Serine/threonine protein kinase SpkG is a candidate for high salt resistance in the unicellular cyanobacterium Synechocystis sp. PCC 6803

The Role of Serine/Threonine-Specific Protein Kinases in Cyanobacteria - SpkB Is Involved in Acclimation to Fluctuating Conditions in Synechocystis sp. PCC 6803

Protein phosphorylation via serine/threonine protein kinases (Spk) is a widespread mechanism to adjust cellular processes toward changing environmental conditions. To study their role(s) in cyanobacteria, we investigated a collection of 11 completely segregated spk mutants among the 12 annotated Spks in the model cyanobacterium Synechocystis sp. PCC 6803. Screening of the mutant collection revealed that especially the mutant defective in SpkB encoded by slr1697 showed clear deviations regarding carbon metabolism, that is, reduced growth rates at low CO2 or in the presence of glucose, and different glycogen accumulation patterns compared to WT. Alterations in the proteome of ΔspkB indicated changes of the cell surface but also metabolic functions. A phospho-proteome analysis revealed the absence of any phosphorylation in two proteins, while decreased phosphorylation of the carboxysome-associated protein CcmM and increased phosphorylation of the allophycocyanin alpha subunit ApcA was detected in ΔspkB. Furthermore, the regulatory PII protein appeared less phosphorylated in the mutant compared to WT, which was verified in Western blot experiments, indicating a clearly delayed PII phosphorylation in cells shifted from nitrate-containing to nitrate-free medium. Our results indicate that SpkB is an important regulator in Synechocystis that is involved in phosphorylation of the PII protein and additional proteins.

SpkH (Sll0005) from Synechocystis sp. PCC 6803 is an active Mn2+-dependent Ser kinase

Twelve genes for the potential serine-threonine protein kinases (STPKs) have been annotated in the genome of Synechocystis sp. PCC 6803. Based on similarities and distinctive domain organization, they were divided into two clusters: serine/threonine-protein N2-like kinases (PKN2-type) and "activity of bc1 complex" kinases (ABC1-type). While the activity of the PKN2-type kinases have been demonstrated, no ABC1-type kinases activity have hitherto been reported. In this study, a recombinant protein previously annotated as a potential STPK of ABC1-type (SpkH, Sll0005) was expressed and purified to homogeneity. We demonstrated SpkH phosphorylating activity and substrate preference for casein in in vitro assays using [γ-32P]ATP. Detailed analyses of activity showed that Mn2+ had the strongest activation effect. The activity of SpkH was significantly inhibited by heparin and spermine, but not by staurosporine. By means of semi-quantitative mass-spectrometric detection of phosphopeptides, we identified a consensus motif recognized by this kinase - X1X2pSX3E. Thus, we first report here that SpkH of Synechocystis represents a true active serine protein kinase, which shares the properties of casein kinases according to its substrate specificity and sensitivity to some activity effectors.

Halotolerance mechanisms in salt‑tolerant cyanobacteria

Cyanobacteria are ubiquitously distributed in nature and are the most abundant photoautotrophs on Earth. Their long evolutionary history reveals that cyanobacteria have a remarkable capacity and strong adaptive tendencies to thrive in a variety of conditions. Thus, they can survive successfully, especially in harsh environmental conditions such as salty environments, high radiation, or extreme temperatures. Among others, salt stress because of excessive salt accumulation in salty environments, is the most common abiotic stress in nature and hampers agricultural growth and productivity worldwide. These detrimental effects point to the importance of understanding the molecular mechanisms underlying the salt stress response. While it is generally accepted that the stress response mechanism is a complex network, fewer efforts have been made to represent it as a network. Substantial evidence revealed that salt-tolerant cyanobacteria have evolved genomic specific mechanisms and high adaptability in response to environmental changes. For example, extended gene families and/or clusters of genes encoding proteins involved in the adaptation to high salinity have been collectively reported. This chapter focuses on recent advances and provides an overview of the molecular basis of halotolerance mechanisms in salt‑tolerant cyanobacteria as well as multiple regulatory pathways. We elaborate on the major protective mechanisms, molecular mechanisms associated with halotolerance, and the global transcriptional landscape to provide a gateway to uncover gene regulation principles. Both knowledge and omics approaches are utilized in this chapter to decipher the mechanistic insights into halotolerance. Collectively, this chapter would have a profound impact on providing a comprehensive understanding of halotolerance in salt‑tolerant cyanobacteria.

Cyanobacteria as cell factories for the photosynthetic production of sucrose

Biofuels and other biologically manufactured sustainable goods are growing in popularity and demand. Carbohydrate feedstocks required for industrial fermentation processes have traditionally been supplied by plant biomass, but the large quantities required to produce replacement commodity products may prevent the long-term feasibility of this approach without alternative strategies to produce sugar feedstocks. Cyanobacteria are under consideration as potential candidates for sustainable production of carbohydrate feedstocks, with potentially lower land and water requirements relative to plants. Several cyanobacterial strains have been genetically engineered to export significant quantities of sugars, especially sucrose. Sucrose is not only naturally synthesized and accumulated by cyanobacteria as a compatible solute to tolerate high salt environments, but also an easily fermentable disaccharide used by many heterotrophic bacteria as a carbon source. In this review, we provide a comprehensive summary of the current knowledge of the endogenous cyanobacterial sucrose synthesis and degradation pathways. We also summarize genetic modifications that have been found to increase sucrose production and secretion. Finally, we consider the current state of synthetic microbial consortia that rely on sugar-secreting cyanobacterial strains, which are co-cultivated alongside heterotrophic microbes able to directly convert the sugars into higher-value compounds (e.g., polyhydroxybutyrates, 3-hydroxypropionic acid, or dyes) in a single-pot reaction. We summarize recent advances reported in such cyanobacteria/heterotroph co-cultivation strategies and provide a perspective on future developments that are likely required to realize their bioindustrial potential.

Ser/Thr Protein Kinase SpkI Affects Photosynthetic Efficiency in Synechocystis sp. PCC 6803 upon Salt Stress

High salinity is a common environmental factor that limits productivity and growth for photosynthetic organisms. Here, we identified a mutant defected in gene sll1770, which encodes a Ser/Thr protein kinase SpkI, with a significantly low maximal quantum yield of PSII under high salt condition in Synechocystis sp. PCC 6803. Physiological characterization demonstrated that the ΔspkI mutant had normal growth and photosynthesis under control condition. And a significantly higher NPQ capacity was also observed in ΔspkI when grown under control condition. However, when grown under high salt condition, ΔspkI exhibited apparently slower growth as well as decreased net photosynthesis and PSII activity. Western blot analysis demonstrated that the amount of major photosynthetic proteins declined sharply in ΔspkI when cells grown under high salt condition. Redox kinetics measurement suggested that the activities of PSI and cytochrome b₆f complex were modified in ΔspkI under high salt condition, which resulted in a more reduced PQ pool in ΔspkI. Chlorophyll fluorescence traces suggested that the O_A⁻ reoxidation and state transition was also impaired in ΔspkI under high salt condition. Above all, we propose that Ser/Thr protein kinase SpkI plays a role in maintaining high-effective photosynthesis during high-salt acclimation process in Synechocystis.

Genome-wide association study reveals a genomic region on 5AL for salinity tolerance in wheat

Soil salinity is a major threat to crop productivity and quality worldwide. In order to reduce the negative effects of salinity stress, it is important to understand the genetic basis of salinity tolerance. Identifying new salinity tolerance QTL or genes is crucial for breeders to pyramid different tolerance mechanisms to improve crop adaptability to salinity. Being one of the major cereal crops, wheat is known as a salt-sensitive glycophyte and subject to substantial yield losses when grown in the presence of salt. In this study, both pot and tank experiments were conducted to investigate the genotypic variation present in 328 wheat varieties in their salinity tolerance at the vegetative stage. A Genome-Wide Association Studies (GWAS) were carried out to identify QTL conferring salinity tolerance through a mixed linear model. Six, five and eight significant marker-trait associations (MTAs) were identified from pot experiments, tank experiments and average damage scores, respectively. These markers are located on the wheat chromosomes 1B, 2B, 2D, 3A, 4B, and 5A. These tolerance alleles were additive in their effects and, when combined, increased tolerance to salinity. Candidate genes identified in these QTL regions encoded a diverse class of proteins involved in salinity tolerance in plants. A Na⁺/H⁺ exchanger and a potassium transporter on chromosome 5A (IWB30519) will be of a potential value for improvement of salt tolerance of wheat cultivars using marker assisted selection programs. Some useful genotypes, which showed consistent tolerance in different trials, can also be effectively used in breeding programs.

Light limitation inducing overcompensatory growth of cyanobacteria and function of serine/threonine kinase (STK) genes involved

The rapid overcompensatory growth that appears when cyanobacteria are supplied with adequate resources after a period of resource deprivation might contribute to the occurrence of cyanobacterial blooms. We investigated the changing characteristics of overcompensatory growth and serine/threonine kinase (STK) genes expression of cyanobacterium Microcystis aeruginosa in response to light limitation. The results showed M. aeruginosa exhibited overcompensatory growth for 2 days after light recovery, during which the increase in growth was inversely related to light intensity. Expression of STK genes, such as spkD, was upregulated significantly at 0.5-4 h after light recovery (P < 0.05). To investigate the function of STK genes in the overcompensatory growth, M. aeruginosa spkD was heterologously expressed in Synechocystis. Transgenic Synechocystis exhibited greater and longer overcompensatory growth than wild-type Synechocystis after light recovery. Relative expression levels of STK genes in transgenic Synechocystis were significantly higher than those in wild-type Synechocystis at 24 h of light recovery (P < 0.05). Heterologous expression of Microcystis spkD might stimulate overcompensatory growth of Synechocystis by affecting its STK gene expression.

Serine/threonine Kinases Play Important Roles in Regulating Polyunsaturated Fatty Acid Biosynthesis in Synechocystis sp. PCC6803

Serine/threonine kinases (STKs) play important roles in prokaryotic cellular functions such as growth, differentiation, and secondary metabolism. When the external environment changes, prokaryotes rely on signal transduction systems, including STKs that quickly sense these changes and alter gene expression to induce the appropriate metabolic changes. In this study, we examined the roles of the STK genes spkD and spkG in fatty acid biosynthesis in the unicellular cyanobacterium Synechocystis sp. PCC6803, using targeted gene knockout. The linoleic acid (C18: 2), γ-linolenic acid (C18: 3n6), α-linolenic acid (C18: 3n3), and stearidonic acid (C18: 4) levels were significantly lower in spkD and spkG gene knockout mutants than in the wild type at a culture temperature of 30°C and a light intensity of 40 μmol⋅m^–2⋅s^–1. The expression levels of fatty acid desaturases and STK genes differed between the spkD and spkG gene knockout mutants. These observations suggest that spkD and spkG may directly or indirectly affect the fatty acid composition in Synechocystis sp. PCC6803 by regulating the expression of fatty acid desaturases genes. Therefore, the STK genes spkD and spkG play important roles in polyunsaturated fatty acid biosynthesis in Synechocystis sp. PCC6803. These findings could facilitate the development of cyanobacteria germplasm resources that yield high levels of fatty acids. In addition, they provide a theoretical basis for the genetic engineering of cyanobacteria with improved yields of secondary metabolites and increased economic benefits.

Revisiting cyanobacterial state transitions

Critical evaluation of “new” and “old” models of cyanobacterial state transitions. Phycobilisome and membrane contributions to this mechanism are addressed. The signaling transduction pathway is discussed.

The Cytochrome b 6 f Complex Is Not Involved in Cyanobacterial State Transitions

Photosynthetic organisms must sense and respond to fluctuating environmental conditions in order to perform efficient photosynthesis and to avoid the formation of dangerous reactive oxygen species. The excitation energy arriving at each photosystem permanently changes due to variations in the intensity and spectral properties of the absorbed light. Cyanobacteria, like plants and algae, have developed a mechanism, named "state transitions," that balances photosystem activities. Here, we characterize the role of the cytochrome b ₆ f complex and phosphorylation reactions in cyanobacterial state transitions using Synechococcus elongatus PCC 7942 and Synechocystis PCC 6803 as model organisms. First, large photosystem II (PSII) fluorescence quenching was observed in State II, a result that does not appear to be related to energy transfer from PSII to PSI (spillover). This membrane-associated process was inhibited by betaine, Suc, and high concentrations of phosphate. Then, using different chemicals affecting the plastoquinone pool redox state and cytochrome b ₆ f activity, we demonstrate that this complex is not involved in state transitions in S. elongatus or Synechocystis PCC6803. Finally, by constructing and characterizing 21 protein kinase and phosphatase mutants and using chemical inhibitors, we demonstrate that phosphorylation reactions are not essential for cyanobacterial state transitions. Thus, signal transduction is completely different in cyanobacterial and plant (green alga) state transitions.

Identification of two two-component signal transduction mutants with enhanced sucrose biosynthesis in Synechococcus elongatus PCC 7942

Metabolic engineering of the freshwater cyanobacterium Synechococcus elongatus PCC 7942 (Syn7942), synthesizing sucrose as the only compatible solute upon salt stress, has greatly improved its sucrose productivity. However, the signaling and regulatory mechanisms of this physiological process are still unknown. To know more about these aspects, a library of inactivation mutants for all 44 predicted signal transduction genes of Syn7942 was constructed. By evaluating sucrose production, two two-component signal transduction mutants Δ1125 and Δ1404, in which Synpcc7942_1125 and Synpcc7942_1404 was inactivated, respectively, were identified. They exhibited stably enhanced sucrose production, but the growth and the expression of sps encoding sucrose-phosphate synthase under salt stress were not affected, indicating that the corresponding signal transduction proteins do not regulate salt-induced sucrose synthesis by directly regulating sps expression. Moreover, the glycogen accumulation was enhanced in Δ1125 and Δ1404, and the salt stress-intensified photodamage of these mutants was also found to be relieved. These results indicated that the basic cell metabolisms such as glycogen metabolism and photosynthesis of the mutants were affected by gene inactivation, which might further affect salt-induced sucrose synthesis. Further studies on gene functions and signaling pathways or networks of Synpcc7942_1125 and Synpcc7942_1404 would reveal more details about the molecular bases for the observed phenotypes of Δ1125 and Δ1404.

Sequences, Domain Architectures, and Biological Functions of the Serine/Threonine and Histidine Kinases in Synechocystis sp. PCC 6803

The cyanobacterium Synechocystis sp. PCC 6803 (hereafter Synechocystis) is a photoautotrophic prokaryote with plant-like photosynthetic machineries which significantly contribute to global carbon fixation and atmospheric oxygen production. Because of the relatively short cell doubling time, small size of the genome, and the ease for genetic manipulation, Synechocystis is a popular model organism for studies including photosynthesis and biofuel production. The cyanobacterium contains 12 eukaryotic type Ser/Thr kinases (SpkA-L) and 49 histidine kinases (Hik1-47 and Sll1334 and Sll5060 are named as Hik48 and Hik49, respectively, in this review) of the two-component system. All SpkA-L kinases have a eukaryotic kinase DFG signature in their A-loops. Based on the types of the kinase domains, the Spks can be separated into three groups: one group contains SpkA and SpkG which are related to human kinases, while SpkH-L are in another group that is distinct from human kinases. The third group contains SpkB-F which are between the first two groups. Four histidine kinases (Hiks17, 36, 45, and 48) lack a clear histidine kinase domain, and the conserved phosphorylatable histidine residue could not be identified for six histidine kinases (Hiks11, 18, 29, 37, 39, and 43) even though they have clear histidine kinase domains. Each of the remaining 39 has a histidine kinase domain with the conserved histidine residue. Eight hybrid histidine kinases contain one or two receiver domains, and they all, except Hik25 (Slr0222), have the conserved phosphorylatable aspartate. The disruptants of all kinases except hik13 and hik15 have been generated, and the majority of them have modest or no obvious phenotypes, indicating other kinases could functionally compensate the loss of a particular kinase. This review presents a comprehensive discussion including a spectrum of sequence, domain architecture, in vivo function, and proteomics investigations of Ser/Thr and histidine kinases. Understanding the sequences, domain architectures, and biology of the kinases will help to integrate "omic" data to clarify their exact biochemical functions.

Hanks-Type Serine/Threonine Protein Kinases and Phosphatases in Bacteria: Roles in Signaling and Adaptation to Various Environments

Reversible phosphorylation is a key mechanism that regulates many cellular processes in prokaryotes and eukaryotes. In prokaryotes, signal transduction includes two-component signaling systems, which involve a membrane sensor histidine kinase and a cognate DNA-binding response regulator. Several recent studies indicate that alternative regulatory pathways controlled by Hanks-type serine/threonine kinases (STKs) and serine/threonine phosphatases (STPs) also play an essential role in regulation of many different processes in bacteria, such as growth and cell division, cell wall biosynthesis, sporulation, biofilm formation, stress response, metabolic and developmental processes, as well as interactions (either pathogenic or symbiotic) with higher host organisms. Since these enzymes are not DNA-binding proteins, they exert the regulatory role via post-translational modifications of their protein targets. In this review, we summarize the current knowledge of STKs and STPs, and discuss how these enzymes mediate gene expression in prokaryotes. Many studies indicate that regulatory systems based on Hanks-type STKs and STPs play an essential role in the regulation of various cellular processes, by reversibly phosphorylating many protein targets, among them several regulatory proteins of other signaling cascades. These data show high complexity of bacterial regulatory network, in which the crosstalk between STK/STP signaling enzymes, components of TCSs, and the translational machinery occurs. In this regulation, the STK/STP systems have been proved to play important roles.

Genome-Wide Association Mapping of Seedling Heat Tolerance in Winter Wheat

Heat stress during the seedling stage of early-planted winter wheat (Triticum aestivum L.) is one of the most abiotic stresses of the crop restricting forage and grain production in the Southern Plains of the United States. To map quantitative trait loci (QTLs) and identify single-nucleotide polymorphism (SNP) markers associated with seedling heat tolerance, a genome-wide association mapping study (GWAS) was conducted using 200 diverse representative lines of the hard red winter wheat association mapping panel, which was established by the Triticeae Coordinated Agricultural Project (TCAP) and genotyped with the wheat iSelect 90K SNP array. The plants were initially planted under optimal temperature conditions in two growth chambers. At the three-leaf stage, one chamber was set to 40/35°C day/night as heat stress treatment, while the other chamber was kept at optimal temperature (25/20°C day/night) as control for 14 days. Data were collected on leaf chlorophyll content, shoot length, number of leaves per seedling, and seedling recovery after removal of heat stress treatment. Phenotypic variability for seedling heat tolerance among wheat lines was observed in this study. Using the mixed linear model (MLM), we detected multiple significant QTLs for seedling heat tolerance on different chromosomes. Some of the QTLs were detected on chromosomes that were previously reported to harbor QTLs for heat tolerance during the flowering stage of wheat. These results suggest that some heat tolerance QTLs are effective from the seedling to reproductive stages in wheat. However, new QTLs that have never been reported at the reproductive stage were found responding to seedling heat stress in the present study. Candidate gene analysis revealed high sequence similarities of some significant loci with candidate genes involved in plant stress responses including heat, drought, and salt stress. This study provides valuable information about the genetic basis of seedling heat tolerance in wheat. To the best of our knowledge, this is the first GWAS to map QTLs associated with seedling heat tolerance targeting early planting of dual-purpose winter wheat. The SNP markers identified in this study will be used for marker-assisted selection (MAS) of seedling heat tolerance during dual-purpose wheat breeding.

The Transcriptional Landscape of the Photosynthetic Model Cyanobacterium Synechocystis sp. PCC6803

Cyanobacteria exhibit a great capacity to adapt to different environmental conditions through changes in gene expression. Although this plasticity has been extensively studied in the model cyanobacterium Synechocystis sp. PCC 6803, a detailed analysis of the coordinated transcriptional adaption across varying conditions is lacking. Here, we report a meta-analysis of 756 individual microarray measurements conducted in 37 independent studies-the most comprehensive study of the Synechocystis transcriptome to date. Using stringent statistical evaluation, we characterized the coordinated adaptation of Synechocystis' gene expression on systems level. Evaluation of the data revealed that the photosynthetic apparatus is subjected to greater changes in expression than other cellular components. Nevertheless, network analyses indicated a significant degree of transcriptional coordination of photosynthesis and various metabolic processes, and revealed the tight co-regulation of components of photosystems I, II and phycobilisomes. Detailed inspection of the integrated data led to the discovery a variety of regulatory patterns and novel putative photosynthetic genes. Intriguingly, global clustering analyses suggested contrasting transcriptional response of metabolic and regulatory genes stress to conditions. The integrated Synechocystis transcriptome can be accessed and interactively analyzed via the CyanoEXpress website (http://cyanoexpress.sysbiolab.eu).

Effects of Phosphorylation of β Subunits of Phycocyanins on State Transition in the Model Cyanobacterium Synechocystis sp. PCC 6803

Synechocystis sp. PCC 6803 (hereafter Synechocystis) is a model cyanobacterium and has been used extensively for studies concerned with photosynthesis and environmental adaptation. Although dozens of protein kinases and phosphatases with specificity for Ser/Thr/Tyr residues have been predicted, only a few substrate proteins are known in Synechocystis. In this study, we report 194 in vivo phosphorylation sites from 149 proteins in Synechocystis, which were identified using a combination of peptide pre-fractionation, TiO(2) enrichment and liquid chromatograpy-tandem mass spectrometry (LC-MS/MS) analysis. These phosphorylated proteins are implicated in diverse biological processes, such as photosynthesis. Among all identified phosphoproteins involved in photosynthesis, the β subunits of phycocyanins (CpcBs) were found to be phosphorylated on Ser22, Ser49, Thr94 and Ser154. Four non-phosphorylated mutants were constructed by using site-directed mutagenesis. The in vivo characterization of the cpcB mutants showed a slower growth under high light irradiance and displayed fluorescence quenching to a lower level and less efficient energy transfer inside the phycobilisome (PBS). Notably, the non-phosphorylated mutants exhibited a slower state transition than the wild type. The current results demonstrated that the phosphorylation status of CpcBs affects the energy transfer and state transition of photosynthesis in Synechocystis. This study provides novel insights into the molecular mechanisms of protein phosphorylation in the regulation of photosynthesis in cyanobacteria and may facilitate the elucidation of the entire regulatory network by linking kinases to their physiological substrates.

RNA-Seq analysis of the wild barley (H. spontaneum) leaf transcriptome under salt stress

Wild salt-tolerant barley (Hordeum spontaneum) is the ancestor of cultivated barley (Hordeum vulgare or H. vulgare). Although the cultivated barley genome is well studied, little is known about genome structure and function of its wild ancestor. In the present study, RNA-Seq analysis was performed on young leaves of wild barley treated with salt (500mM NaCl) at four different time intervals. Transcriptome sequencing yielded 103 to 115 million reads for all replicates of each treatment, corresponding to over 10 billion nucleotides per sample. Of the total reads, between 74.8 and 80.3% could be mapped and 77.4 to 81.7% of the transcripts were found in the H. vulgare unigene database (unigene-mapped). The unmapped wild barley reads for all treatments and replicates were assembled de novo and the resulting contigs were used as a new reference genome. This resulted in 94.3 to 95.3% of the unmapped reads mapping to the new reference. The number of differentially expressed transcripts was 9277, 3861 of which were unigene-mapped. The annotated unigene- and de novo-mapped transcripts (5100) were utilized to generate expression clusters across time of salt stress treatment. Two-dimensional hierarchical clustering classified differential expression profiles into nine expression clusters, four of which were selected for further analysis. Differentially expressed transcripts were assigned to the main functional categories. The most important groups were "response to external stimulus" and "electron-carrier activity". Highly expressed transcripts are involved in several biological processes, including electron transport and exchanger mechanisms, flavonoid biosynthesis, reactive oxygen species (ROS) scavenging, ethylene production, signaling network and protein refolding. The comparisons demonstrated that mRNA-Seq is an efficient method for the analysis of differentially expressed genes and biological processes under salt stress.

Salt acclimation of cyanobacteria and their application in biotechnology

The long evolutionary history and photo-autotrophic lifestyle of cyanobacteria has allowed them to colonize almost all photic habitats on Earth, including environments with high or fluctuating salinity. Their basal salt acclimation strategy includes two principal reactions, the active export of ions and the accumulation of compatible solutes. Cyanobacterial salt acclimation has been characterized in much detail using selected model cyanobacteria, but their salt sensing and regulatory mechanisms are less well understood. Here, we briefly review recent advances in the identification of salt acclimation processes and the essential genes/proteins involved in acclimation to high salt. This knowledge is of increasing importance because the necessary mass cultivation of cyanobacteria for future use in biotechnology will be performed in sea water. In addition, cyanobacterial salt resistance genes also can be applied to improve the salt tolerance of salt sensitive organisms, such as crop plants.

An orphan two-component response regulator Slr1588 involves salt tolerance by directly regulating synthesis of compatible solutes in photosynthetic Synechocystis sp. PCC 6803

We report here the characterization of a novel orphan response regulator Slr1588 directly involved in the synthesis and transport of compatible solutes against salt stress.

Integrated proteomic and transcriptomic analysis reveals novel genes and regulatory mechanisms involved in salt stress responses in Synechocystis sp. PCC 6803

Salt stress is a common stress that limits growth and productivity of photosynthetic microbes in natural environments. Although cellular responses of a model cyanobacterium Synechocystis sp. PCC6803 to high and changing salt concentration have been studied, it remains undefined of the gene components and their regulation in the long-term salt acclimation networks. In this study, we performed an integrated study coupling a quantitative iTRAQ-LC-MS/MS proteomics and a next-generation sequencing-based RNA-seq transcriptomics on Synechocystis under salt stress for an extended period of time. Comparative quantification of protein abundances led to the identification of 68 and 108 proteins differentially regulated by salt treatment at 24 and 48 h, respectively. RNA-seq transcriptomic analysis showed that genes involved in energy metabolism and protein synthesis, and genes encoding hypothetical proteins responded to salt stress in a phase-dependent pattern. Notably, a gene encoding CO2-uptake-related protein (CupA) and three genes encoding hypothetical proteins were induced significantly at either transcript or protein level after long-term salt stress. Gene knockout and comparative growth analysis demonstrated that these four genes were involved in salt tolerance in Synechocystis. In addition, a complementary proteome and transcriptome analysis showed that concordance between protein abundances and their corresponding mRNAs varied significantly between various gene-protein pairs, indicating divergent regulation of transcriptional and post-transcriptional processes during salt stress adaptation in Synechocystis. The study provided new insights on genes and regulatory mechanism involved in salt stress response in Synechocystis.

A suite of new genes defining salinity stress tolerance in seedlings of contrasting rice genotypes

Salinity is one of the major constraints adversely influencing crop productivity. Saltol QTL is a major QTL associated with Na⁺-K⁺ ratio and seedling stage salinity tolerance in rice. With an aim to understand the contribution of individual genes localized within saltol towards salinity tolerance, we analysed the transcript abundance of a set of these genes in seedlings of contrasting genotypes of rice. We hypothesize that this approach may be helpful in identifying new 'candidate genes' for improving salinity tolerance in crops. For this purpose, seedlings of Oryza sativa cv. IR64 (sensitive) and the landrace Pokkali (tolerant) were subjected to short/long durations of salinity. qRT-PCR analysis clearly exhibited differential regulation of genes encoding signaling related protein (SRPs), where higher transcript abundance for most of them was observed in Pokkali than IR64 under non-stress conditions, thereby indicating towards well preparedness of the former to handle stress, in anticipation. Genes encoding proteins of unknown function (PUFs), though, constitute a considerable portion of plant genome, have so far been neglected in most studies. Time course analysis of these genes showed a continuous increase in their abundance in Pokkali, while in IR64, their abundance increased till 24 h followed by a clear decrease, thereby justifying their nomenclature as 'salinity induced factors' (SIFs). This is the first report showing possible involvement of SIFs localized within salinity related QTL towards salinity stress response. Based on the phenotypes of insertional mutants, it is proposed that these SIFs may have a putative function in vegetative growth (SIFVG), fertility (SIFF), viability (SIFV) or early flowering (SIFEF).

Quantitative proteomics reveals dynamic responses of Synechocystis sp. PCC 6803 to next-generation biofuel butanol

Butanol is a promising biofuel, and recent metabolic engineering efforts have demonstrated the use of photosynthetic cyanobacterial hosts for its production. However, cyanobacteria have very low tolerance to butanol, limiting the economic viability of butanol production from these renewable producing systems. The existing knowledge of molecular mechanism involved in butanol tolerance in cyanobacteria is very limited. To build a foundation necessary to engineer robust butanol-producing cyanobacterial hosts, in this study, the responses of Synechocystis PCC 6803 to butanol were investigated using a quantitative proteomics approach with iTRAQ - LC-MS/MS technologies. The resulting high-quality dataset consisted of 25,347 peptides corresponding to 1452 unique proteins, a coverage of approximately 40% of the predicted proteins in Synechocystis. Comparative quantification of protein abundances led to the identification of 303 differentially regulated proteins by butanol. Annotation and GO term enrichment analysis showed that multiple biological processes were regulated, suggesting that Synechocystis probably employed multiple and synergistic resistance mechanisms in dealing with butanol stress. Notably, the analysis revealed the induction of heat-shock protein and transporters, along with modification of cell membrane and envelope were the major protection mechanisms against butanol. A conceptual cellular model of Synechocystis PCC 6803 responses to butanol stress was constructed to illustrate the putative molecular mechanisms employed to defend against butanol stress.

Thiol-based redox modulation of a cyanobacterial eukaryotic-type serine/threonine kinase required for oxidative stress tolerance

AIMS

Protein phosphorylation is a principal signaling mechanism that mediates regulation of enzymatic activities, modulation of gene expression, and adaptation to environmental changes. Recent studies have shown a ubiquitous distribution of eukaryotic-type Serine/Threonine protein kinases in prokaryotic genomes, though the functions, substrates, and possible regulation of these enzymes remain largely unknown. In this study, we investigated whether cyanobacterial protein phosphorylation may be subject to redox regulation through modulation of the cysteine redox state, as has previously been reported for animals and plants. We also explored the role of a cyanobacterial Serine/Threonine kinase in oxidative stress tolerance.

RESULTS

The Synechocystis sp. PCC 6803 Serine/Threonine kinase SpkB was found to be inhibited by oxidation and reactivated by thioredoxin-catalyzed reduction. A Synechocystis mutant devoid of the SpkB kinase was unable to phosphorylate the glycyl-tRNA synthetase β-subunit (GlyS), one of the most prominent phosphoproteins in the wild type, and recombinant purified SpkB could phosphorylate purified GlyS. In vivo characterization of the SpkB mutant showed a pronounced hypersensitivity to oxidative stress and displayed severe growth retardation or death in response to menadione, methyl viologen, and elevated light intensities.

INNOVATION

This study points out a previously unrecognised complexity of prokaryotic regulatory pathways in adaptation to the environment and extends the roles of bacterial eukaryotic-like Serine/Threonine kinases to oxidative stress response.

CONCLUSION

The SpkB kinase is required for survival of the cyanobacterium Synechocystis sp. PCC 6803 under conditions implying increased concentrations of reactive oxygen species, and the activity of SpkB depends on the redox state of its cysteines.