The molecular basis for the broad substrate specificity of human sulfotransferase 1A1

Cytosolic sulfotransferases (SULTs) are mammalian enzymes that detoxify a wide variety of chemicals through the addition of a sulfate group. Despite extensive research, the molecular basis for the broad specificity of SULTs is still not understood. Here, structural, protein engineering and kinetic approaches were employed to obtain deep understanding of the molecular basis for the broad specificity, catalytic activity and substrate inhibition of SULT1A1. We have determined five new structures of SULT1A1 in complex with different acceptors, and utilized a directed evolution approach to generate SULT1A1 mutants with enhanced thermostability and increased catalytic activity. We found that active site plasticity enables binding of different acceptors and identified dramatic structural changes in the SULT1A1 active site leading to the binding of a second acceptor molecule in a conserved yet non-productive manner. Our combined approach highlights the dominant role of SULT1A1 structural flexibility in controlling the specificity and activity of this enzyme.     

Proteins functionally and immunogenically related to pathogenesis‐related proteins are induced during parsley leaf senescence

The advancement of leaf senescence is accompanied by a reduction in cellular protein content together with the induction of specific proteins which are probably involved in the process. In the present study, with parsley, we followed the changes in the levels of proteins functionally and immunogenically related to pathogenesis‐related proteins during both senescence of detached leaves and natural senescence of attached leaves. Both chitinase activity and protein level were found to be induced during senescence, as was the level of two other proteins immunologically related to β‐1,3‐glucanase and P4 pathogenesis‐related proteins of citrus and tomato, respectively. A high correlation between the advancement of senescence and the induction of these proteins was demonstrated. Treatments with CO₂ or gibberellic acid, which retard senescence, reduced both chitinase activity and the level of the pathogenesis‐related proteins, whereas enhancement of senescence with ethylene induced them further. The induction of pathogenesis‐related proteins during senescence suggests that these proteins may have a primary role in this process.     

The efficiency of the CO2-concentrating mechanism during single-cell C4 photosynthesis

The photosynthetic efficiency of the CO₂‐concentrating mechanism in two forms of single‐cell C₄ photosynthesis in the family Chenopodiaceae was characterized. The Bienertioid‐type single‐cell C₄ uses peripheral and central cytoplasmic compartments (Bienertia sinuspersici), while the Borszczowioid single‐cell C₄ uses distal and proximal compartments of the cell (Suaeda aralocaspica). C₄ photosynthesis within a single‐cell raises questions about the efficiency of this type of CO₂‐concentrating mechanism compared with the Kranz‐type. We used measurements of leaf CO₂ isotope exchange (Δ¹³C) to compare the efficiency of the single‐cell and Kranz‐type forms of C₄ photosynthesis under various temperature and light conditions. Comparisons were made between the single‐cell C₄ and a sister Kranz form, S. eltonica[NAD malic enzyme (NAD ME) type], and with Flaveria bidentis[NADP malic enzyme (NADP‐ME) type with Kranz Atriplicoid anatomy]. There were similar levels of Δ¹³C discrimination and CO₂ leakiness (?) in the single‐cell species compared with the Kranz‐type. Increasing leaf temperature (25 to 30 °C) and light intensity caused a decrease in Δ¹³C and ? across all C₄ types. Notably, B. sinuspersici had higher Δ¹³C and ? than S. aralocaspica under lower light. These results demonstrate that rates of photosynthesis and efficiency of the CO₂‐concentrating mechanisms in single‐cell C₄ plants are similar to those in Kranz‐type.     

Differential gene expression analysis of strawberry cultivars that differ in fruit-firmness

Firmness is an important selection criterium in the breeding of fruit, including strawberry ( Fragaria  ×  ananassa Duch.). Clear differences in fruit-firmness are observed between cultivars. In order to identify candidate genes which might be associated with such textural differences, gene expression levels were compared for a soft and a firm cultivar (cv. Gorella and cv. Holiday, respectively). DNA-microarrays representing 1701 strawberry cDNAs were used for simultaneous hybridization of two RNA populations derived from red ripe fruit of both cultivars. In total 61 clones (3.6% of the total cDNAs on the arrays) displayed differential expression, including 10 clones (8 different ones) which showed homology to cell wall related genes in the public databases. The results from the microarray experiments were further confirmed by RNA gel blots, which were also used to examine gene expression in a third cultivar, Elsanta, showing an intermediate texture phenotype (offspring of a cross between Gorella and Holiday). Interestingly, two genes encoding proteins catalysing successive reactions in lignin metabolism (cinnamoyl CoA reductase and cinnamyl alcohol dehydrogenase) showed the highest difference in expression level.     

Variable Myopathic Presentation in a Single Family with Novel Skeletal RYR1 Mutation

We describe an autosomal recessive heterogeneous congenital myopathy in a large consanguineous family. The disease is characterized by variable severity, progressive course in 3 of 4 patients, myopathic face without ophthalmoplegia and proximal muscle weakness. Absence of cores was noted in all patients. Genome wide linkage analysis revealed a single locus on chromosome 19q13 with Zmax = 3.86 at θ = 0.0 and homozygosity of the polymorphic markers at this locus in patients. Direct sequencing of the main candidate gene within the candidate region, RYR1, was performed. A novel homozygous A to G nucleotide substitution (p.Y3016C) within exon 60 of the RYR1 gene was found in patients. ARMS PCR was used to screen for the mutation in all available family members and in an additional 150 healthy individuals. This procedure confirmed sequence analysis and did not reveal the A to G mutation (p.Y3016C) in 300 chromosomes from healthy individuals. Functional analysis on EBV immortalized cell lines showed no effect of the mutation on RyR1 pharmacological activation or the content of intracellular Ca²⁺ stores. Western blot analysis demonstrated a significant reduction of the RyR1 protein in the patient’s muscle concomitant with a reduction of the DHPRα1.1 protein. This novel mutation resulting in RyR1 protein decrease causes heterogeneous clinical presentation, including slow progression course and absence of centrally localized cores on muscle biopsy. We suggest that RYR1 related myopathy should be considered in a wide variety of clinical and pathological presentation in childhood myopathies.     

Epitope mapping of anti‐myelin oligodendrocyte glycoprotein (MOG) antibodies in a mouse model of multiple sclerosis: microwave‐assisted synthesis of the peptide antigens and ELISA screening

The role of pathologic auto‐antibodies against myelin oligodendrocyte glycoprotein (MOG) in multiple sclerosis is a highly controversial matter. As the use of animal models may enable to unravel the molecular mechanisms of the human disorder, numerous studies on multiple sclerosis are carried out using experimental autoimmune encephalomyelitis (EAE). In particular, the most extensively used EAE model is obtained by immunizing C57BL/6 mice with the immunodominant peptide MOG(35–55). In this scenario, we analyzed the anti‐MOG antibody response in this model using the recombinant refolded extracellular domain of the protein, MOG(1–117). To assess the presence of a B‐cell intramolecular epitope spreading mechanism, we tested also five synthetic peptides mapping the 1–117 sequence of MOG, including MOG(35–55). For this purpose, we cloned, expressed in Escherichia coli and on‐column refolded MOG(1–117), and we applied an optimized microwave‐assisted solid‐phase synthetic strategy to obtain the designed peptide sequences. Subsequently, we set up a solid‐phase immunoenzymatic assay testing both naïve and EAE mice sera and using MOG protein and peptides as antigenic probes. The results obtained disclose an intense IgG antibody response against both the recombinant protein and the immunizing peptide, while no response was observed against the other synthetic fragments, thus excluding the presence of an intramolecular epitope spreading mechanism. Furthermore, as the properly refolded recombinant probe is able to bind antibodies with greater efficiency compared with MOG(35–55), we hypothesize the presence of both linear and conformational epitopes on MOG(35–55) sequence. Copyright © 2015 European Peptide Society and John Wiley & Sons, Ltd.     

ABC-type transporters and cuticle assembly: Linking function to polarity in epidermis cells

The aerial organs of plants are covered with a cuticle, a continuous layer overlaying the outermost cell walls of the epidermis. The cuticle is composed of two major classes of the lipid biopolymers: cutin and waxes, collectively termed cuticular lipids. Biosynthesis and transport of cuticular lipids occur predominantly in the epidermis cells. In the transport pathway, cuticular lipids are exported from their site of biosynthesis in the ER/plastid to the extracellular space through the plasma membrane and cell wall. Growing evidence suggests that ATP-binding cassette (ABC) transporters are implicated in transport of cuticular lipids across the plasma membrane of epidermal cells. The Arabidopsis ABC-type transporter protein CER5 (WBC12) was reported to act as a wax monomers transporter. In recent works, our group and others showed that a CER5-related protein, DESPERADO (DSO/WBC11), is required for cutin and wax monomers transport through the plasma membrane of Arabidopsis epidermis cells. Unlike the cer5 mutant, DSO loss-of-function had a profound effect on plant growth and development, particularly dwarfism, postgenital organ fusions, and altered epidermal cell differentiation. The partially overlapping function of CER5 and DSO and the fact that these proteins are half-size ABC transporters suggest that they might form a hetero-dimeric complex while transporting wax components. An intriguing observation was the polar localization of DSO in the distal part of epidermis cells. This polar expression might be explained by DSO localization within lipid rafts, specific plasma membrane microdomains which are associated with polar protein expression. In this review we suggest possible mechanisms for cuticular lipids transport and a link between DSO function and polar expression. Furthermore, we also discuss the subsequent transport of cuticular constituents through the hydrophobic cell wall and the possible involvement of lipid transfer proteins in this process.Key words: ABC transporter, cuticular lipids, polar expression, plasma membrane, epidermis     

The Coordination of C4 Photosynthesis and the CO2-Concentrating Mechanism in Maize and Miscanthus × giganteus in Response to Transient Changes in Light Quality

Unequal absorption of photons between photosystems I and II, and between bundle-sheath and mesophyll cells, are likely to affect the efficiency of the CO₂-concentrating mechanism in C₄ plants. Under steady-state conditions, it is expected that the biochemical distribution of energy (ATP and NADPH) and photosynthetic metabolite concentrations will adjust to maintain the efficiency of C₄ photosynthesis through the coordination of the C₃ (Calvin-Benson-Bassham) and C₄ (CO₂ pump) cycles. However, under transient conditions, changes in light quality will likely alter the coordination of the C₃ and C₄ cycles, influencing rates of CO₂ assimilation and decreasing the efficiency of the CO₂-concentrating mechanism. To test these hypotheses, we measured leaf gas exchange, leaf discrimination, chlorophyll fluorescence, electrochromatic shift, photosynthetic metabolite pools, and chloroplast movement in maize (Zea mays) and Miscanthus × giganteus following transitional changes in light quality. In both species, the rate of net CO₂ assimilation responded quickly to changes in light treatments, with lower rates of net CO₂ assimilation under blue light compared with red, green, and blue light, red light, and green light. Under steady state, the efficiency of CO₂-concentrating mechanisms was similar; however, transient changes affected the coordination of C₃ and C₄ cycles in M. giganteus but to a lesser extent in maize. The species differences in the ability to coordinate the activities of C₃ and C₄ cycles appear to be related to differences in the response of cyclic electron flux around photosystem I and potentially chloroplast rearrangement in response to changes in light quality.The CO₂-concentrating mechanism in C₄ plants reduces the carbon lost through the photorespiratory pathway by limiting the oxygenation of ribulose-1,5-bisphosphate (RuBP) by the enzyme Rubisco (Brown and Smith, 1972; Sage, 1999). Through the compartmentalization of the C₄ cycle in the mesophyll cells and the C₃ cycle in the bundle-sheath cells (Hatch and Slack, 1966), C₄ plants suppress RuBP oxygenation by generating a high CO₂ partial pressure around Rubisco (Furbank and Hatch, 1987). To maintain high photosynthetic rates and efficient light energy utilization, the metabolic flux through the C₃ and C₄ cycles must be coordinated. However, coordination of the C₃ and C₄ cycles is likely disrupted due to rapid changes in environmental conditions, particularly changes in light availability (Evans et al., 2007; Tazoe et al., 2008).Spatial and temporal variations in light environments, including both light quantity and quality, are expected to alter the coordination of the C₃ and C₄ cycles. For example, it has been suggested that the coordination of C₃ and C₄ cycles is altered by changes in light intensity (Henderson et al., 1992; Cousins et al., 2006; Tazoe et al., 2006, 2008; Kromdijk et al., 2008, 2010; Pengelly et al., 2010). However, more recent publications indicate that some of the proposed light sensitivity of the CO₂-concentrating mechanisms in C₄ plants can be attributed to oversimplifications of leaf models of carbon isotope discrimination (Δ13C), in particular, errors in estimates of bundle-sheath CO₂ partial pressure and omissions of respiratory fractionation (Ubierna et al., 2011, 2013). Alternatively, there is little information on the effects of light quality on the coordination of C₃ and C₄ cycle activities and the subsequent impact on net rate of CO₂ assimilation (A_net).In C₃ plants, A_net is reduced under blue light compared with red or green light (Evans and Vogelmann, 2003; Loreto et al., 2009). This was attributed to differences in absorbance and wavelength-dependent differences in light penetration into leaves, where red and green light penetrate farther into leaves compared with blue light (Vogelmann and Evans, 2002; Evans and Vogelmann, 2003). Differences in light quality penetration into a leaf are likely to have profound impacts on C₄ photosynthesis, because the C₄ photosynthetic pathway requires the metabolic coordination of the mesophyll C₄ cycle and the bundle-sheath C₃ cycle. Indeed, Evans et al. (2007) observed a 50% reduction in the rate of CO₂ assimilation in Flaveria bidentis under blue light relative to white light at a light intensity of 350 µmol quanta m⁻² s⁻¹. This was attributed to poor penetration of blue light into the bundle-sheath cells and subsequent insufficient production of ATP in the bundle-sheath cells to match the rates of mesophyll cell CO₂ pumping (Evans et al., 2007). Recently, Sun et al. (2012) observed similar low rates of steady-state CO₂ assimilation under blue light relative to red, green, and blue light (RGB), red light, and green light at a constant light intensity of 900 µmol quanta m⁻² s⁻¹.Because the light penetration into a leaf depends on light quality, with blue light penetrating the least, this potentially results in changes in the energy available for carboxylation reactions in the bundle-sheath (C₃ cycle) and mesophyll (C₄ cycle) cells. Changes in the balance of energy driving the C₃ and C₄ cycles can alter the efficiency of the CO₂-concentrating mechanisms, often represented by leakiness (ϕ), the fraction of CO₂ that is pumped into the bundle-sheath cells that subsequently leaks back out (Evans et al., 2007). Unfortunately, ϕ cannot be measured directly, but it can be estimated through the combined measured and modeled values of Δ13C (Farquhar, 1983). Using measurements of Δ13C, it has been demonstrated that under steady-state conditions, changes in light quality do not affect ϕ (Sun et al., 2012); however, it remains unknown if ϕ is also constant during the transitions between different light qualities. In fact, sudden changes of light quality could temporally alter the coordination of the C₃ and C₄ cycles.To understand the effects of light quality on C₄ photosynthesis and the coordination of the activities of C₃ and C₄ cycles, we measured transitional changes in leaf gas exchange and Δ13C under RGB and broad-spectrum red, green, and blue light in the NADP-malic enzyme C₄ plants maize (Zea mays) and Miscanthus × giganteus. Leaf gas exchange and Δ13C measurements were used to estimate ϕ using the complete model of C₄ leaf Δ13C (Farquhar, 1983; Farquhar and Cernusak, 2012). Additionally, we measured photosynthetic metabolite pools, Rubisco activation state, chloroplast movement, and rates of linear versus cyclic electron flow during rapid transitions from red to blue light and blue to red light. We hypothesized that the limited penetration of blue light into the leaf would result in insufficient production of ATP in the bundle-sheath cells to match the rate of mesophyll cell CO₂ pumping. We predicted that rapid changes in light quality would affect the coordination of the C₃ and C₄ cycles and cause an increase in ϕ, but this would equilibrate as leaf metabolism reached a new steady-state condition.     

Let's connect nature with hypothesis-based experimentation and explore life in context

In a recent paper in Nature, Edith Heard from the European Molecular Biology Laboratory (EMBL) suggested that molecular biologists should ‘reconnect with nature’ by diversifying sampling locations. Although this approach has its own benefits, we suggest that advanced methods should rather be used to take hypothesis-based experiments to nature, thereby supplying a much-needed context for experimentation under controlled conditions. Following the CRISPR (clustered regularly interspaced short palindromic repeats) revolution, this approach has become accessible to many research groups. For the past several years we have developed the groundwork and initiated such experimentation. This included the assembly of a mobile laboratory on a four-wheel drive truck and examining genome-edited metabolic mutants in wild tree tobacco (Nicotiana glauca), grown in nature. Our findings included both targeted answers to focused questions, but also surprising results that could only be reached while working in natural settings.     

Silicon promotes cytokinin biosynthesis and delays senescence in Arabidopsis and Sorghum

Silicate minerals are dominant soil components. Thus, plant roots are constantly exposed to silicic acid. High silicon intake, enabled by root silicon transporters, correlates with increased tolerance to many biotic and abiotic stresses. However, the underlying protection mechanisms are largely unknown. Here, we tested the hypothesis that silicon interacts with the plant hormones, and specifically, that silicic acid intake increases cytokinin biosynthesis. The reaction of sorghum (Sorghum bicolor) and Arabidopsis plants, modified to absorb high versus low amounts of silicon, to dark‐induced senescence was monitored, by quantifying expression levels of genes along the senescence pathway and measuring tissue cytokinin levels. In both species, detached leaves with high silicon content senesced more slowly than leaves that were not exposed to silicic acid. Expression levels of genes along the senescence pathway suggested increased cytokinin biosynthesis with silicon exposure. Mass spectrometry measurements of cytokinin suggested a positive correlation between silicon exposure and active cytokinin concentrations. Our results indicate a similar reaction to silicon treatment in distantly related plants, proposing a general function of silicon as a stress reliever, acting via increased cytokinin biosynthesis.