Identification of nocobactin NA biosynthetic gene clusters in Nocardia farcinica

We identified the biosynthetic gene clusters of the siderophore nocobactin NA. The nbt clusters, which were discovered as genes highly homologous to the mycobactin biosynthesis genes by the genomic sequencing of Nocardia farcinica IFM 10152, consist of 10 genes separately located at two genomic regions. The gene organization of the nbt clusters and the predicted functions of the nbt genes, particularly the cyclization and epimerization domains, were in good agreement with the chemical structure of nocobactin NA. Disruptions of the nbtA and nbtE genes, respectively, reduced and abolished the productivity of nocobactin NA. The heterologous expression of the nbtS gene revealed that this gene encoded a salicylate synthase. These results indicate that the nbt clusters are responsible for the biosynthesis of nocobactin NA. We also found putative IdeR-binding sequences upstream of the nbtA, -G, -H, -S, and -T genes, whose expression was more than 10-fold higher in the low-iron condition than in the high-iron condition. These results suggest that nbt genes are regulated coordinately by IdeR protein in an iron-dependent manner. The ΔnbtE mutant was found to be impaired in cytotoxicity against J774A.1 cells, suggesting that nocobactin NA production is required for virulence of N. farcinica.     

Sequence analysis ofp-hydroxyphenyl-O-β-d-xyloside initiated and radio-iodinated dermatan sulfate from skin fibroblasts

To generate xyloside-primed dermatan sulfate suitable for sequence analysis, skin fibroblasts were incubated withp-hydroxyphenyl--d-xylopyranoside and [³H]galactose, and free [³H]glycosaminoglycan chains were isolated from the culture medium by ion exchange and gel chromatography. After¹²⁵I labelling of their reducing-terminal hydroxyphenyl groups, chains were subjected to various chemical and enzymatic degradations, both partial and complete, followed by gradient polyacrylamide gel electrophoresis and autoradiographic identification of fragments extending from the labelled reducing-end to the point of cleavage. Results of periodate oxidation-alkaline scission indicated that the xylose moiety remained unsubstituted at C-2/C-3; exhaustive treatment with chondroitin AC-I lyase afforded the fragment HexA-Gal-Gal-Xyl-R (R = radio-iodinated hydroxyphenyl group), and complete degradations with chondroitin ABC lyase as well as testicular hyaluronidase yielded the fragments HexA/HexA-GalNAc-GlcA-Gal-Gal-Xyl-R with or without sulfate on theN-acetylgalactosamine. Partial digestions with testicular hyaluronidase or chondroitin B lyase indicated that glucuronic acid was common in the first three repeats after the linkage region and that iduronic acid could occupy any position thereafter. Hence, there were no indications of a repeated, periodic appearance of the clustered GlcA-GalNAc repeats which was previously observed in proteoglycan derived dermatan sulfate [Fransson L-Å, Havsmark B, Silverberg I (1990)Biochem J 269:381–8], suggesting a role for the protein part in controlling the formation of particular copolymeric features during glycosaminoglycan assembly.Abbreviations GAG glycosaminoglycans - CS chondroitin sulfate - DS dermatan sulfate - Ser serine - Xyl d-xylose - Gal d-galactose - GlcA d-glucuronic acid - IdoA l-iduronic acid - GalNAc N-acetyl-d-galactosamine - GlcNAc N-acetyl-d-glucosamine - HexA 4-deoxy-l-threo-hex-4-enopyranosyluronic acid - HO-Phe p-hydroxyphenyl group - HO-Phe-Xyl p-hydroxyphenyl-O--d-xylopyranoside - O₂N-Phe-Xyl p-nitrophenyl--d-xylopyranoside - OSO₃ ester sulfate - PAGE polyacrylamide gel electrophoresis - HPLC high performance liquid chromatography - FPLC fast performance liquid chromatography - LC standard liquid chromatography     

Effects of primer-concentration on uronosyl-epimerization and sulfation patterns in p-hydroxyphenyl-O-β-D-xylopyranoside-primed galactosaminoglycans produced by skin fibroblasts

By supplying skin fibroblasts with different concentrations of the galactosaminoglycan chain-primer p-hydroxyphenyl-O-β-D-xylopyranoside we have produced and recovered glycan-chains that were subsequently radio-iodinated in the hydroxyphenyl group and subjected to sequence analysis by using graded enzymic treatment followed by a combination of gel chromatography and electrophoresis. Fragments extending from the tagged reducing end to the cleavage-point were identified and quantified. Degradation by chondroitin B lyase of chains primed at 0.1 or 0.5 mM xyloside gave profiles indicating a periodic and wave-like distribution of iduronate-containing repeats, with high incidence around positions 2, 5 and onwards, whereas in chains produced at 1.0 mM xyloside the incidence of iduronate was similar in positions 1–4 and then declined. Degradation by chondroitin AC lyase indicated a high incidence of glucuronate in or near the linkage-region. There was a relatively uniform degree of sulfation in chains primed at low xyloside concentration, whereas chains primed at 1.0 mM xyloside gave very heterogeneous charge-patterns in all segments of the chain, including the linkage-region, giving the impression that adequate sulfation, probably at C-4 and at the first opportunity, is necessary to obtain an ordered and periodic epimerization pattern. Abbreviations:CS, chondroitin sulfate; DS, dermatan sulfate; GAG, glycosaminoglycan; Gal, D-galactose, GaINAc, N-acetyl-D-galactosamine; GlcUA, D-glucuronic acid; GlyUA, glycuronic acid; ΔGlyUA, 4,5-unsaturated glycuronic acid; IdoUA, L-iduronic acid; Xyl-Phe-OH, p-hydroxyphenyl-O-β-D-xylopyranoside; Xyl, D-xylose This revised version was published online in November 2006 with corrections to the Cover Date.     

Different Rifampicin Inactivation Mechanisms in Nocardia and Related Taxa

Mycolic acid-containing bacteria inactivate rifampicin in a variety of ways such as glucosylation, ribosylation, phosphorylation and decolorization. These inactivations were found to be a species-specific phenomena in Nocardia and related taxa. Gordona, Tsukamurella and fast-growing Mycobacterium modified rifampicin by ribosylation of the 23-OH group of the antibiotic. Such ribosylation was not observed in Rhodococcus and Corynebacterium, but phosphorylation of the 21-OH group of rifampicin was observed in one strain of Rhodococcus. Nocardia modified the antibiotic by glucosylation (23-OH group) and phosphorylation, but ribosylation was not observed.     

Polyethylene glycol-modified lipase catalyzes asymmetric alcoholysis of δ-decalactone in n-decanol

Summary Lipase from Pseudomonas cepacia was modified with 2,4-bis[O-methoxypoly(ethylene glycol)]-6-chloro-s-triazine(activated PEG₂) to form PEG-lipase. The PEG-lipase, soluble and active in organic solvents, catalyzes asymmetric alcoholysis of racemic -decalactone in alcohols to form (R)-5-hydroxydecanoic acid alkyl esters. The yield was 69% with 83% enantiomeric excess after 3 hr-reaction in n-decanol at 50°C. The advantage of this reaction is that the alcoholysis proceeds efficiently in straight hydrophobic substrates without any organic solvents.     

Phylogenetic Studies of <Emphasis Type="Italic">Gordonia</Emphasis> Species Based on <Emphasis Type="Italic">gyrB</Emphasis> and <Emphasis Type="Italic">secA1</Emphasis> Gene Analyses

Phylogenetic relations within the genus Gordonia were analyzed using partial gyrB and secA1 gene sequences of 23 type species in comparison with those of 16S rRNA gene. The gyrB and secA1 phylogenies showed agreement with that constructed using 16S rRNA gene sequences. The degrees of divergence of the gyrB and secA1 genes were approximately 3.4 and 1.7 times greater, respectively, than that of 16S rRNA gene. The gyrB gene showed more discriminatory power than either the secA1 or 16S rRNA gene, facilitating clear differentiation of any two Gordonia species using gyrB gene analysis. Our data indicate that gyrB and secA1 gene sequences are useful as markers for phylogenetic study and identification at the species level of the genus Gordonia.     

Nocardia beijingensis,is a Pathogenic Bacterium to Humans: The First Infectious Cases in Thailand and Japan

Nocardia beijingensis, a recently established new species, is an isolate from soil in China. During our taxonomic studies on 450 nocardial clinical isolates in Thailand and Japan, 17 strains from Thailand and 1 strain from Japan were found to have a similar physiological characteristic to those of N. beijingensis, such as a drug susceptibility pattern to three antimicrobial agents. Our phylogenetic studies on these 18 strains by 16S rRNA gene sequence analysis confirmed that these strains belong to N. beijingensis species. Phylogenetically, these newly isolated N. beijingensis strains were found to be classified into two distinct clades: one is a Japanese clade and other is a Chinese clade, including a reference strain and 17 Thai strains. This is the first report of human infection due to N. beijingensis strains, and we propose that the bacterium be categorized as an opportunistic infectious group regardless of its original isolation from soil.     

First human case of nocardiosis caused by Nocardia pseudobrasiliensis in Japan

Nocardia sp. IFM 0896, an actinomycete with biochemical characteristics that differed from Nocardia brasiliensis, was isolated from a 71-year-old Japanese man with a history of tuberculosis and cancer. Although the isolate was tentatively identified as N. brasiliensis, the morphological and physiological characteristics of strain IFM 0896 were different from those of N. brasiliensis IFM 0236T. The results of 16S rRNA gene sequence phylogenies and PCR-RFLP analysis of a heat shock protein revealed that Nocardia sp. IFM 0896 belongs to the species N. pseudobrasiliensis. This is the first clinical isolation report of N. pseudobrasiliensis in Japan.