Characterization of a new methylotrophic strain,Methylomonas clara

Summary The organism examined was identified as an obligate methylotroph and as an organism of type I, because it has some characteristics of this group: methanol is utilized via the hexulose phosphate pathway, the enzymes glucose-6-phosphate dehydrogenase, 6-phosphogluconate dehydrogenase, malate dehydrogenase, and isocitrate dehydrogenase (both NAD- and NADP-specific) could be detected, whereas the citric acid cycle is incomplete (in particular -ketoglutarate dehydrogenase could not be found). Furthermore, the organism is able to fix nitrogen. In contrast, there are some different characteristics: carbon dioxide can be fixed in connection with methanol. There is no formate dehydrogenase, and formaldehyde dehydrogenase can be induced by different culture conditions. Moreover, the GC content (49.2%) is distinctly lower than normal, and the hexulose phosphate synthase shows a higher activity with NAD as cosubstrate than with NADP. Carbon is not metabolized via the Embden-Meyerhoff-Parnaß pathway, but via the Entner-Doudoroff pathway. In the disk test, the organism is resistant to some antibiotics: chloramphenicol, fusidic acid, methicillin and lincomycin. A partial resistance can be observed with penicillin, neomycin, novobiocin, and cloxacillin.     

Plasmids in Methylomonas clara,a methylotrophic producer of single cell protein

Summary Three single cell clones of the obligate methylotrophic bacterium Methylomonas clara originating from one fermentor culture were assayed for their DNA content. Apart from chromosomal DNA which showed no difference in the three strains, only two strains were found to carry plasmids with identical buoyant density and GC content but differing in contour length (12.4 m and 4.9 m respectively). According to their restriction pattern they are derived from each other. Both plasmids are not involved in methanol metabolism, since the third strain was found to be devoid of plasmids. The possibility of using these plasmids to establish vectors for gene cloning is evident, since during prolonged vegetative growth the specific plasmid content remains constant.     

Influence of total and oxygen partial pressure on growth and metabolism of Methylomonas clara

The effect of total and oxygen partial pressure on metabolic activities of Methylomonas clara has been investigated in batch and continuous cultivation experiments using a pressurizable airlift loop reactor. At Oxygen partial pressures of more than 1000 mbar growth of M. Clara is retarded and completely inhibited at 1200 mbr. However, after several hours of incubation at elevated oxygen partial pressures, biomass formation is nearly doubled in subsquent continuous operation, Cells pretreated with oxygen are characterized by a change of cytochrome content; they excret carboxylic acids into the medium. The results indicate that, by sparging an aerobic culture intermittently wich pure oxygen, formation of biomass might be enbanced. (c) 1992 John Wiley & Sons, Inc.     

Determination and in vivo characterization of the basic replicon of natural plasmids of Methylomonas clara

The basic replicon of the endogenous Methylomonas clara plasmid pBE-2 and its derivatives was defined to a region of 2.7 kb by in vivo deletions and conjugative transfer experiments using Escherichia coli-M. clara hybrid plasmids. Origin activity was found to be confined to a maximal length of 1.3 kb. The origin consists of two fragments which can be separated more than 4 kb by the integration of foreign DNA fragments without loss of function. A fragment having a maximum size of 2.1 kb supports in trans replication initiation at the origin. In addition, two incompatibility determinants were revealed, one localized in the origin fragment and the other outside the origin. Incompatibility between two basic replicons of the natural M. clara plasmids can be overcome by the integration of one of them in the compatible IncP plasmid R68-Kms. No homology was found between the plasmid basic replicon and the chromosomal DNA of M. clara.     

Molecular cloning and characterization of the recA gene of Methylomonas clara and construction of recA deficient mutant

Summary The recA gene of the methylotrophic bacterium Methylomonas clara has been isolated from a genomic library by hybridization with the Escherichia coli recA gene. Its complete nucleotide sequence consists of 1029 bp encoding a polypeptide of 342 amino acids. Nucleotide sequence analysis of the M. clara recA gene revealed extensive homologies to recA genes from E. coli and Pseudomonas aeruginosa. Part of the physiological activity of the M. clara RecA protein has become evident in that E. coli recA mutant HB101 is complemented. The cloned recA gene has been modified in vitro by site-specific mutagenesis and by insertion of a kanamycin-resistance gene cassette into the recA coding sequence. M. clara recA mutants were obtained by replacement of the active recA gene by an in-vitro inactivated gene copy. Offprint requests to: K. Esser     

Isolation and identification of clara cells from rabbit lung

Summary A procedure has been developed for the isolation of nonciliated bronchiolar epithelial cells (Clara cells) from rabbit lung. Following pulmonary lavage to eliminate macrosphages, cells (5% Clara cells) were released by digestion with 0.1% Protease I in HEPES-buffered balanced salt solution containing 0.5 mM ethylene glycol-bis-(β-aminoethyl ether)-N,N′-tetraacetic acid instilled through the trachea. These cells were then separated on the basis of size using the Beckman JE-6 elutriator rotor. The fourth fraction collected from the elutriator contained about 30% Clara cells. This fraction was then layered on a two-polymer aqueous phase system consisting of 5% dextran T500 (DT) and 3.8% polyethylene glycol 6000 (PEG) in sodium phosphate buffer. A cell fraction was obtained from the PEG phase, which included approximately 70% Clara cells. These cells were found to be greater than 90% viable by trypan blue dye exclusion. Identification of isolated Clara cells was confirmed by light microscopic observation of nitro blue tetrazolium staining and by ultrastructural characteristics as observed by electron microscopy. This research was supported in part by the U.S. Environmental Protection Agency under an interagency agreement relating to the Federal Interagency Energy/Environmental Research and Development Program.     

Methylamine dehydrogenase from the obligate methylotroph Methylomonas methylovora.

An obligate methyltroph Methylomonas methylovora oxidized methylamine, formaldehyde, and formate. Enzymes oxidizing these substrates were detected in a cell-free system. Phenazine methosulfate-linked methylamine dehydrogenase was purified 21-fold. The enzyme had optimum activity at pH 7.5 and was stable at 60 degrees C for 5 min. The enzyme activity was inhibited by parachloromercuric benzoate, isonicotinic acid hydrazide, mercuric chloride, and sodium borate.     

Characterisation of sequences required for RNA initiation from the PGK promoter of Saccharomyces cerevisiae.

In the phosphoglycerate kinase (PGK) gene of yeast, as in other highly expressed yeast genes, the sequences surrounding the site of RNA initiation have a loosely conserved structure of a CT rich stretch followed by the tetranucleotide CAAG. Using internal deletions and insertions we have identified the elements in the PGK promoter which are required for correct RNA initiation at the CAAG sequence at -39. The results indicate that two different components of the PGK promoter contribute to correct RNA initiation, the TATA homologies, located at -152 and -113, and the sequences at the site of initiation. Both TATA elements can function in RNA initiation. Deletion of the upstream TATA element, TATAI, results in slightly heterogeneous RNA initiation, but the majority of the RNA initiates correctly. Deletion of both the PGK TATA elements results in the majority of the RNA initiating at sites downstream from the wild-type I site, within the structural gene between +40 to +80. The CT rich box is not essential for correct mRNA initiation as shown by deletion analysis. The site of RNA initiation in the PGK promoter appears to be determined by sequences located immediately 5' of the CAAG sequence motif. This short sequence, ACAGATC, when located the correct distance from the TATA elements may be sufficient to determine a discrete initiation site.     

Characterisation of a new virus from escarole

A new virus associated with mosaic, yellowing and necrotic symptoms in escarole has been isolated recently in southern Italy. The virus, for which the name escarole mosaic virus (EMV) is proposed, was transmissible by mechanical methods, by seeds and probably by pollen but not by Acyrthosiphon pisum, Aphis gossypii, Myzus persicae, Trialeurodes vaporariorum or Frankliniella occidentalis. The virions showed a single coat protein of about 32 kDa and eight encapsidated RNA species. Viral preparations sedimented as four components in sucrose density gradients. Electron microscopy indicated the presence of spherical particles with a diameter of 25 nm. Ultrastructural investigations on infected tissues revealed the formation of atypical inclusion bodies.     

3-Hexulosephosphate synthase from Methylomonas aminofaciens 77a. Purification, properties and kinetics

3-Hexulosephosphate synthase (D-arabino-3-hexulose 6-phosphate formaldehyde lyase) was purified from an obligate methylotroph, Methylomonas aminofaciens, to homogeneity as judged by polyacrylamide gel electrophoresis and analytical ultracentrifugation. The molecular weight was determined to be 45 000-47 000 by sedimentation velocity and gel filtration. The enzyme appears to be composed of two identical subunits (Mr = 23 000). A bivalent cation is required for the activation and stabilization of the enzyme. The enzyme is specific for formaldehyde and D-ribulose 5-phosphate. The optimum pH is 8.0 (isoelectric point, pH 5.1) and the optimum temperature is 45 degrees C. Initial velocity studies are consistent with a sequential mechanism. The Michaelis constants are 0.29 mM for formaldehyde and 0.059 mM for D-ribulose 5-phosphate.     

Characterisation of a siderophore from Acinetobacter calcoaceticus

Abstract The Gram-negatice bacterium Acinetobacter calcoaceticus was examined for production of siderophores and iron-repressible outer membrane proteins following growth in iron-restricted media. The iron chelator, 2,3-dihydroxybenzoic acid was identified in the culture supernatant bu ¹H nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry (MS). A group of outer membrane proteins between 80 and 85 kDa were induced under iron restriction.     

Characterisation and application of a bovine U6 promoter for expression of short hairpin RNAs

Background  

The use of small interfering RNA (siRNA) molecules in animals to achieve double-stranded RNA-mediated interference (RNAi) has recently emerged as a powerful method of sequence-specific gene knockdown. As DNA-based expression of short hairpin RNA (shRNA) for RNAi may offer some advantages over chemical and in vitro synthesised siRNA, a number of vectors for expression of shRNA have been developed. These often feature polymerase III (pol. III) promoters of either mouse or human origin.     

Characterisation of the expression of a novel constitutive maize promoter in transgenic wheat and maize

A novel constitutive promoter from the maize histone H2Bgene was recently identified. In this study, we characterised H2B promoter activity in both wheat and maize tissues using the gusA reporter gene and two synthetic versions of the pat (phosphinothricin acetyl transferase) selectable marker gene, namely mopat and popat. Analyses of transgenic plants showed that the H2B promoter is able to drive the expression of gusA to strong, constitutive levels in wheat and maize tissues. Using an H2B:mopat construct and phosphinothricin selection, we recovered transgenic wheat plants at efficiencies ranging from 0.3% to 7.4% (mean 1.6%), and the efficiency of selection ranged from 40% to 100% (mean 77.7%). In another application, H2B was combined with the maize Ubi-1 or the maize Adh-1 intron to drive the expression of mopat and popat. Transformation efficiencies with the Ubi-1 intron were between 1.4- to 16-fold greater than with the Adh-1 intron. However, the use of either of the introns was necessary for the recovery of transgenic plants. Mopat gave higher transformation efficiencies and induced higher levels of PAT protein in maize tissues than popat.     

Characterisation of a cell-envelope proteinase from Lactobacillus helveticus

The cell-envelope proteinase from Lactobacillus helveticus CRL 1062 was detected in the cell membrane fraction. The enzyme remained associated with the cells even after treatment with lysozyme and was not released from washed cells in absence of calcium. The proteinase was maximally active at pH 6.5–7.0 and 42°C and hydrolysed - and -caseins at different rates. Activity was inhibited (98%) by 1 mM PMSF, suggesting it was a serine-type protease.     

Characterisation of a novel amylosucrase from Deinococcus radiodurans

The BLAST search for amylosucrases has yielded several gene sequences of putative amylosucrases, however, with various questionable annotations. The putative encoded proteins share 32-48% identity with Neisseria polysaccharea amylosucrase (AS) and contain several amino acid residues proposed to be involved in AS specificity. First, the B-domains of the putative proteins and AS are highly similar. In addition, they also reveal additional residues between putative beta-strand 7 and alpha-helix 7 which could correspond to the AS B'-domain, which turns the active site into a deep pocket. Finally, conserved Asp and Arg residues could form a salt bridge similar to that found in AS, which is responsible for the glucosyl unit transfer specificity. Among these found genes, locus NP_294657.1 (dras) identified in the Deinococcus radiodurans genome was initially annotated as an alpha-amylase encoding gene. The putative encoded protein (DRAS) shares 42% identity with N. polysaccharea AS. To investigate the activity of this protein, gene NP_294657.1 was cloned and expressed in Escherichia coli. When acting on sucrose, the pure recombinant enzyme was shown to catalyse insoluble amylose polymer synthesis accompanied by side-reactions (sucrose hydrolysis, sucrose isomer and soluble maltooligosaccharide formation). Kinetic analyses further showed that DRAS follows a non-Michaelian behaviour toward sucrose substrate and is activated by glycogen, as is AS. This demonstrates that gene NP_294657.1 encodes an amylosucrase.