Identification of novel mutations in FFPE lung adenocarcinomas using DEPArray sorting technology and next-generation sequencing

Formalin-fixed paraffin-embedded (FFPE) tissues are utilized as the standard diagnostic method in pathology laboratories. However, admixture of unwanted tissues and shortage of normal samples, which can be used to detect somatic mutation, are considered critical factors to accurately diagnose cancer. To explore these challenges, we sorted the pure tumor cells from 22 FFPE lung adenocarcinoma tissues via Di-Electro-Phoretic Array (DEPArray) technology, a new cell sorting technology, and analyzed the variants with next-generation sequencing (NGS) for the most accurate analysis. The allele frequencies of the all gene mutations were improved by 1.2 times in cells sorted via DEPArray (tumor suppressor genes, 1.3–10.1 times; oncogenes, 1.3–2.6 times). We identified 16 novel mutations using the sequencing from sorted cells via DEPArray technology, compared to detecting 4 novel mutation by the sequencing from unsorted cells. Using this analysis, we also revealed that five genes (TP53, EGFR, PTEN, RB1, KRAS, and CTNNB1) were somatically mutated in multiple homogeneous lung adenocarcinomas. Together, we sorted pure tumor cells from 22 FFPE lung adenocarcinomas by DEPArray technology and identified 16 novel somatic mutations. We also established the precise genomic landscape for more accurate diagnosis in 22 lung adenocarcinomas with mutations detected in pure tumor cells. The results obtained in this study could offer new avenues for the treatment and the diagnosis of squamous cell lung cancers.     

Dependence of root biomass accumulation on the content and metabolism of cytokinins in ethylene-insensitive plants

Diverse functions of ethylene in plants may depend on its ability to interact with other hormones. We studied the participation of ethylene in the regulation of accumulation and metabolism of cytokinins comparing ethylene-insensitive mutant plants of arabidopsis (Arabidopsis thaliana [L.] Heynh., etr1-1) with the plants of original ecotype Columbia (Col-0). Because cytokinins can regulate growth of both leaves and roots, we determined the weights of these organs and the ratio between them. The content of zeatin and its riboside in the roots of etr1-1 plants was two times greater than in Col-0 plants, which could be accounted for by inhibition of conversion of these forms of cytokinins into 9-N-glucosides. In the leaves of mutant plants, expression of IPT3 gene responsible for the synthesis of cytokinins was more intense than in Col-0 plants, which could also contribute to a rise in the content of cytokinins. In this case, the weight of roots in etr1-1 mutants was lower than in the plants of original ecotype. Because high concentrations of cytokinins can inhibit root growth, suppression of accumulation of their biomass in mutant plants may be related to a greater content of cytokinins therein. The obtained results suggest that ethylene can suppress accumulation of cytokinins and, thereby, maintain redistribution of biomass in favor of the roots, which is important for plant adaptation to a shortage of water and ions.     

The accuracy of the rapid equilibrium assumption in steady-state enzyme kinetics in the case of a multipath arbitrary enzyme mechanism with a number of equilibrium segments

A quantitative evaluation of the accuracy of the rapid-equilibrium assumption in steady-state enzyme kinetics was obtained for a multipath arbitrary enzyme mechanism with a number of equilibrium segments. Explicit expressions for estimating the contribution of any equilibrium segment to the accuracy of the rapid-equilibrium assumption were obtained. This allowed us to determine the accuracy of the rapid-equilibrium assumption (Δ) in general: 1 + Δ = (1 + Δ₁)(1 + Δ₂)... (1 + Δ_k), where Δ₁, Δ₂,..., Δ_k is the contribution of each individual equilibrium segment. The accuracy depends only on the structure and properties of equilibrium segments, which have been accounted for in the rapid-equilibrium assumption, but it is independent of the number of paths in the mechanism of the enzymatic reaction and on the structure and properties of the remaining part (steady-state) of the kinetic scheme.     

Effects of nutritional enrichment on the production of acetone-butanol-ethanol (ABE) by Clostridium acetobutylicum

Clostridium acetobutylicum is an industrially important organism that produces acetone-butanol-ethanol (ABE). The main objective of this study was to characterize the effects of increased cell density on the production of ABE during the phase transition from acidogenesis to solventogenesis in C. acetobutylicum. The increased ABE productivity of C. acetobutylicum was obtained by increasing the cell density using a newly designed medium (designated C. a cetobutylicum medium 1; CAM1). The maximum OD₆₀₀ value of C. acetobutylicum ATCC 824 strain obtained with CAM1 was 19.7, which is 1.8 times higher than that obtained with clostridial growth medium (CGM). The overall ABE productivity obtained in the CAM1-fermetation of the ATCC 824 strain was 0.83 g/L/h, which is 1.5 times higher than that (0.55 g/L/h) obtained with CGM. However, the increased productivity obtained with CAM1 did not result in an increase in the final ABE titer, because phase transition occurred at a high titer of acids.     

RNA transcription and translation in sea urchin oocytes and eggs

The steady-state concentrations and absolute rates of synthesis of ribosomal RNA (rRNA) molecules were measured in oocytes, eggs, embryos, and larvae of the Hawaiian sea urchin Tripneustes gratilla. The steady-state concentration per genome of the RNA precursor sequences measured by hybridization to a cloned rDNA fragment was approximately 100- to 300-fold greater in the RNA obtained from oocytes and eggs than in the RNA extracted from embryos and larvae. Since the rate of processing of the rRNA precursor at different stages is not greatly different, the rates of rRNA synthesis must be considerably greater in oocytes than in embryo cells. The absolute rate of RNA synthesis in oocytes and embryos was determined from the incorporation of [³H]guanosine into cellular GTP pools and into both precursor and mature rRNA species. The data indicate an approximately 40-fold higher rate of rRNA synthesis in oocytes than that measured in embryos or previously in larvae (J. Griffith and T. Humphreys, 1979, Biochemistry18, 2178–2185). Together these results indicate that the ribosomal genes are transcribed much more rapidly during sea urchin oogenesis than during embryogenesis or larval stages.     

Altered Species of Mitochondrial Transfer RNA associated with the <Emphasis Type="Italic">mi</Emphasis>-1 Cytoplasmic Mutation in <Emphasis Type="Italic">Neurospora crassa</Emphasis>

THE mi-1 (poky) strain of Neurospora crassa is a relatively stable, respiration-deficient mutant, which exhibits cyto-plasmically-inherited reduction of growth rate and aberrations in the mitochondrial eytochrome system. In young cultures of mi-1, the cells accumulate up to sixteen times the amount of cytochrome c present in wild-type Neurospora and cytochromes b and a are not detectable spectroscopically in these same cells¹. In sexual crosses the mi-1 mutation is transmitted only through the cytoplasm of the protoperithecial parent and the pleiotropic mi-1 phenotype is caused by an alteration in a cytoplasmic gene², presumably in the mitochondrial DNA.     

Comparison of L-lactate dehydrogenases of different origins produced in the cells of yeast <Emphasis Type="Italic">Schizosaccharomyces pombe</Emphasis>

The expression of L-lactate dehydrogenase genes ldh1 (Bos taurus), ldhA (Homo sapiens), ldhA (Rhizopus oryzae), ldh1 (Lactobacillus plantarum), and ldh1 (Lactobacillus pentosus) in the cells of yeast Schizosaccharomyces pombe VKPM U-3106 has been investigated. The catalytic characteristics of the enzymes encoded by these genes have been compared, and the intensity of lactic acid synthesis by the recombinant strains obtained has been evaluated. The enzymatic activity of L-lactate dehydrogenases from L. plantarum and L. pentosus was the highest (approximately 2 to 2.5 times higher than that of the mammalian enzymes), and these enzymes therefore appear to have the highest potential for the development of lactic-acid producing strains of yeast S. pombe.     

Mutation in the Arabidopsis PASTICCINO1 Gene,Which Encodes a New FK506-Binding Protein-Like Protein,Has a Dramatic Effect on Plant Development

The pasticcino (pas) mutants of Arabidopsis thaliana are a new class of plant developmental mutants; members of this class show ectopic cell proliferation in cotyledons, extra layers of cells in the hypocotyl, and an abnormal apical meristem. This phenotype is correlated with both cell division and cell elongation defects. There are three complementation groups of pas mutants (pas1, pas2, and pas3, with, respectively 2, 1, and 4 alleles). Here we describe in more detail the pas1-1 allele, which was obtained by insertional mutagenesis. The PAS1 gene has been cloned and characterized; it encodes an immunophilin-like protein similar to the p59 FK506-binding protein (FKBP52). PAS1 is characterized by an FKBP-like domain and three tetratricopeptide repeat units. Although the presence of immunophilins in plants has already been demonstrated, the pas1-1 mutant represents the first inactivation of an FKBP-like gene in plants. PAS1 expression is altered in pas1 mutants and in the pas2 and pas3 mutants. The expression of the PAS1 gene is increased in the presence of cytokinins, a class of phytohormones originally discovered because of their ability to stimulate cell division. These results are of particular relevance as they show for the first time that an FKBP-like protein plays an important role in the control of plant development.In flowering plants, morphogenesis depends on the control of the pattern and numbers of cell divisions and on the control of cell elongation. Although there are many examples of controlled patterns of cell division, we still know very little about how local patterns of cell division are established and maintained (30). In Arabidopsis thaliana, the roles of cell division control in the development of the embryo, the shoot, and the root have been extensively studied (reviewed in references 29 and 30). In the last few years, much progress has been made in this field by the isolation of mutants in which single-gene mutations affect specific modes of cell division control. Some of the corresponding genes have been cloned from A. thaliana (SHOOT MERISTEMLESS [STM] and SCARECROW [SCR]) maize (KNOTTED1), and petunia (NO APICAL MERISTEM) (reviewed in reference 30). These genes do not seem to specify components of the cell division machinery, but they are thought to act upstream in the control of cell division. The elements at the interface between genes like STM and SCR and cell cycle regulators, such as cyclins and the CDC genes, are still unknown.The growth and differentiation of higher plants is also greatly dependent on environmental stimuli, such as light and temperature, and on endogenous factors, such as phytohormones. Cytokinins (CKs) were originally discovered because of their ability to promote, along with auxins, plant cell division and organogenesis (reviewed in reference 9). Although this discovery initiated a vast amount of fundamental and applied research on the hormonal control of cell proliferation and regeneration, the mechanisms by which auxins and CKs act and interact at the molecular level are unknown. Steroid-like plant growth factors termed brassinosteroids (BR) were first characterized as inducing cell elongation in synergy with auxin, but recently these hormones have also been found to control plant cell divisions and morphogenesis (15; reviewed in reference 11).The genetic and molecular analysis of hormonal mutants is proving to be a powerful tool for unraveling the mode of action of these molecules. In an attempt to understand the mode of action of CKs and their molecular relationships with auxins in promoting plant cell division, we looked for Arabidopsis mutants with phenotypes which were affected by exogenously applied CKs. We have previously reported the isolation of the pasticcino mutants (pas1, pas2, and pas3) which are affected in both embryonic and vegetative development. Their phenotypes are similar to that of wild-type shoots which have been regenerated in vitro from explants, in the presence of an unbalanced auxin/CK ratio in the medium (12).The pas1-1 mutant was isolated from the transfer DNA (T-DNA) mutant collection of INRA-Centre de Versailles (2, 12). Here we describe the cloning of the PAS1 gene from the T-DNA-tagged pas1-1 allele. PAS1 codes for an immunophilin-like protein similar to the FK506-binding proteins (FKBP). We also demonstrate that the PAS1 mRNA steady-state level is increased in the presence of CK and that PAS1 gene expression is affected in the other pas mutants.     

Estimation of coalescence probabilities and population divergence times from SNP data

We present a method called the G(A|B) method for estimating coalescence probabilities within population lineages from genome sequences when one individual is sampled from each population. Population divergence times can be estimated from these coalescence probabilities if additional assumptions about the history of population sizes are made. Our method is based on a method presented by Rasmussen et al. (2014) to test whether an archaic genome is from a population directly ancestral to a present-day population. The G(A|B) method does not require distinguishing ancestral from derived alleles or assumptions about demographic history before population divergence. We discuss the relationship of our method to two similar methods, one introduced by Green et al. (2010) and called the F(A|B) method and the other introduced by Schlebusch et al. (2017) and called the TT method. When our method is applied to individuals from three or more populations, it provides a test of whether the population history is treelike because coalescence probabilities are additive on a tree. We illustrate the use of our method by applying it to three high-coverage archaic genomes, two Neanderthals (Vindija and Altai) and a Denisovan.Subject terms: Rare variants, Evolutionary genetics

One of the goals of population genetics is to estimate the divergence time of isolated populations. We will review several methods that have been proposed and present a new method that is closely related to two existing methods. We will emphasize the assumptions made when using different methods. It will be useful to make the distinction between estimating coalescence probabilities within populations and estimating population divergence times. We will also introduce a test for a treelike population history based on our method.For distantly related populations, the numbers of mutational differences between sequences indicate relative times of divergence. Relative times are converted to absolute times by assuming a mutation rate. This method traces to Zuckerkandl and Pauling (1962, 1965) and has been used and refined extensively. This class of methods estimates genomic divergence times. Using it to estimate population or species divergence times assumes that those times are so large that the difference between them can be ignored.For recently diverged populations, the numbers of mutational differences probably do not provide a reliable estimate of population divergence times both because there may be too few mutations that differentiate populations and because the difference between the genomic and population divergence times may be substantial. To overcome this problem, Green et al. (2010) (in Supplement 14) introduced a method that accounts for the difference between genomic and population divergence. This method was used in later papers from the same group (Meyer et al. 2012; Prüfer et al. 2014, 2017).The Green et al. (2010) method is applicable when one genome is sampled from each of two populations. It depends on the statistic F(A|B), which is the fraction of sites in population A that carry the derived allele when that site is heterozygous in population B. Green et al. (2010) showed by simulation that the expectation of F(A|B) decreases roughly exponentially with the separation time of A and B. The rate of decrease depends on the history of population sizes both in B and in the population ancestral to A and B. Green et al. (2010) estimated population divergence times by interpolating their simulation results.More recently, Schlebusch et al. (2017), in Section 9.1 of their supplementary materials, introduced a similar method, called the TT method. Their method is based on analytic expressions for the configuration probabilities of SNPs that are polymorphic in the two populations. The TT method assumes that ancestral and derived alleles can be distinguished and the population before divergence was of constant size. The TT method is developed and elaborated on by Sjödin et al. (2020).In the present paper, we present a new method that is closely related to the F(A|B) and TT methods. We call it the G(A|B) method to emphasize its similarity to F(A|B). Our method is based on a method presented by Rasmussen et al. (2014) to test whether an ancient DNA sequence is from a population directly ancestral to a present-day population. We will show that our method provides a way to test whether the history of three or more populations is accurately represented by a population tree even if the demographic histories of those populations are not known.     

Manipulation of Guaiacyl and Syringyl Monomer Biosynthesis in an Arabidopsis Cinnamyl Alcohol Dehydrogenase Mutant Results in Atypical Lignin Biosynthesis and Modified Cell Wall Structure

Modifying lignin composition and structure is a key strategy to increase plant cell wall digestibility for biofuel production. Disruption of the genes encoding both cinnamyl alcohol dehydrogenases (CADs), including CADC and CADD, in Arabidopsis thaliana results in the atypical incorporation of hydroxycinnamaldehydes into lignin. Another strategy to change lignin composition is downregulation or overexpression of ferulate 5-hydroxylase (F5H), which results in lignins enriched in guaiacyl or syringyl units, respectively. Here, we combined these approaches to generate plants enriched in coniferaldehyde-derived lignin units or lignins derived primarily from sinapaldehyde. The cadc cadd and ferulic acid hydroxylase1 (fah1) cadc cadd plants are similar in growth to wild-type plants even though their lignin compositions are drastically altered. In contrast, disruption of CAD in the F5H-overexpressing background results in dwarfism. The dwarfed phenotype observed in these plants does not appear to be related to collapsed xylem, a hallmark of many other lignin-deficient dwarf mutants. cadc cadd, fah1 cadc cadd, and cadd F5H-overexpressing plants have increased enzyme-catalyzed cell wall digestibility. Given that these CAD-deficient plants have similar total lignin contents and only differ in the amounts of hydroxycinnamaldehyde monomer incorporation, these results suggest that hydroxycinnamaldehyde content is a more important determinant of digestibility than lignin content.     

Kinetic Characterization of OmcA and MtrC,Terminal Reductases Involved in Respiratory Electron Transfer for Dissimilatory Iron Reduction in Shewanella oneidensis MR-1

We have used scaling kinetics and the concept of kinetic competence to elucidate the role of hemeproteins OmcA and MtrC in iron reduction by Shewanella oneidensis MR-1. Second-order rate constants for OmcA and MtrC were determined by single-turnover experiments. For soluble iron species, a stopped-flow apparatus was used, and for the less reactive iron oxide goethite, a conventional spectrophotometer was used to measure rates. Steady-state experiments were performed to obtain molecular rate constants by quantifying the OmcA and MtrC contents of membrane fractions and whole cells by Western blot analysis. For reduction of soluble iron, rates determined from transient-state experiments were able to account for rates obtained from steady-state experiments. However, this was not true with goethite; rate constants determined from transient-state experiments were 100 to 1,000 times slower than those calculated from steady-state experiments with membrane fractions and whole cells. In contrast, addition of flavins to the goethite experiments resulted in rates that were consistent with both transient- and steady-state experiments. Kinetic simulations of steady-state results with kinetic constants obtained from transient-state experiments supported flavin involvement. Therefore, we show for the first time that OmcA and MtrC are kinetically competent to account for catalysis of soluble iron reduction in whole Shewanella cells but are not responsible for electron transfer via direct contact alone with insoluble iron-containing minerals. This work supports the hypothesis that electron shuttles are important participants in the reduction of solid Fe phases by this organism.Microbial processes play a central role in the cycling of organic and inorganic compounds on Earth. A select number of these compounds are assimilated by organisms and used as building material for the cell. In addition, a large number of organic and inorganic compounds are used as electron donors and acceptors for respiratory metabolism. Iron, one of the most abundant elements in the Earth''s crust, is both assimilated by life and utilized as an electron donor (Fe²⁺) and acceptor (Fe³⁺) in respiratory metabolism. Due to the importance of iron, microorganisms directly impact the fate and transport of iron, and these Fe impacts indirectly influence the (bio)geochemical cycles of many other elements, including the carbon cycle (38). Furthermore, respiratory metabolism evolved in microorganisms prior to the emergence of oxygenic photosynthesis and was very versatile in using a large number of both organic and inorganic terminal electron acceptors (TEAs) (29). Therefore, the use of iron as a TEA predates the use of molecular oxygen among organisms on Earth. When metals are used as the TEA, this process is referred to as dissimilatory metal reduction (DMR) or, in the case of iron, dissimilatory iron reduction (DIR). Interest in microbial DMR has intensified upon discovery of the ability of DMR bacteria to catalyze reactions of environmentally relevant contaminants, including radionuclides such as U(VI) (1, 19, 20, 24, 30, 45, 47).DMR has been extensively studied in the facultative anaerobe Shewanella oneidensis MR-1 due to its respiratory versatility (for a review, see references 22, 23, 39, and 49). This bacterium also has the ability to utilize soluble and insoluble forms of iron and manganese as TEAs (12, 17, 25, 29, 33, 36). Genetic and biochemical studies show that reduction of the soluble TEAs occurs at the cytoplasmic membrane (CM), the location of the proton motive force-generating electron transport. However, in utilization of insoluble oxides, CM-localized electrons need to traverse the periplasm and the outer membrane (OM) to reach the extracellular matrix. Three mechanisms of transfer of OM-localized electrons to metal oxides have been hypothesized: (i) electron transfer through direct contact with the metal oxide, (ii) cyclic reduction/oxidation of electron shuttles, and (iii) solubilization of the metals with chelators, followed by diffusion to and across the OM to the CM. For a review of the proposed mechanisms, see reference 15.While there are very few reports of bacteria producing chelators for DIR (51), there are more data to support the other two mechanisms. For example, using atomic force microscopy (AFM), Lower et al. (26) measured binding between both OM hemeproteins OmcA and MtrC and the iron oxide hematite and reported that OmcA shows a greater affinity toward hematite than does MtrC. These workers suggested that this tight binding is a prerequisite for direct electron transfer. Xiong et al. (55) also showed tight binding between OmcA and hematite by using dynamic light scattering and fluorescence correlation spectroscopy. Previous work in our laboratory (43, 44) demonstrating the rates of metal oxide reduction by membrane fractions from Shewanella also supported a direct-contact mechanism. Direct contact between cellular components and iron oxides is also consistent with the nanowire mechanism proposed by Gorby et al. (14).In support of the electron shuttle hypothesis, two laboratories independently showed that S. oneidensis produces extracellular flavins, which may act as electron-shuttling agents (31, 52). The involvement of flavins as an electron shuttle would explain previous reports that Shewanella secretes a small, quinone-like compound involved in electron transfer (41) and can utilize sterically sequestered iron located in alginate beads (18).While the previous studies described above provide compelling evidence for their respective mechanisms, none of the mechanisms have been subjected to detailed kinetic analysis. Kinetic studies, while not able to prove a mechanism, can be used to eliminate proposed mechanisms if rates of a reaction measured with purified enzymes, as determined in vitro, cannot account for the rates observed in whole cells. We previously described the importance of kinetic studies and how to apply these kinetic studies to DIR (6, 43, 44). Briefly, rate constants are determined by in vitro studies with purified enzymes. The kinetics of the enzyme of interest is then studied in the whole cell (or in subcellular fractions). The rate constants are then compared between these systems to determine whether the rate of the reactions catalyzed by the enzyme can account for the rates observed in the cell.In our previous work, we performed kinetic studies on membrane fractions of S. oneidensis (43, 44). In the present study, this kinetic characterization is extended to purified enzymes and with whole cells for the purpose of determining kinetic competence. While our major focus is on the reduction of insoluble iron forms, for comparative purposes and as a control to validate our studies with the insoluble oxides, our study also includes a kinetic analysis of soluble chelated iron forms. We have focused our kinetic studies on two OM-localized hemeproteins, OmcA and MtrC. Previous genetic knockout studies show the importance of these enzymes in metal oxide reduction as potential terminal metal reductases (2, 35, 37). We describe both transient- and steady-state kinetic analyses. While both hemeproteins have been studied by stopped-flow analysis (48, 53) and by steady-state methods in whole cells (4), no study has yet attempted to infer mechanisms from scale-up kinetic studies (where kinetic constants from transient-state experiments are compared with those obtained from steady-state experiments). Our studies were thus performed at three different kinetic scales: (i) transient-state iron reduction using purified OmcA and MtrC, (ii) steady-state kinetics with purified total membrane (TM) fractions, and (iii) steady-state whole-cell kinetics.     

Oxidative Cleavage of Diverse Ethers by an Extracellular Fungal Peroxygenase

Many litter-decay fungi secrete heme-thiolate peroxygenases that oxidize various organic chemicals, but little is known about the role or mechanism of these enzymes. We found that the extracellular peroxygenase of Agrocybe aegerita catalyzed the H₂O₂-dependent cleavage of environmentally significant ethers, including methyl t-butyl ether, tetrahydrofuran, and 1,4-dioxane. Experiments with tetrahydrofuran showed the reaction was a two-electron oxidation that generated one aldehyde group and one alcohol group, yielding the ring-opened product 4-hydroxybutanal. Investigations with several model substrates provided information about the route for ether cleavage: (a) steady-state kinetics results with methyl 3,4-dimethoxybenzyl ether, which was oxidized to 3,4-dimethoxybenzaldehyde, gave parallel double reciprocal plots suggestive of a ping-pong mechanism (K_m(peroxide), 1.99 ± 0.25 mm; K_m(ether), 1.43 ± 0.23 mm; k_cat, 720 ± 87 s⁻¹), (b) the cleavage of methyl 4-nitrobenzyl ether in the presence of H₂¹⁸O₂ resulted in incorporation of ¹⁸O into the carbonyl group of the resulting 4-nitrobenzaldehyde, and (c) the demethylation of 1-methoxy-4-trideuteromethoxybenzene showed an observed intramolecular deuterium isotope effect [(k_H/k_D)_obs] of 11.9 ± 0.4. These results suggest a hydrogen abstraction and oxygen rebound mechanism that oxidizes ethers to hemiacetals, which subsequently hydrolyze. The peroxygenase appeared to lack activity on macromolecular ethers, but otherwise exhibited a broad substrate range. It may accordingly have a role in the biodegradation of natural and anthropogenic low molecular weight ethers in soils and plant litter.Recently, a new group of extracellular peroxygenases was described in agaric fungi that are ubiquitous biodegraders of lignocellulose in soils and plant litter. These heme-thiolate enzymes catalyze H₂O₂-dependent halogenations and hydroxylations of numerous aromatic substrates, and thus show some functional similarity to heme chloroperoxidase and to cytochromes P450 (P450s),³ which are also heme-thiolate proteins (1–4). However, the best-characterized fungal peroxygenase, from Agrocybe aegerita, exhibits low sequence identity (∼25%) with heme chloroperoxidase and no significant sequence identity with the P450s (5). On the other hand, the absorption spectrum of the native peroxygenase and of its carbon monoxide adduct closely resemble those of P450s (6). So far, little is known about the catalytic cycle of the A. aegerita peroxygenase.The physiological function of these peroxygenases is also unclear, but their extracellular location suggests a role in the biodegradation or detoxification of organic chemicals encountered by the fungi. Ethers stand out as potential substrates for several reasons. First, ether linkages are widespread in soils and litter, not only in abundant natural substances such as lignin, flavonoids, and lignans, but also in anthropogenic compounds that include many solvents, biocides, and surfactants (7–11). Second, an oxidative mechanism is required for the biodegradation of ethers, which are relatively recalcitrant because they do not hydrolyze at physiological pH values (7). Finally, it is already known that functionally similar monooxygenases, including P450s, are capable of ether scission and have a role in the intracellular metabolism of these compounds by some organisms (7, 12–15).Here we show that the extracellular peroxygenase from A. aegerita cleaves many ethers, including some significant environmental pollutants, and we evaluate some limitations on the etherolytic reactions that the enzyme can accomplish. In addition, we report data from stoichiometrical analyses, steady-state kinetics experiments, an H₂¹⁸O₂-labeling study, and intramolecular deuterium isotope effect determinations. These results provide insights into the enzymatic mechanism for ether cleavage.     

Xylem exudate composition and root-to-shoot nickel translocation in Alyssum species

Aims

An improved understanding of the Ni root-to-shoot translocation mechanism in hyperaccumulators is necessary to increase Ni uptake efficiency for phytoextraction technologies. It has been presumed that an important aspect of Ni translocation and storage involves chelation with organic ligands. It has been reported that exposing several Ni hyperaccumulator species of Alyssum to Ni elicited a large increase in the histidine level of the xylem sap. In later studies it was shown that as time progressed the histidine:Ni ratio dropped considerably. Moreover, previous studies analyzed the relationship between Ni and ligands in plants that were exposed to Ni only for a few hours and therefore obtained results that are unlikely to represent field soils where plants are at steady-state Ni uptake. The aim of this study was to understand the quantitative relationship between Ni and organic ligands in the xylem sap of various Alyssum genotypes or species that reached steady-state Ni uptake after being exposed to Ni in either nutrient solution or serpentine soil for up to 6 weeks.

Methods

Total Ni concentration, 17 amino acids, 9 organic acids, and nicotianamine were measured in xylem sap of 100-day old plants of Alyssum.

Results

Results showed that the concentration of Ni in xylem sap of various Alyssum genotypes was 10–100 fold higher than the concentration of histidine, malate, citrate, and nicotianamine, which were the predominant Ni ligands measured in the sap.

Conclusion

When the physiology of the whole plant is taken into account, our results indicate that the concentration of organic chelators is too low to account for the complexation of all the Ni present in the xylem sap of Alyssum at steady-state Ni hyperaccumulation, and suggest that most of the Ni in xylem sap of this species is present as the hydrated cation.