Genomic Characterization of Methanomicrobiales Reveals Three Classes of Methanogens

Background

Methanomicrobiales is the least studied order of methanogens. While these organisms appear to be more closely related to the Methanosarcinales in ribosomal-based phylogenetic analyses, they are metabolically more similar to Class I methanogens.

Methodology/Principal Findings

In order to improve our understanding of this lineage, we have completely sequenced the genomes of two members of this order, Methanocorpusculum labreanum Z and Methanoculleus marisnigri JR1, and compared them with the genome of a third, Methanospirillum hungatei JF-1. Similar to Class I methanogens, Methanomicrobiales use a partial reductive citric acid cycle for 2-oxoglutarate biosynthesis, and they have the Eha energy-converting hydrogenase. In common with Methanosarcinales, Methanomicrobiales possess the Ech hydrogenase and at least some of them may couple formylmethanofuran formation and heterodisulfide reduction to transmembrane ion gradients. Uniquely, M. labreanum and M. hungatei contain hydrogenases similar to the Pyrococcus furiosus Mbh hydrogenase, and all three Methanomicrobiales have anti-sigma factor and anti-anti-sigma factor regulatory proteins not found in other methanogens. Phylogenetic analysis based on seven core proteins of methanogenesis and cofactor biosynthesis places the Methanomicrobiales equidistant from Class I methanogens and Methanosarcinales.

Conclusions/Significance

Our results indicate that Methanomicrobiales, rather than being similar to Class I methanogens or Methanomicrobiales, share some features of both and have some unique properties. We find that there are three distinct classes of methanogens: the Class I methanogens, the Methanomicrobiales (Class II), and the Methanosarcinales (Class III).     

Efficient biotransformation of herbicide diuron by bacterial strain <Emphasis Type="Italic">Micrococcus</Emphasis> sp. PS-1

A Gram-positive, Micrococcus sp. strain PS-1 capable of utilizing phenylurea herbicide diuron as a sole carbon source at a high concentration (up to 250 ppm) was isolated from diuron storage site by selective enrichment study. The taxonomic characterization with 16S rRNA gene sequencing (1,477 bp) identified PS-1 as a member of Micrococcus sp. It was studied for the degradation of diuron and a range of its analogues (monuron, linuron, monolinuron, chlortoluron and fenuron). The shake flasks experiments demonstrated fast degradation of diuron (up to 96% at 250 ppm within 30 h incubation) with the addition of small quantity (0.01%) of non-ionic detergent. The relative degradation profile by the isolate was in the order of fenuron > monuron > diuron > linuron > monolinuron > chlortoluron. Further, the biochemical characterization of catabolic pathway by spectroscopic and chromatographic techniques demonstrated that the degradation proceeded via formation of dealkylated metabolites to form 3,4-dichloroaniline (3,4-DCA). It was the major metabolite formed, associated with profound increase in degradation kinetics in presence of appropriate additive.     

Discovery in silico and characterization in vitro of novel genes exclusively expressed in the mouse epididymis

Epididymal proteins interact with sperm during their passage through the epididymis and thus contribute to the maturation and fertilizing capacity of the spermatozoa. In the present study we have discovered five novel epididymis-specific genes through in silico analysis of expressed sequence tags (ESTs) at the UniGene library collection. The strategy used is a powerful way to discover novel epididymis-specific genes. The full-length cDNA sequences were determined, and computational tools were used to characterize the genomic structures and to predict putative functions for the encoded proteins. In vitro analyses revealed that all five genes characterized were highly expressed in the defined areas of the epididymis, and they were not expressed at significant levels in any other tissue. Three of the genes were named on the basis of their putative functions: Spint4 (serine protease inhibitor, Kunitz type 4), and Rnase9 and Rnase10 (ribonuclease, Rnase A family 9 and 10), while for the ESTs AV381130 and AV381126 no putative functions could be predicted. The expression of Spint4, Rnase9, and AV381130 was found to be under a direct or indirect regulation by androgens, while the expression of Rnase10 is regulated by a testicular factor(s) other than androgen. None of the genes were expressed in the immature epididymis, while mRNAs were detected from d 17 onward, at the time of maturation of epididymal epithelium. However, the expression of AV381130 was not detected until d 30 after birth, indicating a close connection between gene expression and puberty.     

Intrinsic innervation in the tracheal smooth muscle of the large flying fox (Pteropus vampyrus): an immunohistochemical study

Structure and innervation of the trachea of the large flying fox (Pteropus vampyrus) were examined by mean hematoxylin-eosin staining and immunohistochemical methods. The tracheal rings were predominantly comprised of bone with a small amount of hyaline cartilage. Bone contained bone marrow and hyaline cartilage attached at the ends of the tracheal rings. The tracheal rings in the anterior third of the trachea were connected at each end with connective tissue to almost form a ring. A narrow membranous wall comprising a single layer of smooth muscle was present in the middle third, while inner and outer layers of smooth muscle were present in the posterior third. Protein gene product 9.5 (PGP 9.5)-, nitric oxide synthase (NOS)-, galanin- and vasoactive intestinal peptide (VIP)-immunoreactive nerve fibers were present in the epithelium, lamina propria, smooth muscle layer and tunica adventitia. In the tunica adventitia, many PGP 9.5- and NOS-immunoreactive neurons were found singly or in small ganglia, while some VIP- and galanin-immunoreactive neurons were observed. A few PGP 9.5- and NOS-immunoreactive neurons were found in the submucosal layer. These results suggest that the trachea of the large flying fox has a rigid structure of tracheal rings and that the posterior two-thirds of the trachea probably contract via the actions of smooth muscles innervated with peptidergic or nitrenergic neurons that are located in tracheal ganglia, whereas the anterior third is non-mobile.     

Estimating predation pressure in ecological studies: controlling bias imposed by using sentinel plasticine prey

Sentinel plasticine prey has been increasingly used to estimate predation pressure. The use of plasticine prey may, however, bias the results, as this method was originally designed to account for predation by organisms that can visually recognize the shapes and colors of their prey. To evaluate the limitations of using sentinel plasticine prey, we compared predator attack rates between real prey – dead and live mealworms, Tenebrio molitor L. (Coleoptera: Tenebrionidae) – and plasticine models in a monsoonal tropical rainforest of southeastern China. The attack rates by invertebrates were highest on dead prey followed by live prey and plasticine models, whereas the attack rates by vertebrates were lowest on dead prey, and did not differ between live prey and plasticine models. These results confirm that bias imposed by using the plasticine models is affected by the type of predators. In addition, we tested the validity and generality of the premise that predators can distinguish the shapes of plasticine model prey and preferentially attack a caterpillar-like shape over other shapes. To test this hypothesis, we conducted three independent experiments in China, Papua New Guinea, and Finland. In the two latter localities, predation rates on plasticine caterpillars were higher than on models of other shapes, whereas in China, these differences were not significant. Taken together, our study suggests that plasticine models may underestimate the predation by invertebrates to a greater extent than predation by vertebrates, and the preference of model shape by predators may be locality-specific, presumably due to differences in the composition of the predator community. We propose that predation be estimated on both live and plasticine prey in future studies to measure the potential bias imposed by using plasticine models and its variation among various habitats and predator groups.     

3,5,4′-trihydroxy-6,7-dimethoxyflavone 3-glucoside from Sesuvium portulacastrum

A new flavonol glycoside 3,5,4′-trihydroxy-6,7-dimethoxyflavone 3-O-glucoside has been characterized from Sesuvium portulacastrum, together with its aglycone, eupalitin.     

Structural homologies among type I restriction-modification systems.

Structural homologies among different restriction systems of Escherichia coli and several Salmonella species have been investigated by immunological methods using antibodies prepared against two subunits of the E. coli K12 restriction enzyme, and by DNA hybridization experiments using different fragments of the E. coli K12 hsd genes as probes. The results with both techniques show a strong homology between the E. coli K12 and B restriction-modification systems, weaker but nevertheless marked homology between E. coli K12 and the Salmonella systems SB, SP, and SQ and, surprisingly, no homology between the E. coli K12 and A systems.     

In vitro Hormonal Regulation of Laticifer Differentiation in Calotropis procera

Cultures of Calotropis procera were maintained on MS mediumsupplemented with 4·6 µM FAP and 3 µM NAA.Laticifer initials were observed in 2-week-old cultures whichwere converted into matured, branched, non-articulated laticifersin 4 weeks. It was observed that laticifer differentiation increasedwith the age of cultures, from 2·78% (in the second passage)to 15·11% (in the 12th passage). It has been establishedthat laticifer differentiation in vitro is a cytokinin-dependentprocess and among the cytokinins, FAP was more effective thanBA and 2-iP. But the type of auxin and its concentration alsoplay an important role in modifying the effect of cytokinin.Among the different auxins used IAA was more effective for laticiferdifferentiation than IBA and NAA, while 2,4D was inhibitory.Maximum laticifer differentiation (17·01% was observedon MS medium supplemented with 4·6 µM FAP and 1µM IAA.Copyright 1995, 1999 Academic Press Calotropis procera, callus culture, laticifer, differentiation, hormonal regulation     

Both CAG repeats and inverted DNA repeats stimulate spontaneous unequal sister-chromatid exchange in Saccharomyces cerevisiae

Genomic regions containing trinucleotide repeats (TNRs) are highly unstable, as the repeated sequences exhibit a high rate of mutational change, in which they undergo either a contraction or an expansion of repeat numbers. Although expansion of TNRs is associated with several human genetic diseases, the expansion mechanism is poorly understood. Extensive studies in model organisms have indicated that instability of TNRs occurs by several mechanisms, including replication slippage, DNA repair and recombination. In all models, the formation of secondary structures by disease-associated TNRs is a critical step in the mutation process. In this report, we demonstrate that TNRs and inverted repeats (IRs) both of which have the potential to form secondary structures in vivo, increase spontaneous unequal sister-chromatid exchange (SCE) in vegetatively growing yeast cells. Our results also show that TNR-mediated SCE events are independent of RAD50, MRE11 and RAD51, whereas IR-stimulated SCEs are dependent on the RAD52 epistasis-group genes. We propose that many TNR expansion mutations occur by SCE.     

Immunosensors for pesticide analysis: antibody production and sensor development

Immunosensors, a type of affinity biosensor, are based on the binding interactions between an immobilized biomolecule (antibody/antigen) on the electronic transducer surface with the analyte of interest (antigen/antibody), resulting in a detectable signal. The sensor system takes advantage of the high selectivity provided by the molecular recognition characteristic of an antibody, which binds reversibly with a specific antigen. This review article presents the current status of immunosensors, highlighting their potential benefits and limitations for pesticide analysis. The basic criteria for generating specific antibodies against low-molecular-mass pesticides, which are usually nonimmunogenic in nature, are briefly discussed. The article also describes the fundamentals of important transducer technologies and their use in immunosensor development.