Substitution of tyrosine residues at the aromatic cluster around the betaA-betaB loop of rubisco small subunit affects the structural stability of the enzyme and the in vivo degradation under stress conditions

Magnetic fields exhibit a positive impact on lipid and biomass yield during phototrophic cultivation of Spirulina sp

This study aimed to investigate the effects of magnetic field (MF) application (1, 12 and 24 h day ^-1) to Spirulina sp. LEB 18 in different photosynthesis cycles (dark and/or light) during short (15 days) and long periods (50 days) of cultivation. MF application was performed via two sources: ferrite magnets and solenoids. At the end of cultivation, the biomass was characterized in terms of lipids, proteins, and carbohydrates. In the 15 day cultures, the highest maximum biomass concentrations (2.06 g L^-1 and 1.83 g L^-1) were observed when 30 mT was applied for 24 h day ^-1 or 12 h day ^-1 (on the light cycle), respectively. MF application throughout cultivation (24 h day ^-1) for more than 30 days is not recommended. In all conditions, there was an increase in the lipid concentration (from 14 to 45%). The protein profile suggested important changes in photosystems I and II due to MF application. Cell morphology was not altered by MF application. In conclusion, the effects on the metabolism of Spirulina sp. are directly related to the photosynthesis cycle and time period in which the MF was applied.

Polyhydroxybutyrate production and increased macromolecule content in Chlamydomonas reinhardtii cultivated with xylose and reduced nitrogen levels

The aim of the current study was to evaluate the production of macromolecules such as polyhydroxybutyrate under pentose supplementation and reduced nitrogen levels in Chlamydomonas reinhardtii. Two batches of experiments were carried out: (1) reduction in the nitrogen (NH4Cl) concentration to 6 and 4 g L-1 and (2) supplementation of 10, 20 and 30 mg L-1 D-xylose together with a reduction in the NH4Cl concentration (6 and 4 g L-1). The addition of 20 mg L-1 D-xylose together with 6 g L-1 NH4Cl resulted in polyhydroxybutyrate production (206.0 mg L-1). The reduction of 8 to 6 g L-1 NH4Cl did not trigger a reduction in the production of either proteins (68.3% w w-1) or carbohydrates (23.3% w w-1) in the cells. The current study demonstrated that nutritional modifications, which until now have been unexplored in C. reinhardtii, triggered the production of macromolecules (polymers, carbohydrates and proteins) with high biotechnological potential.

Innovative polyhydroxybutyrate production by Chlorella fusca grown with pentoses

The current study aimed to evaluate if the addition of pentoses along with variations in light intensity and photoperiod can stimulate the production of polyhydroxybutyrate (PHB) and other biomolecules by Chlorella fusca LEB 111. The variables evaluated were the addition of xylose and arabinose as sources of organic carbon, different photoperiods (18 h, 12 h and 6 h light) and variations in light intensities (58, 28 and 9 μmol_photons m^-2 s^-1). The highest PHB accumulation (17.4% w w^-1) and protein production (53.2% ww^-1) were observed in assays with xylose addition and a photoperiod of 6 h of light provided at 28 and 58 μmol_photons m^-2 s^-1, respectively. The highest lipid content (24.7% w w^-1) was obtained with 18 h of light. The current study contributes to the development of sustainable alternatives for the use of wastes and the production of biomolecules from algae.

Initiator tRNA genes template the 3' CCA end at high frequencies in bacteria

Background

While the CCA sequence at the mature 3′ end of tRNAs is conserved and critical for translational function, a genetic template for this sequence is not always contained in tRNA genes. In eukaryotes and Archaea, the CCA ends of tRNAs are synthesized post-transcriptionally by CCA-adding enzymes. In Bacteria, tRNA genes template CCA sporadically.

Results

In order to understand the variation in how prokaryotic tRNA genes template CCA, we re-annotated tRNA genes in tRNAdb-CE database version 0.8. Among 132,129 prokaryotic tRNA genes, initiator tRNA genes template CCA at the highest average frequency (74.1%) over all functional classes except selenocysteine and pyrrolysine tRNA genes (88.1% and 100% respectively). Across bacterial phyla and a wide range of genome sizes, many lineages exist in which predominantly initiator tRNA genes template CCA. Convergent and parallel retention of CCA templating in initiator tRNA genes evolved in independent histories of reductive genome evolution in Bacteria. Also, in a majority of cyanobacterial and actinobacterial genera, predominantly initiator tRNA genes template CCA. We also found that a surprising fraction of archaeal tRNA genes template CCA.

Conclusions

We suggest that cotranscriptional synthesis of initiator tRNA CCA 3′ ends can complement inefficient processing of initiator tRNA precursors, “bootstrap” rapid initiation of protein synthesis from a non-growing state, or contribute to an increase in cellular growth rates by reducing overheads of mass and energy to maintain nonfunctional tRNA precursor pools. More generally, CCA templating in structurally non-conforming tRNA genes can afford cells robustness and greater plasticity to respond rapidly to environmental changes and stimuli.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-3314-x) contains supplementary material, which is available to authorized users.

A reversible decrease in ribulose 1,5-bisphosphate carboxylase/oxygenase carboxylation activity caused by the aggregation of the enzyme's large subunit is triggered in response to the exposure of moderate irradiance-grown plants to low irradiance

Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) is highly regulated in response to fluctuations in the environment, including changes in irradiance. However, no complex data are available on Rubisco regulatory mechanisms triggered in plants which are submitted to moderate-low irradiance shift. Therefore, we investigated in a comprehensive way the changes at the level of amount of Rubisco protein, its structural organization and carboxylase activity of the holoenzyme as triggered by exposure of moderate irradiance-grown Arabidopsis thaliana plants to low irradiance conditions. An exposure of moderate irradiance-grown plants to low irradiance for a single photoperiod caused the exclusion of a certain pool of Rubisco under altered conditions owing to oxidative modifications resulting in the formation of protein aggregates involving Rubisco large subunit (LS). As a result, both initial and total Rubisco carboxylase activities were reduced, whereas Rubisco activation state remained largely unchanged. The results of the determination of reactive oxygen species indicated that a moderate/low irradiance transition had stimulated (1) O2 accumulation and we strongly suggest that Rubisco oxidative modifications leading to formation of aggregates encompassing Rubisco-LS were triggered by (1) O2 . When moderate irradiance regime was resumed, the majority of Rubisco-LS containing aggregates tended to be resolubilized, and this allowed Rubisco carboxylation activities to be largely recovered, without changes in the activation state of the enzyme. In the longer term, these results allow us to better understand a complexity of Rubisco regulatory mechanisms activated in response to abiotic stresses and during recovery from the stresses.

Engineering photosynthetic organisms for the production of biohydrogen

Oxygenic photosynthetic organisms such as green algae are capable of absorbing sunlight and converting the chemical energy into hydrogen gas. This process takes advantage of the photosynthetic apparatus of these organisms which links water oxidation to H2 production. Biological H2 has therefore the potential to be an alternative fuel of the future and shows great promise for generating large scale sustainable energy. Microalgae are able to produce H2 under light anoxic or dark anoxic condition by activating 3 different pathways that utilize the hydrogenases as catalysts. In this review, we highlight the principal barriers that prevent hydrogen production in green algae and how those limitations are being addressed, through metabolic and genetic engineering.  We also discuss the major challenges and bottlenecks facing the development of future commercial algal photobiological systems for H2 production. Finally we provide suggestions for future strategies and potential new techniques to be developed towards an integrated system with optimized hydrogen production.

Substitutions at the opening of the Rubisco central solvent channel affect holoenzyme stability and CO2/O 2 specificity but not activation by Rubisco activase

Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) catalyzes the initial step of carbon metabolism in photosynthesis. The holoenzyme comprises eight large subunits, arranged as a tetramer of dimers around a central solvent channel that defines a fourfold axis of symmetry, and eight small subunits, arranged as two tetramers at the poles of the axis. The phylogenetically divergent small-subunit loops between β-strands A and B form the entrance to the solvent channel. In the green alga Chlamydomonas reinhardtii, Ile-58 from each of the four small-subunit βA-βB loops defines the minimal diameter of the channel opening. To understand the role of the central solvent channel in Rubisco function, directed mutagenesis and transformation of Chlamydomonas were employed to replace Ile-58 with Ala, Lys, Glu, Trp, or three Trp residues (I58W3) to close the entrance to the channel. The I58E, I58K, and I58W substitutions caused only small decreases in photosynthetic growth at 25 and 35 °C, whereas I58W3 had a substantial effect at both temperatures. The mutant enzymes had decreased carboxylation rates, but the I58W3 enzyme had decreases in both carboxylation and CO2/O2 specificity. The I58E, I58W, and I58W3 enzymes were inactivated at lower temperatures than wild-type Rubisco, and were degraded at slower rates under oxidative stress. However, these mutant enzymes were activated by Rubisco activase at normal rates, indicating that the structural transition required for carboxylation is not affected by altering the solvent channel opening. Structural dynamics alone may not be responsible for these distant effects on the Rubisco active site.

Drought tolerance in wheat

Drought is one of the most important phenomena which limit crops' production and yield. Crops demonstrate various morphological, physiological, biochemical, and molecular responses to tackle drought stress. Plants' vegetative and reproductive stages are intensively influenced by drought stress. Drought tolerance is a complicated trait which is controlled by polygenes and their expressions are influenced by various environmental elements. This means that breeding for this trait is so difficult and new molecular methods such as molecular markers, quantitative trait loci (QTL) mapping strategies, and expression patterns of genes should be applied to produce drought tolerant genotypes. In wheat, there are several genes which are responsible for drought stress tolerance and produce different types of enzymes and proteins for instance, late embryogenesis abundant (lea), responsive to abscisic acid (Rab), rubisco, helicase, proline, glutathione-S-transferase (GST), and carbohydrates during drought stress. This review paper has concentrated on the study of water limitation and its effects on morphological, physiological, biochemical, and molecular responses of wheat with the possible losses caused by drought stress.

Hybrid Rubisco of tomato large subunits and tobacco small subunits is functional in tobacco plants

Biogenesis of functional ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) in plants requires specific assembly in the chloroplast of the imported, cytosol-synthesized small subunits (SS) with the chloroplast-made large subunits (LS). Accumulating evidence indicates that chloroplasts (plastids) generally have a low tolerance for assembling foreign or modified Rubisco. To explore Rubisco engineering, we created two lines of transplastomic tobacco plants whose rbcL gene was replaced by tomato-derived rbcL: plant LLS2 with Rubisco composed of tobacco SS and Q437R LS and plant LLS4 with a hybrid Rubisco of tobacco SS and tomato LS (representing four substitutions of Y226F, A230T, S279T and Q437R from tobacco LS). Plant LLS2 exhibited similar phenotypes as the wild type. Plant LLS4 showed lower chlorophyll and Rubisco levels particularly in young emerging leaves, lower photosynthesis rates and biomass during early stages of development, but was able to reach reproductive maturity and somewhat wild type-like phenotype under ambient CO₂ condition. In vitro assays detected similar carboxylase activity and RuBP affinity in LLS2 and LLS4 plants as in wild type. Our studies demonstrated that tomato LS was sufficiently assembled with tobacco SS into functional Rubisco. The hybrid Rubisco of tomato LS and tobacco SS can drive photosynthesis that supports photoautotrophic growth and reproduction of tobacco plants under ambient CO₂ and light conditions. We discuss the effect of these residue substitutions on Rubisco activity and the possible attribution of chlorophyll deficiency to the in planta photosynthesis performance in the hybrid Rubisco plants.

Highly conserved small subunit residues influence rubisco large subunit catalysis

The chloroplast enzyme ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) catalyzes the rate-limiting step of photosynthetic CO(2) fixation. With a deeper understanding of its structure-function relationships and competitive inhibition by O(2), it may be possible to engineer an increase in agricultural productivity and renewable energy. The chloroplast-encoded large subunits form the active site, but the nuclear-encoded small subunits can also influence catalytic efficiency and CO(2)/O(2) specificity. To further define the role of the small subunit in Rubisco function, the 10 most conserved residues in all small subunits were substituted with alanine by transformation of a Chlamydomonas reinhardtii mutant that lacks the small subunit gene family. All the mutant strains were able to grow photosynthetically, indicating that none of the residues is essential for function. Three of the substitutions have little or no effect (S16A, P19A, and E92A), one primarily affects holoenzyme stability (L18A), and the remainder affect catalysis with or without some level of associated structural instability (Y32A, E43A, W73A, L78A, P79A, and F81A). Y32A and E43A cause decreases in CO(2)/O(2) specificity. Based on the x-ray crystal structure of Chlamydomonas Rubisco, all but one (Glu-92) of the conserved residues are in contact with large subunits and cluster near the amino- or carboxyl-terminal ends of large subunit alpha-helix 8, which is a structural element of the alpha/beta-barrel active site. Small subunit residues Glu-43 and Trp-73 identify a possible structural connection between active site alpha-helix 8 and the highly variable small subunit loop between beta-strands A and B, which can also influence Rubisco CO(2)/O(2) specificity.

Drought-tolerant gene screening in wheat using rice microarray

To investigate the wheat transcriptional profile under drought stress, a drought-tolerant variety of wheat (Triticum aestivum), Hanxuan 10, was treated with polyethylene glycol (PEG6000) and samples were collected at 0, 1, 6 and 24 h. Complementary DNA was labelled with fluorescent dye and hybridized with the BGI-RiceChip, a whole genome rice gene chip platform, which contains over 60 000 oligos based on the rice genome sequence. Data analysis detected 166, 207 and 328 differentially expressed genes (DGs), respectively, at 1, 6 and 24 h, indicating that the number of DGs increased with the length of the PEG treatment. Functional category analysis showed that the number of DGs related to energy metabolism pathways increased – 4.2%, 8.2% and 16.8%, respectively, as a proportion of the total number of DGs. Most of the photosynthesis-related genes were up-regulated. It is interesting to note that Psbr and ribulose-bisphosphate carboxylase (Rubisco)-coding genes were down-regulated, suggesting their potential role in the response to drought tolerance.