VsENBP1 regulates the expression of the early nodulin PsENOD12B

A DNA-binding protein, VsENBP1, previously isolated from Vicia sativa was shown to bind in a sequence-specific manner to the early nodulin ENOD12 gene promoter from Pisum sativum. Here, the functional importance of the VsENBP1 binding sites on the PsENOD12B promoter has been studied in vivo. A promoter-gusA fusion in which a mutation was introduced at the putative target sequence, AATAA, was inactive in nodules of transgenic Vicia hirsuta roots. Gel retardation assays showed that VsENBP1 does not bind to the mutated promoter segment, suggesting that VsENBP1 activates the PsENOD12B expression in nodules through its interaction with its target sequence. In the presence of the 35S enhancer, an ENOD12 promoter-GUS construct gave expression in root vascular tissue in addition to the root nodules. Overexpression of Vsenbp1 in transgenic V. hirsuta roots reduced the leaky expression in root vascular tissue in contrast to nodules in which a small increase in GUS expression was observed. The results indicate that VsENBP1 acts as a repressor of ENOD12 expression in root tissue.     

Classification of fungal and bacterial lytic polysaccharide monooxygenases

Background

Lytic polysaccharide monooxygenases are important enzymes for the decomposition of recalcitrant biological macromolecules such as plant cell wall and chitin polymers. These enzymes were originally designated glycoside hydrolase family 61 and carbohydrate-binding module family 33 but are now classified as auxiliary activities 9, 10 and 11 in the CAZy database. To obtain a systematic analysis of the divergent families of lytic polysaccharide monooxygenases we used Peptide Pattern Recognition to divide 5396 protein sequences resembling enzymes from families AA9 (1828 proteins), AA10 (2799 proteins) and AA11 (769 proteins) into subfamilies.

Results

The results showed that the lytic polysaccharide monooxygenases have two conserved regions identified by conserved peptides specific for each AA family. The peptides were used for in silico PCR discovery of the lytic polysaccharide monooxygenases in 79 fungal and 95 bacterial genomes. The bacterial genomes encoded 0 – 7 AA10s (average 0.6). No AA9 or AA11 were found in the bacteria. The fungal genomes encoded 0 – 40 AA9s (average 7) and 0 – 15 AA11s (average 2) and two of the fungi possessed a gene encoding a putative AA10. The AA9s were mainly found in plant cell wall-degrading asco- and basidiomycetes in agreement with the described role of AA9 enzymes. In contrast, the AA11 proteins were found in 36 of the 39 ascomycetes and in only two of the 32 basidiomycetes and their abundance did not correlate to the degradation of cellulose and hemicellulose.

Conclusions

These results provides an overview of the sequence characteristics and occurrence of the divergent AA9, AA10 and AA11 families and pave the way for systematic investigations of the of lytic polysaccharide monooxygenases and for structure-function studies of these enzymes.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1601-6) contains supplementary material, which is available to authorized users.     

Effects of feeding on metabolism, gas transport, and acid-base balance in the bullfrog Rana catesbeiana

Massive feeding in ectothermic vertebrates causes changes in metabolism and acid-base and respiratory parameters. Most investigations have focused on only one aspect of these complex changes, and different species have been used, making comparison among studies difficult. The purpose of the present study was, therefore, to provide an integrative study of the multiple physiological changes taking place after feeding. Bullfrogs (Rana catesbeiana) partly submerged in water were fed meals (mice or rats) amounting to approximately (1)/(10) of their body weight. Oxygen consumption increased and peaked at a value three times the predigestive level 72-96 h after feeding. Arterial PO(2) decreased slightly during digestion, whereas hemoglobin-bound oxygen saturation was unaffected. Yet, arterial blood oxygen content was pronouncedly elevated because of a 60% increase in hematocrit, which appeared mediated via release of red blood cells from the spleen. Gastric acid secretion was associated with a 60% increase in plasma HCO3(-) concentration ([HCO3(-)]) 48 h after feeding. Arterial pH only increased from 7.86 to 7.94, because the metabolic alkalosis was countered by an increase in PCO(2) from 10.8 to 13.7 mm Hg. Feeding also induced a small intracellular alkalosis in the sartorius muscle. Arterial pH and HCO3(-) returned to control values 96-120 h after feeding. There was no sign of anaerobic energy production during digestion as plasma and tissue lactate levels remained low and intracellular ATP concentration stayed high. However, phosphocreatine was reduced in the sartorius muscle and ventricle 48 h after feeding.     

Metabolic arrest and its regulation in anoxic eel hepatocytes

Some vertebrates depress overall metabolism in an abrupt and reversible fashion when challenged with anoxia, ensuring stabilization of cellular [ATP] and long-term survival, but little is known about the eliciting stimuli (e.g., change in O2, adenylates) and downstream effectors responsible for metabolic arrest. Accordingly, eel (Anguilla anguilla) hepatocytes were treated with inhibitors of putative components of the oxygen/metabolite-sensing pathway(s) and exposed to anoxia (Po2=0 mmHg). Anoxia in untreated cells caused a remarkable 85-fold decrease in ATP production rate, but cellular ATP levels stabilized following an initial steep drop. Reoxygenation of cells after 4 h of anoxia caused a fast metabolization of accumulated lactate and reestablishment of preanoxic ATP levels. Unlike physiological anoxia, pharmacological inhibition of the electron transport chain in the presence of oxygen caused extensive cellular ATP depletion, though no loss in viability. In contrast, cellular lactate (i.e., ATP) production rate was affected similarly by either treatment, suggesting that anaerobic glycolysis is regulated by a stimulus other than oxygen tension per se, whereas the continuous matching of ATP consumption and a rapidly ceasing mitochondrial ATP supply require a physiological relevant change in oxygen tension. Protein kinases, notably kinase C (PKC) and A (PKA), have been proposed as key downstream regulators of stress-induced defense mechanisms, but anoxic cell viability, metabolic rate, and [ATP] were not significantly affected by inhibitors of PKC and PKA. Likewise, inhibition of the upstream PKC-activating enzymes phospholipase C (PLC) and phosphatidylinositol 3-kinase (PI 3-K) had no effect on recorded parameters. Anoxic cell survival in complex organisms may, in vivo, also depend on stress hormones released from distant oxygen-sensing cells. Accordingly, adrenaline elevated anaerobic energy production but, apparently, also elevated ATP consumption because cellular ATP levels during oxygen deprivation were slightly lowered by adrenergic stimulation.