Sulfate-driven elemental sparing is regulated at the transcriptional and posttranscriptional levels in a filamentous cyanobacterium

Natural variation of nutrient homeostasis among laboratory and field strains of Chlamydomonas reinhardtii

Natural variation among individuals and populations exists in all species, playing key roles in response to environmental stress and adaptation. Micro- and macronutrients have a wide range of functions in photosynthetic organisms, and mineral nutrition thus plays a sizable role in biomass production. To maintain nutrient concentrations inside the cell within physiological limits and prevent the detrimental effects of deficiency or excess, complex homeostatic networks have evolved in photosynthetic cells. The microalga Chlamydomonas reinhardtii (Chlamydomonas) is a unicellular eukaryotic model for studying such mechanisms. In this work, 24 Chlamydomonas strains, comprising field isolates and laboratory strains, were examined for intraspecific differences in nutrient homeostasis. Growth and mineral content were quantified in mixotrophy, as full nutrition control, and compared with autotrophy and nine deficiency conditions for macronutrients (-Ca, -Mg, -N, -P, and -S) and micronutrients (-Cu, -Fe, -Mn, and -Zn). Growth differences among strains were relatively limited. However, similar growth was accompanied by highly divergent mineral accumulation among strains. The expression of nutrient status marker genes and photosynthesis were scored in pairs of contrasting field strains, revealing distinct transcriptional regulation and nutrient requirements. Leveraging this natural variation should enable a better understanding of nutrient homeostasis in Chlamydomonas.

Disentangling the Impact of Sulfur Limitation on Exopolysaccharide and Functionality of Alr2882 by In Silico Approaches in Anabaena sp. PCC 7120

The wide applications, uniqueness, and high quality of cyanobacterial exopolysaccharides (EPSs) have attracted many biotechnologists. Despite it, the inducers and molecular determinants of EPS biosynthesis in cyanobacteria are lesser known. Although, studies revealed that environmental cues especially C/N ratio as the prime modulator, the factors like light, temperature, moisture, and nutrient availability, etc. have been overlooked. Due to this, the possibilities to modify cyanobacterial system for achieving higher quantity of EPS either by modifying growth medium or metabolic engineering are restricted to few optimisations. Therefore, the present work describes the impact of sulfate limitations on the EPS production and compositions in the cyanobacterium Anabaena sp. PCC 7120. Increased EPS production with enhanced expression of alr2882 was observed in lower sulfate supplementations; however, FTIR analysis depicted an altered composition of supramolecule. Furthermore, in silico analysis of Alr2882 depicted the presence of ExoD domain and three transmembrane regions, thereby indicating its membrane localisation and role in the EPS production. Additionally, the phylogeny and multiple sequence alignment showed vertical inheritance of exoD and conservation among cyanobacteria. The meta-threading template-based modelling and ab initio full atomic relaxation by LOMET and ModRefiner servers, respectively, also exhibited helical topology of Alr2882, with nine α-helices arranged antiparallel to the preceding one. Moreover, post-translational modifications predicted in Alr2882 indicated high order of molecular regulation underlining EPS production in Anabaena sp. PCC 7120. This study provides a foundation for understanding the EPS biosynthesis mechanism under sulfur limitation and the possible role of ExoD in cyanobacteria.

CpeT is the phycoerythrobilin lyase for Cys-165 on β-phycoerythrin from Fremyella diplosiphon and the chaperone-like protein CpeZ greatly improves its activity

Bilin lyases are enzymes which ligate linear tetrapyrrole chromophores to specific cysteine residues on light harvesting proteins present in cyanobacteria and red algae. The lyases responsible for chromophorylating the light harvesting protein phycoerythrin (PE) have not been fully characterized. In this study, we explore the role of CpeT, a putative bilin lyase, in the biosynthesis of PE in the cyanobacterium Fremyella diplosiphon. Recombinant protein studies show that CpeT alone can bind phycoerythrobilin (PEB), but CpeZ, a chaperone-like protein, is needed in order to correctly and efficiently attach PEB to the β-subunit of PE. MS analyses of the recombinant β-subunit of PE coexpressed with CpeT and CpeZ show that PEB is attached at Cys-165. Purified phycobilisomes from a cpeT knockout mutant and wild type (WT) samples from F. diplosiphon were analyzed and compared. The cpeT mutant contained much less PE and more phycocyanin than WT cells grown under green light, conditions which should maximize the production of PE. In addition, Northern blot analyses showed that the cpeCDESTR operon mRNAs were upregulated while the cpeBcpeA mRNAs were downregulated in the cpeT mutant strain when compared with WT, suggesting that CpeT may also play a direct or indirect regulatory role in transcription of these operons or their mRNA stability, in addition to its role as a PEB lyase for Cys-165 on β-PE.

Impact of Zero-Valent Iron Nanoparticles on Fremyella diplosiphon Transesterified Lipids and Fatty Acid Methyl Esters

Efforts to enhance the transformative potential of biofuels is an important step to achieving an environment-friendly and sustainable energy source. Fremyella diplosiphon is an ideal third-generation biofuel agent due to its ability to produce lipids and desirable essential fatty acids. In this study, the impact of Nanofer 25s nanoscale zero-valent iron nanoparticles (nZVIs) on total lipid content and fatty acid composition of F. diplosiphon strains SF33 and B481 was investigated. We observed significant increases (P < 0.05) in the growth of F. diplosiphon treated with 0.2-1.6 mg L^-1 Nanofer 25s, indicating that trace concentrations of nZVIs were not toxic to the organism. Chlorophyll a, carotenoids, and phycobiliprotein levels were not altered in F. diplosiphon treated with nZVIs ranging from 0.4 to 1.6 mg L^-1, confirming that these concentrations did not negatively impact photosynthetic efficacy. In addition, Nanofer 25s ranging from 0.2 to 1.6 mg L^-1 had an optimal impact on SF33 and B481 total lipid content. We identified significant increases in unsaturated fatty acid methyl esters (FAMEs) from F. diplosiphon Nanofer 25s-treated transesterified lipids. Theoretical chemical and physical biofuel properties revealed a product with elevated cetane number and oxidative stability for both strains. Scanning electron microscopy and energy-dispersive X-ray spectroscopy validated the localization of nZVIs. Our findings indicate that Nanofer 25s nZVIs significantly enhance F. diplosiphon total lipid content and essential FAMEs, thus offering a promising approach to augment the potential of the cyanobacterium as a large-scale biofuel agent.

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.

Diurnal Regulation of Cellular Processes in the Cyanobacterium Synechocystis sp. Strain PCC 6803: Insights from Transcriptomic, Fluxomic, and Physiological Analyses

Synechocystis sp. strain PCC 6803 is the most widely studied model cyanobacterium, with a well-developed omics level knowledgebase. Like the lifestyles of other cyanobacteria, that of Synechocystis PCC 6803 is tuned to diurnal changes in light intensity. In this study, we analyzed the expression patterns of all of the genes of this cyanobacterium over two consecutive diurnal periods. Using stringent criteria, we determined that the transcript levels of nearly 40% of the genes in Synechocystis PCC 6803 show robust diurnal oscillating behavior, with a majority of the transcripts being upregulated during the early light period. Such transcripts corresponded to a wide array of cellular processes, such as light harvesting, photosynthetic light and dark reactions, and central carbon metabolism. In contrast, transcripts of membrane transporters for transition metals involved in the photosynthetic electron transport chain (e.g., iron, manganese, and copper) were significantly upregulated during the late dark period. Thus, the pattern of global gene expression led to the development of two distinct transcriptional networks of coregulated oscillatory genes. These networks help describe how Synechocystis PCC 6803 regulates its metabolism toward the end of the dark period in anticipation of efficient photosynthesis during the early light period. Furthermore, in silico flux prediction of important cellular processes and experimental measurements of cellular ATP, NADP(H), and glycogen levels showed how this diurnal behavior influences its metabolic characteristics. In particular, NADPH/NADP(+) showed a strong correlation with the majority of the genes whose expression peaks in the light. We conclude that this ratio is a key endogenous determinant of the diurnal behavior of this cyanobacterium.

IMPORTANCE

Cyanobacteria are photosynthetic microbes that use energy from sunlight and CO2 as feedstock. Certain cyanobacterial strains are amenable to facile genetic manipulation, thus enabling synthetic biology and metabolic engineering applications. Such strains are being developed as a chassis for the sustainable production of food, feed, and fuel. To this end, a holistic knowledge of cyanobacterial physiology and its correlation with gene expression patterns under the diurnal cycle is warranted. In this report, a genomewide transcriptional analysis of Synechocystis PCC 6803, the most widely studied model cyanobacterium, sheds light on the global coordination of cellular processes during diurnal periods. Furthermore, we found that, in addition to light, the redox level of NADP(H) is an important endogenous regulator of diurnal entrainment of Synechocystis PCC 6803.

Role of domain swapping in the hetero-oligomeric cytochrome b6f lipoprotein complex

Domain swapping that contributes to the stability of biologically crucial multisubunit complexes has been implicated in protein oligomerization. In the case of membrane protein assemblies, domain swapping of the iron-sulfur protein (ISP) subunit occurs in the hetero-oligomeric cytochrome b6f and bc1 complexes, which are organized as symmetric dimers that generate the transmembrane proton electrochemical gradient utilized for ATP synthesis. In these complexes, the ISP C-terminal predominantly β-sheet extrinsic domain containing the redox-active [2Fe-2S] cluster resides on the electrochemically positive side of each monomer in the dimeric complex. This domain is bound to the membrane sector of the complex through an N-terminal transmembrane α-helix that is "swapped' to the other monomer of the complex where it spans the complex and the membrane. Detailed analysis of the function and structure of the b6f complex isolated from the cyanobacterium Fremyella diplosiphon SF33 shows that the domain-swapped ISP structure is necessary for function but is not necessarily essential for maintenance of the dimeric structure of the complex. On the basis of crystal structures of the cytochrome complex, the stability of the cytochrome dimer is attributed to specific intermonomer protein-protein and protein-lipid hydrophobic interactions. The geometry of the domain-swapped ISP structure is proposed to be a consequence of the requirement that the anchoring helix of the ISP not perturb the heme organization or quinone channel in the conserved core of each monomer.

Extreme Sensory Complexity Encoded in the 10-Megabase Draft Genome Sequence of the Chromatically Acclimating Cyanobacterium Tolypothrix sp. PCC 7601

Tolypothrix sp. PCC 7601 is a freshwater filamentous cyanobacterium with complex responses to environmental conditions. Here, we present its 9.96-Mbp draft genome sequence, containing 10,065 putative protein-coding sequences, including 305 predicted two-component system proteins and 27 putative phytochrome-class photoreceptors, the most such proteins in any sequenced genome.

Interdependence of tetrapyrrole metabolism, the generation of oxidative stress and the mitigative oxidative stress response

Tetrapyrroles are involved in light harvesting and light perception, electron-transfer reactions, and as co-factors for key enzymes and sensory proteins. Under conditions in which cells exhibit stress-induced imbalances of photosynthetic reactions, or light absorption exceeds the ability of the cell to use photoexcitation energy in synthesis reactions, redox imbalance can occur in photosynthetic cells. Such conditions can lead to the generation of reactive oxygen species (ROS) associated with alterations in tetrapyrrole homeostasis. ROS accumulation can result in cellular damage and detrimental effects on organismal fitness, or ROS molecules can serve as signals to induce a protective or damage-mitigating oxidative stress signaling response in cells. Induced oxidative stress responses include tetrapyrrole-dependent and -independent mechanisms for mitigating ROS generation and/or accumulation. Thus, tetrapyrroles can be contributors to oxidative stress, but are also essential in the oxidative stress response to protect cells by contributing to detoxification of ROS. In this review, we highlight the interconnection and interdependence of tetrapyrrole metabolism with the occurrence of oxidative stress and protective oxidative stress signaling responses in photosynthetic organisms.

•

Tetrapyrroles are involved in light sensing and oxidative stress mitigation.

•

Reactive oxygen species (ROS) can form upon light exposure of free tetrapyrroles.

•

Tetrapyrrole homeostasis must be tightly regulated to avoid oxidative stress.

•

ROS can result in cellular damage or oxidative stress signaling in cells.

In silico proteome-wide amino aCid and elemental composition (PACE) analysis of expression proteomics data provides a fingerprint of dominant metabolic processes

Proteome-wide Amino aCid and Elemental composition (PACE) analysis is a novel and informative way of interrogating the proteome. The PACE approach consists of in silico decomposition of proteins detected and quantified in a proteomics experiment into 20 amino acids and five elements (C, H, N, O and S), with protein abundances converted to relative abundances of amino acids and elements. The method is robust and very sensitive; it provides statistically reliable differentiation between very similar proteomes. In addition, PACE provides novel insights into proteome-wide metabolic processes, occurring, e.g., during cell starvation. For instance, both Escherichia coli and Synechocystis down-regulate sulfur-rich proteins upon sulfur deprivation, but E. coli preferentially down-regulates cysteine-rich proteins while Synechocystis mainly down-regulates methionine-rich proteins. Due to its relative simplicity, flexibility, generality and wide applicability, PACE analysis has the potential of becoming a standard analytical tool in proteomics.

Control of a four-color sensing photoreceptor by a two-color sensing photoreceptor reveals complex light regulation in cyanobacteria

Photoreceptors are biologically important for sensing changes in the color and intensity of ambient light and, for photosynthetic organisms, processing this light information to optimize food production through photosynthesis. Cyanobacteria are an evolutionarily and ecologically important prokaryotic group of oxygenic photosynthesizers that contain cyanobacteriochrome (CBCR) photoreceptors, whose family members sense nearly the entire visible spectrum of light colors. Some cyanobacteria contain 12 to 15 different CBCRs, and many family members contain multiple light-sensing domains. However, the complex interactions that must be occurring within and between these photoreceptors remain unexplored. Here we describe the regulation and photobiology of a unique CBCR called IflA (influenced by far-red light), demonstrating that a second CBCR called RcaE strongly regulates IflA abundance and that IflA uses two distinct photosensory domains to respond to four different light colors: blue, green, red, and far-red. The absorption of red or far-red light by one domain affects the conformation of the other domain, and the rate of relaxation of one of these domains is influenced by the conformation of the other. Deletion of iflA results in delayed growth at low cell density, suggesting that IflA accelerates growth under this condition, apparently by sensing the ratio of red to far-red light in the environment. The types of complex photobiological interactions described here, both between unrelated CBCR family members and within photosensory domains of a single CBCR, may be advantageous for species using these photoreceptors in aquatic environments, where light color ratios are influenced by many biotic and abiotic factors.

Green/red cyanobacteriochromes regulate complementary chromatic acclimation via a protochromic photocycle

Cyanobacteriochromes (CBCRs) are cyanobacterial members of the phytochrome superfamily of photosensors. Like phytochromes, CBCRs convert between two photostates by photoisomerization of a covalently bound linear tetrapyrrole (bilin) chromophore. Although phytochromes are red/far-red sensors, CBCRs exhibit diverse photocycles spanning the visible spectrum and the near-UV (330-680 nm). Two CBCR subfamilies detect near-UV to blue light (330-450 nm) via a "two-Cys photocycle" that couples bilin 15Z/15E photoisomerization with formation or elimination of a second bilin-cysteine adduct. On the other hand, mechanisms for tuning the absorption between the green and red regions of the spectrum have not been elucidated as of yet. CcaS and RcaE are members of a CBCR subfamily that regulates complementary chromatic acclimation, in which cyanobacteria optimize light-harvesting antennae in response to green or red ambient light. CcaS has been shown to undergo a green/red photocycle: reversible photoconversion between a green-absorbing 15Z state ((15Z)P(g)) and a red-absorbing 15E state ((15E)P(r)). We demonstrate that RcaE from Fremyella diplosiphon undergoes the same photocycle and exhibits light-regulated kinase activity. In both RcaE and CcaS, the bilin chromophore is deprotonated as (15Z)P(g) but protonated as (15E)P(r). This change of bilin protonation state is modulated by three key residues that are conserved in green/red CBCRs. We therefore designate the photocycle of green/red CBCRs a "protochromic photocycle," in which the dramatic change from green to red absorption is not induced by initial bilin photoisomerization but by a subsequent change in bilin protonation state.

Elemental economy: microbial strategies for optimizing growth in the face of nutrient limitation

Microorganisms play a dominant role in the biogeochemical cycling of nutrients. They are rightly praised for their facility for fixing both carbon and nitrogen into organic matter, and microbial driven processes have tangibly altered the chemical composition of the biosphere and its surrounding atmosphere. Despite their prodigious capacity for molecular transformations, microorganisms are powerless in the face of the immutability of the elements. Limitations for specific elements, either fleeting or persisting over eons, have left an indelible trace on microbial genomes, physiology, and their very atomic composition. We here review the impact of elemental limitation on microbes, with a focus on selected genetic model systems and representative microbes from the ocean ecosystem. Evolutionary adaptations that enhance growth in the face of persistent or recurrent elemental limitations are evident from genome and proteome analyses. These range from the extreme (such as dispensing with a requirement for a hard to obtain element) to the extremely subtle (changes in protein amino acid sequences that slightly, but significantly, reduce cellular carbon, nitrogen, or sulfur demand). One near-universal adaptation is the development of sophisticated acclimation programs by which cells adjust their chemical composition in response to a changing environment. When specific elements become limiting, acclimation typically begins with an increased commitment to acquisition and a concomitant mobilization of stored resources. If elemental limitation persists, the cell implements austerity measures including elemental sparing and elemental recycling. Insights into these fundamental cellular properties have emerged from studies at many different levels, including ecology, biological oceanography, biogeochemistry, molecular genetics, genomics, and microbial physiology. Here, we present a synthesis of these diverse studies and attempt to discern some overarching themes.