Construction of random transposition mutagenesis system in Rhodococcuserythropolis using IS1415

Unravelling the role of the group 6 soluble di-iron monooxygenase (SDIMO) SmoABCD in alkane metabolism and chlorinated alkane degradation

Soluble di-iron monooxygenases (SDIMOs) are multi-component enzymes catalysing the oxidation of various substrates. These enzymes are characterized by high sequence and functional diversity that is still not well understood despite their key role in biotechnological processes including contaminant biodegradation. In this study, we analysed a mutant of Rhodoccocus aetherivorans BCP1 (BCP1-2.10) characterized by a transposon insertion in the gene smoA encoding the alpha subunit of the plasmid-located SDIMO SmoABCD. The mutant BCP1-2.10 showed a reduced capacity to grow on propane, lost the ability to grow on butane, pentane and n-hexane and was heavily impaired in the capacity to degrade chloroform and trichloroethane. The expression of the additional SDIMO prmABCD in BCP1-2.10 probably allowed the mutant to partially grow on propane and to degrade it, to some extent, together with the other short-chain n-alkanes. The complementation of the mutant, conducted by introducing smoABCD in the genome as a single copy under a constitutive promoter or within a plasmid under a thiostreptone-inducible promoter, allowed the recovery of the alkanotrophic phenotype as well as the capacity to degrade chlorinated n-alkanes. The heterologous expression of smoABCD allowed a non-alkanotrophic Rhodococcus strain to grow on pentane and n-hexane when the gene cluster was introduced together with the downstream genes encoding alcohol and aldehyde dehydrogenases and a GroEL chaperon. BCP1 smoA gene was shown to belong to the group 6 SDIMOs, which is a rare group of monooxygenases mostly present in Mycobacterium genus and in a few Rhodococcus strains. SmoABCD originally evolved in Mycobacterium and was then acquired by Rhodococcus through horizontal gene transfer events. This work extends the knowledge of the biotechnologically relevant SDIMOs by providing functional and evolutionary insights into a group 6 SDIMO in Rhodococcus and demonstrating its key role in the metabolism of short-chain alkanes and degradation of chlorinated n-alkanes.

Development of Efficient Genome-Reduction Tool Based on Cre/loxP System in Rhodococcus erythropolis

Rhodococcus has been extensively studied for its excellent ability to degrade artificial chemicals and its capability to synthesize biosurfactants and antibiotics. In recent years, studies have attempted to use Rhodococcus as a gene expression host. Various genetic tools, such as plasmid vectors, transposon mutagenesis, and gene disruption methods have been developed for use in Rhodococcus; however, no effective method has been reported for performing large-size genome reduction. Therefore, the present study developed an effective plasmid-curing method using the levansucrase-encoding sacB gene and a simple two-step genome-reduction method using a modified Cre/loxP system. For the results, R. erythropolis JCM 2895 was used as the model; a mutant strain that cured all four plasmids and deleted seven chromosomal regions was successfully obtained in this study. The total DNA deletion size was >600 kb, which corresponds mostly to 10% of the genome size. Using this method, a genome-structure-stabilized and unfavorable gene/function-lacking host strain can be created in Rhodococcus. This genetic tool will help develop and improve Rhodococcus strains for various industrial and environmental applications.

Genetic toolkits for engineering Rhodococcus species with versatile applications

Rhodococcus spp. are a group of non-model gram-positive bacteria with diverse catabolic activities and strong adaptive capabilities, which enable their wide application in whole-cell biocatalysis, environmental bioremediation, and lignocellulosic biomass conversion. Compared with model microorganisms, the engineering of Rhodococcus is challenging because of the lack of universal molecular tools, high genome GC content (61% ~ 71%), and low transformation and recombination efficiencies. Nevertheless, because of the high interest in Rhodococcus species for bioproduction, various genetic elements and engineering tools have been recently developed for Rhodococcus spp., including R. opacus, R. jostii, R. ruber, and R. erythropolis, leading to the expansion of the genetic toolkits for Rhodococcus engineering. In this article, we provide a comprehensive review of the important developed genetic elements for Rhodococcus, including shuttle vectors, promoters, antibiotic markers, ribosome binding sites, and reporter genes. In addition, we also summarize gene transfer techniques and strategies to improve transformation efficiency, as well as random and precise genome editing tools available for Rhodococcus, including transposition, homologous recombination, recombineering, and CRISPR/Cas9. We conclude by discussing future trends in Rhodococcus engineering. We expect that more synthetic and systems biology tools (such as multiplex genome editing, dynamic regulation, and genome-scale metabolic models) will be adapted and optimized for Rhodococcus.

An inhibitory compound produced by a soil isolate of Rhodococcus has strong activity against the veterinary pathogen R. equi

Complete genome sequencing of dozens of strains of the soil bacterium Rhodococcus has revealed the presence of many cryptic biosynthetic gene clusters, presumably dedicated to the production of small molecules. This has sparked a renewed interest in this underexplored member of the Actinobacteria as a potential source of new bioactive compounds. Reported here is the discovery of a potent inhibitory molecule produced by a newly isolated strain of Rhodococcus, strain MTM3W5.2. This small inhibitory molecule shows strong activity against all Rhodococcus species tested, including the veterinary pathogen R. equi, and some closely related genera. It is not active against other Gram positive or Gram negative bacteria. A screen of random transposon mutants identified a gene required to produce this inhibitory compound. This gene is a large multi-domain, type I polyketide synthase that is part of a very large multi-gene biosynthetic gene cluster in the chromosome of strain MTM3W5.2. The high resolution mass spectrum of a major chromatogram peak from a broth culture extract of MTM3W5.2 shows the presence of a compound at m/z 911.5490 atomic mass units. This compound is not detected in the culture extracts from a non-producing mutant strain of MTM3W5.2. A large gene cluster containing at least 14 different type I polyketide synthase genes is proposed to be required to synthesize this antibiotic-like compound.

A Transposon Mutagenesis System for Bifidobacterium longum subsp. longum Based on an IS3 Family Insertion Sequence, ISBlo11

Bifidobacteria are a major component of the intestinal microbiota in humans, particularly breast-fed infants. Therefore, elucidation of the mechanisms by which these bacteria colonize the intestine is desired. One approach is transposon mutagenesis, a technique currently attracting much attention because, in combination with next-generation sequencing, it enables exhaustive identification of genes that contribute to microbial fitness. We now describe a transposon mutagenesis system for Bifidobacterium longum subsp. longum 105-A (JCM 31944) based on ISBlo11, a native IS3 family insertion sequence. To build this system, xylose-inducible or constitutive bifidobacterial promoters were tested to drive the expression of full-length or a truncated form at the N terminus of the ISBlo11 transposase. An artificial transposon plasmid, pBFS12, in which ISBlo11 terminal inverted repeats are separated by a 3-bp spacer, was also constructed to mimic the transposition intermediate of IS3 elements. The introduction of this plasmid into a strain expressing transposase resulted in the insertion of the plasmid with an efficiency of >10³ CFU/μg DNA. The plasmid targets random 3- to 4-bp sequences, but with a preference for noncoding regions. This mutagenesis system also worked at least in B. longum NCC2705. Characterization of a transposon insertion mutant revealed that a putative α-glucosidase mediates palatinose and trehalose assimilation, demonstrating the suitability of transposon mutagenesis for loss-of-function analysis. We anticipate that this approach will accelerate functional genomic studies of B. longum subsp. longumIMPORTANCE Several hundred species of bacteria colonize the mammalian intestine. However, the genes that enable such bacteria to colonize and thrive in the intestine remain largely unexplored. Transposon mutagenesis, combined with next-generation sequencing, is a promising tool to comprehensively identify these genes but has so far been applied only to a small number of intestinal bacterial species. In this study, a transposon mutagenesis system was established for Bifidobacterium longum subsp. longum, a representative health-promoting Bifidobacterium species. The system enables the identification of genes that promote colonization and survival in the intestine and should help illuminate the physiology of this species.

Genome-based analysis for the identification of genes involved in o-xylene degradation in Rhodococcus opacus R7

BACKGROUND

Bacteria belonging to the Rhodococcus genus play an important role in the degradation of many contaminants, including methylbenzenes. These bacteria, widely distributed in the environment, are known to be a powerhouse of numerous degradation functions, due to their ability to metabolize a wide range of organic molecules including aliphatic, aromatic, polycyclic aromatic compounds (PAHs), phenols, and nitriles. In accordance with their immense catabolic diversity, Rhodococcus spp. possess large and complex genomes, which contain a multiplicity of catabolic genes, a high genetic redundancy of biosynthetic pathways and a sophisticated regulatory network. The present study aimed to identify genes involved in the o-xylene degradation in R. opacus strain R7 through a genome-based approach.

RESULTS

Using genome-based analysis we identified all the sequences in the R7 genome annotated as dioxygenases or monooxygenases/hydroxylases and clustered them into two different trees. The akb, phe and prm sequences were selected as genes encoding respectively for dioxygenases, phenol hydroxylases and monooxygenases and their putative involvement in o-xylene oxidation was evaluated. The involvement of the akb genes in o-xylene oxidation was demonstrated by RT-PCR/qPCR experiments after growth on o-xylene and by the selection of the R7-50 leaky mutant. Although the akb genes are specifically activated for o-xylene degradation, metabolic intermediates of the pathway suggested potential alternative oxidation steps, possibly through monooxygenation. This led us to further investigate the role of the prm and the phe genes. Results showed that these genes were transcribed in a constitutive manner, and that the activity of the Prm monooxygenase was able to transform o-xylene slowly in intermediates as 3,4-dimethylphenol and 2-methylbenzylalcohol. Moreover, the expression level of phe genes, homologous to the phe genes of Rhodococcus spp. 1CP and UPV-1 with a 90% identity, could explain their role in the further oxidation of o-xylene and R7 growth on dimethylphenols.

CONCLUSIONS

These results suggest that R7 strain is able to degrade o-xylene by the Akb dioxygenase system leading to the production of the corresponding dihydrodiol. Likewise, the redundancy of sequences encoding for several monooxygenases/phenol hydroxylases, supports the involvement of other oxygenases converging in the o-xylene degradation pathway in R7 strain.

Identification of a novel bacteriocin-like protein and structural gene from Rhodococcus erythropolis JCM 2895, using suppression-subtractive hybridization

A novel bacteriocin-like protein and its structural gene (rap) were identified from Rhodococcus erythropolis JCM 2895. The rapA and B genes are located on a 5.4-kb circular plasmid, and were obtained using a modified suppression-subtractive hybridization method. The rapA and B genes were heterologously expressed in Rhodococcus sp. or Escherichia coli, and then characterized. The results indicated that RapA is a small, water-soluble, heat-stable antimicrobial protein, and that RapB is an immunity protein against RapA, estimated to be located on the cell membrane. RapA showed antimicrobial activity particularly against R. erythropolis, and the activity persisted even after SDS-PAGE analysis. For the heterologous expressed RapA protein, N-terminal amino acid sequence was also confirmed. This is the first report of a bacteriocin-like substance obtained from the genus Rhodococcus.

Common origin of methylenedioxy ring degradation and demethylation in bacteria

Plants produce many specific secondary metabolites as a response to environmental stress, especially biological stress. These compounds show strong biological activities and high stability against degradation by microbes and animals. Berberine, a benzylisoquinoline alkaloid, is found in many plant species and has strong antimicrobial activity, and is often included in traditional herbal medicines. We previously investigated how berberine is degraded in nature and we isolated two berberine-utilizing bacteria. In this study, we characterized the gene encoding the enzyme that degrades the 2,3-methylenedioxy ring of berberine; this ring is important for its activity and stability. Further characterization of several other berberine-utilizing bacteria and the genes encoding key demethylenation enzymes revealed that these enzymes are tetrahydrofolate dependent and similar to demethylation enzymes such as GcvT. Because the degradation of O-methyl groups or the methylenedioxy ring in phenolic compounds such as lignin, lignan and many other natural products, including berberine, is the key step for the catabolism of these compounds, our discovery reveals the common origin of the catabolism of these stable chemicals in bacteria.

Abundant Intergenic TAACTGA Direct Repeats and Putative Alternate RNA Polymerase β' Subunits in Marine Beggiatoaceae Genomes: Possible Regulatory Roles and Origins

The genome sequences of several giant marine sulfur-oxidizing bacteria present evidence of a possible post-transcriptional regulatory network that may have been transmitted to or from two distantly related bacteria lineages. The draft genome of a Cand. “Maribeggiatoa” filament from the Guaymas Basin (Gulf of California, Mexico) seafloor contains 169 sets of TAACTGA direct repeats and one indirect repeat, with two to six copies per set. Related heptamers are rarely or never found as direct repeats. TAACTGA direct repeats are also found in some other Beggiatoaceae, Thiocystis violascens, a range of Cyanobacteria, and five Bacteroidetes. This phylogenetic distribution suggests they may have been transmitted horizontally, but no mechanism is evident. There is no correlation between total TAACTGA occurrences and repeats per genome. In most species the repeat units are relatively short, but longer arrays of up to 43 copies are found in several Bacteroidetes and Cyanobacteria. The majority of TAACTGA repeats in the Cand. “Maribeggiatoa” Orange Guaymas (BOGUAY) genome are within several nucleotides upstream of a putative start codon, suggesting they may be binding sites for a post-transcriptional regulator. Candidates include members of the ribosomal protein S1, Csp (cold shock protein), and Csr (carbon storage regulator) families. No pattern was evident in the predicted functions of the open reading frames (ORFs) downstream of repeats, but some encode presumably essential products such as ribosomal proteins. Among these is an ORF encoding a possible alternate or modified RNA polymerase beta prime subunit, predicted to have the expected subunit interaction domains but lacking most catalytic residues. A similar ORF was found in the Thioploca ingrica draft genome, but in no others. In both species they are immediately upstream of putative sensor kinase genes with nearly identical domain structures. In the marine Beggiatoaceae, a role for the TAACTGA repeats in translational regulation is suggested. More speculatively, the putative alternate RNA polymerase subunit could be a negative transcriptional regulator.

Biodegradation of the organic disulfide 4,4'-dithiodibutyric acid by Rhodococcus spp

Four Rhodococcus spp. exhibited the ability to use 4,4'-dithiodibutyric acid (DTDB) as a sole carbon source for growth. The most important step for the production of a novel polythioester (PTE) using DTDB as a precursor substrate is the initial cleavage of DTDB. Thus, identification of the enzyme responsible for this step was mandatory. Because Rhodococcus erythropolis strain MI2 serves as a model organism for elucidation of the biodegradation of DTDB, it was used to identify the genes encoding the enzymes involved in DTDB utilization. To identify these genes, transposon mutagenesis of R. erythropolis MI2 was carried out using transposon pTNR-TA. Among 3,261 mutants screened, 8 showed no growth with DTDB as the sole carbon source. In five mutants, the insertion locus was mapped either within a gene coding for a polysaccharide deacetyltransferase, a putative ATPase, or an acetyl coenzyme A transferase, 1 bp upstream of a gene coding for a putative methylase, or 176 bp downstream of a gene coding for a putative kinase. In another mutant, the insertion was localized between genes encoding a putative transcriptional regulator of the TetR family (noxR) and an NADH:flavin oxidoreductase (nox). Moreover, in two other mutants, the insertion loci were mapped within a gene encoding a hypothetical protein in the vicinity of noxR and nox. The interruption mutant generated, R. erythropolis MI2 noxΩtsr, was unable to grow with DTDB as the sole carbon source. Subsequently, nox was overexpressed and purified, and its activity with DTDB was measured. The specific enzyme activity of Nox amounted to 1.2 ± 0.15 U/mg. Therefore, we propose that Nox is responsible for the initial cleavage of DTDB into 2 molecules of 4-mercaptobutyric acid (4MB).

Isolation and transposition properties of ISBlo11, an active insertion sequence belonging to the IS3 family, from Bifidobacterium longum 105-A

Transposon mutagenesis systems are still under development in bifidobacteria, partly because intrinsic active insertion sequences are not well characterized in bifidobacteria. Here, we isolated an active insertion sequence, ISBlo11, from Bifidobacterium longum 105-A using a sacB-based counterselection system, which is generally used to screen for active insertion sequences from bacterial genomes. ISBlo11 is 1432 bp long and belongs to the IS3 family. It has a single ORF encoding a transposase and 25-bp inverted repeats at its termini. Full-length copies of ISBlo11 are specifically conserved among certain B. longum genomes and exist in different sites. Transposition analysis of an artificial ISBlo11 transposon using an Escherichia coli conjugation system revealed that ISBlo11 has adequate transposition activity, comparable to the reported activity of IS629, another IS3 family element initially isolated from Shigella sonnei. ISBlo11 also showed low transposition selectivity for non-conserved 3- or 4-bp target sequences. These characteristics of ISBlo11 seem suitable for the development of a new transposon mutagenesis system in bifidobacteria.

Utilization of atmospheric ammonia by an extremely oligotrophic bacterium, Rhodococcus erythropolis N9T-4

Rhodococcus erythropolis N9T-4 shows extremely oligotrophic growth and requires CO2 for its growth. In this report, nitrogen sources for the oligotrophic growth of N9T-4 were examined. As is true for most other bacteria, N9T-4 preferred ammonium salt to nitrate as the nitrogen source on an inorganic minimum medium without carbon sources. Interestingly, N9T-4 could also grow on the minimal medium solidified by agarose or silica gel without carbon and nitrogen sources, suggesting that this bacterium is also oligotrophic for nitrogen. We can rule out the possibility of diazotrophic growth of this bacterium, because nitrogenase activity was not detected in the cells and the putative gene encoding nitrogenase was not found in N9T-4 genome. DNA microarray analysis revealed that one of the ammonium transporter genes (amtB) was strongly upregulated 40-50 fold higher under oligotrophic conditions than under heterotrophic conditions. Disruption of amtB led to a growth defect under nitrogen-limiting conditions. Furthermore, additional ammonia vapor enhanced the growth of N9T-4 on the minimum medium without nitrogen sources in a closed culture system. These results suggest that N9T-4 utilizes the trace amount of atmospheric ammonia as the nitrogen source.

Survival of GFP-tagged Rhodococcus sp. D310-1 in chlorimuron-ethyl-contaminated soil and its effects on the indigenous microbial community

The recently isolated bacterial strain Rhodococcus sp. D310-1 can degrade high concentrations of chlorimuron-ethyl (up to 1000 mg L(-1)), indicating its potential for the bioremediation of soil contaminated with high levels of chlorimuron-ethyl. In this study, Rhodococcus sp. D310-1 was tagged with green fluorescent protein gene (gfp) to track its survival in soil. Subsequently, degradation activity of the gfp-tagged strain and its effects on indigenous microbial community were analyzed. Results showed the cell numbers of Rhodococcus sp. D310-1::gfp in non-sterilized soil maintained at 8.5 × 10(4) cells g(-1) dry soil 45 days after inoculation of 7.74 × 10(6) cells g(-1) dry soil and approximately 49% of chlorimuron-ethyl was removed. However, The cell numbers of Rhodococcus sp. D310-1::gfp in sterilized samples increased gradually to 7.85 × 10(7) cells g(-1) dry soil and approximately 78% of chlorimuron-ethyl was removed. PCR-DGGE demonstrated that inoculation of this gfp-tagged strain in chlorimuron-ethyl-contaminated soil has negligible impact on the community structure of bacteria, actinomycetes and fungi. These results indicate that Rhodococcus sp. D310-1 is effective for the remediation of chlorimuron-ethyl-contaminated soil and also provides valuable information about the behavior of the inoculant population during bioremediation, which could be directly used in the risk assessment of inoculant population and optimization of bioremediation process.

Rhodococcus prokaryotic ubiquitin-like protein (Pup) is degraded by deaminase of pup (Dop)

Prokaryotic ubiquitin-like protein (Pup) is a functional analog of ubiquitin. Post-translationally modified pupylated proteins are selectively degraded by a proteasome-dependent proteolytic system. Deaminase of Pup (Dop) activates Pup by deaminating the C-terminal from glutamine to glutamate, and subsequently activated Pup is conjugated to target proteins by proteasome accessory factor A. Dop is also involved in the removal of Pup from pupylated proteins. Deconjugated free Pup is capable of religating to target proteins. Although the pupylation system is well studied in Mycobacterium, little is known about it in other actinomycetes. Both Rhodococcus and Mycobacterium Dop remove Pup from pupylated proteins, but in these two bacteria, no accumulation of deconjugated free Pup from Rhodococcus is observed. Analysis of a model pupylated protein revealed that Rhodococcus Pup is degraded at multiple sites by Dop. The endopeptidase activity of Dop can be detected using a fluorogenic substrate in conjunction with aminopeptidase. Moreover, the enzymatic activity of the model enzyme increases when Pup is deconjugated. These results suggest that depupylated Rhodococcus Pup is not recycled for religation with target proteins, and that Pup not only functions as a degradation signal, but also regulates the enzymatic activity of target proteins by conjugation and deconjugation to them.

Molecular cloning of the gene cluster for lariatin biosynthesis of Rhodococcus jostii K01-B0171

The biosynthetic gene cluster for lariatins A and B, anti-mycobacterial peptide antibiotics with a unique "lasso" structure, was cloned from Gram-positive bacterium Rhodococcus jostii K01-B0171. Random transposition mutagenesis using IS1415 derivative was carried out to identify a chromosomal locus involved in lariatin biosynthesis and six independent lariatin non-producing variants were obtained. Arbitrary PCR revealed that one insertion was located near the region involved in lariatin biosynthesis. Using the lariatin gene as a probe, a genomic library of R. jostii K01-B0171 was screened by colony hybridization, and two clones were obtained. Sequence analysis of these clones revealed that the gene cluster for lariatin biosynthesis spanning about 4.5 kb consisted of five open reading frames (larA to larE). We proposed that the linear precursor LarA is processed by LarB, LarC, and LarD, and the mature lariatin is exported by LarE.

Permeabilization induced by lipid II-targeting lantibiotic nisin and its effect on the bioconversion of vitamin D3 to 25-hydroxyvitamin D3 by Rhodococcus erythropolis

Vitamin D3 (VD3) is a fat-soluble prohormone in mammals. VD3 is inert and must be activated by hydroxylation at the C-25 and C-1α positions to exert its biological activity. We recently accomplished the bioconversion of VD3 to 25(OH)VD3 with a recombinant strain of Rhodococcus erythropolis and found that the permeability of VD3 into the cytoplasm may be the rate-limiting step of 25(OH)VD3 production (Sallam et al., 2010). When the cells were treated with the lipid II-targeting lantibiotic nisin, the permeability of green chemiluminescent cyclodextrin (GCCD), which is used as a model substrate instead of VD3-partially methylated-β-cyclodextrin (PMCD) complex, was drastically induced. Nisin also induced VD3 hydroxylation, and the rate was correlated with the expression levels of Vdh and its redox partner proteins. In the bioconversion reaction, the stability of the redox partner proteins and the additional NADH-regenerating system are crucial for VD3 hydroxylation. The degradation rate of the [2Fe-2S] cluster of ferredoxin ThcC from R. erythropolis NI86/21 is faster than that of AciB from Acinetobacter sp. OC4. Therefore, the nisin-treated R. erythropolis cells coexpressing Vdh and AciBC (1176.5 μg) exhibited much greater 25(OH)VD3 production than the cells coexpressing Vdh and ThcCD (431.7 μg) after four consecutive 16 h reactions. These results suggest that nisin forms nisin-lipid II pore complexes in the Rhodococcus membrane that increase the accessibility of VD3-PMCD complexes to the inside of the cells. Furthermore, nisin-treated Rhodococcus cells can be utilized for the bioconversion of other fat-soluble chemicals.

Biodegradation of the xenobiotic organic disulphide 4,4′-dithiodibutyric acid by Rhodococcus erythropolis strain MI2 and comparison with the microbial utilization of 3,3′-dithiodipropionic acid and 3,3′-thiodipropionic acid

Application of the non-toxic 3,3′-thiodipropionic acid (TDP) and 3,3′-dithiodipropionic acid (DTDP) as precursors for the microbial production of polythioesters (PTEs), a class of biologically persistent biopolymers containing sulphur in the backbone, was successfully established previously. However, synthesis of PTEs containing 4-mercaptobutyrate (4MB) as building blocks could not be achieved. The very harmful 4MB is not used as a PTE precursor or as the carbon source for growth by any known strain. As a promising alternative, the harmless oxidized disulfide of two molecules of 4MB, 4,4′-dithiodibutyric acid (DTDB), was employed for enrichments of bacterial strains capable of biodegradation. Investigation of novel precursor substrates for PTEs and comparison of respective strains growing on TDP, DTDP and DTDB as sole carbon source was accomplished. A broad variety of bacteria capable of using one of these organic sulphur compounds were isolated and compared. TDP and DTDP were degraded by several strains belonging to different genera, whereas all DTDB-utilizing strains were affiliated to the species Rhodococcus erythropolis. Transposon mutagenesis of R. erythropolis strain MI2 and screening of 7500 resulting mutants yielded three mutants exhibiting impaired growth on DTDB. Physiological studies revealed production of volatile hydrogen sulphide and accumulation of significant amounts of 4MB, 4-oxo-4-sulphanylbutanoic acid and succinic acid in the culture supernatants. Based on this knowledge, a putative pathway for degradation of DTDB was proposed: DTDB could be cleaved into two molecules of 4MB, followed by an oxidation yielding 4-oxo-4-sulphanylbutanoic acid. A putative desulphydrase probably catalyses the abstraction of sulphur, thereby generating succinic acid and hydrogen sulphide.

New vector system for random, single-step integration of multiple copies of DNA into the Rhodococcus genome

We designed a new vector system for creating a random mutant library with multiple integrations of DNA fragments into the Rhodococcus genome in a single step. For this, we cotransformed two vectors into Rhodococcus by electroporation: pTip-istAB-sacB regulates the expression of the transposase (IstA) and its helper protein (IstB) under the influence of a thiostrepton-inducible promoter, and pRTSK-sacB provides the transposable-marker DNA. Both are multicopy vectors that are stable in the host cells; transposition of the transposable-marker DNA occurs only after the induction of IstA/IstB expression. With the addition of thiostrepton, all cultured cells harboring the two vectors, irrespective of the volume, can be mutated by random insertion of the transposable-marker DNA into their genome. Among the generated mutants examined, 30% showed multiple (two to five) insertion copies. The multiple integrated DNA copies were stable in the genome for more than 80 generations of serial growth without the addition of any selective antibiotics. This system can also be used for integrating various copy numbers of stably maintained protein expression cassettes in the host cell genome to modulate the expression level of biologically active recombinant proteins. We successfully applied this system to integrate multiple copies of expression cassettes for proline iminopeptidase and vitamin D(3) hydroxylase into the Rhodococcus genome and verified that the clones containing double or multiple copies of the integrated cassettes produced higher levels and showed higher enzymatic activities of the target protein than clones with only a single copy of integration.

An extremely oligotrophic bacterium, Rhodococcus erythropolis N9T-4, isolated from crude oil

Rhodococcus erythropolis N9T-4, which was isolated from crude oil, showed extremely oligotrophic growth and formed its colonies on a minimal salt medium solidified using agar or silica gel without any additional carbon source. N9T-4 did not grow under CO(2)-limiting conditions but could grow on a medium containing NaHCO(3) under the same conditions, suggesting that the oligotrophic growth of N9T-4 depends on CO(2). Proteomic analysis of N9T-4 revealed that two proteins, with molecular masses of 45 and 55 kDa, were highly induced under the oligotrophic conditions. The primary structures of these proteins exhibited striking similarities to those of methanol: N,N'-dimethyl-4-nitrosoaniline oxidoreductase and an aldehyde dehydrogenase from Rhodococcus sp. These enzyme activities were three times higher under oligotrophic conditions than under n-tetradecane-containing heterotrophic conditions, and gene disruption for the aldehyde dehydrogenase caused a lack of growth on the minimal salt medium. Furthermore, 3-hexulose 6-phosphate synthase and phospho-3-hexuloisomerase activities, which are key enzymes in the ribulose monophosphate pathway in methylotrophic bacteria, were detected specifically in the cell extract of oligotrophically grown N9T-4. These results suggest that CO(2) fixation involves methanol (formaldehyde) metabolism in the oligotrophic growth of R. erythropolis N9T-4.

A multipurpose transposon-based vector system mediates protein expression in Rhodococcus erythropolis

In the current study we developed two transposon-based vectors; namely pTNR-KA and pTNR-TA and utilized them for expression of proteasome complex, derived from Streptomyces coelicolor, in Rhodococcus erythropolis. The two vectors can be transposed into Rhodococcus cells by means of electroporation, either individually in two consecutive processes or in combinations by a single step. During transposition, each of the two vectors liberates its transposable-marker gene, which integrated in a single copy into a random site in the Rhodococcus chromosomal DNA. Southern blot analysis indicated that the two transposable-marker genes of both vectors does not alter or knock out each other. To utilize these vectors for Streptomyces proteasome expression, two expression cassettes were constructed; each cassette comprised a constitutive promoter (P(nit)), the DNA fragment, prcA or prcB that encodes alpha- or beta-subunits of Streptomyces proteasome, and T(thcA) transcriptional terminator. The cassettes were then individually introduced into the multiple cloning sites that are located in the transposable-marker gene of the two vectors. The two cassettes-harboring vectors were subsequently co-transposed, in combinations, into the Rhodococcus genome by a single electroporation step and the Streptomyces proteasome was successfully expressed in the rodococcal host cell. The isolated proteasome was further characterized and the peptidase activity was confirmed and indicated that it was biologically active. The present study concluded that both pTNR-KA and pTNR-TA can be used as transposon-based protein expression systems in Rhodococcus species.