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PubMed1967

Metabolism of 4-chloro-2-methylphenoxyacetic Acid by soil bacteria.

A microorganism capable of degrading 4-chloro-2-methylphenoxyacetic acid (MCPA) was isolated from soil and identified as Flavobacterium peregrinum. All of the chlorine of MCPA was released as chloride, and the carboxyl-carbon was converted to volatile products by growing cultures of the bacterium, but a phenol accumulated in the medium. The phenol was identified as 4-chloro-2-methylphenol on the basis of its gas chromatographic and infrared characteristics. Extracts of cells of F. peregrinum and of a phenoxyacetate-metabolizing Arthrobacter sp. dehalogenated MCPA and several catechols but not 4-chloro-2-methylanisole. The Arthrobacter sp. cell extract was fractionated, and an enzyme preparation was obtained which catalyzed the conversion of MCPA to 4-chloro-2-methylphenol. The latter compound was not metabolized unless reduced nicotinamide adenine dinucleotide phosphate was added to the fractionated extract. The phenol in turn was apparently oxidized to a catechol by components of the enzyme preparation.

Journal Article↗

PubMed1975

Microbiological characteristics of Dungeness crab (Cancer magister).

Aerobic, heterotropic microorganisms of Dungeness crab (Cancer magister) were isolated from raw crab, cooked crab, crab meats obtained during commercial processing, and from retail crab meat samples. Each microbial isolate was then identified to the genus level employing the revised replica plating procedure. Microbial groups most commonly isolated from crab meat were, in the order of predominance, Moraxella, Pseudomonas, Acinetobacter, Arthrobacter, Micrococcus, Flavobacterium-Cytophaga, and Bacillus sp. Proteus, Staphylococcus, yeasts, Vibrio, and Lactobacillus sp. were found less frequetly in some samples. Distribution patterns of microbial flora in crab meat revealed the presence of three classes of microorganisms. Microorganisms that originated from the raw crab and gained predominance by growth during refrigerated storage were Moraxella, Pseudomonas, Acinetobacter, and Flavobacterium-Cytophaga sp. Those that originated from the crab but did not grow in meat were Arthrobacter and Bacillus sp. Micrococcus, Staphylococcus, and Proteus sp. were introduced during processing, but they did not grow in the refrigerated crab meat.

Aerobiosis↗

PubMed1987

Metabolism of endogenous trehalose by Streptomyces griseus spores and by spores or cells of other actinomycetes.

The disaccharide trehalose is accumulated as a storage product by spores of Streptomyces griseus. Nongerminating spores used their trehalose reserves slowly when incubated in buffer for several months. In contrast, spores rapidly depleted their trehalose pools during the first hours of germination. Extracts of dormant spores contained a high specific activity of the enzyme trehalase. The level of trehalase remained relatively constant during germination or incubation in buffer. Nongerminating spores of Streptomyces viridochromogenes, Streptomyces antibioticus, and Micromonospora echinospora and nongrowing spherical cells of Arthrobacter crystallopoietes and Nocardia corallina also maintained large amounts of trehalose and active trehalase. These trehalose reserves were depleted during spore germination or outgrowth of spherical Arthrobacter and Nocardia cells into rods.

Actinomycetales↗

PubMed1990

Mechanism of gram variability in select bacteria.

Gram stains were performed on strains of Actinomyces bovis, Actinomyces viscosus, Arthrobacter globiformis, Bacillus brevis, Butyrivibrio fibrisolvens, Clostridium tetani, Clostridium thermosaccharolyticum, Corynebacterium parvum, Mycobacterium phlei, and Propionibacterium acnes, using a modified Gram regimen that allowed the staining process to be observed by electron microscopy (J. A. Davies, G. K. Anderson, T. J. Beveridge, and H. C. Clark, J. Bacteriol. 156:837-845, 1983). Furthermore, since a platinum salt replaced the iodine mordant of the Gram stain, energy-dispersive X-ray spectroscopy could evaluate the stain intensity and location by monitoring the platinum signal. These gram-variable bacteria could be split into two groups on the basis of their staining responses. In the Actinomyces-Arthrobacter-Corynebacterium-Mycobacterium-Propionibacterium group, few cells became gram negative until the exponential growth phase; by mid-exponential phase, 10 to 30% of the cells were gram negative. The cells that became gram negative were a select population of the culture, had initiated septum formation, and were more fragile to the stress of the Gram stain at the division site. As cultures aged to stationary phase, there was a relatively slight increase toward gram negativity (now 15 to 40%) due to the increased lysis of nondividing cells by means of lesions in the side walls; these cells maintained their rod shape but stained gram negative. Those in the Bacillus-Butyrivibrio-Clostridium group also became gram negative as cultures aged but by a separate set of events. These bacteria possessed more complex walls, since they were covered by an S layer. They stained gram positive during lag and the initial exponential growth phases, but as doubling times increased, the wall fabric underlying the S layer became noticeably thinner and diffuse, and the cells became more fragile to the Gram stain. By stationary phase, these cultures were virtually gram negative.

Bacillus↗

PubMed1995

Comparison of 16S ribosomal RNA genes in Clavibacter michiganensis subspecies with other coryneform bacteria.

Nearly complete sequences (97-99%) of the 16S rRNA genes were determined for type strains of Clavibacter michiganensis subsp. michiganensis, Clavibacter michiganensis subsp. insidiosus, Clavibacter michiganensis subsp. sepedonicus, and Clavibacter michiganensis subsp. nebraskensis. The four subspecies had less than 1% dissimilarity in their 16S rRNA genes. Comparative studies indicated that the C. michiganensis subsp. shared relatively high homology with the 16S rRNA gene of Clavibacter xyli. Further comparison with representatives of other Gram-positive coryneform and related bacteria with high G+C% values showed that this group of bacteria was subdivided into three clusters. One cluster consisted of the Clavibacter michiganensis subsp., Clavibacter xyli, Arthrobacter globiformis, Arthrobacter simplex, and Frankia sp.; another cluster consisted of members of the corynebacteria-mycobacteria-nocardia (CMN) group of Mycobacteriaceae including Tsukamurella paurometabolum; and Propionibacterium freudenreichii alone formed a unique cluster, which was remote from other coryneform bacteria analyzed. The three clusters may reflect a systematic rank higher than the genus level among these bacteria.

Actinomycetales↗

PubMed2002

Cultivation-dependent characterization of bacterial diversity from British Columbia forest soils subjected to disturbance.

Bacteria from forest surface organic matter and mineral soil horizons were cultivated using four methods and characterized by fatty acid methyl ester (FAME) analysis. Soil samples from a British Columbia Ministry of Forests Long-Term Soil Productivity (LTSP) installation were collected during winter and summer from two disturbance treatments (whole-tree harvesting with no soil compaction (plot N) and whole-tree harvesting plus complete surface organic matter removal with heavy soil compaction (plot S)) and from an unlogged reference plot (REF). Seventy-five percent of 1795 bacterial isolates were affiliated with 42 genera representing beta- and gamma-Proteobacteria, Actinobacteria, the Bacillus/Clostridium group, and the Cytophaga-Flexibacter-Bacteroides group. Approximately half of the culture collection represented genetic diversity confined to four bacterial genera: Pseudomonas, Bacillus, Paenibacillus, and Arthrobacter. A significantly higher proportion of bacterial isolates belonging to Actinobacteria, and the member genus Arthrobacter, were isolated from plot S soil samples compared with soil samples from plots N and REF. Twenty-five percent of bacterial isolates were not conclusively identified to genus with FAME analysis. Sherlock Tracker cluster analysis and partial 16S rRNA gene sequence analysis enabled classification of a subset of these isolates.

Bacteria↗

PubMed1982

Distribution of beta-lactam and beta-lactone producing bacteria in nature.

Over one million bacteria were isolated from a large variety of soil, plant and water samples collected from different environments and examined in an extremely sensitive and highly specific screen for beta-lactam production. A group of seven related monocyclic beta-lactams (monobactams) were isolated from strains representing four genera-Agrobacterium, Chromobacterium, Gluconobacter and Pseudomonas. Monobactam-producing strains of Agrobacterium and Pseudomonas were isolated only rarely. Producing strains of Chromobacterium were isolated from a relatively limited number of habitats while the Gluconobacter strains appeared to be widespread in nature. In addition, three closely related beta-lactone-containing molecules were isolated from strains representing three genera-Arthrobacter, Bacillus and Pseudomonas. The Bacillus and Pseudomonas strains were isolated infrequently but from a variety of samples. The producing strain of Arthrobacter was isolated only once.

Anti-Bacterial Agents↗

PubMed1999

Cloning and sequencing of the fcbB gene encoding 4-chlorobenzoate-coenzyme A dehalogenase from Pseudomonas sp. DJ-12.

Pseudomonas sp. DJ-12 degrades 4-chlorobenzoate through hydrolytic dechlorination to produce 4-hydroxybenzoate and a chloride ion. The fcbB gene encoding the 4-chlorobenzoate-coenzyme A (4CBA-CoA) dehalogenase which catalyzes the nucleophilic substitution reaction to convert 4CBA-CoA to 4-hydroxybenzoate-coenzyme A (4HBA-CoA) in the consecutive steps of dechlorination was cloned from the chromosome of the organism. A nucleotide sequence analysis of the gene showed an open reading frame consisting of 810 nucleotides, which can encode for a polypeptide of molecular mass 30 kDa, containing 269 amino acid residues. A promoter-like sequence (-35 and -10 region) and a putative ribosome-binding sequence were identified. A deduced amino acid sequence of the 4CBA-CoA dehalogenase showed 86%, 50%, and 50% identity with those of corresponding enzymes in the Pseudomonas sp. CBS3, Arthrobacter sp. SU, and Arthrobacter sp. TM1, respectively.

Amino Acid Sequence↗

PubMed2002

[The existence of contamination in enzymes used for the isolation of Aspergillus and Candida species DNA].

Molecular biological methods which are widely used in different fields, have been replaced with conventional diagnostic tests for the early diagnosis of invasive fungal infections, recently. Polymerase chain reaction (PCR) is one of these methods, with high specificity and sensitivity, which is accepted throughout the world. However, the enzymes that are used for the isolation of target DNA, may be contaminated with the gene sequences of some other fungal species in the preparation steps and may affect the PCR results. The studies showed that, the contamination of these enzymes with any type of fungi during their production steps, leads false positive results in PCR tests. So, the additional studies are recommended for minimizing the contamination. The aim of this study was to search whether the enzymes necessary for the isolation of fungal target DNA, used in PCR, are contaminated or not. For this purpose, five different enzymes namely, Zymolase 20T (from Arthrobacter luteus, two examples from different companies), lyticase (from Arthrobacter luteus), lysing enzyme (from Trichoderma harzianum) and proteinase K (from Tritrachium album) have been investigated for the presence of contamination. As a result, both of zymolase 20T enzymes were found to be contaminated from some fungal species with the demonstration of 18S rRNA gene sequences, while the other enzymes were found non-contaminated. By the help of this method, the most suitable enzyme for PCR was chosen and fungal contamination was prevented.

Aspergillus fumigatus↗

PubMed1965

MICROBIAL DEGRADATION OF ISOPROPYL-N-3 -CHLOROPHENYLCARBAMATE AND 2-CHLOROETHYL-N-3-CHLOROPHENYLCARBAMATE.

Microbial degradation of isopropyl-N-3-chlorophenylcarbamate (CIPC) and 2-chloroethyl-N-3-chlorophenylcarbamate (CEPC) was observed in a soil perfusion system. Degradation in perfused soils, and by pure cultures of effective bacterial isolates, was demonstrated by the production of 3-chloroaniline and the subsequent liberation of free chloride ion. Identified isolates effective in degrading and utilizing CIPC as a sole source of carbon included Pseudomonas striata Chester, a Flavobacterium sp., an Agrobacterium sp., and an Achromobacter sp. Identified isolates, effective in degrading and utilizing CEPC as a sole source of carbon, included an Achromobacter sp. and an Arthrobacter sp. CIPC-effective isolates degraded CEPC more slowly than CIPC, whereas CEPC-effective isolates degraded CIPC more rapidly than CEPC. Both CIPC- and CEPC-effective isolates degraded isopropyl N-phenylcarbamate (IPC) more rapidly than either CIPC or CEPC.

Achromobacter↗

PubMed1965

LYSIS OF BACTERIAL CELL WALLS BY AN ENZYME ISOLATED FROM A MYXOBACTER.

Ensign, J. C. (University of Illinois, Urbana), and R. S. Wolfe. Lysis of bacterial cell walls by an enzyme isolated from a myxobacter. J. Bacteriol. 90:395-402. 1965.-An exoenzyme which lyses intact cells, heat-killed cells, and cell walls of Arthrobacter crystallopoietes was purified 60-fold from the growth liquor obtained from a myxobacter (strain AL-1). The lytic enzyme was produced during growth of the organism in a number of complex media, the maximal amount of enzyme being produced in yeast extract broth. The purified enzyme lysed at different rates a number of gram-positive bacteria. With the exception of Rhodospirillum rubrum, Spirillum itersonii, and S. serpens, the gram-negative bacteria tested were not attacked.

Arthrobacter↗

PubMed1979

Mass-transfer effects on the rate of isomerization of D-glucose into D-fructose, catalyzed by whole-cell immobilized glucose isomerase.

The investigated catalyst system consists of immobilized Arthrobacter cells containing the enzyme glucose isomerase, which catalyzes the isomerization of glucose into fructose. The internal structure of the catalyst was determined from electrom microscope photographs of replicas of freeze-etched catalyst. On the basis of the photographs a model for the internal structure of the catalyst was proposed. This structure was subsequently used to describe the reaction including mass-transfer effects. It appeared that under normal operating conditions the external mass-transfer rate does not influence the overall rate of reaction. The effect of internal mass-transfer resistances on the overall reaction rate can well be accounted for by the so-called porous sphere model. The intrinsic kinetics of the isomerization catalyzed by the present catalyst system can be represented by a modified Michaelis-Menten equation for a reversible one-substrate reaction.

Arthrobacter↗

PubMed2006

Glycopeptide synthesis through endo-glycosidase-catalyzed oligosaccharide transfer of sugar oxazolines: probing substrate structural requirement.

An array of sugar oxazolines was synthesized and tested as donor substrates for the Arthrobacter endo-beta-N-acetylglucosaminidase (Endo-A)-catalyzed glycopeptide synthesis. The experiments revealed that the minimum structure of the donor substrate required for Endo-A catalyzed transglycosylation is a Man beta1-->4-GlcNAc oxazoline moiety. Replacement of the beta-D-Man moiety with beta-D-Glc, beta-D-Gal, and beta-D-GlcNAc monosaccharides resulted in the loss of substrate activity for the disaccharide oxazoline. Despite this, the enzyme could tolerate modifications such as attachment of additional sugar residues or a functional group at the 3- and/or 6-positions of the beta-D-Man moiety, thus allowing a successful transfer of selectively modified oligosaccharides to the peptide acceptor. On the other hand, the enzyme has a great flexibility for the acceptor portion and could take both small and large GlcNAc-peptides as the acceptor. The studies implicate a great potential of the endoglycosidase-catalyzed transglycosylation for constructing both natural and selectively modified glycopeptides.

Amino Acid Sequence↗

PubMed1979

Chitin structures of the cell walls of synchronously grown virgin cells of Saccharomyces cerevisiae.

The ability of a lytic beta-glucanase of Arthrobacter GJM-1 to dissolve cell walls of Saccharomyces cerevisiae with exception of the chitin-containing fraction was employed for the isolation of chitin-rich residues of the cell walls of synchronously growing populations of virgin cells. Electron microscopical examination of such wall residues isolated from cells at various stages of the budding cycle showed that the first phase of chitin deposition in the wall corresponds to the formation of an annular structure found as a part of the bud scar after cell division. The annular chitin-rich structure could not be isolated at cell cycle stages preceding the bud emergence and at earliest stages of bud development. The observations confirmed that the annular structure (chitin ring) formed during bud growth represents a major part of total chitin present in the bud scar after septum closure.

Arthrobacter↗

PubMed1980

A critical analysis of kinetic data of 3-hexulosephosphate synthases. Michaelis-Menten or complex characteristics.

Investigations of the 3-hexulosephosphate synthase (HPS) from different methylotrophic bacteria have revealed apparent discrepancies in kinetic behaviour. In all methanol-utilizing species investigated by us the kinetic characteristics showed intermediary plateau regions. Therefore, this behaviour is assumed to be a general feature of the HPS from all non-methane-utilizing methylotrophic bacteria. However, this assumption is in contrast to the results of other authors. Both for Methylomonas M15 (SAHM et al. 1976) and Methylomonas aminofaciens 77a (KATO et al. 1977, 1978) MICHAELIS-MENTEN kinetics of the HPS were stated. To check the validity of our assumption we have analyzed the kinetic data given by others. Indications of the existence of intermediary plateau regions could be found with the enzyme from Arthrobacter globiformis (BYKOVSKAYA and VORONKOV 1977) and Methylomonas aminofaciens 77a (KATO et al. 1978). Furthermore, biphasic ARRHENIUS plots indicate a multiple character of the HPS from these species as could already be demonstrated with the enzyme from Bacterium MB 58 and Pseudomonas oleovorans. In addition, causes which may obscure the detection of intermediary plateau regions are demonstrated.

Aldehyde-Lyases↗

PubMed2000

Kinetics of biodegradation of p-nitrophenol by different bacteria.

Three bacterial species, i.e., Ralstonia sp. SJ98, Arthrobacter protophormiae RKJ100, and Burkholderia cepacia RKJ200, have been examined for their efficiency and kinetics behavior toward PNP degradation. All the three bacteria utilized PNP as the sole source of carbon, nitrogen, and energy. The rates of radiolabeled [U-(14)C]PNP degradation by all the bacteria were higher in the nitrogen-free medium compared to the medium with nitrogen. The apparent K(m) values of PNP degradation by SJ98, RKJ100, and RKJ200 were 0.32, 0.28, and 0.23 mM, respectively, as determined from the Michaelis-Menten curves. The maximum rates of PNP degradation (V(max)) according to Lineweaver-Burk's plots were 11.76, 7.81, and 3.84 micromol PNP degraded/min/mg dry biomass, respectively. The interpretation drawn from the Lineweaver-Burk's plots showed that the PNP degradation by SJ98 was stimulated by 4-nitrocatechol and 1, 2,4-benzenetriol. Benzoquinone and hydroquinone inhibited PNP degradation by RKJ100 noncompetitively and competitively, respectively, whereas in the case of RKJ200, benzoquinone and hydroquinone inhibited PNP degradation in an uncompetitive manner. beta-Ketoadipate did not affect the rate of PNP degradation in any case.

Arthrobacter↗

PubMed2001

A unique sialidase that cleaves the Neu5Gcalpha2-->5-O(glycolyl)Neu5Gc linkage: comparison of its specificity with that of three microbial sialidases toward four sialic acid dimers.

We found that the hepatopancreas of oyster, Crassostrea virginica, contained a sialidase capable of releasing Neu5Gc from the novel polysialic acid chain (-->5-O(glycolyl)Neu5Gcalpha2-->)n more efficiently than from the conventional type of polysialic acid chains, (-->8Neu5Acalpha2-->)n, or (-->8Neu5Gcalpha2-->)n. We have partially purified this novel sialidase and compared its reactivity with that of microbial sialidases using four different sialic acid dimers, Neu5Gcalpha2-->5-O(glycolyl)Neu5Gc (Gg2), Neu5Acalpha2-->8Neu5Ac (A2), Neu5Gcalpha2-->8Neu5Gc (G2), and KDNalpha2-->8KDN (K2) as substrates. Hydrolysis was monitored by high performance anion-exchange chromatography with a CarboPac PA-100 column and pulsed amperometric detection, the method by which we can accurately quantitate both the substrate (sialiac acid dimers) and the product (sialic acid monomers). The oyster sialidase effectively hydrolyzed Gg2 and K2, whereas A2 and G2 were poor substrates. Neu5Ac2en but not KDN2en effectively inhibited the hydrolysis of Gg2 by the oyster sialidase. Likewise, the hydrolysis of K2 by the oyster sialidase was inhibited by a cognate inhibitor, KDN2en, but not by Neu5Ac2en. Using the new analytical method we found that Gg2 was hydrolyzed less efficiently than A2 but much more readily than G2 by Arthrobacter ureafaciens sialidase. This result was at variance with the previous report using the thiobarbituric acid method to detect the released free sialic acid [Kitazume, S., et al. (1994) Biochem. Biophys. Res. Commun. 205, 893-898]. In agreement with previous results, Gg2 was a poor substrate for Clostridium perfringens sialidase, while K2 was refractory to all microbial sialidases tested. Thus, the oyster sialidase is novel and distinct from microbial sialidases with regards to glycon- and linkage-specificity. This finding adds an example of the presence of diverse sialidases, in line with the diverse sialic acids and sialic acid linkages that exist in nature. The new sialidase should become useful for both structural and functional studies of sialoglycoconjugates.

Animals↗

PubMed2001

Tryptophan-216 is essential for the transglycosylation activity of endo-beta-N-acetylglucosaminidase A.

Endo-beta-N-acetylglucosaminidase from Arthrobacter protophormiae (Endo-A) has a high level of transglycosylation activity. To determine which amino acids are involved in this activity, we employed deletion analysis, as well as random and site-directed mutagenesis. Using PCR random mutagenesis, 11 mutants with greatly decreased levels of enzyme activity were isolated. Six catalytically essential amino acids were identified by site-directed mutagenesis. Mutants E173G, E175Q, D206G, and D270N had markedly reduced hydrolysis activity, while mutants V109D, E173D, and E173Q lost all enzymatic activity, indicating that Val-109 and Glu-173 are important for the catalytic function. Moreover, we isolated a random mutation that abolished the transglycosylation activity without affecting the hydrolysis activity. The Trp-216 to Arg mutation was identified, by site-directed mutagenesis, as that responsible for the loss of transglycosylation activity. While other mutants of Trp-216 showed reduced activity, mutation to another positively charged residue (Lys) also abolished the transglycosylation activity. Sequence comparison with two other endo-beta-N-acetylglucosaminidases, that possess transglycosylation activity and that have been cloned recently, reveals a high degree of identity in the N-terminal regions of the three enzymes. These results indicate that the tryptophan residue at position 216 of Endo-A has a key role in the transglycosylation.

Amino Acid Sequence↗