Identification of different alkane hydroxylase systems in Rhodococcus ruber strain SP2B, an hexane-degrading actinomycete.

AIMS: To investigate the alkane-hydroxylating system of isolate SP2B, closely related to Rhodococcus ruber DSM 43338(T) and uncharacterized so far for its alkane degradation genes. METHODS AND RESULTS: Although isolate SP2B and reference strain can grow on by-products from hexane degradation, the type strain R. ruber was unable, unlike SP2B isolate, to use short-chain alkanes, as assessed by gas chromatography. Using PCR with specific or degenerated primers, inverse PCR and Southern blot, two alkane hydroxylase encoding genes (alkB) were detected in both bacteria, which is in agreement with their alkane range. The first AlkB was related to Rhodococcus AlkB7 enzymes and contains a nonbulky residue at a specific position, suggesting it might be involved in medium- and long-chain alkane oxidation. The second partial alkB gene potentially belongs to alkB5-type, which was found in bacteria unable to use hexane. Moreover, a partial P450 cytochrome alkane hydroxylase, thought to be responsible for the hexane degradation, was detected only in the isolated strain. CONCLUSIONS: Rhodococcus ruber SP2B should prove to be a promising candidate for bioremediation studies of contaminated sites because of its large degradation range of alkanes. SIGNIFICANCE AND IMPACT OF THE STUDY: This is the first thorough study on R.ruber alkane degradation systems.

Detección y caracterización cinética de una contaminación por Candida tropicales durante la producción de levadura forrajera / Detection and kinetic characterization of Candida tropicalis contamination during fodder yeast production

Se identificó a Candia tropicalis como el agente causal de una servera contaminación detectada en la producción de levadura forrajera en una fábrica de la región oriental de Cuba. Posteriormente a un detallado diagnóstico en las materias primas y diferentes secciones de la fábrica con el objetivo de identificar el foco y aislar el microorganismo contaminante, se procedió a su identificación mediante comparación de secuencias nucleotídicas de las regiones adyacentes no codificadoras ITS (internacional transcribed spacer) ITS1 a ITS4 de ADN ribosomal (ADNrib) 5,8S. En paralelo, se simuló la multiplicación celular de la cepa de producción, Candida utilis NRRL Y-660, a volumen de laboratorio (2,5l), observándose los mismos efectos negativos detectados a nivel industrial sobre su comportamiento cinético al conducir un cultivo en condiciones aerobias con melazas contaminadas. La identificación y caracterización cinética primaria permitió la adopción de medidas higiénico-sanitarias y de carácter tecnológico restableciéndose la producción a la vez que se adoptó una metodología para la vigilancia profiláctica de futuras contaminaciones(AU)

Candida tropicalis was identified as the etiologic agent of a severe contamination detected on an industrial fodder yeast production at the Cuban eastern region. After a detailed diagnostic task on raw material carried out on different factory sections, protocols to identify the contamination source and to isolate the microorganism were proposed. The identification was by comparison of the internal transcribed spacers ITS1 and ITS4 from 5.8S ribosomal DNA nucleotide sequences. In parallel, propagation of production strain, Candida utilis NRRL Y-660, at lab scale (2.5 l) was performed. Similar results to those observed in the factory concerning to its kinetic behavior in aerobic propagation with contaminated molasses, were detected at this level. The identification and primary kinetic characterization led to the implementation of sanitary and technological measures to bring production at its normal operational conditions as well as the application of prophylactic surveillance methodologies to avoid future contaminations(AU)

Production of heterologous and chimeric scaffoldins by Clostridium acetobutylicum ATCC 824.

Clostridium acetobutylicum ATCC 824 converts sugars and various polysaccharides into acids and solvents. This bacterium, however, is unable to utilize cellulosic substrates, since it is able to secrete very small amounts of cellulosomes. To promote the utilization of crystalline cellulose, the strategy we chose aims at producing heterologous minicellulosomes, containing two different cellulases bound to a miniscaffoldin, in C. acetobutylicum. A first step toward this goal describes the production of miniCipC1, a truncated form of CipC from Clostridium cellulolyticum, and the hybrid scaffoldin Scaf 3, which bears an additional cohesin domain derived from CipA from Clostridium thermocellum. Both proteins were correctly matured and secreted in the medium, and their various domains were found to be functional.

Maturation of the [NiFe] hydrogenases.

The high degree of similarity that exists between all the [NiFe] hydrogenase operons and the near universality of hydrogen metabolism among microorganisms suggest that the microbial ability to metabolize hydrogen is of great importance and ancient origin. The large number of genes present in these operons, which are mostly involved in the maturation of the structural subunit, is indicative of the complexity of the hydrogenase molecular structure. Two main groups of maturation genes can be differentiated based on the resulting phenotypes when mutated: the 'cis-genes', encoding narrow specificity proteins, are mainly located on the same transcription unit as the structural genes, and the 'trans-genes', encoding broad specificity proteins, are located on a different operon. The maturation of the large subunit starts with the formation of a complex with the chaperone HypC, which remains bound to the amino terminus throughout processing. The ligands CN and CO, which are derived from carbamoylphosphate, are then inserted via HypF and probably other accessory proteins. HypB is responsible for nickel atom delivery in a GTP-hydrolysis-dependent reaction. The last identified step in the large subunit maturation process is proteolytic cleavage at the carboxyl terminus. The possible roles of the other maturation proteins are also discussed.

Cytochrome c(3) mutants of Desulfovibrio desulfuricans.

To explore the physiological role of tetraheme cytochrome c(3) in the sulfate-reducing bacterium Desulfovibrio desulfuricans G20, the gene encoding the preapoprotein was cloned, sequenced, and mutated by plasmid insertion. The physical analysis of the DNA from the strain carrying the integrated plasmid showed that the insertion was successful. The growth rate of the mutant on lactate with sulfate was comparable to that of the wild type; however, mutant cultures did not achieve the same cell densities. Pyruvate, the oxidation product of lactate, served as a poor electron source for the mutant. Unexpectedly, the mutant was able to grow on hydrogen-sulfate medium. These data support a role for tetraheme cytochrome c(3) in the electron transport pathway from pyruvate to sulfate or sulfite in D. desulfuricans G20.

New shuttle vectors for the introduction of cloned DNA in Desulfovibrio.

The pBG1 replicon from the cryptic plasmid of Desulfovibrio desulfuricans G100A was inserted into pTZ18U derivatives to generate a new family of shuttle vectors. These plasmids are stable both in Escherichia coli and in Desulfovibrio, they present a large number of unique restriction sites, and colonies of recombinant clones can be identified by blue/white screening in E. coli. The pBMC, pBMK, and pBMS series carry the cat, npt, or strAB genes as selectable markers, respectively. The pBMC6, pBMK6, and pBMS6 plasmids can be introduced both in D. desulfuricans and in Desulfovibrio fructosovorans by electrotransformation, and the pBMC7, pBMK7, and pBMS7 plasmids contain additional mobilization functions which makes them suitable for conjugation.

Molecular study and partial characterization of iron-only hydrogenase in Desulfovibrio fructosovorans.

An iron-only hydrogenase was partially purified and characterized from Desulfovibrio fructosovorans wild-type strain. The enzyme exhibits a molecular mass of 56 kDa and is composed of two distinct subunits HydA and HydB (46 and 13 kDa, respectively). The N-terminal amino acid sequences of the two subunits of the enzyme were determined with the aim of designing degenerate oligonucleotides. Direct and inverse polymerase chain reaction techniques were used to clone the hydrogenase encoding genes. A 9-nucleotide region located 75 bp upstream from the translational start codon of the D. fructosovorans hydA gene was found to be highly conserved. The analysis of the deduced amino acid sequence of these genes showed the presence of a signal sequence located in the small subunit, exhibiting the consensus sequence which is likely to be involved in the specific export mechanism of hydrogenases. Two ferredoxin-like motives involved in the coordination of [4Fe-4S] clusters were identified in the N-terminal domain of the large subunit. The amino acid sequence of the [Fe] hydrogenase from D. fructosovorans was compared with the amino acid sequences from eight other hydrogenases (cytoplasmic and periplasmic). These enzymes share an overall 18% identity and 28% similarity. The identity reached 73% and 69% when the D. fructosovorans hydrogenase sequence was compared with the hydrogenase sequences from Desulfovibrio vulgaris Hildenborough and Desulfovibrio vulgaris oxamicus Monticello, respectively.