Domain Analysis of a Modular α-l-Arabinofuranosidase with a Unique Carbohydrate Binding Strategy from the Fiber-Degrading Bacterium Fibrobacter succinogenes S85

Family 43 glycoside hydrolases (GH43s) are known to exhibit various activities involved in hemicellulose hydrolysis. Thus, these enzymes contribute to efficient plant cell wall degradation, a topic of much interest for biofuel production. In this study, we characterized a unique GH43 protein from Fibrobacter succinogenes S85. The recombinant protein showed α-l-arabinofuranosidase activity, specifically with arabinoxylan. The enzyme is, therefore, an arabinoxylan arabinofuranohydrolase (AXH). The F. succinogenes AXH (FSUAXH1) is a modular protein that is composed of a signal peptide, a GH43 catalytic module, a unique β-sandwich module (XX domain), a family 6 carbohydrate-binding module (CBM6), and F. succinogenes-specific paralogous module 1 (FPm-1). Truncational analysis and site-directed mutagenesis of the protein revealed that the GH43 domain/XX domain constitute a new form of carbohydrate-binding module and that residue Y484 in the XX domain is essential for binding to arabinoxylan, although protein structural analyses may be required to confirm some of the observations. Kinetic studies demonstrated that the Y484A mutation leads to a higher k_cat for a truncated derivative of FSUAXH1 composed of only the GH43 catalytic module and the XX domain. However, an increase in the K_m for arabinoxylan led to a 3-fold decrease in catalytic efficiency. Based on the knowledge that most XX domains are found only in GH43 proteins, the evolutionary relationships within the GH43 family were investigated. These analyses showed that in GH43 members with a XX domain, the two modules have coevolved and that the length of a loop within the XX domain may serve as an important determinant of substrate specificity.The plant cell wall is composed of a variety of polysaccharides and is the most abundant source of renewable biomass on our planet. There is an increasing effort to convert the cellulosic component to alcohols that can serve as biofuels. A critical step in this process is the enzymatic hydrolysis to release easily fermentable monomeric sugars, such as glucose and xylose, from the complex polysaccharides. However, the conversion of plant cell wall polysaccharides to biofuels is still far from being an ideal cost-effective process (53). Increasing the yields of enzymes during gene expression and bio-prospecting for enzymes with higher catalytic efficiencies are two strategies that can reduce the cost of production of biofuels. Ruminant animals have coevolved with a microbial consortium that harnesses enzymatic hydrolysis to release fermentable sugars from plant cell wall polysaccharides. The released sugars are subsequently fermented by the microbes to short-chain fatty acids that serve as the main energy source of the host (14, 33). Therefore, the genomes of plant cell wall-degrading microbes in the rumen represent a rich source of highly active plant cell wall-degrading enzymes. In addition, a better understanding of the strategies utilized by ruminal plant cell wall-degrading microorganisms should enhance rational design of enzymes with novel functions and/or improved activities through genetic engineering.The enzymes at the core of microbial plant cell wall degradation are the glycoside hydrolases (GHs). GHs frequently display a variety of modular structures. In addition to the catalytic domain, the most commonly observed module in glycoside hydrolases is the carbohydrate-binding module (CBM), which is known to enhance the accessibility of GHs to their appropriate polysaccharide substrates. Currently, there are 115 GH families and 59 CBM families in the carbohydrate active enzyme database (CAZy) (10), and combinations of these modules provide functional diversities to GHs.Hemicellulose is the second most abundant sugar polymer in the plant cell wall, and due to its heterogenous structure, it requires a set of at least five enzymes for its saccharification (12). The family 43 glycoside hydrolases (GH43s) are hemicellulolytic enzymes. They exhibit β-1,4-xylosidase (EC 3.2.1.37), β-1,3-xylosidase (EC 3.2.1.72), α-l-arabinofuranosidase (EC 3.2.1.55), arabinanase (EC 3.2.1.99), xylanase (EC 3.2.1.8), and galactan 1,3-β-galactosidase (EC 3.2.1.145) activities. Recent biophysical studies have revealed domain organizations and catalytic mechanisms in this family (3, 8, 9, 43, 65, 73). Based on their domain organization, these proteins are grouped into three different types. The first group includes 1,5-α-l-arabinanases from Cellvibrio japonicus (43), Bacillus thermodenitrificans (73), and Geobacillus stearothermophilus (3), and these proteins are composed of a single GH43 catalytic domain. The second group includes an arabinoxylan arabinofuranohydrolase enzyme from Bacillus subtilis (BsAXH-m2,3) and, in addition to the GH43 module, the proteins in this group have a family 6 carbohydrate-binding module (CBM6) at their C termini (65). The third group, which includes a β-xylosidase/α-l-arabinofuranosidase from the rumen bacterium Selenomonas ruminantium (SXA) (9) and a β-xylosidase from Geobacillus stearothermophilus (XynB3) (8), possesses in addition to the GH43 modules a C-terminally appended β-sandwich fold structure composed of approximately 200 amino acid residues. GH43 proteins of similar organization as SXA and XynB3 abound in the protein databases, and they are thought to form a cluster of orthologous group of proteins (COG) with β-xylosidase as their functional annotation. The large CBM-like β-sandwich structure in these proteins, however, lacks detailed biochemical characterization. Therefore, one of the aims of this study was to use both truncational and mutational analyses to probe the role of this module in the function of its associated GH43 module.Fibrobacter succinogenes S85 is a highly active cellulolytic ruminal bacterium (15). Interestingly, the genome of this bacterium also codes for many hemicellulolytic enzymes, despite its limited utilization of hemicellulose (41). To gain insight into this unusual metabolism, we have been studying a hemicellulolytic gene cluster that encodes more than 10 hemicellulose-targeting enzymes in the genome of F. succinogenes S85 (74). In this study, it is demonstrated that a GH43 modular protein (FSU2269) in the cluster (see Fig. S1 in the supplemental material) is an arabinoxylan arabinofuranohydrolase (AXH), which has been named FSUAXH1. Furthermore, the truncational and biochemical studies of this enzyme suggest that the unique β-sandwich domain (XX domain), which shares significant homology with the β-sandwich domains of SXA and XynB3, is important for binding to arabinoxylan. Since the majority of XX domains are only observed in GH43 proteins, we probed the relationship between the two different structural folds. The data presented here demonstrate interdependence between the two folds for substrate binding and suggest discovery of a new form of carbohydrate-binding module, likely composed of the interface between the GH43 module and the XX domain.     

Preimplantation genetic diagnosis--an overview.

Since the early 1990s, preimplantation genetic diagnosis (PGD) has been expanding in scope and applications. Selection of female embryos to avoid X-linked disease was carried out first by polymerase chain reaction, then by fluorescence in situ hybridization (FISH), and an ever-increasing number of tests for monogenic diseases have been developed. Couples with chromosome rearrangements such as Robertsonian and reciprocal translocations form a large referral group for most PGD centers and present a special challenge, due to the large number of genetically unbalanced embryos generated by meiotic segregation. Early protocols used blastomeres biopsied from cleavage-stage embryos; testing of first and second polar bodies is now a routine alternative, and blastocyst biopsy can also be used. More recently, the technology has been harnessed to provide PGD-AS, or aneuploidy screening. FISH probes specific for chromosomes commonly found to be aneuploid in early pregnancy loss are used to test blastomeres for aneuploidy, with the aim of replacing euploid embryos and increasing pregnancy rates in groups of women who have poor IVF success rates. More recent application of PGD to areas such as HLA typing and social sex selection have stoked public controversy and concern, while provoking interesting ethical debates and keeping PGD firmly in the public eye.     

Endocannabinoid system in frog and rodent testis: type-1 cannabinoid receptor and fatty acid amide hydrolase activity in male germ cells

N-arachidonoylethanolamide (anandamide [AEA]) is the main endocannabinoid described to date in the testis. It exerts its effects through the activation of G-protein coupled cannabinoid receptors (CNR). However, the activity of AEA in controlling male reproduction is still poorly known. Here we provide direct evidence on the presence of the "endocannabinoid system," constituted by type-1 cannabinoid receptor (CNR1) and fatty acid amide hydrolase (FAAH), in the frog Rana esculenta testis demonstrating its expression in tubular compartment. In fact, during the annual reproductive cycle, both proteins increase in September, when the appearance of spermatids (SPT) occurs. Immunocytochemistry confirms their localization in germ cells and, in particular, in elongated SPT. Signals are still present in spermatozoa (SPZ), as demonstrated by Western blot analysis. Furthermore, the activation of CNR1 reduces sperm motility. Comparative research, carried out using mouse and rat SPZ, definitely indicates that the endocannabinoid system operates in SPZ of phylogenetically distant species. A conserved physiological role of endocannabinoid system in controlling the inhibition of sperm motility is suggested.     

Cannabinoid CB2 receptors in the enteric nervous system modulate gastrointestinal contractility in lipopolysaccharide-treated rats

Enhanced intestinal transit due to lipopolysaccharide (LPS) is reversed by cannabinoid (CB)2 receptor agonists in vivo, but the site and mechanism of action are unknown. We have tested the hypothesis that CB2 receptors are expressed in the enteric nervous system and are activated in pathophysiological conditions. Tissues from either saline- or LPS-treated (2 h; 65 microg/kg ip) rats were processed for RT-PCR, Western blotting, and immunohistochemistry or were mounted in organ baths where electrical field stimulation was applied in the presence or absence of CB receptor agonists. Whereas the CB2 receptor agonist JWH133 did not affect the electrically evoked twitch response of the ileum under basal conditions, in the LPS-treated tissues JWH133 was able to reduce the enhanced contractile response in a concentration-dependent manner. Rat ileum expressed CB2 receptor mRNA and protein under physiological conditions, and this expression was not affected by LPS treatment. In the myenteric plexus, CB2 receptors were expressed on the majority of neurons, although not on those expressing nitric oxide synthase. LPS did not alter the distribution of CB2 receptor expression in the myenteric plexus. In vivo LPS treatment significantly increased Fos expression in both enteric glia and neurons. This enhanced expression was significantly attenuated by JWH133, whose action was reversed by the CB2 receptor antagonist AM630. Taking these facts together, we conclude that activation of CB2 receptors in the enteric nervous system of the gastrointestinal tract dampens endotoxin-induced enhanced intestinal contractility.     

Effect of Condensed Tannins on Bacterial Diversity and Metabolic Activity in the Rat Gastrointestinal Tract

The effect of dietary condensed tannins (proanthocyanidins) on rat fecal bacterial populations was ascertained in order to determine whether the proportion on tannin-resistant bacteria increased and if there was a change in the predominant bacterial populations. After 3 weeks of tannin diets the proportion of tannin-resistant bacteria increased significantly (P < 0.05) from 0.3% ± 5.5% to 25.3% ± 8.3% with a 0.7% tannin diet and to 47.2% ± 5.1% with a 2% tannin diet. The proportion of tannin-resistant bacteria returned to preexposure levels in the absence of dietary tannins. A shift in bacterial populations was confirmed by molecular fingerprinting of fecal bacterial populations by denaturing gradient gel electrophoresis (DGGE). Posttreatment samples were generally still distinguishable from controls after 3.5 weeks. Sequence analysis of DGGE bands and characterization of tannin-resistant isolates indicated that tannins selected for Enterobacteriaceae and Bacteroides species. Dot blot quantification confirmed that these gram-negative bacterial groups predominated in the presence of dietary tannins and that there was a corresponding decrease in the gram-positive Clostridium leptum group and other groups. Metabolic fingerprint patterns revealed that functional activities of culturable fecal bacteria were affected by the presence of tannins. Condensed tannins of Acacia angustissima altered fecal bacterial populations in the rat gastrointestinal tract, resulting in a shift in the predominant bacteria towards tannin-resistant gram-negative Enterobacteriaceae and Bacteroides species.     

Inactivation of cytochrome P450 and inhibition of ferrochelatase by analogues of 3,5-diethoxycarbonyl-1,4-dihydro-2,4,6-trimethylpyridine with 4-nonyl and 4-dodecyl substituents.

Cytochrome P450- and heme-destructive effects of the 4-nonyl and 4-dodecyl analogues of 3,5-diethoxycarbonyl-1,4-dihydro-2,4,6-trimethylpyridine (DDC) were determined using hepatic microsomal preparations obtained from untreated, beta-naphthoflavone-treated, and phenobarbital-treated chick embryos. The 4-nonyl analogue of DDC was less efficacious than 4-ethyl DDC and 4-hexyl DDC, but more efficacious than 4-dodecyl DDC with respect to cytochrome P450-destructive activity. In all hepatic microsomal preparations, cytochrome P450 destruction by 4-nonyl DDC was accompanied by loss of microsomal heme. In contrast, 4-dodecyl DDC caused loss of heme only in hepatic microsomal preparations obtained from phenobarbital-treated chick embryos. The ability of 4-nonyl DDC and 4-dodecyl DDC to lower ferrochelatase activity was compared with that of 4-ethyl DDC and 4-hexyl DDC in cultured chick embryo hepatocytes. As the length of the 4-alkyl group was increased, the ferrochelatase-lowering efficacy and potency of the DDC analogue decreased. The 4-dodecyl DDC analogue was unable to lower ferrochelatase activity, which accorded with the finding that the administration of 4-dodecyl DDC to phenobarbital-treated rats did not lead to the accumulation of an N-alkylprotoporphyrin. The ability of 4-nonyl DDC to lower ferrochelatase activity was attributed to the formation of N-nonylprotoporphyrin IX following the administration of 4-nonyl DDC to phenobarbital-treated rats.     

Ectopic RNase E sites promote bypass of 5'-end-dependent mRNA decay in Escherichia coli

In Escherichia coli, 5'-terminal stem-loops form major impediments to mRNA decay, yet conditions that determine their effectiveness or the use of alternative decay pathway(s) are unclear. A synthetic 5'-terminal hairpin stabilizes the rpsT mRNA sixfold. This stabilization is dependent on efficient translational initiation and ribosome transit through at least two-thirds of the coding sequence past a major RNase E cleavage site in the rpsT mRNA. Insertion of a 12-15 residue 'ectopic' RNase E cleavage site from either the rne leader or 9S pre-rRNA into the 5'-non-coding region of the rpsT mRNA significantly reduces the stabilizing effect of the terminal stem-loop, dependent on RNase E. A similar insertion into the rpsT coding sequence is partially destabilizing. These findings demonstrate that RNase E can bypass an interaction with the 5'-terminus, and exploit an alternative 'internal entry' pathway. We propose a model for degradation of the rpsT mRNA, which explains the hierarchy of protection afforded by different 5'-termini, the use of internal entry for bypass of barriers to decay, 'ectopic sites' and the role of translating ribosomes.