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Helvella bachu, an ectomycorrhizal fungus, forms a symbiotic relationship with Populus euphratica, a rare and endangered species crucial to desert riparian ecosystems. In this study, endofungal bacteria (EFBs) within the fruiting bodies of H. bachu were confirmed by a polyphasic approach, including genomic sequencing, real-time quantitative PCR targeting the 16S rRNA gene, full-length and next-generation sequencing (NGS) of the 16S rRNA gene, and culture methods. The genera Stenotrophomonas, Variovorax, Acidovorax, and Pedobacter were abundant in the EFBs of fruiting bodies associated with three Populus hosts and were consistently present across different developmental stages. Notably, S. maltophilia and V. paradoxus were detected in high abundance, as revealed by full-length 16S rRNA sequencing, with S. maltophilia also isolated by culture methods. KO-pathway analysis indicated that pathways related to primary, secondary, and energy metabolism were predominantly enriched, suggesting these bacteria may promote H. bachu growth by producing essential compounds, including sugars, proteins, and vitamins, and secondary metabolites. This study confirmed the presence of EFBs in H. bachu and provided the first comprehensive overview of their structure, functional potential, and dynamic changes throughout fruiting body maturation, offering valuable insights for advancing the artificial domestication of this species. [ABSTRACT FROM AUTHOR]

By decreasing root 1-aminocyclopropane-1-carboxylate (ACC) content and plant ethylene production, the microbial enzyme ACC deaminase is a widespread beneficial trait of plant growth-promoting rhizobacteria (PGPR), ameliorating ethylene-mediated root growth inhibition. However, relatively little is known about whether bacterial ACC deaminase modulates root architecture and root hair traits. Thus the dwarf tomato (Solanum lycopersicum) cultivar Micro-Tom was inoculated in vitro with Pseudomonas brassicacearum Am3, its ACC deaminase deficient mutant T8-1, a known PGPR strain Variovorax paradoxus 5C-2 or chemically treated with agents that promoted or inhibited ethylene production or sensitivity (Ag+, Co2+, and ACC). ACC treatment reduced both root elongation and the number of lateral roots, while ethylene inhibitors (Ag+, Co2+) and V. paradoxus 5C-2 promoted primary root elongation, but differentially affected lateral root length and number. Ag+ stimulated lateral root development, while Co2+ and V. paradoxus 5C-2 did not. Inoculation with P. brassicacearum Am3 and T8-1 inhibited elongation of the primary and lateral roots at a high inoculum concentration (106 cells cm3). All bacterial strains significantly increased the length and number of root hairs, with these effects more pronounced in P. brassicacearum Am3 than in the mutant T8-1. Treatment with Ag+ inhibited root hair formation and elongation, while Co2+ had the opposite effects. ACC treatment had no effect on root hair elongation but increased root hair density. While root growth inhibition caused by P. brassicacearum Am3 was independent of ACC deaminase, the promotion of root hair elongation and density by this strain was augmented by ACC deaminase activity. Thus ACC deaminase can modulate the morphological impacts of bacteria on root hair response by affecting plant ethylene content.

By decreasing root 1-aminocyclopropane-1-carboxylate (ACC) content and plant ethylene production, the microbial enzyme ACC deaminase is a widespread beneficial trait of plant growth-promoting rhizobacteria (PGPR), ameliorating ethylene-mediated root growth inhibition. However, relatively little is known about whether bacterial ACC deaminase modulates root architecture and root hair traits. Thus the dwarf tomato (Solanum lycopersicum) cultivar Micro-Tom was inoculated in vitro with Pseudomonas brassicacearum Am3, its ACC deaminase deficient mutant T8-1, a known PGPR strain Variovorax paradoxus 5C-2 or chemically treated with agents that promoted or inhibited ethylene production or sensitivity (Ag+, Co2+, and ACC). ACC treatment reduced both root elongation and the number of lateral roots, while ethylene inhibitors (Ag+, Co2+) and V. paradoxus 5C-2 promoted primary root elongation, but differentially affected lateral root length and number. Ag+ stimulated lateral root development, while Co2+ and V. paradoxus 5C-2 did not. Inoculation with P. brassicacearum Am3 and T8-1 inhibited elongation of the primary and lateral roots at a high inoculum concentration (106 cells cm3). All bacterial strains significantly increased the length and number of root hairs, with these effects more pronounced in P. brassicacearum Am3 than in the mutant T8-1. Treatment with Ag+ inhibited root hair formation and elongation, while Co2+ had the opposite effects. ACC treatment had no effect on root hair elongation but increased root hair density. While root growth inhibition caused by P. brassicacearum Am3 was independent of ACC deaminase, the promotion of root hair elongation and density by this strain was augmented by ACC deaminase activity. Thus ACC deaminase can modulate the morphological impacts of bacteria on root hair response by affecting plant ethylene content. [ABSTRACT FROM AUTHOR]

The N-acyl-D-amino acid amidohydrolase (N-d-AAase) of Variovorax paradoxus Iso1 can enantioselectively catalyze the zinc-assisted deacetylation of N-acyl-Damino acids to yield consistent D-amino acids. A putative FAD-binding glycine/Damino acid oxidase was located immediately upstream of the N-d-AAase gene. The gene encoding this protein was cloned into Escherichia coli BL21 (DE3)pLysS and overexpressed at 25°C for 6 h with 0.5 mM isopropyl β-D-1-thiogalactopyranoside induction. After purification, the tag-free recombinant protein was obtained. The enzyme could metabolize glycine, sarcosine, and D-alanine, but not L-amino acids or bulky D-amino acids. Protein modeling further supported these results, demonstrating that glycine, sarcosine, and D-alanine could fit into the pocket of the enzyme's activation site, while L-alanine and D-threonine were out of position. Therefore, this protein was proposed as a glycine oxidase, and we designated it VpGO. Interestingly, VpGO showed low sequence similarity to other well-characterized glycine oxidases. We found that VpGO and N-d-AAase were expressed on the same mRNA and could be transcriptionally induced by various N-acetyl-D-amino acids. Western blotting and zymography showed that both proteins had similar expression patterns in response to different types of inducers. Thus, we have identified a novel glycine oxidase that is co-regulated with N-d-AAase in an operon, and metabolizes N-acyl-D-amino acids in the metabolically versatile V. paradoxus Iso1. [ABSTRACT FROM AUTHOR]

Abstract Here, we report and discuss the applicability of Variovorax paradoxus strain BFB1_13 in the bioremediation of BTEX contaminated sites. Strain BFB1_13 was capable of degrading all the six BTEX-compounds under both aerobic (O2 conc. 8 mg l−1) and micro-aerobic/oxygen-limited (O2 conc. 0.5 mg l−1) conditions using either individual (8 mg‧l−1) or a mixture of compounds (~ 1.3 mg‧l−1 of each BTEX compound). The BTEX biodegradation capability of SBP-encapsulated cultures (SBP—Small Bioreactor Platform) was also assessed. The fastest degradation rate was observed in the case of aerobic benzene biodegradation (8 mg l−1 per 90 h). Complete biodegradation of other BTEX occurred after at least 168 h of incubation, irrespective of the oxygenation and encapsulation. No statistically significant difference was observed between aerobic and microaerobic BTEX biodegradation. Genes involved in BTEX biodegradation were annotated and degradation pathways were predicted based on whole-genome shotgun sequencing and metabolic analysis. We conclude that V. paradoxus strain BFB1_13 could be used for the development of reactive biobarriers for the containment and in situ decontamination of BTEX contaminated groundwater plumes. Our results suggest that V. paradoxus strain BFB1_13—alone or in co-culture with other BTEX degrading bacterial isolates—can be a new and efficient commercial bioremediation agent for BTEX contaminated sites.

Effective biocatalysts for the synthesis of optically pure amines from keto precursors are highly required in organic synthesis. Transaminases are a large group of PLP-dependent enzymes, which can be utilized for production of chiral amines or amino acids. The bioinformatic approach previously made to search for promising transaminases with unusual characteristics surprisingly revealed mysterious genes in some Gram-negative bacteria, which products were annotated as aminotransferases, but they lacked the key catalytic lysine residue required for covalent binding of the PLP-cofactor. To address the question of which products these genes encode, we obtained the first structure of such a type of protein from the bacterium Variovorax paradoxus (VP5454) and provided its comprehensive analysis. We demonstrated that VP5454 has a typical aminotransferase fold and architecture of the active site, where substitution of the catalytic lysine with asparagine was observed. Despite that no covalent adduct can be formed between PLP and asparagine residue, using X-ray analysis and molecular dynamic (MD) simulation, we demonstrated that VP5454 is able to bind the PLP molecule in the transaminase in a specific manner, with PLP coordinated via its phosphate moiety. Taking into account a number of sequences homologous to VP5454 with a substituted catalytic lysine found in the genomes of various bacteria, we speculate that the proteins encoded by these sequences may have hidden functional roles. [ABSTRACT FROM AUTHOR]

By decreasing root 1-aminocyclopropane-1-carboxylate (ACC) content and plant ethylene production, the microbial enzyme ACC deaminase is a widespread beneficial trait of plant growth-promoting rhizobacteria (PGPR), ameliorating ethylene-mediated root growth inhibition. However, relatively little is known about whether bacterial ACC deaminase modulates root architecture and root hair traits. Thus the dwarf tomato (Solanum lycopersicum) cultivar Micro-Tom was inoculated in vitro with Pseudomonas brassicacearum Am3, its ACC deaminase deficient mutant T8-1, a known PGPR strain Variovorax paradoxus 5C-2 or chemically treated with agents that promoted or inhibited ethylene production or sensitivity (Ag+, Co2+, and ACC). ACC treatment reduced both root elongation and the number of lateral roots, while ethylene inhibitors (Ag+, Co2+) and V. paradoxus 5C-2 promoted primary root elongation, but differentially affected lateral root length and number. Ag+ stimulated lateral root development, while Co2+ and V. paradoxus 5C-2 did not. Inoculation with P. brassicacearum Am3 and T8-1 inhibited elongation of the primary and lateral roots at a high inoculum concentration (106 cells cm3). All bacterial strains significantly increased the length and number of root hairs, with these effects more pronounced in P. brassicacearum Am3 than in the mutant T8-1. Treatment with Ag+ inhibited root hair formation and elongation, while Co2+ had the opposite effects. ACC treatment had no effect on root hair elongation but increased root hair density. While root growth inhibition caused by P. brassicacearum Am3 was independent of ACC deaminase, the promotion of root hair elongation and density by this strain was augmented by ACC deaminase activity. Thus ACC deaminase can modulate the morphological impacts of bacteria on root hair response by affecting plant ethylene content. [ABSTRACT FROM AUTHOR]

Here, we report and discuss the applicability of Variovorax paradoxus strain BFB1_13 in the bioremediation of BTEX contaminated sites. Strain BFB1_13 was capable of degrading all the six BTEX-compounds under both aerobic (O2 conc. 8 mg l−1) and micro-aerobic/oxygen-limited (O2 conc. 0.5 mg l−1) conditions using either individual (8 mg‧l−1) or a mixture of compounds (~ 1.3 mg‧l−1 of each BTEX compound). The BTEX biodegradation capability of SBP-encapsulated cultures (SBP—Small Bioreactor Platform) was also assessed. The fastest degradation rate was observed in the case of aerobic benzene biodegradation (8 mg l−1 per 90 h). Complete biodegradation of other BTEX occurred after at least 168 h of incubation, irrespective of the oxygenation and encapsulation. No statistically significant difference was observed between aerobic and microaerobic BTEX biodegradation. Genes involved in BTEX biodegradation were annotated and degradation pathways were predicted based on whole-genome shotgun sequencing and metabolic analysis. We conclude that V. paradoxus strain BFB1_13 could be used for the development of reactive biobarriers for the containment and in situ decontamination of BTEX contaminated groundwater plumes. Our results suggest that V. paradoxus strain BFB1_13—alone or in co-culture with other BTEX degrading bacterial isolates—can be a new and efficient commercial bioremediation agent for BTEX contaminated sites. [ABSTRACT FROM AUTHOR]

3,3′-Thiodipropionic acid (TDP) is an antioxidant, which can be used as precursor carbon source to synthesize polythioesters. The bacterium Variovorax paradoxus TBEA6 strain can use TDP as a single source of carbon and energy. In the present study, experiments were carried out to identify proteins involved in the transport of TDP into the cells of strain TBEA6. Hence, eight putative tctC genes, which encode for the TctC proteins, were amplified from genomic DNA of TBEA6 strain using polymerase chain reaction and expressed in E. coli BL21 cells. Cells were grown in auto-induction medium, and protein purification was done using His Spin Trap affinity columns. Purity and molecular weight of each protein were confirmed by SDS-PAGE analysis. Protein-ligand interactions were monitored in thermoshift assays using the real-time PCR system. Two TctC proteins (locus tags VPARA-44430 and VPARA-01760) out of eight proteins showed a significant shift in their melting temperatures when they interact with the ligand (TDP or gluconate). The responsible genes were deleted in the genome of TBEA6 using suicide plasmid pJQ200mp18Tc, and single deletion mutants of the two candidate genes were subsequently generated. Finally, growth of the wild-type strain (TBEA6) and the two mutant strains (ΔVPARA-44430 and ΔVPARA-01760) were monitored and compared using TDP or gluconate as carbon sources. Wild type strains were successfully grown with TDP or gluconate. From the two mutant strains, one (ΔVPARA-44430) was unable to grow with TDP indicating that the tctC gene with locus tag VPARA-44430 is involved in the uptake of TDP. Key Points • Putative tctC genes from V. paradoxus TBEA6 were heterologously expressed in E. coli. • Protein-ligand interactions monitored in thermoshift assays using the real-time PCR. • tctC gene with locus tag VPARA-44430 is involved in the uptake of TDP. [ABSTRACT FROM AUTHOR]

Effective biocatalysts for the synthesis of optically pure amines from keto precursors are highly required in organic synthesis. Transaminases are a large group of PLP-dependent enzymes, which can be utilized for production of chiral amines or amino acids. The bioinformatic approach previously made to search for promising transaminases with unusual characteristics surprisingly revealed mysterious genes in some Gram-negative bacteria, which products were annotated as aminotransferases, but they lacked the key catalytic lysine residue required for covalent binding of the PLP-cofactor. To address the question of which products these genes encode, we obtained the first structure of such a type of protein from the bacterium Variovorax paradoxus (VP5454) and provided its comprehensive analysis. We demonstrated that VP5454 has a typical aminotransferase fold and architecture of the active site, where substitution of the catalytic lysine with asparagine was observed. Despite that no covalent adduct can be formed between PLP and asparagine residue, using X-ray analysis and molecular dynamic (MD) simulation, we demonstrated that VP5454 is able to bind the PLP molecule in the transaminase in a specific manner, with PLP coordinated via its phosphate moiety. Taking into account a number of sequences homologous to VP5454 with a substituted catalytic lysine found in the genomes of various bacteria, we speculate that the proteins encoded by these sequences may have hidden functional roles.

• Plant growth promoting rhizobacteria (PGPR) alleviate crop losses during drought. • The microbiome, plant and environment determine PGPR fate post-inoculation. • Variovorax paradoxus has high metabolic versatility, directing its fitness and competitiveness in the rhizosphere. • Applying V. paradoxus to plants grown in drying soil promoted plant growth. • Matching inocula to target environments offers biotechnological opportunities. Drought affects plant hormonal homeostasis, including root to shoot signalling. The plant is intimately connected below-ground with soil-dwelling microbes, including plant growth promoting rhizobacteria (PGPR) that can modulate plant hormonal homeostasis. Incorporating PGPR into the rhizosphere often delivers favourable results in greenhouse experiments, while field applications are much less predictable. We review the natural processes that affect the formation and dynamics of the rhizosphere, establishing a model for successful field application of PGPR utilizing an example microbial inoculum, Variovorax paradoxus 5C-2. [ABSTRACT FROM AUTHOR]

3,3'-Thiodipropionic acid (TDP) is used as an additive in food and cosmetic industry and as precursor substrate for biotechnical polythioester production. Its catabolism was investigated in Variovorax paradoxus TBEA6 previous to this study. It was reported that the insertion of the transposon Tn5::mob into a gene showing high homology to flavin-dependent oxidoreductases (fox) resulted in impaired growth with TDP. Therefore, it was assumed that the initial cleavage of TDP is catalyzed by an FAD-dependent oxidoreductase (Fox, VPARA 05580). Accordingly, fox was heterologously expressed as a thioredoxin fusion protein. Analytical size exclusion chromatography revealed a homodimeric structure and the presence of the cofactor FAD. In vitro experiments showed that FoxTBEA6 is a D-2-hydroxy acid specific dehydrogenase and that its activity is enhanced in presence of either Ni2+, Co2+ or Zn2+. Cleavage of TDP by FoxTBEA6 was not observed. The findings are contrary to restricted growth with TDP of the transposon mutants and the previously published deletion mutant V. paradoxus TBEA6 Δfox. In this study, this contradiction was investigated by generation of additional deletion mutants, in which partial or complete deletion of fox did not affect utilization of TDP, and the mapping of single nucleotide polymorphisms (SNPs) in V. paradoxus TBEA6 Δfox. [ABSTRACT FROM AUTHOR]

The use of bioresources such as bio-fertilizers especially those containing plant growth promoting rhizobacteria (PGPR), may be a strategy for sustainable agriculture that respects the environment while ensuring optimal plant growth. The objective of this study was to investigate the effects of selected PGPR strains on the growth, yield and quality of saffron. The bacteria tested were isolated from the saffron rhizosphere and selected for important plant beneficial activities (phosphate solubilization, siderophore, and auxin production). The best strains were identified by 16S rRNA gene sequence analysis. Strains S11P1 and S11A1a were identified as Rahnella aquatilis , while strain S12S4 belonged to the species Variovorax paradoxus. An inoculation field experiment was conducted in a 1575 m2 field area in Taliouine (Morocco). Four different inoculants were set-up: the three single selected strains and their mixture. Using the PGPR isolates as inoculum affects positively different saffron plant parameters, such as the number of leaves (28.87 ± 6.1 vs. 22.47 ± 8.19 for control treatment) and chlorophyll content. Underground parts, in particular, daughter corms production was significantly increased about 1.91 times more than the control. In addition, the quality of inoculated saffron was in accordance with the category I specifications (Crocin > 200, Picrocrocin > 70 and Safaranal >20). Overall these results bode well the possibility of using these rhizobacteria, and specially the treatment T2 (Rahnella aquatilis S11P1), as effective biofertilizers for saffron organic cultivation. [Display omitted] • Three local rhizobacterial strains were selected in vitro for their higher PGP activities. • Single strains inoculants and their mixture were applied to saffron plants under field conditions. • Biofertilizers beneficial effects concerned saffron aerial parts growth, the number and biomass of daughter corms. • PGPR inoculation improved the quality of saffron by increasing the rate of essential secondary metabolites. [ABSTRACT FROM AUTHOR]

There is a great interest in the removal of heavy metals from aqueous media by various biomass. In this study, the potential of using live and dead cells ofVariovorax paradoxusandArthrobacter viscosusbacteria for the removal of Zn(II) were investigated for the first time. The bacteria were isolated from the ceramic industry sludge. Remaining concentrations of Zn(II) in the metal solutions after biosorption by bacteria were measured by ICP-OES. The removal of Zn(II) from aqueous solution increased with increasing pH and initial ion concentration. The maximum removal efficiency ofV. paradoxuslive and dead cells was calculated as 92.7 and 91.3%, respectively, whereas the maximum removal efficiency ofA. viscosuslive and dead cells was calculated as 89.4 and 90.8%, respectively. The experimental data was found to comply with the Freundlich isotherm model and the biosorption mechanism was expressed with the pseudo-second-order model. [ABSTRACT FROM PUBLISHER]

Two novel plasmids, coined pHB44 and pBS64, were recently found in Variovorax paradoxus strains HB44 and BS64 isolated from the mycosphere of Laccaria proxima, on two different sampling occasions. We here describe the full sequences of pHB44 and pBS64 and establish their evolutionary placement and ecological function. Both plasmids, unique for mycospheric V paradoxus, were around 58 kb in size. They possessed, in a very similar fashion, three main plasmid backbone regions, which were predicted to be involved in plasmid replication, central control of maintenance, and conjugational transfer. Phylogenetic inference on the basis of seven selected and concatenated plasmid backbone genes provided solid evidence for the placement of the two plasmids in the IncP-1β1 group, with the recently isolated IncP-1β1 plasmid pMBUI8 as the closest relative. A comparative analysis of the sequences present in each of the recombinational hot spots (RHS) I to III across plasmids pHB44, pBS64, and pMBUI8 revealed the insertions found in plasmids pHB44 and pBS64 to be different from those of pMBUI8. Whereas, in the former two plasmids, RHS I and III were devoid of any major inserts, their RHS II regions contained inserts of 15,043 (pHB44) and 16,406 kb (pBS64), against about 9,3 kb for pMBUI8. Interestingly, these regions were highly similar across plasmids pHB44 and pBS64, and differed from that of pMBUI8. Closer inspection revealed the insert in the former plasmids to contain, next to transposases, an "mmf" gene cassette previously reported to encode metal "responsiveness" in the PromA plasmid pMOL98. Whereas the plasmid pHB44 RHS II contained the canonical mmf sequence, that in pBS64 contained, in addition, a "two-gene duplicated region" flanking the mmfC2 gene. In vitro experiments on the growth and survival of strains with or without plasmid pHB44 suggested this plasmid was involved in the binding and import of Fe3+ as well as V3+ ions into the host cells, thus yielding a growth advantage under "metal ion-limiting" conditions. In addition, pHB44 was found to confer a bacitracin resistance phenotype to its host strain HB44. The metal import and bacitracin resistance traits were tentatively attributed to specific genes present in the RHS II inserts. [ABSTRACT FROM AUTHOR]

Methotrexate degrading enzymes are required to overcome the toxicity of the methotrexate while treating the cancer. The enzyme from Variovorax paradoxus converts the methotrexate in to non toxic products. Methotrexate degrading enzyme from V. paradoxus is a dimeric protein with a molecular mass of 46 kDa and it acts on casein and gelatin. This enzyme is optimally active at pH 7.5 and 40 °C and nanoparticles of this enzyme were prepared by desolvation-crosslinking method. Enzyme nanoparticles could degrade methotrexate faster than the native enzyme and they show lower K m compare to the native enzyme. Enzyme nanoparticles show better thermostability and they were stable for much longer time in the serum compare to the native enzyme. Enzyme nanoparticles show better functionality than the native enzyme while clearing the methotrexate added to the serum suggesting their advantage over the native enzyme for the therapeutic and biotechnological applications. [ABSTRACT FROM AUTHOR]

The betaproteobacterium Variovorax paradoxus strain TBEA6 is capable of using 3,3′-thiodipropionic acid (TDP) as sole carbon and energy source for growth. This thioether is employed for several industrial applications. It can be applied as precursor for the biotechnical production of polythioesters (PTE), which represent persistent bioplastics. Consequently, the genome of V. paradoxus strain TBEA6 was sequenced. The draft genome sequence comprises approximately 7.2 Mbp and 6852 predicted open reading frames. Furthermore, transposon mutagenesis to unravel the catabolism of TDP in strain TBEA6 was performed. Screening of 20,000 mutants mapped the insertions of Tn 5 :: mob in 32 mutants, which all showed no growth with TDP as sole carbon source. Based on the annotated genome sequence together with transposon-induced mutagenesis, defined gene deletions, in silico analyses and comparative genomics, a comprehensive pathway for the catabolism of TDP is proposed: TDP is imported via the tripartite tricarboxcylate transport system and/or the TRAP-type dicarboxylate transport system. The initial cleavage of TDP into 3-hydroxypropionic acid (3HP) and 3-mercaptopropionic acid (3MP), which serves as precursor substrate for PTE synthesis, is most probably performed by the FAD-dependent oxidoreductase Fox. 3HP is presumably catabolized via malonate semialdehyde, whereas 3MP is oxygenated by the 3MP-dioxygenase Mdo yielding 3-sulfinopropionic acid (3SP). Afterwards, 3SP is linked to coenzyme A. The next step is the abstraction of sulfite by a desulfinase, and the resulting propionyl-CoA enters the central metabolism. Sulfite is oxidized to sulfate by the sulfite-oxidizing enzyme SoeABC and is subsequently excreted by the cells by the sulfate exporter Pse. [ABSTRACT FROM AUTHOR]

2-Mercaptosuccinic acid (MS) is an important and versatile substance for diverse fields of applications of which the most significant are surveyed in this article. Biological, chemical, and physical properties of MS as well as the knowledge of its synthesis and microbial degradation are illustrated. In addition, exemplary structural analogs of the organic sulfur compound are commented. The key application of MS in nanotechnology is discussed in detail with particular emphasis on quantum dots (nanocrystals) and self-assembled monolayers in combination with gold or silver. Furthermore, some medical and pharmaceutical applications are given, inter alia in bioimaging, as a nanocarrier, and with regard to the antimicrobial activity of MS-silver and MS-gold nanoparticles. Moreover, biological and chemical applications of MS are exemplified: the thiol compound can serve as an inhibitor for glutathione peroxidase, or the toxicity of substances can be increased due to the presence of MS in the respective cells or tissues. In the field of cosmetics, MS is widely utilized as a reducing agent for numerous products as explained in this article. Additionally, the microbial utilization of MS as a carbon and energy source for growth is elucidated in-depth, providing insight into different catabolic mechanisms. [ABSTRACT FROM AUTHOR]

Variovorax paradoxus B4 was isolated due to its ability to degrade the organic thiol compound mercaptosuccinate, which could be a promising precursor for novel polythioesters. The analysis of the proteome of this Gram-negative bacterium revealed several proteins with significantly increased expression during growth of cells with mercaptosuccinate as carbon source when compared to cells grown with gluconate or succinate. Among those, a large number of proteins involved in amino acid metabolism were identified, e.g., adenosylhomocysteinase and glutamate-ammonia ligase. Additionally, detection of superoxide dismutase strengthened the assumption of enhanced stress levels in mercaptosuccinate-grown cells. Several isoforms of a rhodanese domain-containing protein exhibited particularly increased expression during growth with mercaptosuccinate in comparison to gluconate (factor 14.2, stationary phase) or to succinate (factor 15.4, stationary phase). Besides this, augmented expression of the hypothetical protein VAPA_1c41240 raised attention. VAPA_1c41240 exhibited up to 13.3-fold (mercaptosuccinate vs gluconate) or 9.5-fold (mercaptosuccinate vs succinate) increased expression levels, and in silico searches revealed that this protein might be a thiol dioxygenase. Based on these results, a novel degradation pathway is proposed for mercaptosuccinate. The newly identified putative mercaptosuccinate dioxygenase could convert mercaptosuccinate to sulfinosuccinate by the introduction of two molecules of oxygen. Subsequently, sulfinosuccinate would be cleaved into succinate and sulfite either by a yet unknown enzyme, by spontaneous hydrolysis, or by the putative mercaptosuccinate dioxygenase itself. Succinate could then enter the central metabolism, while detoxification of sulfite could be achieved by the previously identified putative molybdopterin oxidoreductase. Biochemical studies will be done in the future to confirm this pathway. [ABSTRACT FROM AUTHOR]

This review outlines information about the Gram-negative, aerobic bacterium Variovorax paradoxus. The genomes of these species have G+C contents of 66.5-69.4 mol%, and the cells form yellow colonies. Some strains of V. paradoxus are facultative lithoautotrophic, others are chemoorganotrophic. Many of them are associated with important catabolic processes including the degradation of toxic and/or complex chemical compounds. The degradation pathways or other skills related to the following compounds, respectively, are described in this review: sulfolane, 3-sulfolene, 2-mercaptosuccinic acid, 3,3′-thiodipropionic acid, aromatic sulfonates, alkanesulfonates, amino acids and other sulfur sources, polychlorinated biphenyls, dimethyl terephthalate, linuron, 2,4-dinitrotoluene, homovanillate, veratraldehyde, 2,4-dichlorophenoxyacetic acid, anthracene, poly(3-hydroxybutyrate), chitin, cellulose, humic acids, metal-EDTA complexes, yttrium, rare earth elements, As(III), trichloroethylene, capsaicin, 3-nitrotyrosine, acyl-homoserine lactones, 1-aminocyclopropane-1-carboxylate, methyl tert-butyl ether, geosmin, and 2-methylisoborneol. Strains of V. paradoxus are also engaged in mutually beneficial interactions with other plant and bacterial species in various ecosystems. This species comprises probably promising strains for bioremediation and other biotechnical applications. Lately, the complete genomes of strains S110 and EPS have been sequenced for further investigations. [ABSTRACT FROM AUTHOR]

Resolving the physiological mechanisms by which rhizobacteria enhance plant growth is difficult, since many such bacteria contain multiple plant growth-promoting properties. To understand further how the 1-aminocyclopropane-1-carboxylate (ACC) deaminase (ACCd)-containing rhizobacterium Variovorax paradoxus 5C-2 affects plant growth, the flows and partitioning of mineral nutrients and abscisic acid (ABA) and ABA metabolism were studied in pea (Pisum sativum) plants following rhizosphere bacterial inoculation. Although root architecture was not affected, inoculation increased root and shoot biomass, and stomatal conductance, by 20, 15, and 24%, respectively, and increased N, P, K, Ca, and Mg uptake by 16, 81, 50, 46, and 58%, respectively. P deposition in inoculated plant roots was 4.9 times higher than that in uninoculated controls. Rhizobacterial inoculation increased root to shoot xylem flows and shoot to root phloem flows of K by 1.8- and 2.1-fold, respectively. In control plants, major sinks for K deposition were the roots and upper shoot (43% and 49% of total uptake, respectively), while rhizobacterial inoculation increased K distribution to the lower shoot at the expense of other compartments (xylem, phloem, and upper shoot). Despite being unable to metabolize ABA in vitro, V. paradoxus 5C-2 decreased root ABA concentrations and accumulation by 40–60%. Although inoculation decreased xylem ABA flows, phloem ABA flows increased. Whether bacterial ACCd attenuates root to shoot ABA signalling requires further investigation, since ABA is critical to maintain growth of droughted plants, and ACCd-containing organisms have been advocated as a means of minimizing growth inhibition of plants in drying soil. [ABSTRACT FROM AUTHOR]

The identification and discrimination of functional sequences or mutations is very helpful in the medical area. Promoter and splice-junction identification, gene finding, DNA or Aminoacid database searching are some examples. Pattern recognition algorithms are candidates to perform this tasks. In this work we present a model, based on AlphaBeta associative memory and NeedlemanWunsch algorithm, to correctly recall altered version of learning patterns with one or more of the following modifications: insertions, deletions, and mutations, very common alterations in DNA and Aminoacid sequences. Moreover, this model preserve one of the most important advantages in associative memories, the correct recall of the fundamental set. To test the performance of the algorithm on bioinformatics and biomedical applications, the model presented here was tested using two datasets; one from the UCI repository; refered to promoter identification and the second one to using the genome of the Variovorax paradoxus organism obtained from the NCBI repository. [ABSTRACT FROM AUTHOR]

Abstract: Inoculation of growing media with plant growth promoting rhizobacteria (PGPR) has a number of potential benefits for the production of ornamental plants. Certain rhizobacteria synthesise the enzyme ACC deaminase, which cleaves ACC, the precursor of the plant hormone ethylene. Bacterial metabolism is now known to lead to a reduction in [ACC] in the plant transpiration stream and bacteria are hypothesised to act on ACC exuded from roots. This in turn reduces the ethylene generated in plants growing in growing media inoculated with these bacteria. Here we tested if applications of the ACC deaminase containing rhizobacteria Variovorax paradoxus 5C–2could be of benefit to ornamental growers by reducing ethylene generation in stressed plants. Ethylene is produced at levels that are inhibitory to growth and development under a number of abiotic stresses. The propagation and production of hardy ornamentals is deleteriously affected by abiotic stresses that involve ethylene signalling, including drought and physical wounding. Inoculation of growing media with V. paradoxus 5C-2 lowered ethylene emission from mature leaves of Cytisus × praecox experiencing drought stress. In addition, bacterial inoculation of the growing media resulted in significantly reduced abscission of the mature leaves under drought treatment. Beneficial effects of inoculation where also found in the wounding response of Fargesia murielae following divisional propagation and late season senescence in Aquilegia × hybrida in response to drought stress. Together these results demonstrate that V. paradoxus 5C–2has real potential for use on ornamental nurseries in situations where plant stresses are unavoidable. [Copyright &y& Elsevier]

Abstract: In previous work, Variovorax paradoxus strain HB44, next to Burkholderia terrae BS001 and Dyella japonica BS003, were found to be selected in the mycosphere of the tricholomataceous fungi Laccaria proxima and Lyophyllum sp. strain Karsten in an acid soil denoted G. V. paradoxus HB44 showed poor survival in G bulk soil, irrespective of prior soil sterilization, and this poor survival also occurred for B. terrae BS001 and D. japonica BS003. In contrast, the survival rate of strain HB44 in two other soils, with pH values>5.5, was significantly raised. Also, significantly enhanced strain HB44 survival in G soil was found if the pH was raised to 5.5 or 6.5, and it was even shown to grow (in the presence of the exogenous carbon source glycerol) at such pH values in the sterile G soil. This behaviour was similar to that of the V. paradoxus type strain. Strikingly, Lyophyllum sp. strain Karsten, when colonizing the sterilized G soil, significantly raised the soil pH from about 4.6 to ≥5.0. The pH raise was dependent on time, hyphal development, as well as on initial soil pH, but was consistent throughout. The modulated soil pH conditions were shown to be permissive for the survival and growth of strain HB44, and this was extended to strains BS001 and BS003. These findings corroborate the hypothesis that L. sp. strain Karsten provides a suitable habitat for acid-sensitive strains like HB44, BS001 and BS003 in its mycosphere in acid soil, which is strongly defined by the establishment of a growth-permissive pH. [ABSTRACT FROM AUTHOR]

Abstract: At two occasions (2004 and 2006), a similar cluster of culturable bacteria was found to be selected in the mycosphere of the basidiomycetous fungus Laccaria proxima (Agaricales, Tricholomataceae) in the field. The bacteria, identified as related to Variovorax paradoxus, comprised 7.3–9% of the total culturable bacterial community in the L. proxima mycosphere, but were not found in corresponding bulk soil (<0.3%). One strain, denoted HB44, was selected in order to unravel the basis of the V. paradoxus mycosphere competence in in vitro experiments with the former Laccaria laccata, which was recently reclassified as Lyophyllum sp. strain Karsten (Agaricales, Tricholomataceae). In liquid culture experiments, L. strain Karsten was shown to be an avid producer of glycerol, next to acetate and formate, which constituted the most abundant carbonaceous compounds released. Strain HB44 was able to grow avidly at the expense of the glycerol liberated by the fungus, as evidenced by proton NMR analysis of the fungal exudates in the medium before and after bacterial growth. In sterilized field soil, strain HB44 survived significantly better in the presence than in the absence of L. strain Karsten. Addition of a glycerol series to the sterilized soil (without the fungus) resulted in the persistence or growth of strain HB44, but only if the pH of this soil was previously set at 5.5. Thus, we provide evidence for the contention that tricholomataceous fungi can create specific niches in soil for the V. paradoxus-related strain HB44 and that glycerol may be a main carbon source that drives the selection of this organism. [ABSTRACT FROM AUTHOR]

The article studies the alpha-methylserine aldolase gene from the NBRC15150, NBRC15149 and AJ110406 strains of Variovorax paradoxus that was expressed and cloned in Escherichia coli. It includes an in-depth analysis of the characterization and purification of the recombinant enzyme, as well as a discussion on the issues' implications for biotechnology.

An arsenic-resistant bacterium, AsRB1, was isolated from the fronds of Pteris vittata grown in a site contaminated with copper chromium arsenate. The bacterium exhibited resistance to arsenate, arsenite, and antimony in the culture medium. AsRB1, like Pseudomonas putida, grew on MacConkey and xylose–lactose–desoxycholate agars and utilized citrate but, unlike P. putida, was positive for indole test and negative for oxidase test. A phylogenetic analysis of the 16S rRNA gene showed that AsRB1 is a proteobacterium of the beta subclass, related to Pseudomonas saccharophila and Variovorax paradoxus. Following an exogenous supply of arsenate, most arsenic occurred as arsenite in the medium and the cell extracts, suggesting reduction and extrusion of arsenic as the mechanism for arsenic resistance in AsRB1. [ABSTRACT FROM AUTHOR]

Abstract: Eleven cadmium-tolerant bacterial strains were isolated from the root zone of Indian mustard (Brassica juncea L. Czern.) seedlings grown in Cd-supplemented soils as well as sewage sludge and mining waste highly contaminated with Cd. The bacteria also showed increased tolerance to other metals including Zn, Cu, Ni and Co. The isolated strains included Variovorax paradoxus, Rhodococcus sp. and Flavobacterium sp., and were capable of stimulating root elongation of B. juncea seedlings either in the presence or absence of toxic Cd concentrations. Some of the strains produced indoles or siderophores, but none possessed C2H2-reduction activity. All the strains, except Flavobacterium sp. strain 5P-3, contained the enzyme 1-aminocyclopropane-1-carboxylate (ACC) deaminase, which hydrolyses ACC (the immediate precursor of plant hormone ethylene) to NH3 and α-ketobutyrate. V. paradoxus utilized ACC as a sole source of N or energy. A positive correlation between the in vitro ACC deaminase activity of the bacteria and their stimulating effect on root elongation suggested that utilization of ACC is an important bacterial trait determining root growth promotion. The isolated bacteria offer promise as inoculants to improve growth of the metal accumulating plant B. juncea in the presence of toxic Cd concentrations and for the development of plant-inoculant systems useful for phytoremediation of polluted soils. [Copyright &y& Elsevier]