The complete genome sequence of Fibrobacter succinogenes S85 reveals a cellulolytic and metabolic specialist

Fibrobacter succinogenes is an important member of the rumen microbial community that converts plant biomass into nutrients usable by its host. This bacterium, which is also one of only two cultivated species in its phylum, is an efficient and prolific degrader of cellulose. Specifically, it has a particularly high activity against crystalline cellulose that requires close physical contact with this substrate. However, unlike other known cellulolytic microbes, it does not degrade cellulose using a cellulosome or by producing high extracellular titers of cellulase enzymes. To better understand the biology of F. succinogenes, we sequenced the genome of the type strain S85 to completion. A total of 3,085 open reading frames were predicted from its 3.84 Mbp genome. Analysis of sequences predicted to encode for carbohydrate-degrading enzymes revealed an unusually high number of genes that were classified into 49 different families of glycoside hydrolases, carbohydrate binding modules (CBMs), carbohydrate esterases, and polysaccharide lyases. Of the 31 identified cellulases, none contain CBMs in families 1, 2, and 3, typically associated with crystalline cellulose degradation. Polysaccharide hydrolysis and utilization assays showed that F. succinogenes was able to hydrolyze a number of polysaccharides, but could only utilize the hydrolytic products of cellulose. This suggests that F. succinogenes uses its array of hemicellulose-degrading enzymes to remove hemicelluloses to gain access to cellulose. This is reflected in its genome, as F. succinogenes lacks many of the genes necessary to transport and metabolize the hydrolytic products of non-cellulose polysaccharides. The F. succinogenes genome reveals a bacterium that specializes in cellulose as its sole energy source, and provides insight into a novel strategy for cellulose degradation.     

Complete genome sequence of Thermomonospora curvata type strain (B9)

Thermomonospora curvata Henssen 1957 is the type species of the genus Thermomonospora. This genus is of interest because members of this clade are sources of new antibiotics, enzymes, and products with pharmacological activity. In addition, members of this genus participate in the active degradation of cellulose. This is the first complete genome sequence of a member of the family Thermomonosporaceae. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 5,639,016 bp long genome with its 4,985 protein-coding and 76 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.     

The state of the antioxidant system during therapy of patients with multiple sclerosis

Activity of erythrocyte glutathione peroxidase (GPx), glutathione reductase (GR), glutathione transferase (GT), glucose-6-phosphate dehydrogenase (G6PDH), catalase and superoxide dismutase (SOD), the level of erythrocyte malonic dialdehyde (MDA) and also total antioxidant activity of blood serum were studied in patients with different types of multiple sclerosis (MS). Investigation of peripherical blood was carried out on the first day of admission to the hospital and after the standard therapy with copaxone. During the whole period of observation all MS patients had a high level of MDA and activity of erythrocyte GP compared with a control group. Other erythrocyte antioxidant enzymes and total antioxidant activity of blood serum exhibited weak positive dynamics in patients with relapsing-remitting multiple sclerosis (RRMS). The pathological decrease of antioxidant system activity in patients with secondary progressive multiple sclerosis (SPMS) was more pronounced and remained unchanged after the treatment. This is consistent with a more severe clinical course of this disease.     

Investigations into the processes of sorption and desorption of polypeptide antibiotics on Taunit multiwalled carbon nanotubes

A modern nanomaterial made of Taunit multiwalled carbon nanotubes (MWCNTs) was used for the first time to adsorb and desorb gramicidin S and teicoplanin A2 polypeptide antibiotics. Taunit was found to absorb efficiently antibiotics under particular conditions when MWCNTs were taken in excess at 20°C for 18 h. The desorption efficiency depended on the eluent content and the structure of antibiotics. The teicoplanin A2 antibiotic was eluted with a higher yield because of its higher polarity compared to gramicidin S (86% against 65% of the total Taunit-bound antibiotic).     

Effect of Cytokinin 4-PU-30 on the Lipid Composition of Water Stressed Bean Plants

Fourteen days-old bean plants, grown on sand with Knop's nutrient solution were subjected to water stress (three days without irrigation). The stress led to a decrease in almost all lipid classes except phospholipids in the primary leaves. The content of palmitic acid increased, and that of the linolenic acid decreased. An increase of hexadecenoic acid in phospholipids was also observed. Rewatering for 24 h led to the recovery of the stressed plants including that of the photosynthetic apparatus, but the changes in the lipid composition were insignificant. The spraying of the plants before and after the water stress with 5 × 10-6 M solution of the phenylurea cytokinin 4-PU-30 alleviated negative effect of water stress on the lipid membrane composition permitting the plants to resist the harmful environment. This revised version was published online in July 2006 with corrections to the Cover Date.     

Complete genome sequence of Coraliomargarita akajimensis type strain (04OKA010-24)

Coraliomargarita akajimensis Yoon et al. 2007 is the type species of the genus Coraliomargarita. C. akajimensis is an obligately aerobic, Gram-negative, non-spore-forming, non-motile, spherical bacterium that was isolated from seawater surrounding the hard coral Galaxea fascicularis. C. akajimensis is of special interest because of its phylogenetic position in a genomically under-studied area of the bacterial diversity. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of a member of the family Puniceicoccaceae. The 3,750,771 bp long genome with its 3,137 protein-coding and 55 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.     

Calcium Signaling Controls Pathogenic Th17 Cell-Mediated Inflammation by Regulating Mitochondrial Function

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Complete genome sequence of Ignisphaera aggregans type strain (AQ1.S1)

Ignisphaera aggregans Niederberger et al. 2006 is the type and sole species of genus Ignisphaera. This archaeal species is characterized by a coccoid-shape and is strictly anaerobic, moderately acidophilic, heterotrophic hyperthermophilic and fermentative. The type strain AQ1.S1(T) was isolated from a near neutral, boiling spring in Kuirau Park, Rotorua, New Zealand. This is the first completed genome sequence of the genus Ignisphaera and the fifth genome (fourth type strain) sequence in the family Desulfurococcaceae. The 1,875,953 bp long genome with its 2,009 protein-coding and 52 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.     

Inositol 1,4,5-trisphosphate receptor-isoform diversity in cell death and survival

Cell-death and -survival decisions are critically controlled by intracellular Ca^2 + homeostasis and dynamics at the level of the endoplasmic reticulum (ER). Inositol 1,4,5-trisphosphate (IP₃) receptors (IP₃Rs) play a pivotal role in these processes by mediating Ca^2 + flux from the ER into the cytosol and mitochondria. Hence, it is clear that many pro-survival and pro-death signaling pathways and proteins affect Ca^2 + signaling by directly targeting IP₃R channels, which can happen in an IP₃R-isoform-dependent manner. In this review, we will focus on how the different IP₃R isoforms (IP₃R1, IP₃R2 and IP₃R3) control cell death and survival. First, we will present an overview of the isoform-specific regulation of IP₃Rs by cellular factors like IP₃, Ca^2 +, Ca^2 +-binding proteins, adenosine triphosphate (ATP), thiol modification, phosphorylation and interacting proteins, and of IP₃R-isoform specific expression patterns. Second, we will discuss the role of the ER as a Ca^2 + store in cell death and survival and how IP₃Rs and pro-survival/pro-death proteins can modulate the basal ER Ca^2 + leak. Third, we will review the regulation of the Ca^2 +-flux properties of the IP₃R isoforms by the ER-resident and by the cytoplasmic proteins involved in cell death and survival as well as by redox regulation. Hence, we aim to highlight the specific roles of the various IP₃R isoforms in cell-death and -survival signaling. This article is part of a Special Issue entitled: Calcium signaling in health and disease. Guest Editors: Geert Bultynck, Jacques Haiech, Claus W. Heizmann, Joachim Krebs, and Marc Moreau.