Correction to: Spatiotemporal plant hormone analysis from cryosections using laser microdissection-liquid chromatography-mass spectrometry

Journal of Plant Research - Laser microdissection (LMD) is used for isolating specific regions or single cells from a wide variety of tissue samples under direct microscopic observation. The LMD...     

Visualization of acetaminophen-induced liver injury by time-of-flight secondary ion mass spectrometry

Time-of-flight secondary ion mass spectrometry (MS) provides secondary ion images that reflect distributions of substances with sub-micrometer spatial resolution. To evaluate the use of time-of-flight secondary ion MS to capture subcellular chemical changes in a tissue specimen, we visualized cellular damage showing a three-zone distribution in mouse liver tissue injured by acetaminophen overdose. First, we selected two types of ion peaks related to the hepatocyte nucleus and cytoplasm using control mouse liver. Acetaminophen-overdosed mouse liver was then classified into three areas using the time-of-flight secondary ion MS image of the two types of peaks, which roughly corresponded to established histopathological features. The ion peaks related to the cytoplasm decreased as the injury became more severe, and their origin was assumed to be mostly glycogen based on comparison with periodic acid–Schiff staining images and reference compound spectra. This indicated that the time-of-flight secondary ion MS image of the acetaminophen-overdosed mouse liver represented the chemical changes mainly corresponding to glycogen depletion on a subcellular scale. In addition, this technique also provided information on lipid species related to the injury. These results suggest that time-of-flight secondary ion MS has potential utility in histopathological applications.     

Focus on Metabolism: Glutathionylation and Reduction of Methacrolein in Tomato Plants Account for Its Absorption from the Vapor Phase

A large portion of the volatile organic compounds emitted by plants are oxygenated to yield reactive carbonyl species, which have a big impact on atmospheric chemistry. Deposition to vegetation driven by the absorption of reactive carbonyl species into plants plays a major role in cleansing the atmosphere, but the mechanisms supporting this absorption have been little examined. Here, we performed model experiments using methacrolein (MACR), one of the major reactive carbonyl species formed from isoprene, and tomato (Solanum lycopersicum) plants. Tomato shoots enclosed in a jar with MACR vapor efficiently absorbed MACR. The absorption efficiency was much higher than expected from the gas/liquid partition coefficient of MACR, indicating that MACR was likely metabolized in leaf tissues. Isobutyraldehyde, isobutyl alcohol, and methallyl alcohol (MAA) were detected in the headspace and inside tomato tissues treated with MACR vapor, suggesting that MACR was enzymatically reduced. Glutathione (GSH) conjugates of MACR (MACR-GSH) and MAA (MAA-GSH) were also detected. MACR-GSH was essentially formed through spontaneous conjugation between endogenous GSH and exogenous MACR, and reduction of MACR-GSH to MAA-GSH was likely catalyzed by an NADPH-dependent enzyme in tomato leaves. Glutathionylation was the metabolic pathway most responsible for the absorption of MACR, but when the amount of MACR exceeded the available GSH, MACR that accumulated reduced photosynthetic capacity. In an experiment simulating the natural environment using gas flow, MACR-GSH and MAA-GSH accumulation accounted for 30% to 40% of the MACR supplied. These results suggest that MACR metabolism, especially spontaneous glutathionylation, is an essential factor supporting MACR absorption from the atmosphere by tomato plants.Plants emit vast amounts of volatile organic chemicals (VOCs) into the atmosphere. The annual emission of VOCs other than methane is estimated to be approximately 1,300 Tg of carbon (Goldstein and Galbally, 2007), with approximately 90% originating from biogenic sources, of which one-third (approximately 500 Tg of carbon/year) is isoprene (Guenther et al., 1995). In the atmosphere, VOCs undergo the chemical processes of photolysis and reaction with hydroxyl and nitrate radicals (Atkinson and Arey, 2003). Isoprene, for example, is converted into a series of isomeric hydroxyl-substituted alkyl peroxyl radicals, which are further converted into methyl vinyl ketone (MVK; but-3-en-2-one) and methacrolein (MACR; 2-methylprop-2-enal; Liu et al., 2013). These VOCs and their oxygenated products (oVOCs) are important components for the production of ozone and aerosols, and thus have a big impact on atmospheric chemistry and even on the climate system (Goldstein and Galbally, 2007). VOCs and oVOCs are removed from the atmosphere through oxidation to carbon monoxide or dioxide, dry or wet deposition, or secondary aerosol formation (Goldstein and Galbally, 2007). Among these, deposition to vegetation plays a major role in the removal of VOCs and oVOCs from the atmosphere (Karl et al., 2010).A significant portion of the deposition to vegetation is attributable to the uptake of VOCs and oVOCs by plants, and a field study showed that MVK and MACR were immediately lost once they entered a leaf through stomata (Karl et al., 2010). Under growth conditions where stomatal conductance is high enough, the partitioning of VOCs between air and leaf water phases in equilibrium and the capacity of the plant to metabolize, translocate, and store VOCs determine their uptake rate (Tani et al., 2013). The immediate loss in leaves observed with MVK and MACR is indicative of efficient enzymatic reactions metabolizing them; however, the details of the metabolism of these oVOCs have been little investigated so far.The absorption and metabolism of several VOCs by plants have been reported. Airborne ent-kaurene was absorbed by Arabidopsis (Arabidopsis thaliana), Japanese cypress (Chamaecyparis obtusa), and Japanese cedar (Cryptomeria japonica) plants and converted into GAs (Otsuka et al., 2004). Arabidopsis absorbed (Z)-3-hexenal and converted it into (Z)-3-hexen-1-ol or further into (Z)-3-hexen-1-yl acetate using NADPH and acetyl-CoA, probably inside the plant tissues (Matsui et al., 2012). Nicotiana attenuata plants absorbed dimethyl disulfide formed by rhizobacteria (Meldau et al., 2013). The sulfur atom derived from volatile dimethyl disulfide was assimilated into plant proteins. Karl et al. (2010) assumed that aldehyde dehydrogenase, which is involved in detoxification that limits aldehyde accumulation and oxidative stress (Kirch et al., 2004), is involved in the uptake of oVOCs containing an aldehyde moiety; however, they did not provide direct evidence supporting their assumption.Conjugation of VOCs and oVOCs with sugar or glutathione (GSH) is another way to metabolize them. (Z)-3-Hexen-1-ol in the vapor phase was taken up by tomato (Solanum lycopersicum) plants and converted into its glycoside (Sugimoto et al., 2014). (E)-2-Hexenal reacts with GSH spontaneously and/or via glutathione S-transferase (GST) to form hexanal-GSH, which is subsequently reduced to hexanol-GSH (Davoine et al., 2006), although it is uncertain whether airborne (E)-2-hexenal is converted into its corresponding GSH adduct. Glutathionylation of (E)-2-hexenal is common and has been confirmed in grapevine (Vitis vinifera) and passion fruit (Passiflora edulis; Kobayashi et al., 2011; Fedrizzi et al., 2012). The catabolites formed from the GSH adduct in these crops are precursors for important flavor components.Although it is clear that oVOCs are absorbed by vegetation and that their efficient uptake is probably supported by metabolism in plant tissues, the metabolic fates of oVOCs taken up from the vapor phase into plants have been little studied. Here, we performed a series of model experiments using tomato seedlings and MACR to dissect the fates of oVOCs once they entered into plant tissues. To clearly see absorption of MACR and its fates in plant tissues, a model experiment under enclosed conditions with a high concentration of MACR was first carried out. Subsequently, an airflow system with a realistically low concentration of MACR was used. Tomato plants efficiently absorbed MACR. Reduction of the carbonyl moiety and the double bond conjugated to the carbonyl and conjugation with GSH were the major methods of metabolism of exogenous MACR. The metabolism seemed to be involved in the detoxification of reactive carbonyl species, which, in turn, accounted for the oVOC deposition to vegetation.     

Water exchange in manganese-based water-oxidizing catalysts in photosynthetic systems: From the water-oxidizing complex in photosystem II to nano-sized manganese oxides

The water-oxidizing complex (WOC), also known as the oxygen-evolving complex (OEC), of photosystem II in oxygenic photosynthetic organisms efficiently catalyzes water oxidation. It is, therefore, responsible for the presence of oxygen in the Earth's atmosphere. The WOC is a manganese–calcium (Mn₄CaO₅(H₂O)₄) cluster housed in a protein complex. In this review, we focus on water exchange chemistry of metal hydrates and discuss the mechanisms and factors affecting this chemical process. Further, water exchange rates for both the biological cofactor and synthetic manganese water splitting are discussed. The importance of fully unveiling the water exchange mechanism to understand the chemistry of water oxidation is also emphasized here. This article is part of a Special Issue entitled: Photosynthesis Research for Sustainability: Keys to Produce Clean Energy.     

Ideal Osmotic Spaces for Chlorobionts or Cyanobionts Are Differentially Realized by Lichenized Fungi

Lichens result from symbioses between a fungus and either a green alga or a cyanobacterium. They are known to exhibit extreme desiccation tolerance. We investigated the mechanism that makes photobionts biologically active under severe desiccation using green algal lichens (chlorolichens), cyanobacterial lichens (cyanolichens), a cephalodia-possessing lichen composed of green algal and cyanobacterial parts within the same thallus, a green algal photobiont, an aerial green alga, and a terrestrial cyanobacterium. The photosynthetic response to dehydration by the cyanolichen was almost the same as that of the terrestrial cyanobacterium but was more sensitive than that of the chlorolichen or the chlorobiont. Different responses to dehydration were closely related to cellular osmolarity; osmolarity was comparable between the cyanolichen and a cyanobacterium as well as between a chlorolichen and a green alga. In the cephalodium-possessing lichen, osmolarity and the effect of dehydration on cephalodia were similar to those exhibited by cyanolichens. The green algal part response was similar to those exhibited by chlorolichens. Through the analysis of cellular osmolarity, it was clearly shown that photobionts retain their original properties as free-living organisms even after lichenization.Lichens are ubiquitously found in all terrestrial environments, including those with extreme climates such as Antarctica and deserts; they are pioneer organisms in primary succession (Longton, 1988; Ahmadjian, 1993). Colonization ability is largely owed to lichens’ extreme tolerance for desiccation (Ahmadjian, 1993). Although lichens harbor photosynthetic green algae or cyanobacteria (blue-green algae) within their thalli, they show metabolic activity even when dried at 20°C and under conditions of 54% relative humidity (Cowan et al., 1979). This desiccation tolerance partially results from drought resistance originally exhibited by the photobiont. It is further strengthened by lichen symbiosis (Kosugi et al., 2009). Cyanolichens (symbiosis between a fungus and a cyanobacterium) are desiccation-tolerant organisms that favor humid and shady environments, whereas chlorolichens (symbiosis between a fungus and a green alga) tolerate dry and high-light environments (James and Henssen, 1976; Lange et al., 1988). Chlorolichens can perform photosynthesis when the surrounding humidity is high, but cyanolichens require some water in a liquid state (Lange et al., 1986, 2001; Nash et al., 1990; Ahmadjian, 1993).Most poikilohydric photosynthetic organisms can tolerate rapid drying. Biological activity during desiccation and recovery following drought are scarcely affected by protein synthesis inhibitors (Proctor and Smirnoff, 2000). Moderate drought tolerance is attained by increasing compatible solutes (amino acids, sugars, and sugar alcohols) as protective agents during drought stress (Mazur, 1968; Parker, 1968; Hoekstra et al., 2001). An increase in compatible solutes prevents water loss or increases water uptake from the air when humidity is high (Lange et al., 1988). It has been observed, however, that the intracellular solute concentration is low (corresponding to a sorbitol concentration of approximately 0.22 m) in the desiccation-tolerant terrestrial cyanobacterium Nostoc commune (Satoh et al., 2002; Hirai et al., 2004). N. commune photosynthetic activity is lost when incubated in low sorbitol concentrations (Hirai et al., 2004), whereas a Trebouxia spp. chlorobiont freshly isolated from the desiccation-tolerant chlorolichen Ramalina yasudae remains active under the same conditions (Kosugi et al., 2009).Different solute concentrations in photobionts may dictate habitat preferences for chlorolichens and cyanolichens (James and Henssen, 1976; Lange et al., 1988). One might expect that the ideal cellular osmotic pressure (or cellular solute concentration) of a lichenized fungus is problematic, as both the fungus and the photobiont are closely associated in the thallus (Kranner et al., 2005). Thus, we may be able to further hypothesize that the solute concentration itself in original photobionts determines the nature of desiccation tolerance in chlorolichens and cyanolichens.To better understand symbiosis in lichens, it is important to examine how the cellular osmotic pressures of both symbionts contribute to lichen photosynthesis. In this study, cellular osmotic pressures of lichens and photobionts were determined by assessing water potential. The cephalodia-possessing lichen Stereocaulon sorediiferum was chosen as a desiccation-tolerant model organism because it separately harbors a green alga and a cyanobacterium in different compartments of the lichen body. The green algal photobiont is contained in the stem- and branch-like structures, whereas the cyanobacterial photobiont (cyanobiont) is contained in the organism’s cephalodia. For comparison, several chlorolichens (R. yasudae, Parmotrema tinctorum, and Graphis spp.), cyanolichens (Collema subflaccidum and Peltigera degenii), green algae (Prasiola crispa, Trebouxia spp., and Trentepohlia aurea), and cyanobacteria (N. commune, Scytonema spp., and Stigonema spp.) were also analyzed (Fig. 1). The cyanobiont of C. subflaccidum is closely related to N. commune (Ahmadjian, 1993), and the cyanobiont of S. sorediiferum belongs to the genus Stigonema (Kurina and Vitousek, 1999). Green algal photobionts of R. yasudae and S. sorediiferum are Trebouxia spp. (Bergman and Huss-Danell, 1983). For the measurements of water potential, we had to use specimens larger than 0.1 g dry weight for one measurement. Furthermore, the specimens should cover approximately 70% of the surface area of a sample cup with 4 cm diameter that was equipped in our dewpoint potentiometer. Considering the statistical analyses, we needed large amounts of lichen and algal samples for the measurement of water potential. To conduct this study, we wanted to use free-living green algae and cyanobacteria, not the photobionts isolated from a lichen body. This is because inconsistent results were reported previously for chlorobionts liberated from lichens (Brock, 1975; Lange et al., 1990). Three major photobionts of lichens, Trebouxia, Trentepohlia, and Nostoc spp., were considered for inclusion. Until now, free-living Trebouxia spp. were not observed convincingly in nature. Therefore, cultivated Trebouxia spp. were used. Other green algae and cyanobacteria were chosen from among free-living species that (1) are closely related to some photobionts, (2) form large communities sufficient to cover the required quantity that will not destroy the local ecosystem by our sampling, (3) are easy to remove from other attached algae/microorganisms, and (4) are tolerant to desiccation. P. crispa forms large communities in nature, and the closely related species Prasiola borealis is known to be a photobiont of Mastodia tessellata. Only two freshwater species of genus Prasiola are found in Japan; P. crispa inhabits a limited area of Hokkaido Island, and Prasiola japonica is a rare species. P. crispa harvested in Antarctica and shown to be desiccation tolerant in our previous work (Kosugi et al., 2010b) was used in this study.Open in a separate windowFigure 1.Lichens analyzed in this study. A, Cyanolichen C. subflaccidum on a rock. B, Wet (left) and dry (right) thalli of cyanolichen Peltigera degenii with green moss. C, Chlorolichen R. yasudae on a rock. D, Chlorolichen Graphis spp. on a Zelkova serrata tree trunk. The grayish basal part of Graphis spp. is the site where the photobiont resides, and the dark-colored streaks are the apothecia. E, Chlorolichen Parmotrema tinctorum on a Z. serrata tree trunk. F, Cephalodia-possessing lichen S. sorediiferum. Some cephalodia are indicated by arrows. The stem- and branch-like structures are the green algae-containing compartments.     

Mitochondrial genomic investigation of flatfish monophyly

We present the first study to use whole mitochondrial genome sequences to examine phylogenetic affinities of the flatfishes (Pleuronectiformes). Flatfishes have attracted attention in evolutionary biology since the early history of the field because understanding the evolutionary history and patterns of diversification of the group will shed light on the evolution of novel body plans. Because recent molecular studies based primarily on DNA sequences from nuclear loci have yielded conflicting results, it is important to examine phylogenetic signal in different genomes and genome regions. We aligned and analyzed mitochondrial genome sequences from thirty-nine pleuronectiforms including nine that are newly reported here, and sixty-six non-pleuronectiforms (twenty additional clade L taxa [Carangimorpha or Carangimorpharia] and forty-six secondary outgroup taxa). The analyses yield strong support for clade L and weak support for the monophyly of Pleuronectiformes. The suborder Pleuronectoidei receives moderate support, and as with other molecular studies the putatively basal lineage of Pleuronectiformes, the Psettodoidei is frequently not most closely related to other pleuronectiforms. Within the Pleuronectoidei, the basal lineages in the group are poorly resolved, however several flatfish subclades receive consistent support. The affinities of Lepidoblepharon and Citharoides among pleuronectoids are particularly uncertain with these data.     

Mitogenomic circumscription of a novel percomorph fish clade mainly comprising “Syngnathoidei” (Teleostei)

Percomorpha, comprising about 60% of modern teleost fishes, has been described as the “(unresolved) bush at the top” of the tree, with its intrarelationships still being ambiguous owing to huge diversity (> 15,000 species). Recent molecular phylogenetic studies based on extensive taxon and character sampling, however, have revealed a number of unexpected clades of Percomorpha, and one of which is composed of Syngnathoidei (seahorses, pipefishes, and their relatives) plus several groups distributed across three different orders. To circumscribe the clade more definitely, we sampled several candidate taxa with reference to the previous studies and newly determined whole mitochondrial genome (mitogenome) sequences for 16 percomorph species across syngnathoids, dactylopterids, and their putatively closely-related fishes (Mullidae, Callionymoidei, Malacanthidae). Unambiguously aligned sequences (13,872 bp) from those 16 species plus 78 percomorphs and two outgroups (total 96 species) were subjected to partitioned Bayesian and maximum likelihood analyses. The resulting trees revealed a highly supported clade comprising seven families in Syngnathoidei (Gasterosteiformes), Dactylopteridae (Scorpaeniformes), Mullidae in Percoidei and two families in Callionymoidei (Perciformes). We herein proposed to call this clade “Syngnathiformes” following the latest nuclear DNA studies with some revisions on the included families.