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Phylogenomic and comparative analysis of the distribution and regulatory patterns of TPP riboswitches in fungi.
Mukherjee, S, Retwitzer, MD, Barash, D, Sengupta, S
Scientific reports. 2018;(1):5563
Abstract
Riboswitches are metabolite or ion sensing cis-regulatory elements that regulate the expression of the associated genes involved in biosynthesis or transport of the corresponding metabolite. Among the nearly 40 different classes of riboswitches discovered in bacteria so far, only the TPP riboswitch has also been found in algae, plants, and in fungi where their presence has been experimentally validated in a few instances. We analyzed all the available complete fungal and related genomes and identified TPP riboswitch-based regulation systems in 138 fungi and 15 oomycetes. We find that TPP riboswitches are most abundant in Ascomycota and Basidiomycota where they regulate TPP biosynthesis and/or transporter genes. Many of these transporter genes were found to contain conserved domains consistent with nucleoside, urea and amino acid transporter gene families. The genomic location of TPP riboswitches when correlated with the intron structure of the regulated genes enabled prediction of the precise regulation mechanism employed by each riboswitch. Our comprehensive analysis of TPP riboswitches in fungi provides insights about the phylogenomic distribution, regulatory patterns and functioning mechanisms of TPP riboswitches across diverse fungal species and provides a useful resource that will enhance the understanding of RNA-based gene regulation in eukaryotes.
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2.
Comparison of the potency of a variety of β-glucans to induce cytokine production in human whole blood.
Noss, I, Doekes, G, Thorne, PS, Heederik, DJ, Wouters, IM
Innate immunity. 2013;(1):10-9
Abstract
β-Glucans are components of fungal cell walls and potent stimulants of innate immunity. The majority of research on biological activities of glucans has focused on β-(1→3)-glucans, which have been implicated in relation to fungal exposure-associated respiratory symptoms and as important stimulatory agents in anti-fungal immune responses. Fungi-and bacteria and plants-produce a wide variety of glucans with vast differences in the proportion and arrangement of their β-(1→3)-, -(1→4)- and -(1→6)-glycosidic linkages. Thus far, the pro-inflammatory potential of different β-glucans has not been studied within the same experimental model. Therefore, we compared the potency of 13 different glucan preparations to induce in vitro production of IL-1β, IL-6, IL-8 and TNF-α in human, whole blood cultures. The strongest inducers of all cytokines were pustulan [β-(1→6)-glucan], lichenan [β-(1→3)-(1→4)-glucan], xyloglucan [β-(1→4)-glucan] and pullulan [α-(1→4)-(1→6)-glucan]. Moderate-to-strong cytokine production was observed for curdlan [β-(1→3)-glucan], baker's yeast glucan [β-(1→3)-(1→6)-glucan] and barley glucan [β-(1→3)-(1→4)-glucan], while all other glucan preparations induced very low, or no, detectable levels of cytokines. We therefore conclude that innate immunity reactions are not exclusively induced by β-(1→3)-glucans, but also by β-(1→6)- and β-(1→4)-structures. Thus, not only β-(1→3)-glucan, but also other β-glucans and particularly β-(1→6)-glucans should be considered in future research.
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3.
Influence of bulking agents and microbial activator on thermophilic aerobic transformation of sewage sludge.
Pasda, N, Limtong, P, Oliver, R, Montange, D, Panichsakpatana, S
Environmental technology. 2005;(10):1127-35
Abstract
Bangkok, while improving the wastewater treatment in order to alleviate the river pollution, faces important amounts of sewage sludge. The sewage sludge contains organic matter, nitrogen and phosphorus available for plant growth. However, it may contain pathogenic microorganisms. To be used for agricultural purposes, these pathogens should be destroyed, which can be achieved with the thermophilic phase of composting. As the sewage sludge is dense and unable to compost alone (low C/N ratio), it should be mixed with an organic by-product. Two by-products available in large quantities in Thailand (wood chips and rice husk) have been tested for mixture with sewage sludge. As these products are not easy to decompose (presence of silica in rice husk and lignin/tannins in wood chips), the addition of a microbial activator for composting has been tested in controlled conditions (small quantities of organic mixtures, 55 degrees C, moisture maintained at 60-70% of water holding capacity). The monitoring of the decomposition has been made by measuring the carbon dioxide respiration, pH, organic matter and nitrogen contents and the evolution of enzymatic activities. When mixed with sewage sludge, wood chips and rice husk do not show significant differences concerning decomposition after 63 days. The use of an activator within the experimental conditions does not improve the decomposition of organic matter contained in the mixture of sewage sludge and rice husk or wood chips.
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4.
The arbuscular mycorrhizal fungus Glomus mosseae induces growth and metal accumulation changes in Cannabis sativa L.
Citterio, S, Prato, N, Fumagalli, P, Aina, R, Massa, N, Santagostino, A, Sgorbati, S, Berta, G
Chemosphere. 2005;(1):21-9
Abstract
The effect of arbuscular mycorrhiza on heavy metal uptake and translocation was investigated in Cannabis sativa. Hemp was grown in the presence and absence of 100 microg g-1 Cd and Ni and 300 microg g-1 Cr(VI), and inoculated or not with the arbuscular mycorrhizal fungus Glomus mosseae. In our experimental condition, hemp growth was reduced in inoculated plants and the reduction was related to the degree of mycorrhization. The percentage of mycorrhizal colonisation was 42% and 9% in plants grown in non-contaminated and contaminated soil, suggesting a significant negative effect of high metal concentrations on plant infection by G. mosseae. Soil pH, metal bioavailability and plant metal uptake were not influenced by mycorrhization. The organ metal concentrations were not statistically different between inoculated and non-inoculated plants, apart from Ni which concentration was significantly higher in stem and leaf of inoculated plants grown in contaminated soil. The distribution of absorbed metals inside plant was related to the soil heavy metal concentrations: in plant grown in non-contaminated soil the greater part of absorbed Cr and Ni was found in shoots and no significant difference was determined between inoculated and non-inoculated plants. On the contrary, plants grown in artificially contaminated soil accumulated most metal in root organ. In this soil, mycorrhization significantly enhanced the translocation of all the three metals from root to shoot. The possibility to increase metal accumulation in shoot is very interesting for phytoextraction purpose, since most high producing biomass plants, such as non-mycorrhized hemp, retain most heavy metals in roots, limiting their application.
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5.
XIP-I, a xylanase inhibitor protein from wheat: a novel protein function.
Juge, N, Payan, F, Williamson, G
Biochimica et biophysica acta. 2004;(2):203-11
Abstract
Endo-(1,4)-beta-xylanases of plant and fungal origin play an important role in the degradation of arabinoxylans. Two distinct classes of proteinaceous endoxylanase inhibitors, the Triticum aestivum xylanase inhibitor (TAXI) and the xylanase inhibitor protein (XIP), have been identified in cereals. Engineering of proteins in conjunction with enzyme kinetics, thermodynamic, real-time interaction, and X-ray crystallographic studies has provided knowledge on the mechanism of inhibition of XIP-I towards endoxylanases. XIP-I is a 30 kDa protein which belongs to glycoside hydrolase family 18, and folds as a typical (beta/alpha)8 barrel. Although the inhibitor shows highest homology with plant chitinases, XIP-I does not hydrolyse chitin; probably due to structural differences in the XIP-I binding cleft. The inhibitor is specific for fungal xylanases from glycoside hydrolases families 10 and 11, but does not inhibit bacterial enzymes. The inhibition is competitive and, depending on the xylanase, the Ki value can be as low as 3.4 nM. Site-directed mutagenesis of a xylanase from Aspergillus niger suggested that the XIP-I binding site was the conserved hairpin loop "thumb" region of family 11 xylanases. Furthermore, XIP-I shows the ability to inhibit barley alpha-amylases of glycoside hydrolase family 13, providing the first example of a protein able to inhibit members of different glycoside hydrolase families (10, 11, and 13), and additionally a novel function for a protein of glycoside hydrolase family 18.
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6.
Arbuscular mycorrhizal symbiosis regulates plasma membrane H+-ATPase gene expression in tomato plants.
Ferrol, N, Pozo, MJ, Antelo, M, Azcón-Aguilar, C
Journal of experimental botany. 2002;(374):1683-7
Abstract
Regulation by arbuscular mycorrhizal symbiosis of three tomato plasma membrane H+-ATPase genes (LHA1, LHA2 and LHA4) has been analysed in wild-type and mycorrhiza-defective tomato plants. Expression of these genes was differentially regulated in leaves and roots of both tomato phenotypes after inoculation with Glomus mosseae.