Degradation of 4-nitrobenzoate via 4-hydroxylaminobenzoate and 3,4-dihydroxybenzoate in Comamonas acidovorans NBA-10

Comamonas acidovorans NBA-10 was previously shown to degrade 4-nitrobenzoate via 4-hydroxylaminobenzoate and 3,4-dihydroxybenzoate. Washed cells, grown on a mixture of 4-nitrobenzoate and ethanol, stoichiometrically produced ammonium and 3,4-dihydroxybenzoate from 4-nitrobenzoate under anaerobic conditions provided ethanol was present. In cell extracts 4-hydroxylaminobenzoate was degraded to ammonium and 3,4-dihydroxybenzoate, but this activity was lost upon dialysis. No requirement for a cofactor was found, but rather reduced incubation conditions were necessary to restore enzyme activity. The 4-hydroxylamino-degrading enzyme was purified and the role of this novel type of enzyme in the degradation of nitroaromatic compounds is discussed.Abbreviation 4-ABA 4-aminobenzoate - 4-NBA 4-nitrobenzoate - 4-HABA 4-hydroxylaminobenzoate - 3,4-diHBA 3,4-dihydroxybenzoate     

The Fat and Warts signaling pathways: new insights into their regulation, mechanism and conservation

A cassette of cytoplasmic Drosophila tumor suppressors, including the kinases Hippo and Warts, has recently been linked to the transmembrane tumor suppressor Fat. These proteins act within interconnected signaling pathways, the principal functions of which are to control the growth and polarity of developing tissues. Recent studies have enhanced our understanding of the basis for signal transduction by Fat and Warts pathways, including the identification of a DNA-binding protein at the end of the pathway, have established the conservation of Fat and Warts signaling from flies to mammals, and have given us new insights into their regulation and biological functions.     

A new two-dimensional thallium(I) coordination polymer with 4-hydroxybenzylidene-4-aminobenzoate: Thermal, structural, solution and solvatochromic studies

A new one-dimensional thallium(I) coordination polymer with a Schiff base ligand, {[Tl(L)(HL)](H₂O)_0.77}_n (1) [HL = 4-hydroxybenzylidene-4-aminobenzoic acid], has been synthesized and characterized. The single-crystal X-ray data of compound 1 show the coordination number of the Tl^I ions to be seven. The thermal stability of 1 was studied by thermal gravimetric (TG) and differential thermal analyses (DTA). The overall stoichiometry in the solid state is 1:2, but both spectrophotometric and conductometric methods did not support formation of a complex with this stoichiometry in solution. The solvatochromic behaviour of 4-hydroxybenzylidene-4-aminobenzoic acid was also investigated by studying its spectra in a selection of different organic solvents. The observed bands are assigned to electronic transitions.     

Biodegradation of 4-nitrophenol in a two-phase sequencing batch reactor: concept demonstration,kinetics and modelling

The objectives of this work were to demonstrate the potential of a two-phase sequencing batch reactor in degrading xenobiotics and to evaluate the kinetic parameters leading to a mathematical model of the system. 4-Nitrophenol (4NP), a typical representative of substituted phenols, was selected as the target xenobiotic; this compound has never been remediated in a two-phase bioreactor before. Partition tests were conducted to determine the most appropriate partitioning solvent, and among the three investigated solvents (1-undecanol, 2-undecanone and oleyl alcohol), 2-undecanone was chosen because of its favourable partition coefficient and its negligible emulsion-forming tendencies. Moreover, the selected solvent showed satisfactory biocompatibility characteristics with respect to the biomass, with only minor effects on the intrinsic microbial kinetics. Kinetic tests were then performed in a sequencing batch reactor (2-l volume) operated in both conventional one- and two-phase configurations, with the two-phase system showing a significant improvement in the process kinetics in terms of reduced inhibition and increased maximum removal rate. The obtained kinetic parameters suggest that the two-phase sequencing batch system may find full-scale application, as the maximum removal rate k _max (~3 mg 4NP mgVSS⁻¹ day⁻¹) is of the same order of magnitude of heterotrophic bacteria operating in wastewater treatment plants.     

Improved degradation of 4-chlorobiphenyl, 2,3-dihydroxybiphenyl, and catecholic compounds by recombinant bacterial strains

ThepcbC gene encoding (4-chloro-)2,3-dihydroxybiphenyl dioxygenase was cloned from the genomic DNA ofPseudomonas sp. P20 using pKT230 to construct pKK1. A recombinant strain,E. coli KK1, was selected by transforming the pKK1 intoE. coli XL1-Blue. Another recombinant strain,Pseudomonas sp. DJP-120, was obtained by transferring the pKK1 ofE. coli KK1 intoPseudomonas sp. DJ-12 by conjugation. Both recombinant strains showed a 23.7 to 26.5 fold increase in the degradation activity to 2,3-dihydroxybiphenyl compared with that of the natural isolate,Pseudomonas sp. DJ-12. The DJP-120 strain showed 24.5, 3.5, and 4.8 fold higher degradation activities to 4-chlorobiphenyl, catechol, and 3-methylcatechol than DJ-12 strain, respectively. The pKK1 plasmid of both strains and their ability to degrade 2,3-dihydroxybiphenyl were stable even after about 1,200 generations.     

Comparative genomics of yeast species: new insights into their biology

The genomes of two hemiascomycetous yeasts (Saccharomyces cerevisiae and Candida albicans) and one archiascomycete (Schizosaccharomyces pombe) have been completely sequenced and the genes have been annotated. In addition, the genomes of 13 more Hemiascomycetes have been partially sequenced. The amount of data thus obtained provides information on the evolutionary relationships between yeast species. In addition, the differential genetic characteristics of the microorganisms explain a number of distinctive biological traits. Gene order conservation is observed between phylogenetically close species and is lost in distantly related species, probably due to rearrangements of short regions of DNA. However, gene function is much more conserved along evolution. Compared to S. cerevisiae and S. pombe, C. albicans has a larger number of specific genes, i.e., genes not found in other organisms, a fact that can account for the biological characteristics of this pathogenic dimorphic yeast which is able to colonize a large variety of environments.     

G4-quadruplex-binding proteins: review and insights into selectivity

There are over 700,000 putative G4-quadruplexes (G4Qs) in the human genome, found largely in promoter regions, telomeres, and other regions of high regulation. Growing evidence links their presence to functionality in various cellular processes, where cellular proteins interact with them, either stabilizing and/or anchoring upon them, or unwinding them to allow a process to proceed. Interest in understanding and manipulating the plethora of processes regulated by these G4Qs has spawned a new area of small-molecule binder development, with attempts to mimic and block the associated G4-binding protein (G4BP). Despite the growing interest and focus on these G4Qs, there is limited data (in particular, high-resolution structural information), on the nature of these G4Q-G4BP interactions and what makes a G4BP selective to certain G4Qs, if in fact they are at all. This review summarizes the current literature on G4BPs with regards to their interactions with G4Qs, providing groupings for binding mode, drawing conclusions around commonalities and highlighting information on specific interactions where available.     

Biodegradation of the mixtures of 4-chlorophenol and phenol by Comamonas testosteroni CPW301

A 4-chlorophenol (4-CP)-degrading bacterium, strain CPW301, was isolated from soil and identified as Comamonas testosteroni. This strain dechlorinated and degraded 4-CP via a meta-cleavage pathway. CPW301 could also utilize phenol as a carbon and energy source without the accumulation of any metabolites via the same meta-cleavage pathway. When phenol was added as a additional substrate, CPW301 could degrade 4-CP and phenol simultaneously. The addition of phenol greatly accelerated the degradation of 4-CP due to the increased cell mass. The simultaneous degradation of the 4-CP and phenol is useful not only for enhanced cell growth but also for the bioremediation of both compounds, which are normally present in hazardous waste sites as a mixture.     

Lipoproteins in Gram-negative bacteria: new insights into their biogenesis,subcellular targeting and functional roles

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Oxysterols: Sources,cellular storage and metabolism,and new insights into their roles in cholesterol homeostasis

Oxysterols are structurally identical to cholesterol, but with one or more additional oxygen containing functional groups (such as alcohol, carbonyl or epoxide groups). The wide array of oxysterols encountered in human health and disease vary in their origin (either enzymic or non-enzymic), and their putative effects and/or function(s). Some are thought to be damaging, whereas others may play important physiological roles, including in the regulation of cholesterol homeostasis. In this review, we will concentrate on the major cellular oxysterols. We summarise their location, generation, metabolism and elimination, as well as providing insights into the latest research into their regulatory roles in cholesterol homeostasis.     

Biodegradation of trinitrotoluene (TNT) by indigenous microorganisms from TNT-contaminated soil,and their application in TNT bioremediation

Soil and groundwater contaminated by munitions compounds is a crucial issue in environmental protection. Trinitrotoluene (TNT) is highly toxic and carcinogenic; therefore, the control and remediation of TNT contamination is a critical environmental issue. In this study, the authors characterized the indigenous microbial isolates from a TNT-contaminated site and evaluated their activity in TNT biodegradation. The bacteria Achromobacter sp. BC09 and Citrobacter sp. YC4 isolated from TNT-contaminated soil by enrichment culture with TNT as the sole carbon and nitrogen source (strain BC09) and as the sole nitrogen but not carbon source (strain YC4) were studied for their use in TNT bioremediation. The efficacy of degradation of TNT by indigenous microorganisms in contaminated soil without any modification was insufficient in the laboratory-scale pilot experiments. The addition of strains BC09 and YC4 to the contaminated soil did not significantly accelerate the degradation rate. However, the addition of an additional carbon source (e.g., 0.25% sucrose) could significantly increase the bioremediation efficiency (ca. decrease of 200 ppm for 10 days). Overall, the results suggested that biostimulation was more efficient as compared with bioaugmentation. Nevertheless, the combination of biostimulation and bioaugmentation using these indigenous isolates is still a feasible approach for the development of bioremediation of TNT pollution.     

Closing the loops: new insights into the role and regulation of actin during cell polarization

In this review, we summarize recent results on the understanding of actin organization and cell polarization with an emphasis on the critical role of actin during this process. We first report on the advances made in understanding the function and mechanism of formin family proteins in the nucleation of actin filaments. We also discuss how formins and other regulators of actin dynamics are thought to be involved in the generation of cell polarity. In the second part we discuss new findings indicating that, rather than using a linear pathway from signal transduction to cytoskeleton re-organization, cell polarity is established through bidirectional interplay between these processes. We describe the various types of feedback loops identified and point out common schemes. Finally we briefly summarize the emerging role of actinlike proteins in the generation of polarity in prokaryotes that implies an early origin of actin's role in cell polarity.     

Biodegradation of phenoxyacetic acid in soil by Pseudomonas putida PP0301(pR0103), a constitutive degrader of 2, 4–dichlorophenoxyacetate

The efficacy of using genetically engineered microbes (GEMs) to degrade recalcitrant environmental toxicants was demonstrated by the application of Pseudomonas putida PP0301(pR0103) to an Oregon agricultural soil amended with 500 micrograms/g of a model xenobiotic, phenoxyacetic acid (PAA). P. putida PP0301(pR0103) is a constitutive degrader of 2,4-dichlorophenoxyacetate (2,4-D) and is also active on the non-inducing substrate, PAA. PAA is the parental compound of 2,4-dichlorophenoxyacetic acid (2,4-D) and whilst the indigenous soil microbiota degraded 500 micrograms/g 2,4-D to less than 10 micrograms/g, PAA degradation was insignificant during a 40-day period. No significant degradation of PAA occurred in soil inoculated with the parental strain P. putida PP0301 or the inducible 2,4-D degrader P. putida PP0301(pR0101). Moreover, co-amendment of soil with 2,4-D and PAA induced the microbiota to degrade 2,4-D; PAA was not degraded. P. putida PP0301-(pR0103) mineralized 500-micrograms/g PAA to trace levels within 13 days and relieved phytotoxicity of PAA to Raphanus sativus (radish) seeds with 100% germination in the presence of the GEM and 7% germination in its absence. In unamended soil, survival of the plasmid-free parental strain P. putida PP0301 was similar to the survival of the GEM strain P. putida PP0301(pR0103). However, in PAA amended soil, survival of the parent strain was over 10,000-fold lower (< 3 colony forming units per gram of soil) than survival of the GEM strain after 39 days.     

Repeat-protein folding: new insights into origins of cooperativity, stability, and topology

Although our understanding of globular protein folding continues to advance, the irregular tertiary structures and high cooperativity of globular proteins complicates energetic dissection. Recently, proteins with regular, repetitive tertiary structures have been identified that sidestep limitations imposed by globular protein architecture. Here we review recent studies of repeat-protein folding. These studies uniquely advance our understanding of both the energetics and kinetics of protein folding. Equilibrium studies provide detailed maps of local stabilities, access to energy landscapes, insights into cooperativity, determination of nearest-neighbor interaction parameters using statistical thermodynamics, relationships between consensus sequences and repeat-protein stability. Kinetic studies provide insight into the influence of short-range topology on folding rates, the degree to which folding proceeds by parallel (versus localized) pathways, and the factors that select among multiple potential pathways. The recent application of force spectroscopy to repeat-protein unfolding is providing a unique route to test and extend many of these findings.     

Fate of Enrofloxacin in Lake Sediment: Biodegradation,Transformation Product Identification,and Ecotoxicological Implications

Various pharmaceutical drugs are being detected in different environmental compartments such as surface waters, groundwater, and sediment; a major concern since they are biologically active substances which can interfere with biological systems affecting the native biota. Among these drugs, antimicrobials are especially worrisome mainly due to the development of bacterial resistance. The aims of this study were to investigate if enrofloxacin, an emergent antibiotic pollutant, could be biodegraded in lake sediment, identify its break down products and to determine if these products have antimicrobial properties or are toxic. Three biodegradation products were identified and the antibiotic susceptibility assay proved that the products formed did not display antibiotic effects. Ecotoxicity testing with green algae suggested that the degradation products do not cause adverse effects statistically. However, it is suggested that further investigations are needed to identify the mechanism of degradation and the microbes involved.     

An epigenetic integrator: new insights into genome regulation, environmental stress responses and developmental controls by histone deacetylase 6

Histone acetylation ranks with DNA methylation as one of major epigenetic modifications in eukaryotes. Deacetylation of histone N-terminal tails is intimately correlated with gene silencing and heterochromatin formation. In Arabidopsis, histone deacetylase 6 (HDA6) is a well-studied histone deacetylase that functions in gene silencing. Recently, it has been reported that HDA6 cooperates with DNA methylation on its direct target locus in the gene silencing mechanism. HDA6 has the multifaceted role in regulation of genome maintenance, development and environmental stress responses in plants. Elucidation of HDA6 function provides important information for understanding of epigenetic regulation in plants. In this review, we highlight recent progress in elucidating the HDA6-mediated gene silencing mechanisms and deciphering the biological function of HDA6.     

Comparative genomic analysis of nine Sphingobium strains: insights into their evolution and hexachlorocyclohexane (HCH) degradation pathways

Background

Sphingobium spp. are efficient degraders of a wide range of chlorinated and aromatic hydrocarbons. In particular, strains which harbour the lin pathway genes mediating the degradation of hexachlorocyclohexane (HCH) isomers are of interest due to the widespread persistence of this contaminant. Here, we examined the evolution and diversification of the lin pathway under the selective pressure of HCH, by comparing the draft genomes of six newly-sequenced Sphingobium spp. (strains LL03, DS20, IP26, HDIPO4, P25 and RL3) isolated from HCH dumpsites, with three existing genomes (S. indicum B90A, S. japonicum UT26S and Sphingobium sp. SYK6).

Results

Efficient HCH degraders phylogenetically clustered in a closely related group comprising of UT26S, B90A, HDIPO4 and IP26, where HDIPO4 and IP26 were classified as subspecies with ANI value >98%. Less than 10% of the total gene content was shared among all nine strains, but among the eight HCH-associated strains, that is all except SYK6, the shared gene content jumped to nearly 25%. Genes associated with nitrogen stress response and two-component systems were found to be enriched. The strains also housed many xenobiotic degradation pathways other than HCH, despite the absence of these xenobiotics from isolation sources. Additionally, these strains, although non-motile, but posses flagellar assembly genes. While strains HDIPO4 and IP26 contained the complete set of lin genes, DS20 was entirely devoid of lin genes (except linKLMN) whereas, LL03, P25 and RL3 were identified as lin deficient strains, as they housed incomplete lin pathways. Further, in HDIPO4, linA was found as a hybrid of two natural variants i.e., linA1 and linA2 known for their different enantioselectivity.

Conclusion

The bacteria isolated from HCH dumpsites provide a natural testing ground to study variations in the lin system and their effects on degradation efficacy. Further, the diversity in the lin gene sequences and copy number, their arrangement with respect to IS6100 and evidence for potential plasmid content elucidate possible evolutionary acquisition mechanisms for this pathway. This study further opens the horizon for selection of bacterial strains for inclusion in an HCH bioremediation consortium and suggests that HDIPO4, IP26 and B90A would be appropriate candidates for inclusion.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-1014) contains supplementary material, which is available to authorized users.