Conversion of guaiacyl to syringyl moieties on the cinnamyl alcohol pathway during the biosynthesis of lignin in angiosperms

Aglycons derived from 4-O-β-D-glucosides of both caffeyl and 5-hydroxyconiferyl alcohols were incorporated into guaiacyl (G) and syringyl (S) units in the lignin of newly formed xylem of several angiosperms. It is likely that these aglycons enter the cinnamyl alcohol pathway as intermediates in the introduction of methoxyl groups onto aromatic rings, and serve as precursors for the biosynthesis of lignin. The S/G ratio in this pathway was coincident with the ratio in the cell wall lignin of each tree. Our results indicate that the cinnamyl alcohol pathway involves the same mechanisms as the cinnamic acid and cinnamyl CoA pathways and they suggest that this novel pathway might be part of a metabolic grid in the biosynthesis of lignin. Received: 8 September 1999 / Accepted: 4 October 1999     

Impact of functionalized coligands on the pharmacokinetics of 99mTcIII '4+1' mixed-ligand complexes conjugated to bombesin

Bombesins (BN) containing ^99mTc ‘4 + 1’ complexes may be useful to detect tumors expressing the gastrin-releasing peptide receptor (GRPR). Derivatives of the formula [^99mTc(NS₃R)(L2-BN_st)] were synthesized, in which Tc(III) is coordinated by an isocyanide L2-BN_st bearing the peptide (BN_st = βAla-βAla-Gln-Trp-Ala-Val-Gly-His-Cha-Nle-NH₂) and a tetradentate chelator NS₃R. NS₃R consists of 2,2′,2″-nitrilotriethanethiol (NS₃) bearing a crown ether (NS₃crown), an aliphatic amine (NS₃en) and a tricarboxylic acid (NS₃(COOH)₃). Non-radioactive Re compounds were prepared and analysed by electrospray ionization mass spectrometry. The structural similarity to the ^99mTc conjugates was demonstrated by their identical HPLC elution profiles. The lipophilicity of [^99mTc(NS₃R)(L2-BN_st)] decreased depending on the coligands NS₃crown (log D_O/W, pH = 7.4, 0.98 ± 0.11), NS₃en (− 0.49 ± 0.07) and NS₃(COOH)₃ (− 2.01 ± 0.09). Biodistribution in normal rats was characterized by an increasing kidney uptake and a decreasing uptake into the liver corresponding to the reduced lipophilicity of the conjugates. The pancreatic uptake expressed by the organ/blood ratio of standardized uptake values at 60 min p.i. in rats was 8.6 ± 1.2 for [^99mTc(NS₃en)(L2-BN_st)] and higher compared to the other conjugates. The pancreas/liver ratio of the SUV at 60 min p.i. in rats was highest for [^99mTc(NS₃(COOH)₃)(L2-BN_st)] at 8.4 ± 1.3. [^99mTc(NS₃en)(L2-BN_st)] was further studied in tumor-bearing mice and its pancreas/blood and pancreas/liver ratios were lower, however the pancreas/kidney ratios were higher in mice compared to rats. The activity uptake of [^99mTc(NS₃en)(L2-BN_st)] into the PC-3 tumor xenografts was low (%ID/g: 0.83 ± 0.18 at 60 min; SUV: 0.21 ± 0.05 at 60 min) but specific.     

From genetic diversity to metabolic unity: studies on the biosynthesis of aurafurones and aurafuron-like structures in myxobacteria and streptomycetes

The myxobacterial polyketide secondary metabolites aurafuron A and B were identified by genome mining in the myxobacterial strain Stigmatella aurantiaca DW4/3-1. The compounds contain an unusual furanone moiety and resemble metabolites isolated from soil-dwelling and marine actinobacteria, a fungus and mollusks. We describe here the cloning and functional analysis of the aurafuron biosynthetic gene cluster, including site-directed mutagenesis and feeding studies using labeled precursors. The polyketide core of the aurafurones is assembled by a modular polyketide synthase (PKS). As with many such systems described from myxobacteria, the aurafuron PKS exhibits a number of unusual features, including the apparent iterative use of a module, redundant modules and domains, a trans acting dehydratase and the absence of a terminal thioesterase domain. Four oxidoreductases are encoded within the gene locus, some of which likely participate in formation of the furanone moiety via a Baeyer-Villiger type oxidation. Indeed, inactivation of a gene encoding a cytochrome P₄₅₀ monooxygenase completely abolished production of both compounds. We also compare the complete gene locus to biosynthetic gene clusters from two Streptomyces sp., which produce close structural analogues of the aurafurones. A portion of the post-PKS biosynthetic machinery is strikingly similar in all three cases, in contrast to the PKS genes, which are highly divergent. Phylogenetic analysis of the ketosynthase domains further indicates that the PKSs have developed independently (polyphyletically) during evolution. These findings point to a currently unknown but important biological function of aurafuron-like compounds for the producing organisms.     

Inhibitory effects of some phenolic compounds on the activities of carbonic anhydrase: from in vivo to ex vivo

Carbonic anhydrase (CA) inhibitors have been used for more than 60 years for therapeutic purposes in many diseases table such as in medications against antiglaucoma and as diuretics. Phenolic compounds are a new class of CA inhibitor. In our study, we tested the effects of arachidonoyl dopamine, 2,4,6-trihydroxybenzaldehyde and 3,4-dihydroxy-5-methoxybenzoic acid on esterase and the CO₂-hydratase activities of CA I and II isozymes purified from in vivo to ex vivo. The K_i values of arachidonoyl dopamine, 2,4,6-trihydroxybenzaldehyde and 3,4-dihydroxy-5-methoxybenzoic acid were 203.80, 1170.00 and 910.00?μM, respectively for hCA I and 75.25, 354.00 and 1510.00?μM, respectively for hCA II. Additionally, IC₅₀ values from in vivo studies were found to be in the range of 173.25–1360.0?μM for CA I and II, respectively, using CO₂-hydratase activity methods. These results demonstrated that phenolic compounds used in in vivo studies could be used in different biomedical applications to inhibit approximately 30% of the CO₂-hydratase activity of the total CA enzyme of rat erythrocytes.     

Shifting the paradigm in Evolve and Resequence studies: From analysis of single nucleotide polymorphisms to selected haplotype blocks

For almost a decade the combination of whole genome sequencing with experimental evolution (Evolve and Resequence, E&R; Turner, Stewart, Fields, Rice, & Tarone, 2011) has been used to study adaptation in outcrossing organisms. However, complications caused by inversions and hitchhiking variants have prevented this powerful approach from living up to its potential. In this issue of Molecular Ecology, Michalak, Kang, Schou, Garner, and Loeschke (2018), provide an important step ahead by using a population of Drosophila melanogaster devoid of segregating inversions to identify the genetic basis of resistance to five environmental stressors. They further address the challenge of hitchhiking variants by reconstructing selected haplotype blocks. While it is apparent that the haplotype block reconstruction needs further refinements, their work underpins the potential of E&R studies in Drosophila to address fundamental questions in evolutionary biology.     

Matching Biochemical Reaction Kinetics to the Timescales of Life: Structural Determinants That Influence the Autodephosphorylation Rate of Response Regulator Proteins

In two-component regulatory systems, covalent phosphorylation typically activates the response regulator signaling protein, and hydrolysis of the phosphoryl group reestablishes the inactive state. Despite highly conserved three-dimensional structures and active-site features, the rates of catalytic autodephosphorylation for different response regulators vary by a factor of almost 10⁶. Previous studies identified two variable active-site residues, corresponding to Escherichia coli CheY residues 59 and 89, that modulate response regulator autodephosphorylation rates about 100-fold. Here, a set of five CheY mutants, which match other “model” response regulators (ArcA, CusR, DctD, FixJ, PhoB, or Spo0F) at variable active-site positions corresponding to CheY residues 14, 59, and 89, were characterized functionally and structurally in an attempt to identify mechanisms that modulate autodephosphorylation rate. As expected, the autodephosphorylation rates of the CheY mutants were reduced 6- to 40-fold relative to wild-type CheY, but all still autodephosphorylated 12- to 80-fold faster than their respective model response regulators. Comparison of X-ray crystal structures of the five CheY mutants (complexed with the phosphoryl group analogue BeF₃⁻) to wild-type CheY or corresponding model response regulator structures gave strong evidence for steric obstruction of the phosphoryl group from the attacking water molecule as one mechanism to enhance phosphoryl group stability. Structural data also suggested that impeding the change of a response regulator from the active to the inactive conformation might retard the autodephosphorylation reaction if the two processes are coupled, and that the residue at position ‘58’ may contribute to rate modulation. A given combination of amino acids at positions ‘14’, ‘59’, and ‘89’ adopted similar conformations regardless of protein context (CheY or model response regulator), suggesting that knowledge of residue identity may be sufficient to predict autodephosphorylation rate, and hence the kinetics of the signaling response, in the response regulator family of proteins.     

A conformational approach to the study of the dynamics of enzyme inhibition: studies on thermolysin

The preferred conformations of β-phenylpropionyl-l-phenylalanine (β-PPP) and $\text{N-}\text{carbobenzoxy-}\text{l}\text{-phenylalanine}$ (Cb_z-Phe), two inhibitors of thermolysin, have been determined by computing potential energy using empirial potential energy functions. Of the 15 to 20 conformations that are favoured for each of these inhibitors only a few have the right conformation to reach the active site of the enzyme. The conformer of β-PPP that initiates binding with the enzyme is different from the bound one, while for Cb_z-Phe the bound and initiating conformers are quite similar. Thus, β-PPP favours the ‘induced fit’ model while Cb_z-Phe follows the ‘lock and key’ model of binding. The inhibitors differ in their alignment at the active site.     

Substrate inhibition in human hydroxysteroid sulfotransferase SULT2A1: studies on the formation of catalytically non-productive enzyme complexes

The cytosolic sulfotransferase hSULT2A1 is the major hydroxysteroid (alcohol) sulfotransferase in human liver, and it catalyzes the 3′-phosphoadenosine-5′-phosphosulfate (PAPS)-dependent sulfation of various endogenous hydroxysteroids as well as many xenobiotics that contain alcohol and phenol functional groups. The hSULT2A1 often displays substrate inhibition, and we have hypothesized that a key element in this response to increasing substrate concentration is the formation of non-productive ternary dead-end enzyme complexes involving the nucleotide product, adenosine 3′,5′-diphosphate (PAP). One of these substrates for hSULT2A1 is dehydroepiandrosterone (DHEA), a major circulating steroid hormone in humans that serves as precursor to both androgens and estrogens. We have utilized DHEA in both initial velocity studies and equilibrium binding experiments in order to evaluate the potential role of ternary complexes in substrate inhibition of the enzyme. Our results indicate that hSULT2A1 forms non-productive ternary complexes that involve either DHEA or dehydroepiandrosterone sulfate, and the formation of these ternary complexes displays negative cooperativity in the binding of DHEA.     

From nature to the laboratory: the impact of founder effects on adaptation

Most founding events entail a reduction in population size, which in turn leads to genetic drift effects that can deplete alleles. Besides reducing neutral genetic variability, founder effects can in principle shift additive genetic variance for phenotypes that underlie fitness. This could then lead to different rates of adaptation among populations that have undergone a population size bottleneck as well as an environmental change, even when these populations have a common evolutionary history. Thus, theory suggests that there should be an association between observable genetic variability for both neutral markers and phenotypes related to fitness. Here, we test this scenario by monitoring the early evolutionary dynamics of six laboratory foundations derived from founders taken from the same source natural population of Drosophila subobscura. Each foundation was in turn three‐fold replicated. During their first few generations, these six foundations showed an abrupt increase in their genetic differentiation, within and between foundations. The eighteen populations that were monitored also differed in their patterns of phenotypic adaptation according to their immediately ancestral founding sample. Differences in early genetic variability and in effective population size were found to predict differences in the rate of adaptation during the first 21 generations of laboratory evolution. We show that evolution in a novel environment is strongly contingent not only on the initial composition of a newly founded population but also on the stochastic changes that occur during the first generations of colonization. Such effects make laboratory populations poor guides to the evolutionary genetic properties of their ancestral wild populations.     

From OCR and ECAR to energy: Perspectives on the design and interpretation of bioenergetics studies

Biological energy transduction underlies all physiological phenomena in cells. The metabolic systems that support energy transduction have been of great interest due to their association with numerous pathologies including diabetes, cancer, rare genetic diseases, and aberrant cell death. Commercially available bioenergetics technologies (e.g., extracellular flux analysis, high-resolution respirometry, fluorescent dye kits, etc.) have made practical assessment of metabolic parameters widely accessible. This has facilitated an explosion in the number of studies exploring, in particular, the biological implications of oxygen consumption rate (OCR) and substrate level phosphorylation via glycolysis (i.e., via extracellular acidification rate (ECAR)). Though these technologies have demonstrated substantial utility and broad applicability to cell biology research, they are also susceptible to historical assumptions, experimental limitations, and other caveats that have led to premature and/or erroneous interpretations. This review enumerates various important considerations for designing and interpreting cellular and mitochondrial bioenergetics experiments, some common challenges and pitfalls in data interpretation, and some potential “next steps” to be taken that can address these highlighted challenges.     

From the hemangioblast to self-tolerance: a series of innovations gained from studies on the avian embryo

During the last decades of the 20th century, studies on the vertebrate hematopoietic and immune systems have largely been performed, on mammalian models. The mouse has been the preferred material for several cogent reasons: (i) numerous well defined genetic strains are available; (ii) this species has been and still is instrumental in the study of gene activity through transgenesis; and (iii) in vitro culture techniques and in vivo assays for blood cells together with a wide array of antibodies and nucleic acid probes have been developed to investigate the cellular interactions occurring during hematopoiesis and immune reactivity. However, important and fundamental notions have emerged from using another higher vertebrate model, the avian embryo. The distinction among small lymphocytes of two populations, the T and B lymphocytes, endowed with different roles in adaptive immunity and dependant on different environments for their specification, has relied on experiments carried out in birds. The avian model has been critical for the analysis of the origin and traffic of hematopoietic precursor cells. It allowed the demonstration that both hematopoietic and angioblastic lineages arise from a common precursor, a cell whose existence had been proposed but never undoubtedly proven, the hemangioblast. Finally a form of thymus-dependant 'dominant' tolerance was demonstrated on the basis of experiments in the avian embryo, which initiated a large current of studies on 'regulatory T-cells'. Work in this model during the last decades has relied strongly on the construction of chimeras between quail and chick embryos that allowed a refined analysis of cell behaviour during embryogenesis. The novel perception of developmental neuropoiesis and immunopoiesis that followed proved to be largely applicable to lower and higher vertebrates, notably mammals.     

From species to communities: the signature of recreational use on a tropical river ecosystem

Disturbance can impact natural communities in multiple ways. However, there has been a tendency to focus on single indicators of change when examining the effects of disturbance. This is problematic as classical diversity measures, such as Shannon and Simpson indices, do not always detect the effects of disturbance. Here, we instead take a multilevel, hierarchical approach, looking for signatures of disturbance in the capacity and diversity of the community, and also in allocation and demography at the population level. Using recreational use as an example of disturbance, and the freshwater streams of Trinidad as a model ecosystem, we repeatedly sampled the fish communities and physical parameters of eight pairs of recreational and nonrecreational sites every 3 months over a 28‐month period. We also chose the Trinidadian guppy (Poecilia reticulata) as the subject of our population‐level analyses. Regression tree analysis, together with analysis of deviance, revealed that community capacity and community species richness were greater at sites with higher levels of recreational use. Interestingly, measures of community diversity that took into account the proportional abundance of each species were not significantly associated with recreational use. Neither did we find any direct association between recreational use and proportion of guppy biomass in the community. However, population‐level differences were detected in the guppy: Sex ratio was significantly more female‐biased at more disturbed sites. Our findings emphasize the importance of considering multiple levels when asking how disturbance impacts a community. We advocate the use of a multilevel approach when monitoring the effects of disturbance, and highlight gaps in our knowledge when it comes to interpreting these effects.     

Caffeine biosynthesis in young leaves of Camellia sinensis: In vitro studies on N-methyltransferase activity involved in the conversion of xanthosine to caffeine

The aim of this study was to investigate the S -adenosylmethionine dependent N -methyltransferase(s) (NMT) associated with the three methylation steps in the caffeine biosynthesis pathway in tea ( Camellia sinensis L.). NMT activity in cell-free preparations from young leaves was purified by anion-exchange and gel-filtration column chromatography. In both systems, a single zone of NMT activity, with broad substrate specificity was detected. The N-3 position of dimethylxanthine and monomethylxanthines was methylated more readily than N-1 while comparatively little substitution occurred at the N-7 locus. When xanthosine was used as a substrate only the N-7 position was methylated. These results indicate that a single NMT may participate in the conversion of xanthosine to caffeine. The apparent M_r of the NMT, estimated by gel filtration chromatography, was 61 000. The substrate specificity of the NMT is compatible with the operation of a xanthosine → 7-methylxanthosine → 7-methylxanthine → theobromine → caffeine pathway as the main biosynthetic route to caffeine in young tea leaves. The data also indicate that the conversion of 7-methylxanthine → paraxanthine → caffeine may function as one of a number of minor pathways that also contribute to the production of caffeine.     

Caffeine biosynthesis in young leaves of Camellia sinensis: In vitro studies on N-methyltransferase activity involved in the conversion of xanthosine to caffeine

The aim of this study was to investigate the S -adenosylmethionine dependent N -methyltransferase(s) (NMT) associated with the three methylation steps in the caffeine biosynthesis pathway in tea ( Camellia sinensis L.). NMT activity in cell-free preparations from young leaves was purified by anion-exchange and gel-filtration column chromatography. In both systems, a single zone of NMT activity, with broad substrate specificity was detected. The N-3 position of dimethylxanthine and monomethylxanthines was methylated more readily than N-1 while comparatively little substitution occurred at the N-7 locus. When xanthosine was used as a substrate only the N-7 position was methylated. These results indicate that a single NMT may participate in the conversion of xanthosine to caffeine. The apparent M_r of the NMT, estimated by gel filtration chromatography, was 61 000. The substrate specificity of the NMT is compatible with the operation of a xanthosine → 7-methylxanthosine → 7-methylxanthine → theobromine → caffeine pathway as the main biosynthetic route to caffeine in young tea leaves. The data also indicate that the conversion of 7-methylxanthine → paraxanthine → caffeine may function as one of a number of minor pathways that also contribute to the production of caffeine.     

Ecophysiological studies on citrate synthase: (II) enzyme regulation of selected crustaceans with regard to life-style and the climatic zone

Citrate synthase is a regulatory enzyme of the energy metabolism pathway controlling the citric acid cycle. It was studied in order to determine modes of enzyme regulation with regard to the life-style of the investigated species. Citrate synthase from crustaceans with different life-styles were compared: the pelagic euphausiids Euphausia superba from the Antarctic and Meganyctiphanes norvegica from the Scandinavian Kattegat and the Mediterranean were compared to the benthic isopods Serolis polita from the Antarctic and Idotea baltica from the Baltic. Citrate synthase was partly purified chromatographically and the influence of adenosine 5′-triphosphate on enzyme activity was examined. Mechanisms of inhibition and inhibitor constants were determined. Two different mechanisms of enzyme regulation by ATP were found. Citrate synthase from isopods was only competitively inhibited, while citrate synthase from euphausiids showed not only competitive inhibition but also activation by low concentrations of ATP. This activation is equivalent to the reversed methanism of uncompetitive inhibition. The ecophysiological relevances of the coupling of these mechanisms are discussed. The degree of competitive inhibition was different in the two groups of investigated crustaceans. Inhibitor constants were similar within the euphausiids but not in isopods, which showed higher or lower inhibition depending on the climatic zone: the colder the ambient temperature the lower the ATP inhibition. A possible mechanism of temperature adaptation through effects of varying inhibition constants is concluded.     

Photosynthesis and phage: early studies on phosphorus metabolism in photosynthetic microorganisms with 32P,and how they led to the serendipic discovery of 32P-decay suicide of bacteriophage

During my PhD thesis research (1946–1949), I explored the effects of light on the uptake of ³²P-labeled inorganic phosphate (P_i) by cells of photosynthetic bacteria and microalgae, and the dynamics of P turnover between low and high molecular weight cell constituents. The results were interpreted as evidence for the conversion of light energy to the chemical energy of phosphorylated compounds. The experimental results also suggested to me that the precursors of the P in DNA bacteriophages of Escherichia coli must be low molecular weight phosphorylated compounds present within the host cells and led to the design of an experiment to determine the conservation of ³²P of an infecting phage particle in its numerous progeny. The experiment envisaged was never conducted because phage labeled with ³²P of high specific activity showed unexpected loss of viability. Thus, by serendipity, ‘suicide’ of phage due to ³²P-β decay was discovered. ³²P-decay ‘suicide’ provided a technique that was useful for analysis of phage genetic structure and replication. This memoir describes the unusual circumstances leading to the decisive role of serendipity in revealing an extraordinary phenomenon. This revised version was published online in June 2006 with corrections to the Cover Date.