton distribution patterns and the potential shaping mechanisms during a typical wet season. During the cruise, picophytoplankton, especially Syn, and Nano-eukaryotes contributed importantly to the total phytoplankton biomass of the estuary. Syn can be further divided into phycoerythrin (PE)-rich Syn and phycocyanin (PC)-rich Syn, with PC-rich Syn about 1.5 times higher than PE-rich Syn in abundance. Both PE-rich Syn (60.75 × 10³ cells ml^-1) and PC-rich Syn (604.05 × 10³ cells ml^-1) reach the highest abundance at the lower part of the estuary. Moreover, PE-rich Syn can be divided into two subgroups which showed different salinity preference, with PE1 distributed in the high salinity area (with salinity >25) while PE2 in the middle salinity area (with salinity 7-20). Our results from the 16S rDNA sequencing also indicated abundant diversity and different niche adaptation of Syn with the operational taxonomic units (OTUs) along the estuary. Besides, analysis also indicated a tight correlation between estuarine Syn and active heterotrophic bacteria, especially groups of Rhodobacteria and Actionobacteria.

The endogenous redox rhythm is controlled by a central circadian oscillator in cyanobacterium Synechococcus elongatus PCC7942

The intracellular redox and the circadian clock in photosynthetic organisms are two major regulators globally affecting various biological functions. Both of the global control systems have evolved as systems to adapt to regularly or irregularly changing light environments. Here, we report that the two global regulators mutually interact in cyanobacterium Synechococcus elongatus PCC7942, a model photosynthetic organism whose clock molecular mechanism is well known. Electrochemical assay using a transmembrane electron mediator revealed that intracellular redox of S. elongatus PCC7942 cell exhibited circadian rhythms under constant light conditions. The redox rhythm disappeared when transcription/translation of clock genes is defunctionalized, indicating that the transcription/translation controlled by a core KaiABC oscillator generates the circadian redox rhythm. Importantly, the amplitude of the redox rhythm at a constant light condition was large enough to affect the KaiABC oscillator. The findings indicated that the intracellular redox state is actively controlled to change in a 24-h cycle under constant light conditions by the circadian clock system.

Extensive remodeling of the photosynthetic apparatus alters energy transfer among photosynthetic complexes when cyanobacteria acclimate to far-red light

Some cyanobacteria remodel their photosynthetic apparatus by a process known as Far-Red Light Photoacclimation (FaRLiP). Specific subunits of the phycobilisome (PBS), photosystem I (PSI), and photosystem II (PSII) complexes produced in visible light are replaced by paralogous subunits encoded within a conserved FaRLiP gene cluster when cells are grown in far-red light (FRL; λ = 700-800 nm). FRL-PSII complexes from the FaRLiP cyanobacterium, Synechococcus sp. PCC 7335, were purified and shown to contain Chl a, Chl d, Chl f, and pheophytin a, while FRL-PSI complexes contained only Chl a and Chl f. The spectroscopic properties of purified photosynthetic complexes from Synechococcus sp. PCC 7335 were determined individually, and energy transfer kinetics among PBS, PSII, and PSI were analyzed by time-resolved fluorescence (TRF) spectroscopy. Direct energy transfer from PSII to PSI was observed in cells (and thylakoids) grown in red light (RL), and possible routes of energy transfer in both RL- and FRL-grown cells were inferred. Three structural arrangements for RL-PSI were observed by atomic force microscopy of thylakoid membranes, but only arrays of trimeric FRL-PSI were observed in thylakoids from FRL-grown cells. Cells grown in FRL synthesized the FRL-specific complexes but also continued to synthesize some PBS and PSII complexes identical to those produced in RL. Although the light-harvesting efficiency of photosynthetic complexes produced in FRL might be lower in white light than the complexes produced in cells acclimated to white light, the FRL-complexes provide cells with the flexibility to utilize both visible and FRL to support oxygenic photosynthesis. This article is part of a Special Issue entitled Light harvesting, edited by Dr. Roberta Croce.

Energy transfer from chlorophyll f to the trapping center in naturally occurring and engineered Photosystem I complexes

Certain cyanobacteria can thrive in environments enriched in far-red light (700-800 nm) due to an acclimation process known as far-red light photoacclimation (FaRLiP). During FaRLiP, about 8% of the Chl a molecules in the photosystems are replaced by Chl f and a very small amount of Chl d. We investigated the spectroscopic properties of Photosystem I (PSI) complexes isolated from wild-type (WT) Synechococcus sp. PCC 7335 and a chlF mutant strain (lacking Chl f synthase) grown in white and far-red light (WL-PSI and FRL-PSI, respectively). WT-FRL-PSI complexes contain Chl f and Chl a but not Chl d. The light-minus dark difference spectrum of the trapping center at high spectral resolution indicates that the special pair in WT-FRL-PSI consists of Chl a molecules with maximum bleaching at 703-704 nm. The action spectrum for photobleaching of the special pair showed that Chl f molecules absorbing at wavelengths up to 800 nm efficiently transfer energy to the trapping center in FRL-PSI complexes to produce a charge-separated state. This is ~ 50 nm further into the near IR than WL-PSI; Chl f has a quantum yield equivalent to that of Chl a in the antenna, i.e., ~ 1.0. PSI complexes from Synechococcus 7002 carrying 3.8 Chl f molecules could promote photobleaching of the special pair by energy transfer at wavelengths longer than WT PSI complexes. Results from these latter studies are directly relevant to the issue of whether introduction of Chl f synthase into plants could expand the wavelength range available for oxygenic photosynthesis in crop plants.

A microcin processing peptidase-like protein of the cyanobacterium Synechococcus elongatus is essential for secretion of biofilm-promoting proteins

Small secreted compounds, e.g. microcins, are characterized by a double-glycine (GG) secretion motif that is cleaved off upon maturation. Genomic analysis suggests that small proteins that possess a GG motif are widespread in cyanobacteria; however, the roles of these proteins are largely unknown. Using a biofilm-proficient mutant of the cyanobacterium Synechococcus elongatus PCC 7942 in which the constitutive biofilm self-suppression mechanism is inactivated, we previously demonstrated that four small proteins, Enable biofilm formation with a GG motif (EbfG1-4), each with a GG motif, enable biofilm formation. Furthermore, a peptidase belonging to the C39 family, Peptidase transporter enabling Biofilm (PteB), is required for secretion of these proteins. Here, we show that the microcin processing peptidase-like protein encoded by gene Synpcc7942_1127 is also required for biofilm development - inactivation of this gene in the biofilm-proficient mutant abrogates biofilm development. Additionally, this peptidase-like protein (denoted EbfE - enables biofilm formation peptidase) is required for secretion of the EbfG biofilm-promoting small proteins. Given their protein-domain characteristics, we suggest that PteB and EbfE take part in a maturation-secretion system, with PteB being located to the cell membrane while EbfE is directed to the periplasmic space via its secretion signal.

Characterization of chlorophyll f synthase heterologously produced in Synechococcus sp. PCC 7002

In diverse terrestrial cyanobacteria, Far-Red Light Photoacclimation (FaRLiP) promotes extensive remodeling of the photosynthetic apparatus, including photosystems (PS)I and PSII and the cores of phycobilisomes, and is accompanied by the concomitant biosynthesis of chlorophyll (Chl) d and Chl f. Chl f synthase, encoded by chlF, is a highly divergent paralog of psbA; heterologous expression of chlF from Chlorogloeopsis fritscii PCC 9212 led to the light-dependent production of Chl f in Synechococcus sp. PCC 7002 (Ho et al., Science 353, aaf9178 (2016)). In the studies reported here, expression of the chlF gene from Fischerella thermalis PCC 7521 in the heterologous system led to enhanced synthesis of Chl f. N-terminally [His]₁₀-tagged ChlF⁷⁵²¹ was purified and identified by immunoblotting and tryptic-peptide mass fingerprinting. As predicted from its sequence similarity to PsbA, ChlF bound Chl a and pheophytin a at a ratio of ~ 3-4:1, bound β-carotene and zeaxanthin, and was inhibited in vivo by 3-(3,4-dichlorophenyl)-1,1-dimethylurea. Cross-linking studies and the absence of copurifying proteins indicated that ChlF forms homodimers. Flash photolysis of ChlF produced a Chl a triplet that decayed with a lifetime (1/e) of ~ 817 µs and that could be attributed to intersystem crossing by EPR spectroscopy at 90 K. When the chlF⁷⁵²¹ gene was expressed in a strain in which the psbD1 and psbD2 genes had been deleted, significantly more Chl f was produced, and Chl f levels could be further enhanced by specific growth-light conditions. Chl f synthesized in Synechococcus sp. PCC 7002 was inserted into trimeric PSI complexes.

Allelopathic effects of Chara species (C. aspera, C. baltica, and C. canescens) on the bloom-forming picocyanobacterium Synechococcus sp

The role of macroalgal allelopathy in aquatic systems has received increasing attention as a potential means of controlling cyanobacterial blooms. However, the allelopathic activity of Chara sp. on coexisting and bloom-forming picocyanobacteria is still largely unknown. Therefore, the laboratory experiments were conducted to investigate the allelopathic activity of extracts of Chara aspera, C. baltica, and C. canescens on the growth, the fluorescence parameters: maximum and effective quantum yield of photosystem II (PSII) photochemistry (F_v/F_m and ΦPSII, respectively) and photosynthesis parameters such as the initial slope of photosynthesis-irradiance (P-E) curves (alpha) and photosynthetic capacity (P_m) of the picocyanobacterium Synechococcus sp. Batch cultures of picocyanobacterium were exposed to three concentrations of extracts originating from three charophyte cultures and the effect was followed at three sampling times. Dried specimens of C. aspera, C. baltica, and C. canescens were extracted in the water-based matrix and the initial Synechococcus sp. inoculum, derived from unialgal culture media, was used. We found both negative and positive allelopathic effects of all tested Chara extracts on Synechococcus sp. The strongest adverse impact of picocyanobacterium growth was caused by C. baltica. This study clearly demonstrated that the allelopathic effect depends on the Chara species identity. Our results also suggested that some allelopathic Chara sp. have the potential to mitigate harmful cyanobacterial blooms in systems dominated by Synechococcus sp.

Cell size control driven by the circadian clock and environment in cyanobacteria

How cells maintain their size has been extensively studied under constant conditions. In the wild, however, cells rarely experience constant environments. Here, we examine how the 24-h circadian clock and environmental cycles modulate cell size control and division timings in the cyanobacterium Synechococcus elongatus using single-cell time-lapse microscopy. Under constant light, wild-type cells follow an apparent sizer-like principle. Closer inspection reveals that the clock generates two subpopulations, with cells born in the subjective day following different division rules from cells born in subjective night. A stochastic model explains how this behavior emerges from the interaction of cell size control with the clock. We demonstrate that the clock continuously modulates the probability of cell division throughout day and night, rather than solely applying an on-off gate to division, as previously proposed. Iterating between modeling and experiments, we go on to identify an effective coupling of the division rate to time of day through the combined effects of the environment and the clock on cell division. Under naturally graded light-dark cycles, this coupling narrows the time window of cell divisions and shifts divisions away from when light levels are low and cell growth is reduced. Our analysis allows us to disentangle, and predict the effects of, the complex interactions between the environment, clock, and cell size control.

Cell size control driven by the circadian clock and environment in cyanobacteria

How cells maintain their size has been extensively studied under constant conditions. In the wild, however, cells rarely experience constant environments. Here, we examine how the 24-h circadian clock and environmental cycles modulate cell size control and division timings in the cyanobacterium Synechococcus elongatus using single-cell time-lapse microscopy. Under constant light, wild-type cells follow an apparent sizer-like principle. Closer inspection reveals that the clock generates two subpopulations, with cells born in the subjective day following different division rules from cells born in subjective night. A stochastic model explains how this behavior emerges from the interaction of cell size control with the clock. We demonstrate that the clock continuously modulates the probability of cell division throughout day and night, rather than solely applying an on-off gate to division, as previously proposed. Iterating between modeling and experiments, we go on to identify an effective coupling of the division rate to time of day through the combined effects of the environment and the clock on cell division. Under naturally graded light-dark cycles, this coupling narrows the time window of cell divisions and shifts divisions away from when light levels are low and cell growth is reduced. Our analysis allows us to disentangle, and predict the effects of, the complex interactions between the environment, clock, and cell size control.

Complementary chromatic and far-red photoacclimations in Synechococcus ATCC 29403 (PCC 7335). I: The phycobilisomes, a proteomic approach

Synechococcus ATCC 29403 (PCC 7335) is a unicellular cyanobacterium isolated from Puerto Peñasco, Sonora Mexico. This cyanobacterium performs complementary chromatic acclimation (CCA), far-red light photoacclimation (FaRLiP), and nitrogen fixation. The Synechococcus PCC 7335 genome contains at least 31 genes for proteins of the phycobilisome (PBS). Nine constitutive genes were expressed when cells were grown under white or red lights and the resulting proteins were identified by mass spectrometry in isolated PBS. Five inducible genes were expressed under white light, and phycoerythrin subunits and associated linker proteins were detected. The proteins of five inducible genes expressed under red light were identified, the induced phycocyanin subunits, two rod linkers and the rod-capping linker. The five genes for FaRLiP phycobilisomes were expressed under far-red light together with the apcF gene, and the proteins were identified by mass spectrometry after isoelectric focusing and SDS-PAGE. Based on in silico analysis, Phylogenetic trees, and the observation of a highly conserved amino acid sequence in far-red light absorbing alpha allophycoproteins encoded by FaRLiP gene cluster, we propose a new nomenclature for the genes. Based on a ratio of ApcG2/ApcG3 of six, a model with the arrangement of the allophycocyanin trimers of the core is proposed.

Elemental Stoichiometry and Photophysiology Regulation of Synechococcus sp. PCC7002 Under Increasing Severity of Chronic Iron Limitation

Iron (Fe) is an essential cofactor for many metabolic enzymes of photoautotrophs. Although Fe limits phytoplankton productivity in broad areas of the ocean, phytoplankton have adapted their metabolism and growth to survive in these conditions. Using the euryhaline cyanobacterium Synechococcus sp. PCC7002, we investigated the physiological responses to long-term acclimation to four levels of Fe availability representative of the contemporary ocean (36.7, 3.83, 0.47 and 0.047 pM Fe'). With increasing severity of Fe limitation, Synechococcus sp. cells gradually decreased their volume and growth while increasing their energy allocation into organic carbon and nitrogen cellular pools. Furthermore, the total cellular content of pigments decreased. Additionally, with increasing severity of Fe limitation, intertwined responses of PSII functional cross-section (σPSII), re-oxidation time of the plastoquinone primary acceptor QA (τ) and non-photochemical quenching revealed a shift in the photophysiological response between mild to strong Fe limitation compared with severe limitation. Under mild and strong Fe limitation, there was a decrease in linear electron transport accompanied by progressive loss of state transitions. Under severe Fe limitation, state transitions seemed to be largely supplanted by alternative electron pathways. In addition, mechanisms to dissipate energy excess and minimize oxidative stress associated with high irradiances increased with increasing severity of Fe limitation. Overall, our results establish the sequence of physiological strategies adopted by the cells under increasing severity of chronic Fe limitation, within a range of Fe concentrations relevant to modern ocean biogeochemistry.

Detecting signatures of a sponge-associated lifestyle in bacterial genomes

Sponges interact with diverse and rich communities of bacteria that are phylogenetically often distinct from their free-living counterparts. Recent genomics and metagenomic studies have indicated that bacterial sponge symbionts also have distinct functional features from free-living bacteria; however, it is unclear, if such genome-derived functional signatures are common and present in different symbiont taxa. We therefore compared here a large set of genomes from cultured (Pseudovibrio, Ruegeria and Aquimarina) and yet-uncultivated (Synechococcus) bacteria found in either sponge-associated or free-living sources. Our analysis revealed only very few genera-specific functions that could be correlated with a sponge-associated lifestyle. Using different sets of sponge-associated and free-living bacteria for each genus, we could however show that the functions identified as 'sponge-associated' are dependent on the reference comparison being made. Using simulation approaches, we show how this influences the robustness of identifying functional signatures and how evolutionary divergence and genomic adaptation can be distinguished. Our results highlight the future need for robust comparative analyses to define genomic signatures of symbiotic lifestyles, whether it is for symbionts of sponges or other host organisms.

Effects of PSII Manganese-Stabilizing Protein Succinylation on Photosynthesis in the Model Cyanobacterium Synechococcus sp. PCC 7002

Lysine succinylation is a newly identified protein post-translational modification and plays important roles in various biological pathways in both prokaryotes and eukaryotes, but its extent and function in photosynthetic organisms remain largely unknown. Here, we performed the first systematic studies of lysine succinylation in cyanobacteria, which are the only prokaryotes capable of oxygenic photosynthesis and the established model organisms for studying photosynthetic mechanisms. By using mass spectrometry analysis in combination with the enrichment of succinylated peptides from digested cell lysates, we identified 1,704 lysine succinylation sites on 691 proteins in a model cyanobacterium Synechococcus sp. PCC 7002. Bioinformatic analysis revealed that a large proportion of the succinylation sites were present on proteins in photosynthesis and metabolism. Among all identified succinylated proteins involved in photosynthesis, the PSII manganese-stabilizing protein (PsbO) was found to be succinylated on Lys99 and Lys234. Functional studies of PsbO were performed by site-directed mutagenesis, and mutants mimicking either constitutively succinylated (K99E and K234E) or non-succinylated states (K99R and K234R) were constructed. The succinylation-mimicking K234E mutant exhibited a decreased oxygen evolution rate of the PSII center and the efficiency of energy transfer during the photosynthetic reaction. Molecular dynamics simulations suggested a mechanism that may allow succinylation to influence the efficiency of photosynthesis by altering the conformation of PsbO, thereby hindering the interaction between PsbO and the PSII core. Our findings suggest that reversible succinylation may be an important regulatory mechanism during photosynthesis in Synechococcus, as well as in other photosynthetic organisms.

Physiological response of 10 phytoplankton species exposed to macondo oil and the dispersant, Corexit

Culture experiments were conducted on ten phytoplankton species to examine their biological and physiological responses during exposure to oil and a combination of oil and dispersant. The species tested included a range of taxa typically found in the Gulf of Mexico such as cyanobacteria, chlorophytes, and diatoms. Cultures were exposed to Macondo surrogate oil using the water accommodated fraction (WAF), and dispersed oil using a chemically enhanced WAF (CEWAF) and diluted CEWAF, to replicate conditions following the Deepwater Horizon spill in the Gulf of Mexico. A range of responses were observed, that could broadly class the algae as either "robust" or "sensitive" to oil and/or dispersant exposure. Robust algae were identified as Synechococcus elongatus, Dunaliella tertiolecta, two pennate diatoms Phaeodactylum tricornutum and Navicula sp., and Skeletonema grethae CCMP775, and were largely unaffected by any of the treatments (no changes to growth rate or time spent in lag phase relative to controls). The rest of the phytoplankton, all centric diatoms, exhibited at least some combination of reduced growth rates or increased lag time in response to oil and/or dispersant exposure. Photophysiology did not have a strong treatment effect, with significant inhibition of photosynthetic efficiency (F_v /F_m ) only observed in the CEWAF, if at all. We found that the effects of oil and dispersants on phytoplankton physiology were species-dependent, and not always detrimental. This has significant implications on how oil spills might impact phytoplankton community structure and bloom dynamics in the Gulf of Mexico, which in turn impacts higher trophic levels.

Phosphatidylglycerol is implicated in divisome formation and metabolic processes of cyanobacteria

Phosphatidylglycerol is an essential phospholipid for photosynthesis and other cellular processes. We investigated the role of phosphatidylglycerol in cell division and metabolism in a phophatidylglycerol-auxotrophic strain of Synechococcus PCC7942. Here we show that phosphatidylglycerol is essential for the photosynthetic electron transfer and for the oligomerisation of the photosynthetic complexes, notably, we revealed that this lipid is important for non-linear electron transport. Furthermore, we demonstrate that phosphatidylglycerol starvation elevated the expressions of proteins of nitrogen and carbon metabolism. Moreover, we show that phosphatidylglycerol-deficient cells changed the morphology, became elongated, the FtsZ ring did not assemble correctly, and subsequently the division was hindered. However, supplementation with phosphatidylglycerol restored the ring-like structure at the mid-cell region and the normal cell size, demonstrating the phosphatidylglycerol is needed for normal septum formation. Taken together, central roles of phosphatidylglycerol were revealed; it is implicated in the photosynthetic activity, the metabolism and the fission of bacteria.

Photosynthetic functions of Synechococcus in the ocean microbiomes of diverse salinity and seasons

Synechococcus is an important photosynthetic picoplankton in the temperate to tropical oceans. As a photosynthetic bacterium, Synechococcus has an efficient mechanism to adapt to the changes in salinity and light intensity. The analysis of the distributions and functions of such microorganisms in the ever changing river mouth environment, where freshwater and seawater mix, should help better understand their roles in the ecosystem. Toward this objective, we have collected and sequenced the ocean microbiome in the river mouth of Kwangyang Bay, Korea, as a function of salinity and temperature. In conjunction with comparative genomics approaches using the sequenced genomes of a wide phylogeny of Synechococcus, the ocean microbiome was analyzed in terms of their composition and clade-specific functions. The results showed significant differences in the compositions of Synechococcus sampled in different seasons. The photosynthetic functions in such enhanced Synechococcus strains were also observed in the microbiomes in summer, which is significantly different from those in other seasons.

A Carbon Dioxide Limitation-Inducible Protein, ColA, Supports the Growth of Synechococcus sp. PCC 7002

A limitation in carbon dioxide (CO₂), which occurs as a result of natural environmental variation, suppresses photosynthesis and has the potential to cause photo-oxidative damage to photosynthetic cells. Oxygenic phototrophs have strategies to alleviate photo-oxidative damage to allow life in present atmospheric CO₂ conditions. However, the mechanisms for CO₂ limitation acclimation are diverse among the various oxygenic phototrophs, and many mechanisms remain to be discovered. In this study, we found that the gene encoding a CO₂ limitation-inducible protein, ColA, is required for the cyanobacterium Synechococcus sp. PCC 7002 (S. 7002) to acclimate to limited CO₂ conditions. An S. 7002 mutant deficient in ColA (ΔcolA) showed lower chlorophyll content, based on the amount of nitrogen, than that in S. 7002 wild-type (WT) under ambient air but not high CO₂ conditions. Both thermoluminescence and protein carbonylation detected in the ambient air grown cells indicated that the lack of ColA promotes oxidative stress in S. 7002. Alterations in the photosynthetic O₂ evolution rate and relative electron transport rate in the short-term response, within an hour, to CO₂ limitation were the same between the WT and ΔcolA. Conversely, these photosynthetic parameters were mostly lower in the long-term response of a few days in ΔcolA than in the WT. These data suggest that ColA is required to sustain photosynthetic activity for living under ambient air in S. 7002. The unique phylogeny of ColA revealed diverse strategies to acclimate to CO₂ limitation among cyanobacteria.

Influence of Interaction Between α-Fe2O3 Nanoparticles and Dissolved Fulvic Acid on the Physiological Responses in Synechococcus sp. PCC7942

The ecotoxicity of α-Fe₂O₃ nanoparticles (NPs) and its interaction with a typical natural organic matter (NOM), fulvic acid (FA) on the physiological responses of Synechococcus sp. PCC7942 was studied. α-Fe₂O₃ NPs inhibited the algae growth at concentration higher than 10 mg L^-1 and induced oxidative stress, indicated by enhanced antioxidant enzymes activities, elevated protein and sugar content. FA could efficiently recover cell growth and reduce antioxidant enzyme activities which induced by α-Fe₂O₃ NPs, indicating the toxicity of NPs was alleviated in the presence of FA. α-Fe₂O₃ NPs could form large aggregates coating on cell surface and inhibit cell growth. FTIR spectra verified FA interacted with α-Fe₂O₃ NPs through carboxyl groups, partly replaced the binding sites of α-Fe₂O₃ NPs on algal cell walls, thus reduced NPs aggregates coating on cell surface. This favors reducing the oxidative stress caused by direct contact and increasing light availability, thus mitigate NPs toxicity.

The microbiome associated with two Synechococcus ribotypes at different levels of ecological interaction

Planktonic cyanobacteria belonging to the genus Synechococcus are ubiquitously distributed in marine and fresh waters, substantially contributing to total carbon fixation on a global scale. While their ecological relevance is acknowledged, increasing resolution in molecular techniques allows disentangling cyanobacteria's role at the micro-scale, where complex microbial interactions may drive the overall community assembly. The interplay between phylogenetically different Synechococcus clades and their associated bacterial communities can affect their ecological fate and susceptibility to protistan predation. In this study, we experimentally promoted different levels of ecological interaction by mixing two Synechococcus ribotypes (MW101C3 and LL) and their associated bacteria, with and without a nanoflagellate grazer (Poterioochromonas sp.) in laboratory cultures. The beta-diversity of the Synechococcus-associated microbiome in laboratory cultures indicated that the presence of the LL ribotype was the main factor determining community composition changes (41% of total variance), and prevailed over the effect of protistan predation (18% of total variance). Our outcomes also showed that species coexistence and predation may promote microbial diversity, thus highlighting the underrated ecological relevance of such micro-scale factors.

Minimal tool set for a prokaryotic circadian clock

BACKGROUND

Circadian clocks are found in organisms of almost all domains including photosynthetic Cyanobacteria, whereby large diversity exists within the protein components involved. In the model cyanobacterium Synechococcus elongatus PCC 7942 circadian rhythms are driven by a unique KaiABC protein clock, which is embedded in a network of input and output factors. Homologous proteins to the KaiABC clock have been observed in Bacteria and Archaea, where evidence for circadian behavior in these domains is accumulating. However, interaction and function of non-cyanobacterial Kai-proteins as well as homologous input and output components remain mainly unclear.

RESULTS

Using a universal BLAST analyses, we identified putative KaiC-based timing systems in organisms outside as well as variations within Cyanobacteria. A systematic analyses of publicly available microarray data elucidated interesting variations in circadian gene expression between different cyanobacterial strains, which might be correlated to the diversity of genome encoded clock components. Based on statistical analyses of co-occurrences of the clock components homologous to Synechococcus elongatus PCC 7942, we propose putative networks of reduced and fully functional clock systems. Further, we studied KaiC sequence conservation to determine functionally important regions of diverged KaiC homologs. Biochemical characterization of exemplary cyanobacterial KaiC proteins as well as homologs from two thermophilic Archaea demonstrated that kinase activity is always present. However, a KaiA-mediated phosphorylation is only detectable in KaiC1 orthologs.

CONCLUSION

Our analysis of 11,264 genomes clearly demonstrates that components of the Synechococcus elongatus PCC 7942 circadian clock are present in Bacteria and Archaea. However, all components are less abundant in other organisms than Cyanobacteria and KaiA, Pex, LdpA, and CdpA are only present in the latter. Thus, only reduced KaiBC-based or even simpler, solely KaiC-based timing systems might exist outside of the cyanobacterial phylum, which might be capable of driving diurnal oscillations.

Characterization of zinc stress response in Cyanobacterium Synechococcus sp. IU 625

The ability of cyanobacteria to survive many environmental stress factors is a testament to their resilience in nature. Of these environmental stress factors, overexposure to zinc is important to study since excessive zinc intake can be a severe hazard. Zinc toxicity in freshwater has been demonstrated to affects organisms such as invertebrates, algae and cyanobacteria. Cyanobacteria which possess increased resistance to zinc have been isolated. It is therefore important to elucidate the mechanism of survival and response to determine what factors allow their survival; as well as any remediation implications they may have. To characterize the effects of zinc in freshwater cyanobacteria, we investigated the response of Synechococcus sp. IU 625 (S. IU 625) over 29days to various concentrations (10, 25, and 50mg/L) of ZnCl₂. S. IU 625 was shown to be tolerant up to 25mg/L ZnCl₂ exposure, with 10mg/L ZnCl₂ having no outward physiological change and 50mg/L ZnCl₂ proving lethal to the cells. To determine a potential mechanism Inductive Coupled Plasma-Mass Spectrometry (ICP-MS) and RNA-seq analysis were performed on zinc exposed cells. Analysis performed on days 4 and 7 indicated that response is dose-dependent, with 10mg/L ZnCl₂ exhibiting nearly all zinc extracellular, corresponding with upregulation of cation transport response. Whereas the 25mg/L ZnCl₂ exhibited half of total zinc sequestered by the cells, which corresponds with the upregulation of sequestering proteins such as metallothionein and the downregulation of genes involved with ATP synthesis and phycobilisome assembly. These analyses were combined with growth monitoring, microscopy, quantitative polymerase chain reaction (qPCR) and flow cytometry to present a full spectrum of mechanisms behind zinc response in S. IU 625.

A thermodynamically consistent model of the post-translational Kai circadian clock

The principal pacemaker of the circadian clock of the cyanobacterium S. elongatus is a protein phosphorylation cycle consisting of three proteins, KaiA, KaiB and KaiC. KaiC forms a homohexamer, with each monomer consisting of two domains, CI and CII. Both domains can bind and hydrolyze ATP, but only the CII domain can be phosphorylated, at two residues, in a well-defined sequence. While this system has been studied extensively, how the clock is driven thermodynamically has remained elusive. Inspired by recent experimental observations and building on ideas from previous mathematical models, we present a new, thermodynamically consistent, statistical-mechanical model of the clock. At its heart are two main ideas: i) ATP hydrolysis in the CI domain provides the thermodynamic driving force for the clock, switching KaiC between an active conformational state in which its phosphorylation level tends to rise and an inactive one in which it tends to fall; ii) phosphorylation of the CII domain provides the timer for the hydrolysis in the CI domain. The model also naturally explains how KaiA, by acting as a nucleotide exchange factor, can stimulate phosphorylation of KaiC, and how the differential affinity of KaiA for the different KaiC phosphoforms generates the characteristic temporal order of KaiC phosphorylation. As the phosphorylation level in the CII domain rises, the release of ADP from CI slows down, making the inactive conformational state of KaiC more stable. In the inactive state, KaiC binds KaiB, which not only stabilizes this state further, but also leads to the sequestration of KaiA, and hence to KaiC dephosphorylation. Using a dedicated kinetic Monte Carlo algorithm, which makes it possible to efficiently simulate this system consisting of more than a billion reactions, we show that the model can describe a wealth of experimental data.

Circadian clocks are biological timekeeping devices with a rhythm of 24 hours in living cells pertaining to all kingdoms of life. They help organisms to coordinate their behavior with the day-night cycle. The circadian clock of the cyanobacterium Synechococcus elongatus is one of the simplest and best characterized clocks in biology. The central clock component is the protein KaiC, which is phosphorylated and dephosphorylated in a cyclical manner with a 24 hr period. While we know from elementary thermodynamics that oscillations require a net turnover of fuel molecules, in this case ATP, how ATP hydrolysis drives the clock has remained elusive. Based on recent experimental observations and building on ideas from existing models, we construct the most detailed mathematical model of this system to date. KaiC consists of two domains, CI and CII, which each can bind ATP, yet only CII can be phosphorylated. Moreover, KaiC can exist in two conformational states, an active one in which the phosphorylation level tends to rise, and an inactive one in which it tends to fall. Our model predicts that ATP hydrolysis in the CI domain is the principal energetic driver of the clock, driving the switching between the two conformational states, while phosphorylation in the CII domain provides the timer for the conformational switch. The coupling between ATP hydrolysis in the CI domain and phosphorylation in the CII domain leads to novel testable predictions.

Synechococcus production and grazing loss rates in nearshore tropical waters

Temporal variation of Synechococcus, its production (μ) and grazing loss (g) rates were studied for 2 years at nearshore stations, i.e. Port Dickson and Port Klang along the Straits of Malacca. Synechococcus abundance at Port Dickson (0.3-2.3 × 10⁵ cell ml^-1) was always higher than at Port Klang (0.3-7.1 × 10⁴ cell ml^-1) (p < 0.001). μ ranged up to 0.98 day^-1 (0.51 ± 0.29 day^-1), while g ranged from 0.02 to 0.31 day^-1 (0.15 ± 0.07 day^-1) at Port Klang. At Port Dickson, μ and g averaged 0.47 ± 0.13 day^-1 (0.29-0.82 day^-1) and 0.31 ± 0.14 day^-1 (0.13-0.63 day^-1), respectively. Synechococcus abundance did not correlate with temperature (p > 0.25), but nutrient and light availability were important factors for their distribution. The relationship was modelled as log Synechococcus = 0.37Secchi - 0.01DIN + 4.52 where light availability (as Secchi disc depth) was a more important determinant. From a two-factorial experiment, nutrients were not significant for Synechococcus growth as in situ nutrient concentrations exceeded the threshold for saturated growth. However, light availability was important and elevated Synechococcus growth rates especially at Port Dickson (F = 5.94, p < 0.05). As for grazing loss rates, they were independent of either nutrients or light intensity (p > 0.30). In nearshore tropical waters, an estimated 69 % of Synechococcus production could be grazed.

Far-red light photoacclimation (FaRLiP) in Synechococcus sp. PCC 7335: I. Regulation of FaRLiP gene expression

Far-red light photoacclimation (FaRLiP) is a mechanism that allows some cyanobacteria to utilize far-red light (FRL) for oxygenic photosynthesis. During FaRLiP, cyanobacteria remodel photosystem (PS) I, PS II, and phycobilisomes while synthesizing Chl d, Chl f, and far-red-absorbing phycobiliproteins, and these changes enable these organisms to use FRL for growth. In this study, a conjugation-based genetic system was developed for Synechococcus sp. PCC 7335. Three antibiotic cassettes were successfully used to generate knockout mutations in genes in Synechococcus sp. PCC 7335, which should allow up to three gene loci to be modified in one strain. This system was used to delete the rfpA, rfpB, and rfpC genes individually, and characterization of the mutants demonstrated that these genes control the expression of the FaRLiP gene cluster in Synechococcus sp. PCC 7335. The mutant strains exhibited some surprising differences from similar mutants in other FaRLiP strains. Notably, mutations in any of the three master transcription regulatory genes led to enhanced synthesis of phycocyanin and PS II. A time-course study showed that acclimation of the photosynthetic apparatus from that produced in white light to that produced in FRL occurs very slowly over a period 12-14 days in this strain and that it is associated with a substantial reduction (~34 %) in the chlorophyll a content of the cells. This study shows that there are differences in the detailed responses of cyanobacteria to growth in FRL in spite of the obvious similarities in the organization and regulation of the FaRLiP gene cluster.

Far-red light photoacclimation (FaRLiP) in Synechococcus sp. PCC 7335. II.Characterization of phycobiliproteins produced during acclimation to far-red light

Phycobilisomes (PBS) are antenna complexes that harvest light for photosystem (PS) I and PS II in cyanobacteria and some algae. A process known as far-red light photoacclimation (FaRLiP) occurs when some cyanobacteria are grown in far-red light (FRL). They synthesize chlorophylls d and f and remodel PS I, PS II, and PBS using subunits paralogous to those produced in white light. The FaRLiP strain, Leptolyngbya sp. JSC-1, replaces hemidiscoidal PBS with pentacylindrical cores, which are produced when cells are grown in red or white light, with PBS with bicylindrical cores when cells are grown in FRL. This study shows that the PBS of another FaRLiP strain, Synechococcus sp. PCC 7335, are not remodeled in cells grown in FRL. Instead, cells grown in FRL produce bicylindrical cores that uniquely contain the paralogous allophycocyanin subunits encoded in the FaRLiP cluster, and these bicylindrical cores coexist with red-light-type PBS with tricylindrical cores. The bicylindrical cores have absorption maxima at 650 and 711 nm and a low-temperature fluorescence emission maximum at 730 nm. They contain ApcE2:ApcF:ApcD3:ApcD2:ApcD5:ApcB2 in the approximate ratio 2:2:4:6:12:22, and a structural model is proposed. Time course experiments showed that bicylindrical cores were detectable about 48 h after cells were transferred from RL to FRL and that synthesis of red-light-type PBS continued throughout a 21-day growth period. When considered in comparison with results for other FaRLiP cyanobacteria, the results here show that acclimation responses to FRL can differ considerably among FaRLiP cyanobacteria.

Inhibition by ultraviolet and photosynthetically available radiation lowers model estimates of depth-integrated picophytoplankton photosynthesis: global predictions for Prochlorococcus and Synechococcus

Phytoplankton photosynthesis is often inhibited by ultraviolet (UV) and intense photosynthetically available radiation (PAR), but the effects on ocean productivity have received little consideration aside from polar areas subject to periodic enhanced UV-B due to depletion of stratospheric ozone. A more comprehensive assessment is important for understanding the contribution of phytoplankton production to the global carbon budget, present and future. Here, we consider responses in the temperate and tropical mid-ocean regions typically dominated by picophytoplankton including the prokaryotic lineages, Prochlorococcus and Synechococcus. Spectral models of photosynthetic response for each lineage were constructed using model strains cultured at different growth irradiances and temperatures. In the model, inhibition becomes more severe once exposure exceeds a threshold (E_max ) related to repair capacity. Model parameters are presented for Prochlorococcus adding to those previously presented for Synechococcus. The models were applied to estimate midday, water column photosynthesis based on an atmospheric model of spectral radiation, satellite-derived spectral water transparency and temperature. Based on a global survey of inhibitory exposure severity, a full-latitude section of the mid-Pacific and near-equatorial region of the east Pacific were identified as representative regions for prediction of responses over the entire water column. Comparing predictions integrated over the water column including versus excluding inhibition, production was 7-28% lower due to inhibition depending on strain and site conditions. Inhibition was consistently greater for Prochlorococcus compared to two strains of Synechococcus. Considering only the surface mixed layer, production was inhibited 7-73%. On average, including inhibition lowered estimates of midday productivity around 20% for the modeled region of the Pacific with UV accounting for two-thirds of the reduction. In contrast, most other productivity models either ignore inhibition or only include PAR inhibition. Incorporation of E_max model responses into an existing spectral model of depth-integrated, daily production will enable efficient global predictions of picophytoplankton productivity including inhibition.

Diversity in photosynthetic electron transport under [CO2]-limitation: the cyanobacterium Synechococcus sp. PCC 7002 and green alga Chlamydomonas reinhardtii drive an O2-dependent alternative electron flow and non-photochemical quenching of chlorophyll fluorescence during CO2-limited photosynthesis

Some cyanobacteria, but not all, experience an induction of alternative electron flow (AEF) during CO₂-limited photosynthesis. For example, Synechocystis sp. PCC 6803 (S. 6803) exhibits AEF, but Synechococcus elongatus sp. PCC 7942 does not. This difference is due to the presence of flavodiiron 2 and 4 proteins (FLV2/4) in S. 6803, which catalyze electron donation to O₂. In this study, we observed a low-[CO₂] induced AEF in the marine cyanobacterium Synechococcus sp. PCC 7002 that lacks FLV2/4. The AEF shows high affinity for O₂, compared with AEF mediated by FLV2/4 in S. 6803, and can proceed under extreme low [O₂] (about a few µM O₂). Further, the transition from CO₂-saturated to CO₂-limited photosynthesis leads a preferential excitation of PSI to PSII and increased non-photochemical quenching of chlorophyll fluorescence. We found that the model green alga Chlamydomonas reinhardtii also has an O₂-dependent AEF showing the same affinity for O₂ as that in S. 7002. These data represent the diverse molecular mechanisms to drive AEF in cyanobacteria and green algae. In this paper, we further discuss the diversity, the evolution, and the physiological function of strategy to CO₂-limitation in cyanobacterial and green algal photosynthesis.

Effects of exogenous β-carotene, a chemical scavenger of singlet oxygen, on the millisecond rise of chlorophyll a fluorescence of cyanobacterium Synechococcus sp. PCC 7942

Singlet-excited oxygen (¹O ₂^* ) has been recognized as the most destructive member of the reactive oxygen species (ROS) which are formed during oxygenic photosynthesis by plants, algae, and cyanobacteria. ROS and ¹O ₂^* are known to damage protein and phospholipid structures and to impair photosynthetic electron transport and de novo protein synthesis. Partial protection is afforded to photosynthetic organism by the β-carotene (β-Car) molecules which accompany chlorophyll (Chl) a in the pigment-protein complexes of Photosystem II (PS II). In this paper, we studied the effects of exogenously added β-Car on the initial kinetic rise of Chl a fluorescence (10-1000 μs, the OJ segment) from the unicellular cyanobacterium Synechococcus sp. PCC7942. We show that the added β-Car enhances Chl a fluorescence when it is excited at an intensity of 3000 μmol photons m^-2 s^-1 but not when excited at 1000 μmol photons m^-2 s^-1. Since β-Car is an efficient scavenger of ¹O ₂^* , as well as a quencher of ³Chl a ^* (precursor of ¹O ₂^* ), both of which are more abundant at higher excitations, we assume that the higher Chl a fluorescence in its presence signifies a protective effect against photo-oxidative damages of Chl proteins. The protective effect of added β-Car is not observed in O₂-depleted cell suspensions. Lastly, in contrast to β-Car, a water-insoluble molecule, a water-soluble scavenger of ¹O ₂^* , histidine, provides no protection to Chl proteins during the same time period (10-1000 μs).

Increased Photochemical Efficiency in Cyanobacteria via an Engineered Sucrose Sink

In plants, a limited capacity to utilize or export the end-products of the Calvin-Benson cycle (CB) from photosynthetically active source cells to non-photosynthetic sink cells can result in reduced carbon capture and photosynthetic electron transport (PET), and lowered photochemical efficiency. The down-regulation of photosynthesis caused by reduced capacity to utilize photosynthate has been termed 'sink limitation'. Recently, several cyanobacterial and algal strains engineered to overproduce target metabolites have exhibited increased photochemistry, suggesting that possible source-sink regulatory mechanisms may be involved. We directly examined photochemical properties following induction of a heterologous sucrose 'sink' in the unicellular cyanobacterium Synechococcus elongatus PCC 7942. We show that total photochemistry increases proportionally to the experimentally controlled rate of sucrose export. Importantly, the quantum yield of PSII (ΦII) increases in response to sucrose export while the PET chain becomes more oxidized from less PSI acceptor-side limitation, suggesting increased CB activity and a decrease in sink limitation. Enhanced photosynthetic activity and linear electron flow are detectable within hours of induction of the heterologous sink and are independent of pigmentation alterations or the ionic/osmotic effects of the induction system. These observations provide direct evidence that secretion of heterologous carbon bioproducts can be used as an alternative approach to improve photosynthetic efficiency, presumably by by-passing sink limitation. Our results also suggest that engineered microalgal production strains are valuable alternative models for examining photosynthetic sink limitation because they enable greater control and monitoring of metabolite fluxes relative to plants.

Reduction-Induced Suppression of Electron Flow (RISE) in the Photosynthetic Electron Transport System of Synechococcus elongatus PCC 7942

Accumulation of electrons under conditions of environmental stress produces a reduced state in the photosynthetic electron transport (PET) system and causes the reduction of O₂ by PSI in the thylakoid membranes to produce the reactive oxygen species superoxide radical, which irreversibly inactivates PSI. This study aims to elucidate the molecular mechanism for the oxidation of reaction center Chl of PSI, P700, after saturated pulse (SP) light illumination of the cyanobacterium Synechococcus elongatus PCC 7942 under steady-state photosynthetic conditions. Both P700 and NADPH were transiently oxidized after SP light illumination under CO₂-depleted photosynthesis conditions. In contrast, the Chl fluorescence intensity transiently increased. Compared with the wild type, the increase in Chl fluorescence and the oxidations of P700 and NADPH were greatly enhanced in a mutant (Δflv1/3) deficient in the genes encoding FLAVODIIRON 1 (FLV1) and FLV3 proteins even under high photosynthetic conditions. Furthermore, oxidation of Cyt f was also observed in the mutant. After SP light illumination, a transient suppression of O₂ evolution was also observed in Δflv1/3. From these observations, we propose that the reduction in the plastquinone (PQ) pool suppresses linear electron flow at the Cyt b₆/f complex, which we call the reduction-induced suppression of electron flow (RISE) in the PET system. The accumulation of the reduced form of PQ probably suppresses turnover of the Q cycle in the Cyt b₆/f complex.

Light Modulates the Biosynthesis and Organization of Cyanobacterial Carbon Fixation Machinery through Photosynthetic Electron Flow

Cyanobacteria have evolved effective adaptive mechanisms to improve photosynthesis and CO2 fixation. The central CO2-fixing machinery is the carboxysome, which is composed of an icosahedral proteinaceous shell encapsulating the key carbon fixation enzyme, Rubisco, in the interior. Controlled biosynthesis and ordered organization of carboxysomes are vital to the CO2-fixing activity of cyanobacterial cells. However, little is known about how carboxysome biosynthesis and spatial positioning are physiologically regulated to adjust to dynamic changes in the environment. Here, we used fluorescence tagging and live-cell confocal fluorescence imaging to explore the biosynthesis and subcellular localization of β-carboxysomes within a model cyanobacterium, Synechococcus elongatus PCC7942, in response to light variation. We demonstrated that β-carboxysome biosynthesis is accelerated in response to increasing light intensity, thereby enhancing the carbon fixation activity of the cell. Inhibition of photosynthetic electron flow impairs the accumulation of carboxysomes, indicating a close coordination between β-carboxysome biogenesis and photosynthetic electron transport. Likewise, the spatial organization of carboxysomes in the cell correlates with the redox state of photosynthetic electron transport chain. This study provides essential knowledge for us to modulate the β-carboxysome biosynthesis and function in cyanobacteria. In translational terms, the knowledge is instrumental for design and synthetic engineering of functional carboxysomes into higher plants to improve photosynthesis performance and CO2 fixation.

Effects of low temperature on tropical and temperate isolates of marine Synechococcus

Temperature is an important factor influencing the distribution of marine picocyanobacteria. However, molecular responses contributing to temperature preferences are poorly understood in these important primary producers. We compared the temperature acclimation of a tropical Synechococcus strain WH8102 with temperate strain BL107 at 18 °C relative to 22 °C and examined their global protein expression, growth patterns, photosynthetic efficiency and lipid composition. Global protein expression profiles demonstrate the partitioning of the proteome into major categories: photosynthesis (>40%), translation (10-15%) and membrane transport (2-8%) with distinct differences between and within strains grown at different temperatures. At low temperature, growth and photosynthesis of strain WH8102 was significantly decreased, while BL107 was largely unaffected. There was an increased abundance of proteins involved in protein biosynthesis at 18 °C for BL107. Each strain showed distinct differences in lipid composition with higher unsaturation in strain BL107. We hypothesize that differences in membrane fluidity, abundance of protein biosynthesis machinery and the maintenance of photosynthesis efficiency contribute to the acclimation of strain BL107 to low temperature. Additional proteins unique to BL107 may also contribute to this strain's improved fitness at low temperature. Such adaptive capacities are likely important factors favoring growth of temperate strains over tropical strains in high latitude niches.

Analysis of the Fine-Tuning of Cyanobacterial Circadian Phase by Monochromatic Light and Long-Day Conditions

The cyanobacterial circadian-related protein, Pex, accumulates in the dark period of the diurnal light-dark cycle. After the diurnal cycle, an approximately 3 h advance in the phase of the circadian bioluminescence rhythm is observed in pex-deficient mutants, as compared with the wild type. However, it is unclear what type of photosensing mechanism regulates the accumulation and the phase change. In monochromatic light irradiation experiments, Pex accumulation was strongly repressed under blue light conditions; however, only small reductions in Pex accumulation were observed under red or green light conditions. After the diurnal cycle of 12 h of white fluorescent light and 12 h of blue light, the phase advance was repressed more than that of the cycle of 12 h red (or green) light. The phase advance also occurred after 16 h light/8 h dark cycles (long-day cycles) but did not occur after 8 h light/16 h dark cycles (short-day cycles). While Pex is a unique winged helix transcription factor harboring secondary structures (α0 and α4 helices), the importance of the structures is not understood. In in vivo experiments with site-directed mutations in the α0 helix, the obtained mutants, in which Pex was missing the hydrophobic side chain at the 28th or 32nd amino acid residue, exhibited no phase delay after the light/dark cycle. In in vitro DNA binding assays, the mutant proteins showed no binding to the promoter region of the clock gene kaiA. From these results, we propose a molecular model which describes the phase delay in cyanobacteria.

A mutant Synechococcus gene encoding glutamate 1-semialdehyde aminotransferase confers gabaculine resistance when expressed in tobacco plastids

KEY MESSAGE

A mutant glutamate 1-semialdehyde aminotransferase gene from the Synechococcus , inserted into tobacco plastid DNA by means of particle bombardment and antibiotic selection, conferred gabaculine resistance allowing to attain homoplasmy. Many plant species are recalcitrant to plastid genome transformation. New selections systems may help to overcome this limitation and to extend the application of this technology. A mutant hemL gene from the photosynthetic cyanobacterium Synechococcus, encoding a gabaculine-insensitive glutamate 1-semialdehyde aminotransferase (GSA), is an efficient selectable marker gene for nuclear transformation of tobacco, alfalfa and durum wheat. Since GSA functions in the plastid, we introduced the mutant hemL gene into the tobacco plastid genome along with the conventional antibiotic resistance aadA gene, in the attempt to develop a new selection system for plastome transformation. Although we were unable to directly regenerate gabaculine resistant transplastomic plants, we demonstrated the functionality of hemL in tobacco plastids by using gabaculine selection in the second and third rounds of in vitro selection that permitted to obtain the homoplasmic state in transgenic plants. Thus, the mutant hemL gene functions as a secondary selection marker in tobacco plastids. Our results encourage further attempts to test gabaculine resistant GSA for plastome transformation of crop plants in which gabaculine has stronger regeneration-inhibiting effects with respect to tobacco.

Changes in the Synechococcus Assemblage Composition at the Surface of the East China Sea Due to Flooding of the Changjiang River

The aim of this study was to elucidate how flooding of the Changjiang River affects the assemblage composition of phycoerythrin-rich (PE-rich) Synechococcus at the surface of the East China Sea (ECS). During non-flooding summers (e.g., 2009), PE-rich Synechococcus usually thrive at the outer edge of the Changjiang River diluted water coverage (CDW; salinity ≤31 PSU). In the summer of 2010, a severe flood occurred in the Changjiang River basin. The plentiful freshwater injection resulted in the expansion of the CDW over half of the ECS and caused PE-rich cells to show a uniform distribution pattern, with decreased abundance compared with the non-flooding summer. The phylogenetic diversity of 16S rRNA gene sequences indicated that the flooding event also shifted the picoplankton community composition from being dominated by Synechococcus, mainly attributed to the clade II lineage, to various orders of heterotrophic bacteria, including Actinobacteria, Flavobacteria, α-Proteobacteria, and γ-Proteobacteria. As an increasing number of studies have proposed that global warming might result in more frequent floods, combining this perspective with the information obtained from our previous [1] and this studies yield a more comprehensive understanding of the relationship between the composition of the marine Synechococcus assemblage and global environmental changes.