Richard F. Helm

Lignin–feruloyl ester cross-links in grasses. Part 1. Incorporation of feruloyl esters into coniferyl alcohol dehydrogenation polymers

Methyl 5-O-(E)-[γ-13C]feruloyl-α-L-arabinofuranoside (FA-Ara) has been synthesized and incorporated into a synthetic lignin dehydrogenation polymer (DHP) of coniferyl alcohol. Inverse-detected long-range C–H correlation NMR experiments on the DHP lignin gave correlation peaks indicative of the copolymerization of the FA-Ara and coniferyl alcohol into the DHP polymer. The bonding sites and modes, as determined by analysis of the carbonyl region of the long-range C–H correlated 2D NMR experiment, are predictable from free-radical coupling mechanisms. In addition to the abundant 4-O-α′ and 4-O-β′ ether couplings, structures involving the β-position of the feruloyl moiety of FA-Ara in β-ether, phenylcoumaran and pinoresinolide structures were present. The incorporation of feruloyl esters into a lignin DHP results in some structures which would not release ferulic acid by solvolytic schemes currently used for quantitation of ferulic acid in plant materials. Thus the degree to which hydroxycinnamic acids are involved in the lignification of forages may be significantly underestimated.

Auxin and ethylene induce flavonol accumulation through distinct transcriptional networks

Auxin and ethylene are key regulators of plant growth and development, and thus the transcriptional networks that mediate responses to these hormones have been the subject of intense research. This study dissected the hormonal cross talk regulating the synthesis of flavonols and examined their impact on root growth and development. We analyzed the effects of auxin and an ethylene precursor on roots of wild-type and hormone-insensitive Arabidopsis (Arabidopsis thaliana) mutants at the transcript, protein, and metabolite levels at high spatial and temporal resolution. Indole-3-acetic acid (IAA) and 1-aminocyclopropane-1-carboxylic acid (ACC) differentially increased flavonol pathway transcripts and flavonol accumulation, altering the relative abundance of quercetin and kaempferol. The IAA, but not ACC, response is lost in the transport inhibitor response1 (tir1) auxin receptor mutant, while ACC responses, but not IAA responses, are lost in ethylene insensitive2 (ein2) and ethylene resistant1 (etr1) ethylene signaling mutants. A kinetic analysis identified increases in transcripts encoding the transcriptional regulators MYB12, Transparent Testa Glabra1, and Production of Anthocyanin Pigment after hormone treatments, which preceded increases in transcripts encoding flavonoid biosynthetic enzymes. In addition, myb12 mutants were insensitive to the effects of auxin and ethylene on flavonol metabolism. The equivalent phenotypes for transparent testa4 (tt4), which makes no flavonols, and tt7, which makes kaempferol but not quercetin, showed that quercetin derivatives are the inhibitors of basipetal root auxin transport, gravitropism, and elongation growth. Collectively, these experiments demonstrate that auxin and ethylene regulate flavonol biosynthesis through distinct signaling networks involving TIR1 and EIN2/ETR1, respectively, both of which converge on MYB12. This study also provides new evidence that quercetin is the flavonol that modulates basipetal auxin transport.

Active Fe-Containing Superoxide Dismutase and Abundant sodF mRNA in Nostoc commune(Cyanobacteria) after Years of Desiccation

Active Fe-superoxide dismutase (SodF) was the third most abundant soluble protein in cells of Nostoc commune CHEN/1986 after prolonged (13 years) storage in the desiccated state. Upon rehydration, Fe-containing superoxide disumutase (Fe-SOD) was released and the activity was distributed between rehydrating cells and the extracellular fluid. The 21-kDa Fe-SOD polypeptide was purified, the N terminus was sequenced, and the data were used to isolate sodF from the clonal isolate N. commune DRH1. sodF encodes an open reading frame of 200 codons and is expressed as a monocistronic transcript (of approximately 750 bases) from a region of the genome which includes genes involved in nucleic acid synthesis and repair, including dipyrimidine photolyase (phr) and cytidylate monophosphate kinase (panC). sodF mRNA was abundant and stable in cells after long-term desiccation. Upon rehydration of desiccated cells, there was a turnover of sodF mRNA within 15 min and then a rise in the mRNA pool to control levels (quantity of sodF mRNA in cells in late logarithmic phase of growth) over approximately 24 h. The extensive extracellular polysaccharide (glycan) of N. commune DRH1 generated superoxide radicals upon exposure to UV-A or -B irradiation, and these were scavenged by SOD. Despite demonstrated roles for the glycan in the desiccation tolerance of N. commune, it may in fact be a significant source of damaging free radicals in vivo. It is proposed that the high levels of SodF in N. commune, and release of the enzyme from dried cells upon rehydration, counter the effects of oxidative stress imposed by multiple cycles of desiccation and rehydration during UV-A or -B irradiation in situ.

Extracellular polysaccharide of Nostoc commune (Cyanobacteria) inhibits fusion of membrane vesicles during desiccation

Cells of the cyanobacterium Nostoc commune secrete a complex, high molecular weight, extracellular polysaccharide (EPS) which accumulates to more than 60% of the dry weight of colonies. The EPS was purified from the clonal isolate N. commune DRH1. The midpoint of the membrane phase transition (Tm) of desiccated cells of N. commune CHEN was low (Tmdry = 8 °C) and was comparable to the Tm of rehydrated cells((Tm)H20 = 6 °C). The EPS was not responsible for the depression of Tm. However, the EPS, at low concentrations, inhibited specifically the fusion of phosphatidylcholine membrane vesicles when they were dried in vitro at0% relative humidity (−400 MPa). Low concentrations of a trehalose:sucrose mixture, in a molar ratio which corresponded with that present in cells in vivo, together with small amounts of the EPS, were efficient in preventing leakage of carboxyfloroscein (CF) from membrane vesicles. Freeze-fracture electron microscopy resolved complex changes in the structure of the EPS and the outer membrane in response to rehydration of desiccated cells. The capacity of the EPS to prevent membrane fusion, the maintenance of a low Tmdry in desiccated cells, and the changes in rheological properties of the EPS in response to water availability, constitute what are likely important mechanisms for desiccation tolerance in this cyanobacterium.

Structural Characterization of the Released Polysaccharide of Desiccation-Tolerant Nostoc commune DRH-1

The structure of the viscous extracellular polysaccharide (glycan) of desiccation-tolerant Nostoc commune DRH-1 was determined through chromatographic and spectroscopic methods. The polysaccharide is novel in that it possesses a 1-4-linked xylogalactoglucan backbone with D-ribofuranose and 3-O-[(R)-1-carboxyethyl]-D-glucuronic acid (nosturonic acid) pendant groups. The presence of D-ribose and nosturonic acid as peripheral groups is unusual, and their potential roles in modulating the rheological properties of the glycan are discussed. Nosturonic acid was present in the glycans of N. commune from diverse geographic locations, suggesting that this uronic acid is an integral component of this cosmopolitan anhydrophile.

The effect of overliming on the toxicity of dilute acid pretreated lignocellulosics: the role of inorganics, uronic acids and ether-soluble organics.

Although the treatment of dilute acid pretreated lignocellulosics with calcium hydroxide or carbonate (overliming) is known to improve the fermentability of carbohydrate-rich hydrolyzate streams, a firm understanding of the chemistry behind the process is lacking. Quantitative evaluation of inorganics, uronic acids, and non-polar organics indicates that only a portion of the improvement can be ascribed to these materials. Upon overliming the concentrations of inorganics either increase (Ca, Mg), decrease (Fe, P, Zn, K) or remain relatively the same (Al, Na). Furthermore, organic compounds that are not extractable with tert-butyl methyl ether (MTBE) are toxic to Zymomonas mobilis CP4(pZB5). Overliming and direct neutralization are somewhat effective in removing sulfate anions, although sulfate toxicity is considerably less than that of acetic acid. Uronic acids were found to be non-toxic under pH controlled conditions.

Identification of inhibitory components toxic toward Zymomonas mobilis CP4(pZB5) xylose fermentation

Zymomonas mobilis CP4(pZB5) is a recombinant bacterium that can produce ethanol from both xylose and glucose. The ethanol-producing efficiency of this organism is substantially impeded by toxic substances present in pretreated hydrolyzates or solid biomass substrates. Acetic acid and furfural (a pentose degradation product) are highly toxic to this organism at levels envisioned for a pretreated-hardwood liquid hydrolyzate. In addition, lignin degradation products and 5-hydroxymethylfurfural (a hexose degradation product) have a moderately toxic effect on the organism. Of the compounds studied, organic acids and aldehydes were found to be more inhibitory than lignin acids or the one alkaloid studied. Acetone:water and methanol extracts of solid biomass samples from red oak, white oak, and yellow poplar are toxic toZymomonas cell growth and ethanol production, with the extracts from white oak being the most toxic.

Transcriptional Response of Saccharomyces cerevisiae to Desiccation and Rehydration

ABSTRACT A transcriptional analysis of the response of Saccharomyces cerevisiae strain BY4743 to controlled air-drying (desiccation) and subsequent rehydration under minimal glucose conditions was performed. Expression of genes involved in fatty acid oxidation and the glyoxylate cycle was observed to increase during drying and remained in this state during the rehydration phase. When the BY4743 expression profile for the dried sample was compared to that of a commercially prepared dry active yeast, strikingly similar expression changes were observed. The fact that these two samples, dried by different means, possessed very similar transcriptional profiles supports the hypothesis that the response to desiccation is a coordinated event independent of the particular conditions involved in water removal. Similarities between “stationary-phase-essential genes” and those upregulated during desiccation were also noted, suggesting commonalities in different routes to reduced metabolic states. Trends in extracellular and intracellular glucose and trehalose levels suggested that the cells were in a “holding pattern” during the rehydration phase, a concept that was reinforced by cell cycle analyses. Application of a “redescription mining” algorithm suggested that sulfur metabolism is important for cell survival during desiccation and rehydration.

Engineering desiccation tolerance in Escherichia coli.

ABSTRACT Recombinant sucrose-6-phosphate synthase (SpsA) was synthesized inEscherichia coli BL21DE3 by using the spsA gene of the cyanobacterium Synechocystis sp. strain PCC 6803. Transformants exhibited a 10,000-fold increase in survival compared to wild-type cells following either freeze-drying, air drying, or desiccation over phosphorus pentoxide. The phase transition temperatures and vibration frequencies (PO stretch) in phospholipids suggested that sucrose maintained membrane fluidity during cell dehydration.

Desiccation tolerance of prokaryotes: application of principles to human cells.

Abstract The loss of water from cells is a stress that was likely imposed very early in evolution. An understanding of the sensitivity or tolerance of cells to depletion of intracellular water is relevant to the study of quiescence, longevity and aging, because one consequence of air-drying is full metabolic arrest, sometimes for extended periods. When considering the adaptation of cells to physiological extremes of pH, temperature or pressure, it is generally assumed that evolution is driven toward optimum function rather than maximum stability. However, adaptation to desiccation has the singular and crucial distinction that dried cells do not grow, and the time the cell is dried may represent the greater part of the life (the time the cell remains viable) of that cell and its component macromolecules. Is a consideration of “function” relevant in the context of desiccated cells? The response of prokaryotic cells to desiccation, and the mechanisms they employ to tolerate this stress at the level of the cell, genome and proteome are considered. Fundamental principles were then implemented in the design of strategies to achieve air-dry stabilization of sensitive eukaryotic (human) cells. The responses of the transcriptomes and proteomes of prokaryotic cells and eukaryotic cells (yeast and human) to drying in air are compared and contrasted to achieve an evolutionary context. The concept of the “desiccome” is developed to question whether there is common set of structural, physiological and molecular mechanisms that constitute desiccation tolerance.