A distinct class of GTP-binding proteins mediates chloroplast protein import in Rhodophyta.

Chloroplast protein import is mediated by translocons named TOC and TIC on the outer and inner envelope membranes, respectively. Translocon constituents are conserved among green lineages, including plants and green algae. However, it remains unclear whether Rhodophyta (red algae) share common chloroplast protein import mechanisms with the green lineages. We show that in the rhodophyte Cyanidioschyzon merolae, plastome-encoded Tic20pt localized to the chloroplast envelope and was transiently associated with preproteins during import, suggesting its conserved function as a TIC constituent. Besides plastome-encoded FtsHpt and several chaperones, a class of GTP (guanosine 5'-triphosphate)-binding proteins distinct from the Toc34/159 GTPase family associated transiently with preproteins. This class of proteins resides mainly in the cytosol and shows sequence similarities with Sey1/RHD3, required for endoplasmic reticulum membrane fusion, and with the periplastid-localized import factor PPP1, previously identified in the Apicomplexa and diatoms. These GTP-binding proteins, named plastid targeting factor for protein import 1 (PTF1) to PTF3, may act as plastid targeting factors in Rhodophyta.

Biosynthesis of Sulfur-Containing Small Biomolecules in Plants.

Sulfur is an essential element required for plant growth. It can be found as a thiol group of proteins or non-protein molecules, and as various sulfur-containing small biomolecules, including iron-sulfur (Fe/S) clusters, molybdenum cofactor (Moco), and sulfur-modified nucleotides. Thiol-mediated redox regulation has been well investigated, whereas biosynthesis pathways of the sulfur-containing small biomolecules have not yet been clearly described. In order to understand overall sulfur transfer processes in plant cells, it is important to elucidate the relationships among various sulfur delivery pathways as well as to investigate their interactions. In this review, we summarize the information from recent studies on the biosynthesis pathways of several sulfur-containing small biomolecules and the proteins participating in these processes. In addition, we show characteristic features of gene expression in Arabidopsis at the early stage of sulfate depletion from the medium, and we provide insights into sulfur transfer processes in plant cells.

tRNA Wobble Modification Affects Leaf Cell Development in Arabidopsis thaliana.

The tRNA modification at the wobble position of Lys, Glu and Gln (wobbleU* modification) is responsible for the fine-tuning of protein translation efficiency and translation rate. This modification influences organism function in accordance with growth and environmental changes. However, the effects of wobbleU* modification at the cellular, tissue, or individual level have not yet been elucidated. In this study, we show that sulfur modification of wobbleU* of the tRNAs affects leaf development in Arabidopsis thaliana. The sulfur modification was impaired in the two wobbleU*-modification mutants: the URM1-like protein-defective mutant and the Elongator complex-defective mutants. Analyses of the mutant phenotypes revealed that the deficiency in the wobbleU* modification increased the airspaces in the leaves and the leaf size without affecting the number and the area of palisade mesophyll cells. On the other hand, both mutants exhibited increased number of leaf epidermal pavement cells but with reduced cell size. The deficiency in the wobbleU* modification also delayed the initiation of the endoreduplication processes of mesophyll cells. The phenotype of ASYMMETRIC LEAVES2-defective mutant was enhanced in the Elongator-defective mutants, while it was unchanged in the URM1-like protein-defective mutant. Collectively, the findings of this study suggest that the tRNA wobbleU* modification plays an important role in leaf morphogenesis by balancing the development between epidermal and mesophyll tissues.

Beech Wood Pyrolysis in Polyethylene Melt as a Means of Enhancing Levoglucosan and Methoxyphenol Production.

Recycling wood/plastic composites in municipal and industrial wastes currently represents a challenge which needs to be overcome. In this work, we considered the concept of independent pyrolysis of wood and plastic in wood/plastic mixtures for enabling a versatile catalytic process design which is capable of producing recoverable final products from both components. In order to reveal the influence of plastic on wood pyrolysis, the pyrolysis of beech wood (BW, wood material) in a polyethylene (PE) melt (polyolefin material) was performed at 350 °C. The combined use of thermogravimetric analysis, product recovery studies, in situ radical characterisations, and microscopic analysis revealed the influence of the PE melt on the BW pyrolysis. More specifically, a physical prevention of the intermolecular condensation and hydrogen abstraction from PE pyrolysates in the liquid/solid phase was observed. These interactions enhanced the production of levoglucosan and methoxyphenols by factors of 1.7 and 1.4, respectively, during the BW pyrolysis in the PE melt. Based on these results, we concluded that the observed synergistic effects could potentially control the yield and quality of useful products, as well as the utilisation of mixed wood/plastic wastes, which cannot be effectively recycled otherwise.

Interaction of Quinone-Related Electron Acceptors with Hydropersulfide Na2S2: Evidence for One-Electron Reduction Reaction.

We previously reported that 9,10-phenanthraquinone (9,10-PQ), an atmospheric electron acceptor, undergoes redox cycling with dithiols as electron donors, resulting in the formation of semiquinone radicals and monothiyl radicals; however, monothiols have little reactivity. Because persulfide and polysulfide species are highly reducing, we speculate that 9,10-PQ might undergo one-electron reduction with these reactive sulfides. In the present study, we explored the redox cycling capability of a variety of quinone-related electron acceptors, including 9,10-PQ, during interactions with the hydropersulfide Na2S2 and its related polysulfides. No reaction occurred when 9,10-PQ was incubated with Na2S; however, when 5 µM 9,10-PQ was incubated with either 250 µM Na2S2 or Na2S4, we detected extensive consumption of dissolved oxygen (84 µM). Under these conditions, both the semiquinone radicals of 9,10-PQ and their thiyl radical species were also detected using ESR, suggesting that a redox cycle reaction occurred utilizing one-electron reduction processes. Notably, the perthiyl radicals remained stable even under aerobic conditions. Similar phenomenon has also been observed with other electron acceptors, such as pyrroloquinoline quinone, vitamin K3, and coenzyme Q10. Our experiments with N-methoxycarbonyl penicillamine persulfide (MCPSSH), a precursor for endogenous cysteine persulfide, suggested the possibility of a redox coupling reaction with 9,10-PQ inside cells. Our study indicates that hydropersulfide and its related polysulfides are efficient electron donors that interact with quinones. Redox coupling reactions between quinoid electron acceptors and such highly reactive thiols might occur in biological systems.

A Ycf2-FtsHi Heteromeric AAA-ATPase Complex Is Required for Chloroplast Protein Import.

Chloroplasts import thousands of nucleus-encoded preproteins synthesized in the cytosol through the TOC and TIC translocons on the outer and inner envelope membranes, respectively. Preprotein translocation across the inner membrane requires ATP; however, the import motor has remained unclear. Here, we report that a 2-MD heteromeric AAA-ATPase complex associates with the TIC complex and functions as the import motor, directly interacting with various translocating preproteins. This 2-MD complex consists of a protein encoded by the previously enigmatic chloroplast gene ycf2 and five related nuclear-encoded FtsH-like proteins, namely, FtsHi1, FtsHi2, FtsHi4, FtsHi5, and FtsH12. These components are each essential for plant viability and retain the AAA-type ATPase domain, but only FtsH12 contains the zinc binding active site generally conserved among FtsH-type metalloproteases. Furthermore, even the FtsH12 zinc binding site is dispensable for its essential function. Phylogenetic analyses suggest that all AAA-type members of the Ycf2/FtsHi complex including Ycf2 evolved from the chloroplast-encoded membrane-bound AAA-protease FtsH of the ancestral endosymbiont. The Ycf2/FtsHi complex also contains an NAD-malate dehydrogenase, a proposed key enzyme for ATP production in chloroplasts in darkness or in nonphotosynthetic plastids. These findings advance our understanding of this ATP-driven protein translocation system that is unique to the green lineage of photosynthetic eukaryotes.

Carbocatalytic reductive coupling reactions via electron transfer from graphene to aryldiazonium salt.

A reductive coupling reaction using two-dimensional nanocarbon, i.e., reduced graphene oxide (rGO), as a carbocatalyst and/or a reaction initiator was developed. The radical species on the rGO played an important role in the coupling reaction.

Sulfur Modifications of the Wobble U34 in tRNAs and their Intracellular Localization in Eukaryotic Cells.

The wobble uridine (U34) of transfer RNAs (tRNAs) for two-box codon recognition, i.e., tRNALysUUU, tRNAGluUUC, and tRNAGlnUUG, harbor a sulfur- (thio-) and a methyl-derivative structure at the second and fifth positions of U34, respectively. Both modifications are necessary to construct the proper anticodon loop structure and to enable them to exert their functions in translation. Thio-modification of U34 (s²U34) is found in both cytosolic tRNAs (cy-tRNAs) and mitochondrial tRNAs (mt-tRNAs). Although l-cysteine desulfurase is required in both cases, subsequent sulfur transfer pathways to cy-tRNAs and mt-tRNAs are different due to their distinct intracellular locations. The s²U34 formation in cy-tRNAs involves a sulfur delivery system required for the biosynthesis of iron-sulfur (Fe/S) clusters and certain resultant Fe/S proteins. This review addresses presumed sulfur delivery pathways for the s²U34 formation in distinct intracellular locations, especially that for cy-tRNAs in comparison with that for mt-tRNAs.

NADPH-cytochrome P450 reductase-mediated denitration reaction of 2,4,6-trinitrotoluene to yield nitrite in mammals.

While the biodegradation of 2,4,6-trinitrotoluene (TNT) via the release of nitrite is well established, mechanistic details of the reaction in mammals are unknown. To address this issue, we attempted to identify the enzyme from rat liver responsible for the production of nitrite from TNT. A NADPH-cytochrome P450 reductase (P450R) was isolated and identified from rat liver microsomes as the enzyme responsible for not only the release of nitrite from TNT but also formation of superoxide and 4-hydroxyamino-2,6-dinitrotoluene (4-HADNT) under aerobic conditions. In this context, reactive oxygen species generated during P450R-catalyzed TNT reduction were found to be, at least in part, a mediator for the production of 4-HADNT from TNT via formation of 4-nitroso-2,6-dinitrotoluene. P450R did not catalyze the formation of the hydride-Meisenheimer complex (H(-)-TNT) that is thought to be an intermediate for nitrite release from TNT. Furthermore, in a time-course experiment, 4-HADNT formation reached a plateau level and then declined during the reaction between TNT and P450R with NADPH, while the release of nitrite was subjected to a lag period. Notably, the produced 4-HADNT can react with the parent compound TNT to produce nitrite and dimerized products via formation of a Janovsky complex. Our results demonstrate for the first time that P450R-mediated release of nitrite from TNT results from the process of chemical interaction of TNT and its 4-electron reduction metabolite 4-HADNT.

Arabidopsis molybdopterin biosynthesis protein Cnx5 collaborates with the ubiquitin-like protein Urm11 in the thio-modification of tRNA.

The thio-modification of tRNA that occurs in virtually all organisms affects the accuracy and efficiency of protein translation and is therefore biologically important. However, the molecular mechanism responsible for this tRNA modification in plants is largely unclear. We demonstrate here that Arabidopsis sulfurtransferase Cnx5, a ubiquitin-activating enzyme-like (UBA) protein involved in molybdopterin (MPT) biosynthesis, is strictly required for the thio-modification of cytosolic tRNAs in vivo. A previously uncharacterized ubiquitin-like (Ubl) protein Urm11 is also essential for tRNA thio-modification in Arabidopsis. When expressed in Saccharomyces cerevisiae, Cnx5 and Urm11 can substitute for the corresponding yeast orthologs ScUba4 and ScUrm1, respectively, in the thio-modification of yeast cytosolic tRNAs. However, another Ubl protein, Cnx7 of Arabidopsis, which is involved in MPT biosynthesis in conjunction with Cnx5, cannot replace yeast ScUrm1. Interestingly, the expression of a mutant form of Cnx7 in which the carboxyl-terminal six amino acids are substituted by those of Urm11 can significantly restore the thio-modification of tRNAs in the yeast urm1Δ mutant. These findings suggest that in Arabidopsis the common UBA protein Cnx5 collaborates with two functionally differentiated Ubl proteins, Urm11 and Cnx7, in the thio-modification of tRNA and MPT biosynthesis, respectively. Phylogenetic analysis revealed that although most eukaryotes contained a Cnx5-Urm11 ortholog pair and the tRNA thio-modification some fungi, including S. cerevisiae, had lost the Cnx7 ortholog and the ability to synthesize the molybdenum cofactor.

Arabidopsis cytosolic Nbp35 homodimer can assemble both [2Fe-2S] and [4Fe-4S] clusters in two distinct domains.

Iron-sulfur proteins play physiologically important roles in a variety of metabolic processes in eukaryotes. In plants, iron-sulfur cluster biosynthesis is known to take place both in mitochondria and chloroplasts. However no components that mediate iron-sulfur cluster delivery in the plant cell cytosol have been identified so far. Here we report identification and characterization of a cytosolic Nbp35 homolog named AtNbp35 from Arabidopsis thaliana. AtNbp35-deficient Arabidopsis mutants were seedling lethal. Unlike the previously characterized yeast ScNbp35 which forms a heterotetramer with ScCfd1, AtNbp35 forms a homodimer in the cytosol and can harbor both [4Fe-4S] and [2Fe-2S] clusters on its amino- and carboxyl-terminal domains, respectively. Taken together, our data suggest that Nbp35 plays a pivotal role in iron-sulfur cluster assembly and delivery in the plant cell cytosol as a bifunctional molecular scaffold.

Thio-modification of yeast cytosolic tRNA requires a ubiquitin-related system that resembles bacterial sulfur transfer systems.

The wobble uridine in yeast cytosolic tRNA(Lys2)(UUU) and tRNA(Glu3)(UUC) undergoes a thio-modification at the second position (s(2) modification) and a methoxycarbonylmethyl modification at the fifth position (mcm(5) modification). We previously demonstrated that the cytosolic and mitochondrial iron-sulfur (Fe/S) cluster assembly machineries termed CIA and ISC, including a cysteine desulfurase called Nfs1, were essential for the s(2) modification. However, the cytosolic component that directly participates in this process remains unclear. We found that ubiquitin-like protein Urm1 and ubiquitin-activating enzyme-like protein Uba4, as well as Tuc1 and Tuc2, were strictly required for the s(2) modification. The carboxyl-terminal glycine residue of Urm1 was critical for the s(2) modification, indicating direct involvement of the unique ubiquitin-related system in this process. We also demonstrated that the s(2) and mcm(5) modifications in cytosolic tRNAs influence each other's efficiency. Taken together, our data indicate that the s(2) modification of cytosolic tRNAs is a more complex process that requires additional unidentified components.

An approach to evaluate two-electron reduction of 9,10-phenanthraquinone and redox activity of the hydroquinone associated with oxidative stress.

Quinones are widely used as medicines or redox agents. The chemical properties are based on the reactions against an electron donor. 9,10-Phenanthraquinone (PQ), which is a quinone contaminated in airborne particulate matters, forms redox cycling, not Michael addition, with electron donors. Redox cycling of PQ contributes to its toxicity, following generation of reactive oxygen species (ROS). Detoxification of quinones is generally thought to be two-electron reduction forming hydroquinones. However, a hydroquinone of PQ, 9,10-dihydroxyphenanthrene (PQH(2)), has been never detected itself, because it is quite unstable. In this paper, we succeeded in detecting PQH(2) as its stable derivative, 9,10-diacetoxyphenanthrene (DAP). However, higher concentrations of PQ (>4 microM) form disproportionately with PQH(2), producing the 9,10-phenanthraquinone radical (PQ(-)) which is a one-electron reducing product of PQ. In cellular experiments using DAP as a precursor of PQH(2), it was shown that PQH(2) plays a critical role in the oxidative protein damage and cellular toxicity of PQ, showing that two-electron reduction of PQ can also initiate redox cycling to cause oxidative stress-dependent cytotoxicity.

Superoxide anion radical scavenging activities of herbs and pastures in northern Japan determined using electron spin resonance spectrometry.

Free radicals are not only destructive to the living cells but also reduce the quality of animal products through oxidation. As a result the superoxide anion radical (O2-), one of the most destructive reactive oxygen species, is a matter of concern for the animal scientists as well as feed manufacturers to ensure the quality of product to reach consumers demand. The superoxide anion radical scavenging activities (SOSA) of water and MeOH extracts of 2 herbs and 9 pasture samples collected from lowland and highland swards were determined against a 5,5-dimethyl-1-pyroline-N-oxide-O2-spin adduct based on a hypoxanthine-xanthine oxidase reaction using electron spin resonance spectrometry. Both the water and MeOH extracted SOSA differed among the herbs and pastures. Species and altitudinal variations were observed between extraction methods. The herbs were higher in both water and MeOH extracted SOSA than the pastures except for water extracts of one pasture, white clover (Trifolium repens L.). Among the pastures, quackgrass (Agrophyron repens L.) showed higher SOSA in both the MeOH and water extracts, and timothy (Phleum pretense L.) showed higher MeOH extracted SOSA. It is apparent that the kind and amount of antioxidants differ among herbs and pastures. Animal health and quality of animal products could be improved by adequate selection and combining of herbs and pastures having higher SOSA.

Thio modification of yeast cytosolic tRNA is an iron-sulfur protein-dependent pathway.

Defects in the yeast cysteine desulfurase Nfs1 cause a severe impairment in the 2-thio modification of uridine of mitochondrial tRNAs (mt-tRNAs) and cytosolic tRNAs (cy-tRNAs). Nfs1 can also provide the sulfur atoms of the iron-sulfur (Fe/S) clusters generated by the mitochondrial and cytosolic Fe/S cluster assembly machineries, termed ISC and CIA, respectively. Therefore, a key question remains as to whether the biosynthesis of Fe/S clusters is a prerequisite for the 2-thio modification of the tRNAs in both of the subcellular compartments of yeast cells. To elucidate this question, we asked whether mitochondrial ISC and/or cytosolic CIA components besides Nfs1 were involved in the 2-thio modification of these tRNAs. We demonstrate here that the three CIA components, Cfd1, Nbp35, and Cia1, are required for the 2-thio modification of cy-tRNAs but not of mt-tRNAs. Interestingly, the mitochondrial scaffold proteins Isu1 and Isu2 are required for the 2-thio modification of the cy-tRNAs but not of the mt-tRNAs, while mitochondrial Nfs1 is required for both 2-thio modifications. These results clearly indicate that the 2-thio modification of cy-tRNAs is Fe/S protein dependent and thus requires both CIA and ISC machineries but that of mt-tRNAs is Fe/S cluster independent and does not require key mitochondrial ISC components except for Nfs1.

Gallate, the component of HIF-inducing catechins, inhibits HIF prolyl hydroxylase.

Catechins have recently been reported to increase the cellular content of the hypoxia-inducible factor (HIF)-1alpha within mammalian cells. These catechins have a gallate moiety as a common structure. We now report that n-propyl gallate (nPG) also increases the HIF-1alpha protein in the rat heart-derived H9c2 cells. The increase was dose-dependent and reached a maximum at 2-4h after the addition of nPG to the cells. nPG did not change the HIF-1alpha mRNA level, showing that the increase is a posttranscriptional event. Although nPG did not inhibit the HIF prolyl hydroxylase, gallate, the hydrolysis product of nPG, inhibited the enzyme completely at submillimolar concentrations. Model building studies on the human HIF prolyl hydroxylase 2 showed that the two phenolate oxygen atoms of gallate form a chelate with the active site Fe(2+), while the carboxyl group of gallate forms a strong ionic/hydrogen bonding interaction with Arg383, explaining why nPG, which has an esterified carboxyl group, is unable to inhibit the hydroxylase. Together with the observation that gallate was detected in the H9c2 cells treated with nPG, these results suggest that nPG incorporated into the cells is hydrolyzed and the released gallate inhibits the HIF prolyl hydroxylase, thereby reducing the HIF degradation rate and increasing the HIF-1alpha content.

Role of human mitochondrial Nfs1 in cytosolic iron-sulfur protein biogenesis and iron regulation.

The biogenesis of iron-sulfur (Fe/S) proteins in eukaryotes is a complex process involving more than 20 components. So far, functional investigations have mainly been performed in Saccharomyces cerevisiae. Here, we have analyzed the role of the human cysteine desulfurase Nfs1 (huNfs1), which serves as a sulfur donor in biogenesis. The protein is located predominantly in mitochondria, but small amounts are present in the cytosol/nucleus. huNfs1 was depleted efficiently in HeLa cells by a small interfering RNA (siRNA) approach, resulting in a drastic growth retardation and striking morphological changes of mitochondria. The activities of both mitochondrial and cytosolic Fe/S proteins were strongly impaired, demonstrating that huNfs1 performs an essential function in Fe/S protein biogenesis in human cells. Expression of murine Nfs1 (muNfs1) in huNfs1-depleted cells restored both growth and Fe/S protein activities to wild-type levels, indicating the specificity of the siRNA depletion approach. No complementation of the growth retardation was observed, when muNfs1 was synthesized without its mitochondrial presequence. This extramitochondrial muNfs1 did not support maintenance of Fe/S protein activities, neither in the cytosol nor in mitochondria. In conclusion, our study shows that the essential huNfs1 is required inside mitochondria for efficient maturation of cellular Fe/S proteins. The results have implications for the regulation of iron homeostasis by cytosolic iron regulatory protein 1.

Inhibitory effects of beer on mutation in the Ames test and DNA adduct formation in mouse organs induced by 2-Amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP).

An evaluation of the antigenotoxic potential of beer components against carcinogens contained in the human diet, namely heterocyclic amines (HCAs) including 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP), was determined. The protective mechanism involved was also investigated. Beer samples were found to inhibit the mutagenicity of HCAs in the Ames test. Beer solution, consisting of a freeze-dried and dissolved sample, given as drink-water significantly reduced the formation of PhIP-DNA adducts in mouse colon and lung compared to control mice fed with PhIP in the absence of beer solution. Furthermore, beer solution added in the diet as a food additive mimic significantly reduced the amount of DNA adducts present in the liver and lung of mice fed with PhIP. In an effort to investigate the mechanism responsible for the observed protective effect, the effect of beer solutions on HCA metabolizing enzymes was investigated. Beer solutions inhibited the activity of CYP1A1 and CYP1A2, as determined from deethylation and demethylation assays using 7-ethoxy- and 7-methoxyresolufin, respectively. Considering the overall suppression of PhIP genotoxicity by beer, this study confirmed that beer components can interfere with the enzyme activity involved in the metabolism of HCAs and subsequently suppress the observed genotoxicity. The results of this study showed that beer components act in a protective capacity against the genotoxic effects of heterocyclic amines in vivo.

9,10-Phenanthraquinone in diesel exhaust particles downregulates Cu,Zn-SOD and HO-1 in human pulmonary epithelial cells: intracellular iron scavenger 1,10-phenanthroline affords protection against apoptosis.

9,10-Phenanthraquinone (PQ), a major quinone contained in diesel exhaust particles and atmospheric PM(2.5), undergoes one-electron reduction by flavin enzymes such as NADPH-cytochrome P450 reductase, leading to production of reactive oxygen species in vitro. We have detected an ESR signal for superoxide (O(2)(-)) and hydroxyl radicals ((.)OH) by the spin trap method when PQ was mixed with P450 reductase, NADPH, and iron(III). When we examined the effects of PQ on A549 human pulmonary epithelial cells, PQ induced apoptosis with a LC(50) of approximately 7 microM. Formation of protein carbonyls was also detected in cells after treatment with PQ, suggesting that PQ induces oxidative damage. Iron chelators such as 1,10-phenanthroline (OP), desferrioxamine mesylate, and deferiprone respectively afforded protection against the toxic effects of PQ. Furthermore, treatment of A549 cells with 10-20 microM PQ for 12 h specifically down-regulated protein levels of Cu,Zn-superoxide dismutase (Cu,Zn-SOD) and heme oxygenase-1 (HO-1) by more than 50%. Pretreatment of cells with OP (10 microM) markedly reduced the down-regulation of Cu,Zn-SOD and HO-1 and protein carbonyl formation in response to PQ. The inhibitor of Cu,Zn-SOD, diethyldithiocarbamate, enhanced the toxic effects of 5 microM PQ. The present findings suggest that PQ causes iron-mediated oxidative damage that is exacerbated by the concomitant down-regulation of Cu,Zn-SOD.