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At least 1,063 records · Page 59Linked to original sources
PubMed1998

Description of Arthrobacter creatinolyticus sp. nov., isolated from human urine.

Three strains of creatinine-hydrolysing bacteria isolated from human urine were characterized taxonomically. They were aerobic, non-spore-forming, Gram-positive rods with the peptidoglycan of the cell wall containing lysine. MK-8 and MK-9 were found to be the major types of menaquinone. The G + C content of the DNA was 66-67 mol%. The 16S rRNA sequence of one strain (GIFU 12498) was determined and aligned with other high-G + C-content Gram-positive rods from different genera. Following phylogenetic analysis, this strain was placed in the genus Arthrobacter. Arthrobacter protophormiae was the most closely related species in the phylogenetic tree, and this species also showed the highest sequence homology value (97%) with GIFU 12498. However, DNA-DNA hybridization indicated that GIFU 12498 did not belong to A. protophormiae (33.8 +/- 3.5% chromosomal similarity). The three urine strains belonged to one species because they shared more than 95% DNA-DNA similarity. It is proposed that these strains are placed in the genus Arthrobacter as a new species, Arthrobacter creatinolyticus sp. nov. The type strain of A. creatinolyticus is GIFU 12498, which has been deposited in the Japan Collection of Microorganisms (JCM) with the accession number JCM 10102.

Amino Acids↗
PubMed2004

Phenylobacterium lituiforme sp. nov., a moderately thermophilic bacterium from a subsurface aquifer, and emended description of the genus Phenylobacterium.

A facultative anaerobic bacterium, strain FaiI3(T), was isolated from samples collected from the free-flowing waters of a bore well (Fairlea Bore, registration number 3768) which taps into the Australian Great Artesian Basin subsurface thermal aquifer. Strain FaiI3(T) developed yellow to pale-yellow colonies (0.5-1.5 mm) after 48 h. The non-spore forming rods (0.5x1-3 microm) were slightly curved, occurred singly and as pairs and were motile with a single polar flagellum. Cells tended to form clumps in liquid medium and rosettes were commonly observed. The cells stained Gram-negative and electron micrographs of thin sections revealed a multi-layered complex Gram-negative cell wall structure. Strain FaiI3(T) grew optimally at 40-41 degrees C, with growth observed at 45 degrees C but not at 50 degrees C. The pH growth range was between pH 6 and 9 and optimal growth occurred between pH 6 and 6.5. Strain FaiI3(T) grew best with yeast extract as the sole carbon and energy source. Peptone, yeast extract, acetate, xylose, sucrose, glucose, glycerol, succinate, butyrate, lactate, fumarate, citrate, L-phenylalanine, cellobiose and gelatin supported growth but maltose, fructose, glycine, ethanol, benzoate and oxalate did not. Tyrosine was produced from L-phenylalanine. Strain FaiI3(T) was catalase-positive and oxidase-negative and did not hydrolyse starch. Growth was inhibited by neomycin, tetracycline, streptomycin, chloramphenicol, ampicillin, vancomycin and spectinomycin. The G+C content was determined to be 66.5+/-0.5 mol%. On the basis of the 16S rRNA gene sequence analysis, strain FaiI3(T) was assigned as a novel species of the genus Phenylobacterium, Phenylobacterium lituiforme sp. nov. in the order Caulobacterales, subclass alpha-Proteobacteria, class Proteobacteria. The type strain is FaiI3(T) (=ATCC BAA-294(T)=DSM 14363(T)).

Anaerobiosis↗
PubMed2004

Reclassification of Cellulosimicrobium variabile Bakalidou et al. 2002 as Isoptericola variabilis gen. nov., comb. nov.

As already depicted in the original publication, the type strain of the species Cellulosimicrobium variabile Bakalidou et al. 2002, DSM 10177(T), does not cluster unambiguously with the type species, Cellulosimicrobium cellulans DSM 43879(T), in phylogenetic analysis. Strain DSM 10177(T) is moderately related to the recently described species Xylanimonas cellulosilytica, Promicromonospora pachnodae and Xylanibacterium ulmi, forming a lineage that branches between C. cellulans and members of the genus Promicromonospora in most dendrograms generated on the basis of different algorithms and reference strains. The type strains of the two Cellulosimicrobium species resemble each other in morphology, composition of fatty acids, DNA G+C content, phospholipids and the presence of lysine in position 3 of the peptide subunit of peptidoglycan. However, the two strains differ from each other in cell-wall sugars and in the amino acid composition of the A4alpha-type peptidoglycan, which contains serine and aspartic acid in C. cellulans, whereas only aspartic acid is present in the interpeptide bridge of C. variabile. This type is also present in Xylanimonas cellulosilytica XIL07(T), but not in the neighbouring species P. pachnodae DSM 12657(T), which exhibits the L-lys-L-ser-D-Glu type. On the basis of distinct phylogenetic position and the amino acid composition of peptidoglycan, a novel genus and combination for C. variabile, Isoptericola variabilis gen. nov., comb. nov., is proposed.

Actinomycetales↗
PubMed1979

Characterization of the carbohydrate component of fraction I in the Neurospora crassa cell wall.

The carbohydrate portion of fraction I of the Neurospora crassa cell wall has been analyzed for sugar composition by gas-liquid chromatography and colorimetric methods. The analysis was performed comparatively in a wild-type strain (RL 3-8A) and three morphological mutants: scumbo (FGSC 49), peak-2a (a mutant known to be allelic to biscuit), and ragged (FGSC 296). Fraction I of all strains studied contains glucose, mannose, and galactose as the main sugars. Uronic acids and amino sugars are also present in small amounts. The glycosidic linkages binding the neutral sugars were analyzed by Lindberg's combined gas chromatography-mass spectrometry techniques for identification of the partially methylated alditol acitate sugar derivatives. The main polymeric portion of fraction I seems to be a linear glucan with the glucose residues linked by 1 leads to 3 and 1 leads to 4 bonds. A mannan portion with a branched configuration is also present, with galactose as the sugar residue which serves as branches in the molecule(s). The branched mannan portion appears to increase in amount in correlation with more drastic morphological changes of the mycelia. In this respect, the mutant ragged has the lowest mycelial growth rate and the largest amount of mannan. The importance of the polysaccharide structure of fraction I on the colonial morphology of the mycelia is discussed.

Carbohydrates↗
PubMed2004

Streptomyces hebeiensis sp. nov.

A novel actinomycete strain, YIM 001(T), was isolated from a soil sample collected from Hebei province, People's Republic of China. The strain was characterized by white to grey aerial mycelium. Long spore chains, borne on the aerial mycelium, were straight to Rectiflexibiles; the spore chains were composed of non-motile and coccoid spores with a warty surface. The cell wall of strain YIM 001(T) contained LL-diaminopimelic acid (A(2)pm) and traces of meso-A(2)pm. Whole-cell hydrolysates contained mainly glucose and small amounts of xylose, galactose and arabinose. The menaquinones were MK-9(H(4)) (4.6 %), MK-9(H(6)) (60 %), MK-9(H(8)) (30.7 %) and MK-9(H(10)) (4.7 %). Phosphatidylethanolamine was the diagnostic phospholipid. The DNA G+C content of strain YIM 001(T) was 71.4 mol%. Phylogenetic analysis indicated that strain YIM 001(T) belongs to the genus Streptomyces. Based on its phenotypic and genotypic characteristics, strain YIM 001(T) (=CCTCC AA 203005(T)=CIP 107974(T)=DSM 41837(T)) is proposed as the type strain of a novel species, Streptomyces hebeiensis sp. nov.

Base Composition↗
PubMedDate not supplied

Immunological study on the wall proteins of different fruiting portions in Pleurotus ostreatus (Jacq. ex Fr.) Kummer and Agaricus bisporus (Lge.) Sing.

Immunological techniques are useful to clarify the sistematic scheme utilized for mushrooms. By comparing the various fruiting portions, a different composition in protein was observed in the cell wall of spores, pileus and stipe. The differences were present both in Agaricus bisporus and in Pleurotus ostreatus. The results indicate that a well definite choice of the utilized portions is necessary for comparative studies. In the Basidiomycetes the meiospores represent the more useful development stage to carry out immunological comparisons.

Agaricales↗
PubMed1994

Cell Wall Metabolism in Ripening Fruit (VII. Biologically Active Pectin Oligomers in Ripening Tomato (Lycopersicon esculentum Mill.) Fruits).

A water-soluble, ethanol-insoluble extract of autolytically inactive tomato (Lycopersicon esculentum Mill.) pericarp tissue contains a series of galacturonic acid-containing (pectic) oligosaccharides that will elicit a transient increase in ethylene biosynthesis when applied to pericarp discs cut from mature green fruit. The concentration of these oligosaccharides in extracts (2.2 [mu]g/g fresh weight) is in excess of that required to promote ethylene synthesis. Oligomers in extracts of ripening fruits were partially purified by preparative high-performance liquid chromatography, and their compositions are described. Pectins were extracted from cell walls prepared from mature green fruit using chelator and Na2CO3 solutions. These pectins are not active in eliciting ethylene synthesis. However, treatment of the Na2CO3-soluble, but not the chelator-soluble, pectin with pure tomato polygalacturonase 1 generates oligomers that are similar to those extracted from ripening fruit (according to high-performance liquid chromatography analysis) and are active as elicitors. The possibility that pectin-derived oligomers are endogenous regulators of ripening is discussed.

Journal Article↗
PubMed1997

Structural characterization of molecular phospholipid species in cytoplasmic membranes of the cell wall-less Streptomyces hygroscopicus L form by use of electrospray ionization coupled with collision-induced dissociation mass spectrometry.

A comparative analysis of the lipid compositions and fatty acids in the cytoplasmic membranes of Streptomyces hygroscopicus and its stable cell wall-less L form has been carried out to detect the differences which may be involved in the altered properties of the L-form membranes. Because only quantitative differences could be found (8), we analyzed the lipid components at the molecular level. Electrospray ionization (ESI), collision-induced dissociation (CID), and tandem mass spectrometry (MS-MS) were used for qualitative detection and quantitative determination of the molecular lipid species in phosphatidylethanolamine (PE1), lyso-cardiolipin (LCL), and cardiolipin (CL). Each phospholipid, isolated by preparative high-performance liquid chromatography showed several homologous molecular ion groups (PE1, four groups; LCL, six groups; CL, six groups) in the negative ESI-MS spectra. The sizes of the peaks represent their relative amounts in the corresponding phospholipid classes. Structural details about individual components of the molecular ion groups were obtained by mass selection and CID with MS-MS. Product ions derived from CID (daughter ions) give information about the molecular weights of the acyl constituents. The qualitative and quantitative compositions of the molecular species were determined by combining the data from the fatty acid pattern obtained by gas chromatography (GC), the relative quantities of the molecular ion groups, and the acyl constituents detected in these molecular ions. Because the ESI-MS-CID-MS data do not allow us to distinguish between n, iso, and anteiso fatty acids of the same molecular weight, it has been assumed that the ratio of these equal-numbered fatty acids determined by GC analysis of the isolated fatty acids is also present in the CID-MS peaks. In this way, 18 species were found in PE1, 43 species were estimated in LCL, and 59 species were ascertained for CL.

Cell Membrane↗
PubMed1997

beta-Glucosylated proteins in the cell wall of the black yeast Exophiala (Wangiella) dermatitidis.

Wild-type cells of the pathogenic black yeast Exophiala (Wangiella) dermatitidis grown in a low-pH ascorbate medium became less melanized and less resistant to Zymolyase. This was accompanied by increased staining with fluorescently labelled concanavalin A. The sugar composition of wild-type and mutant cell walls was, except for the presence of galactose, similar to that of Saccharomyces cerevisiae. Digestion of mutant cell walls with laminarinase released galactomannoproteins. In addition, the released cell wall proteins contained glucose and reacted with affinity-purified 1,6-beta-glucan antiserum, indicating that they are linked to 1,6-beta-glucan. It is proposed that 1,6-beta-glucosylated cell wall proteins generally occur among ascomycetes.

Carbohydrate Conformation↗
PubMed2006

Plant glycoside hydrolases involved in cell wall polysaccharide degradation.

The cell wall plays a key role in controlling the size and shape of the plant cell during plant development and in the interactions of the plant with its environment. The cell wall structure is complex and contains various components such as polysaccharides, lignin and proteins whose composition and concentration change during plant development and growth. Many studies have revealed changes in cell walls which occur during cell division, expansion, and differentiation and in response to environmental stresses; i.e. pathogens or mechanical stress. Although many proteins and enzymes are necessary for the control of cell wall organization, little information is available concerning them. An important advance was made recently concerning cell wall organization as plant enzymes that belong to the superfamily of glycoside hydrolases and transglycosidases were identified and characterized; these enzymes are involved in the degradation of cell wall polysaccharides. Glycoside hydrolases have been characterized using molecular, genetic and biochemical approaches. Many genes encoding these enzymes have been identified and functional analysis of some of them has been performed. This review summarizes our current knowledge about plant glycoside hydrolases that participate in the degradation and reorganisation of cell wall polysaccharides in plants focussing particularly on those from Arabidopsis thaliana.

Arabidopsis↗
PubMed1989

Validity of Candida natalensis van der Walt et Tscheuschner.

In order to verify whether Candida natalensis is a synonym of Candida sake or not, we investigated DNA base composition, DNA-DNA hybridization, the electrophoretic patterns of enzymes, and proton magnetic resonance (PMR) spectra of cell wall mannans of representative strains of C. natalensis and C. sake. No significant differences in DNA base compositions were found among strains of C. natalensis and C. sake. Very low DNA relatedness was detected between the type strain of C. natalensis and the type strain of C. sake, and little DNA relatedness was demonstrated between a strain of C. natalensis and the type strain of C. sake. Furthermore, little DNA relatedness was found between the type strain and a strain of C. natalensis. These results well correlated with those of the electrophoretic patterns of seven enzymes and PMR spectra of cell wall mannans. C. natalensis is a distinct species from C. sake. Also, one strain, which was previously identified as C. natalensis, is a different species from C. natalensis and C. sake.

Base Composition↗
PubMed2004

Enzymatic high digestion of soybean milk residue (okara).

The objective of this study was to digest okara in high yield by food-processing enzymes. Autoclaving of okara was effective in increasing cellulase digestion for the primary cell wall, and the digestion was accelerated by the formation of single cells by stirring. Most of the residual okara after autoclaving and cellulase digestion was found to be the secondary cell walls compared with the cellulase-treated soybean single cells. The secondary cell wall was found to be composed of galacturonic acid, neutral sugars, and protein and was considered to be a complex of these compositions. Many cellulolytic and proteolytic enzymes could not digest the secondary cell wall; however, it was found that two pectinases could digest the secondary cell wall. A series of digestions resulted in yields of 83-85% from the raw okara, and the final residues were identified as oil body complexes in the soybean cells and fiber-like organ between the cells.

Cell Wall↗
PubMed1992

Mechanism of chlorpromazine binding by gram-positive and gram-negative bacteria.

Chlorpromazine forms charge-transfer complexes with xanthene dyes in bacteria. These complexes permit the differentiation of Gram-positive and Gram-negative bacteria in both light and polarization microscopy. The birefringence induced by the charge-transfer complex might explain the molecular basis of bacterial staining. The charge-transfer complexes formed between chlorpromazine and xanthene dyes accumulate in the bacterial cell, mainly inside the bacterial cell wall. The complexes give the cells a color, which depends on the chemical composition of the staining structure, and in particular the polysaccharides of the cell wall in bacteria. Metachromatic granules were seen inside Gram-positive bacteria after chlorpromazine and rose bengal staining. Although the nature of these granules remains unclear, this type of binding may have a role in the inhibition of biochemical processes in the bacterial cells.

Binding Sites↗
PubMed1980

Lipopolysacharides from anaerobic gram-negative rods.

The chemical composition and antigenic specificity of the cell wall lipopolysaccharides of the two main groups of Bacteroidaceae, Fusobacterium and Bacteroides species, are reviewed. Cell wall lipopolysaccharides from Fusobacterium species contain 2-keto-3-deoxy-octonate and heptose, but lipopolysaccharides isolated from Bacteroides species do not.

Bacteroidaceae↗
PubMed1990

Logic of the Escherichia coli cell cycle.

The logic of Escherichia coli's responses to environmental changes gives hope that its cell cycle will be equally well designed. During growth in a constant environment, internal signals trigger cell-cycle events such as replication initiation and cell division. Internal signals must also provide the cell with information about its present state, enabling it to coordinate the synthesis of cytoplasm, DNA and cell wall and maintain proper cell shape and composition. How the cell regulates these aspects of its growth is a fascinating--and as yet unfinished--story.

Cell Cycle↗
PubMed1998

Identification and molecular characterization of a gene homologous to epr (endopeptidase resistance gene) in Staphylococcus aureus.

Certain Staphylococci possess a gene called epr or lif that renders the cells resistant to lysis by glycylglycine endopeptidase. The resistance is conferred by modifying the amino acid composition of interpeptide chains in cell-wall peptidoglycan by increasing serine content and decreasing glycine content. A gene homologous to epr/lif was cloned from S. aureus RN450 genomic libraries and designated eprh. eprh was found to localize 27bp downstream of a novel cell-wall hydrolase gene lytN, which is in the same orientation with eprh. By analogy with epr/lif, eprh is suggested to be involved in the transfer of certain amino acids, possibly serine or amino acids other than glycine, to interpeptide chains of cell-wall peptidoglycan. Unlike epr/lif, overexpression of eprh in S. aureus did not result in an increased resistance to lysostaphin. Insertional inactivation of eprh or lytN by Campbell-type integration did not affect the susceptibility of the cells to lysostaphin, either. These results suggest that eprh and lytN are not essential genes for S. aureus growth. The physiological function of eprh remains unknown.

Amino Acid Sequence↗
PubMed2002

Use of the nuclear gene glyceraldehyde 3-phosphate dehydrogenase for phylogeny reconstruction of recently diverged lineages in Mitthyridium (Musci: Calymperaceae).

A portion of the nuclear gene glyceraldehyde 3-phosphate dehydrogenase (gpd) was sequenced in 26 representatives of the paleotropical moss, Mitthyridium, and a group of 20 outgroup taxa to assess its utility for phylogenetic reconstruction compared with the better understood chloroplast markers, rps4 and trnL. Primers based on plant and fungal sequences were designed to amplify gpd in plants universally with the exclusion of fungal contaminants. The piece amplified spanned 4 introns and 3 of 9 exons, based on comparisons with complete sequence from Arabidopsis. Size variation in gpd ranged from 891 to 1007 bp, in part attributable to 6 indels of variable length found within the introns. Intron 6 contributed most of the length variation and contained a variable purine-repeat motif of possible use as a microsatellite. Phylogenetic analyses of the full gpd amplicon yielded well-resolved trees that were in nearly full accord with the trees derived from the cpDNA partitions for analyses of both the ingroup and ingroup + outgroup taxon sets. Pairwise nucleotide substitution rates of gpd were as much as 2.2 times higher than those in rps4 and 2.8 times higher than in trnL. Excision of the introns left suitable numbers of parsimony informative characters and demonstrated that the full gpd amplicon could be compartmentalized to provide resolution for both shallow and deep phylogenetic branches. Exons of gpd were found to behave in a clock-like fashion for the 26 ingroup taxa and select outgroups. In general, gpd was found to hold great promise not only for improving resolution of chloroplast-derived phylogenies, but also for phylogenetic reconstruction of recent, diversifying lineages.

Base Composition↗
PubMed1990

A putative protein kinase gene (kin1+) is important for growth polarity in Schizosaccharomyces pombe.

Mixed synthetic oligonucleotides encoding a sequence conserved among tyrosine-specific protein kinases were used to probe the genome of the fission yeast Schizosaccharomyces pombe. A single gene (kin1+) was isolated that encodes a putative protein kinase closely related to the KIN1- and KIN2-encoded serine/threonine-specific protein kinases of Saccharomyces cerevisiae. kin1+ is transcribed into a 3.5-kilobase mRNA that contains an uninterrupted open reading frame encoding a polypeptide of 98 kDa. In contrast to results obtained with kin mutants of S. cerevisiae, disruption of the Sc. pombe kin1+ gene resulted in recessive morphological and growth defects. kin1-disrupted cells grew slowly on enriched medium and grew as spheres, in contrast to wild-type Sc. pombe cells, which grow as rods. Relative to kin1+ cells, kin1-disrupted cells were differentially sensitive to lysis by treatment with alpha- and beta-glucanases, suggesting an alteration in either the composition or the organization of their cell walls.

Amino Acid Sequence↗