Two Zn2Cys6-type transcription factors respond to aromatic compounds and regulate the expression of laccases in the white-rot fungus Trametes hirsuta.

White-rot fungi differentially express laccases when they encounter aromatic compounds. However, the underlying mechanisms are still being explored. Here, proteomics analysis revealed that in addition to increased laccase activity, proteins involved in sphingolipid metabolism and toluene degradation as well as some cytochrome P450s (CYP450s) were differentially expressed and significantly enriched during 48 h of o-toluidine exposure, in Trametes hirsuta AH28-2. Two Zn2Cys6-type transcription factors (TFs), TH8421 and TH4300, were upregulated. Bioinformatics docking and isothermal titration calorimetry assays showed that each of them could bind directly to o-toluidine and another aromatic monomer, guaiacol. Binding to aromatic compounds promoted the formation of TH8421/TH4300 heterodimers. TH8421 and TH4300 silencing in T. hirsuta AH28-2 led to decreased transcriptional levels and activities of LacA and LacB upon o-toluidine and guaiacol exposure. EMSA and ChIP-qPCR analysis further showed that TH8421 and TH4300 bound directly with the promoter regions of lacA and lacB containing CGG or CCG motifs. Furthermore, the two TFs were involved in direct and positive regulation of the transcription of some CYP450s. Together, TH8421 and TH4300, two key regulators found in T. hirsuta AH28-2, function as heterodimers to simultaneously trigger the expression of downstream laccases and intracellular enzymes. Monomeric aromatic compounds act as ligands to promote heterodimer formation and enhance the transcriptional activities of the two TFs.IMPORTANCEWhite-rot fungi differentially express laccase isoenzymes when exposed to aromatic compounds. Clarification of the molecular mechanisms underlying differential laccase expression is essential to elucidate how white-rot fungi respond to the environment. Our study shows that two Zn2Cys6-type transcription factors form heterodimers, interact with the promoters of laccase genes, and positively regulate laccase transcription in Trametes hirsuta AH28-2. Aromatic monomer addition induces faster heterodimer formation and rate of activity. These findings not only identify two new transcription factors involved in fungal laccase transcription but also deepen our understanding of the mechanisms underlying the response to aromatics exposure in white-rot fungi.

Sulfonamide Per- and Polyfluoroalkyl Substances Can Impact Microorganisms Used in Aromatic Hydrocarbon and Trichloroethene Bioremediation.

Per- and polyfluoroalkyl substances (PFASs) from aqueous film forming foams (AFFFs) can hinder bioremediation of co-contaminants such as trichloroethene (TCE) and benzene, toluene, ethylbenzene, and xylene (BTEX). Anaerobic dechlorination can require bioaugmentation of Dehalococcoides, and for BTEX, oxygen is often sparged to stimulate in situ aerobic biodegradation. We tested PFAS inhibition to TCE and BTEX bioremediation by exposing an anaerobic TCE-dechlorinating coculture, an aerobic BTEX-degrading enrichment culture, and an anaerobic toluene-degrading enrichment culture to n-dimethyl perfluorohexane sulfonamido amine (AmPr-FHxSA), perfluorohexane sulfonamide (FHxSA), perfluorohexanesulfonic acid (PFHxS), or nonfluorinated surfactant sodium dodecyl sulfate (SDS). The anaerobic TCE-dechlorinating coculture was resistant to individual PFAS exposures but was inhibited by >1000× diluted AFFF. FHxSA and AmPr-FHxSA inhibited the aerobic BTEX-degrading enrichment. The anaerobic toluene-degrading enrichment was not inhibited by AFFF or individual PFASs. Increases in amino acids in the anaerobic TCE-dechlorinating coculture compared to the control indicated stress response, whereas the BTEX culture exhibited lower concentrations of all amino acids upon exposure to most surfactants (both fluorinated and nonfluorinated) compared to the control. These data suggest the main mechanisms of microbial toxicity are related to interactions with cell membrane synthesis as well as protein stress signaling.

Bacterial crude oil and polyaromatic hydrocarbon degraders from Kazakh oil fields as barley growth support.

Bacterial strains of the genera Arthrobacter, Bacillus, Dietzia, Kocuria, and Micrococcus were isolated from oil-contaminated soils of the Balgimbaev, Dossor, and Zaburunye oil fields in Kazakhstan. They were selected from 1376 isolated strains based on their unique ability to use crude oil and polyaromatic hydrocarbons (PAHs) as sole source of carbon and energy in growth experiments. The isolated strains degraded a wide range of aliphatic and aromatic components from crude oil to generate a total of 170 acid metabolites. Eight metabolites were detected during the degradation of anthracene and of phenanthrene, two of which led to the description of a new degradation pathway. The selected bacterial strains Arthrobacter bussei/agilis SBUG 2290, Bacillus atrophaeus SBUG 2291, Bacillus subtilis SBUG 2285, Dietzia kunjamensis SBUG 2289, Kocuria rosea SBUG 2287, Kocuria polaris SBUG 2288, and Micrococcus luteus SBUG 2286 promoted the growth of barley shoots and roots in oil-contaminated soil, demonstrating the enormous potential of isolatable and cultivable soil bacteria in soil remediation. KEY POINTS: • Special powerful bacterial strains as potential crude oil and PAH degraders. • Growth on crude oil or PAHs as sole source of carbon and energy. • Bacterial support of barley growth as resource for soil remediation.

Biodegradation of aliphatic and aromatic hydrocarbons by bacteria isolated from Bahregan area.

Environmental pollution with aromatic and aliphatic hydrocarbons caused by oil and petrochemical industries has very toxic and carcinogenic effects on living organisms and should be removed from the environment. In this research, after analyzing the oil sludge of the Bahregan area, it was found that most aliphatic paraffin compounds are related to octadecane, most liquid aliphatic compounds are related to hexadecane, and most aromatic compounds are related to naphthalene, phenanthrene, fluoranthene, and anthracene. Then, we investigated the ability of native bacteria from this area, such as Thalassospira, Chromohalobacter, and a bacterial consortium, to biodegrade the dominant aromatic and aliphatic hydrocarbons found in oil sludge. The results of Gas Chromatography-Mass Spectrometry analysis showed that among the tested hydrocarbon sources, Thalassospira can completely remove octadecane and hexadecane, and Chromohalobacter can reduce hexadecane from 15.9 to 9.9%. The bacterial consortium can completely remove octadecane and reduce hexadecane from 15.9 to 5.1%, toluene from 25.6 to 0.6%, and phenanthrene from 12.93 to 6%. According to the obtained results, the bacterial consortium effectively plays a role in the biodegradation of aromatic and aliphatic hydrocarbons, making it a viable solution for treating hydrocarbon pollutants in various environments.

Insights into the susceptibility of Pseudomonas putida to industrially relevant aromatic hydrocarbons that it can synthesize from sugars.

Pseudomonas putida DOT-T1E is a highly solvent tolerant strain for which many genetic tools have been developed. The strain represents a promising candidate host for the synthesis of aromatic compounds-opening a path towards a green alternative to petrol-derived chemicals. We have engineered this strain to produce phenylalanine, which can then be used as a raw material for the synthesis of styrene via trans-cinnamic acid. To understand the response of this strain to the bioproducts of interest, we have analyzed the in-depth physiological and genetic response of the strain to these compounds. We found that in response to the exposure to the toxic compounds that the strain can produce, the cell launches a multifactorial response to enhance membrane impermeabilization. This process occurs via the activation of a cis to trans isomerase that converts cis unsaturated fatty acids to their corresponding trans isomers. In addition, the bacterial cells initiate a stress response program that involves the synthesis of a number of chaperones and ROS removing enzymes, such as peroxidases and superoxide dismutases. The strain also responds by enhancing the metabolism of glucose through the specific induction of the glucose phosphorylative pathway, Entner-Doudoroff enzymes, Krebs cycle enzymes and Nuo. In step with these changes, the cells induce two efflux pumps to extrude the toxic chemicals. Through analyzing a wide collection of efflux pump mutants, we found that the most relevant pump is TtgGHI, which is controlled by the TtgV regulator.

Combined Omics Approach Reveals Key Differences between Aerobic and Microaerobic Xylene-Degrading Enrichment Bacterial Communities: Rhodoferax─A Hitherto Unknown Player Emerges from the Microbial Dark Matter.

Among monoaromatic hydrocarbons, xylenes, especially the ortho and para isomers, are the least biodegradable compounds in oxygen-limited subsurface environments. Although much knowledge has been gained regarding the anaerobic degradation of xylene isomers in the past 2 decades, the diversity of those bacteria which are able to degrade them under microaerobic conditions is still unknown. To overcome this limitation, aerobic and microaerobic xylene-degrading enrichment cultures were established using groundwater taken from a xylene-contaminated site, and the associated bacterial communities were investigated using a polyphasic approach. Our results show that the xylene-degrading bacterial communities were distinctly different between aerobic and microaerobic enrichment conditions. Although members of the genus Pseudomonas were the most dominant in both types of enrichments, the Rhodoferax and Azovibrio lineages were only abundant under microaerobic conditions, while Sphingobium entirely replaced them under aerobic conditions. Analysis of a metagenome-assembled genome of a Rhodoferax-related bacterium revealed aromatic hydrocarbon-degrading ability by identifying two catechol 2,3-dioxygenases in the genome. Moreover, phylogenetic analysis indicated that both enzymes belonged to a newly defined subfamily of type I.2 extradiol dioxygenases (EDOs). Aerobic and microaerobic xylene-degradation experiments were conducted on strains Sphingobium sp. AS12 and Pseudomonas sp. MAP12, isolated from the aerobic and microaerobic enrichments, respectively. The obtained results, together with the whole-genome sequence data of the strains, confirmed the observation that members of the genus Sphingobium are excellent aromatic hydrocarbon degraders but effective only under clear aerobic conditions. Overall, it was concluded that the observed differences between the bacterial communities of aerobic and microaerobic xylene-degrading enrichments were driven primarily by (i) the method of aromatic ring activation (monooxygenation vs dioxygenation), (ii) the type of EDO enzymes, and (iii) the ability of degraders to respire utilizing nitrate.

Mixed polyaromatic hydrocarbon degradation by halotolerant bacterial strains from marine environment and its metabolic pathway.

Accidents involving diesel oil spills are prevalent in sea- and coastal regions. Polycyclic aromatic hydrocarbons (PAHs) can be adsorbed in soil and constitute a persistent contaminant due to their poor water solubility and complex breakdown. PAHs pollution is a pervasive environmental concern that poses serious risks to human life and ecosystems. Thus, it is the need of the hour to degrade and decontaminate the toxic pollutant to save the environment. Among all the available techniques, microbial degradation of the PAHs is proving to be greatly beneficial and effective. Bioremediation overcomes the drawbacks of most physicochemical procedures by eliminating numerous organic pollutants at a lower cost in ambient circumstances and has therefore become a prominent remedial option for pollutant removal, including PAHs. In the present study, we have studied the degradation of Low molecular Weight and High Molecular Weight PAH in combination by bacterial strains isolated from a marine environment. Optimum pH, temperature, carbon, and nitrogen sources, NaCl concentrations were found for efficient degradation using the isolated bacterial strains. At 250 mg/L concentration of the PAH mixture an 89.5% degradation was observed. Vibrio algiolytcus strains were found to be potent halotolerant bacteria to degrade complex PAH into less toxic simple molecules. GC-MS and FTIR data were used to probe the pathway of degradation of PAH.

A peroxisomal ß-oxidative pathway contributes to the formation of C6-C1 aromatic volatiles in poplar.

Benzenoids (C6-C1 aromatic compounds) play important roles in plant defense and are often produced upon herbivory. Black cottonwood (Populus trichocarpa) produces a variety of volatile and nonvolatile benzenoids involved in various defense responses. However, their biosynthesis in poplar is mainly unresolved. We showed feeding of the poplar leaf beetle (Chrysomela populi) on P. trichocarpa leaves led to increased emission of the benzenoid volatiles benzaldehyde, benzylalcohol, and benzyl benzoate. The accumulation of salicinoids, a group of nonvolatile phenolic defense glycosides composed in part of benzenoid units, was hardly affected by beetle herbivory. In planta labeling experiments revealed that volatile and nonvolatile poplar benzenoids are produced from cinnamic acid (C6-C3). The biosynthesis of C6-C1 aromatic compounds from cinnamic acid has been described in petunia (Petunia hybrida) flowers where the pathway includes a peroxisomal-localized chain shortening sequence, involving cinnamate-CoA ligase (CNL), cinnamoyl-CoA hydratase/dehydrogenase (CHD), and 3-ketoacyl-CoA thiolase (KAT). Sequence and phylogenetic analysis enabled the identification of small CNL, CHD, and KAT gene families in P. trichocarpa. Heterologous expression of the candidate genes in Escherichia coli and characterization of purified proteins in vitro revealed enzymatic activities similar to those described in petunia flowers. RNA interference-mediated knockdown of the CNL subfamily in gray poplar (Populus x canescens) resulted in decreased emission of C6-C1 aromatic volatiles upon herbivory, while constitutively accumulating salicinoids were not affected. This indicates the peroxisomal ß-oxidative pathway participates in the formation of volatile benzenoids. The chain shortening steps for salicinoids, however, likely employ an alternative pathway.

Enzymatic C-H activation of aromatic compounds through CO2 fixation.

The direct C-H carboxylation of aromatic compounds is an attractive route to the corresponding carboxylic acids, but remains challenging under mild conditions. It has been proposed that the first step in anaerobic microbial degradation of recalcitrant aromatic compounds is a UbiD-mediated carboxylation. In this study, we use the UbiD enzyme ferulic acid decarboxylase (Fdc) in combination with a carboxylic acid reductase to create aromatic degradation-inspired cascade reactions, leading to efficient functionalization of styrene through CO2 fixation. We reveal that rational structure-guided laboratory evolution can expand the substrate scope of Fdc, resulting in activity on a range of mono- and bicyclic aromatic compounds through a single mutation. Selected variants demonstrated 150-fold improvement in the conversion of coumarillic acid to benzofuran + CO2 and unlocked reactivity towards naphthoic acid. Our data demonstrate that UbiD-mediated C-H activation is a versatile tool for the transformation of aryl/alkene compounds and CO2 into commodity chemicals.

Pinisolibacter aquiterrae sp. nov., a novel aromatic hydrocarbon-degrading bacterium isolated from benzene-, and xylene-degrading enrichment cultures, and emended description of the genus Pinisolibacter.

Two Gram-reaction-negative strains, designated as B13T and MA2-2, were isolated from two different aromatic hydrocarbon-degrading enrichment cultures and characterized using a polyphasic approach to determine their taxonomic position. The two strains had identical 16S rRNA gene sequences and were most closely related to Pinisolibacter ravus E9T (97.36 %) and Siculibacillus lacustris SA-279T (96.33 %). Cells were facultatively aerobic rods and motile with a single polar flagellum. The strains were able to degrade ethylbenzene as sole source of carbon and energy. The assembled genome of strain B13T had a total length of 4.91 Mb and the DNA G+C content was 68.8 mol%. The predominant fatty acids (>5 % of the total) of strains B13T and MA2-2 were C18 : 1 ω7c/C18 : 1 ω6c, C16 : 1 ω7c/C16 : 1 ω6c and C16 : 0. The major ubiquinone of strain B13T was Q10, while the major polar lipids were phosphatidyl-N-methylethanolamine, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and a phospholipid. Based on phenotypic characteristics and phylogenetic data, it is concluded that strains B13T and MA2-2 are members of the genus Pinisolibacter and represent a novel species for which the name Pinisolibacter aquiterrae sp. nov. is proposed. The type strain of the species is strain B13T (=LMG 32346T=NCAIM B.02665T).

Protein-Activatable Diarylethene Monomer as a Smart Trigger of Noninvasive Control Over Reversible Generation of Singlet Oxygen: A Facile, Switchable, Theranostic Strategy for Photodynamic-Immunotherapy.

The development of activatable photosensitizers to allow for the reversible control of singlet oxygen (1O2) production for photodynamic therapy (PDT) faces great challenges. Fortunately, the flourishing field of supramolecular biotechnology provides more effective strategies for activatable PDT systems. Here, we developed a new reversible PDT on a switch that controls the 1O2 generation of self-assembled albumin nanotheranostics in vitro and in vivo. A new molecular design principle of aggregation-induced self-quenching photochromism and albumin on-photoswitching was demonstrated using a new asymmetric, synthetic diarylethene moiety DIA. The photosensitizer porphyrin and DIA were incorporated as building blocks in a glutaraldehyde-induced covalent albumin cross-linking nanoplatform, HSA-DIA-porphyrin nanoparticles (NPs). More importantly, the excellent photoswitching property of DIA enables the resultant nanoplatform to act as a facile, switchable strategy for photodynamic-immunotherapy.

Oxygen detoxification by dienoyl-CoA oxidase involving flavin/disulfide cofactors.

Class I benzoyl-CoA reductases (BCRs) are oxygen-sensitive key enzymes in the degradation of monocyclic aromatic compounds in anaerobic prokaryotes. They catalyze the ATP-dependent reductive dearomatization of their substrate to cyclohexa-1,5-diene-1-carboxyl-CoA (1,5-dienoyl-CoA). An aromatizing 1,5-dienoyl-CoA oxidase (DCO) activity has been proposed to protect BCRs from oxidative damage, however, the gene and its product involved have not been identified, yet. Here, we heterologously produced a DCO from the hyperthermophilic euryarchaeon Ferroglobus placidus that coupled the oxidation of two 1,5-dienoyl-CoA to benzoyl-CoA to the reduction of O2 to water at 80°C. DCO showed similarities to members of the old yellow enzyme family and contained FMN, FAD and an FeS cluster as cofactors. The O2 -dependent activation of inactive, reduced DCO is assigned to a redox thiol switch at Eo ' = -3 mV. We propose a catalytic cycle in which the active site FMN/disulfide redox centers are reduced by two 1,5-dienoyl-CoA (reductive half-cycle), followed by two consecutive two-electron transfer steps to molecular oxygen via peroxy- and hydroxyflavin intermediates yielding water (oxidative half-cycle). This work identified the enzyme involved in a unique oxygen detoxification process for an oxygen-sensitive catabolic enzyme.

Application of lipase immobilized on a hydrophobic support for the synthesis of aromatic esters.

The present study aimed at preparing three biocatalysts via physical adsorption of lipases from Candida rugosa (CRL), Mucor javanicus, and Candida sp. on a hydrophobic and mesoporous support (Diaion HP-20). These biocatalysts were later applied to the synthesis of aromatic esters of apple peel and citrus (hexyl butyrate), apple and rose (geranyl butyrate), and apricot and pineapple (propyl butyrate). Scanning electron microscopy and gel electrophoresis confirmed a selective adsorption of lipases on Diaion, thus endorsing simultaneous immobilization and purification. Gibbs free energy (∆G) evinced the spontaneity of the process (-17.9 kJ/mol ≤ ∆G ≤ -5.1 kJ/mol). Maximum immobilized protein concentration of 30 mg/g support by CRL. This biocatalyst was the most active in olive oil hydrolysis (hydrolytic activity of 126.0 ± 2.0 U/g) and in the synthesis of aromatic esters. Maximum conversion yield of 89.1% was attained after 150 Min for the synthesis of hexyl butyrate, followed by the synthesis of geranyl butyrate (87.3% after 240 Min) and propyl butyrate (80.0% after 150 Min). CRL immobilized on Diaion retained around 93% of its original activity after six consecutive cycles of 150 Min for the synthesis of hexyl butyrate.

The ever-expanding limits of enzyme catalysis and biodegradation: polyaromatic, polychlorinated, polyfluorinated, and polymeric compounds.

Biodegradation is simply the metabolism of anthropogenic, or otherwise unwanted, chemicals in our environment, typically by microorganisms. The metabolism of compounds commonly found in living things is limited to several thousand metabolites whereas ∼100 million chemical substances have been devised by chemical synthesis, and ∼100 000 are used commercially. Since most of those compounds are not natively found in living things, and some are toxic or carcinogenic, the question arises as to whether there is some organism somewhere with the enzymes that can biodegrade them. Repeatedly, anthropogenic chemicals have been denoted 'non-biodegradable,' only to find they are reactive with one or more enzyme(s). Enzyme reactivity has been organized into categories of functional group transformations. The discovery of new functional group transformations has continually expanded our knowledge of enzymes and biodegradation. This expansion of new-chemical biodegradation is driven by the evolution and spread of newly evolved enzymes. This review describes the biodegradation of widespread commercial chemicals with a focus on four classes: polyaromatic, polychlorinated, polyfluorinated, and polymeric compounds. Polyaromatic hydrocarbons include some of the most carcinogenic compounds known. Polychlorinated compounds include polychlorinated biphenyls (PCBs) and many pesticides of the twentieth century. Polyfluorinated compounds are a major focus of bioremediation efforts today. Polymers are clogging landfills, killing aquatic species in the oceans and increasingly found in our bodies. All of these classes of compounds, each thought at one time to be non-biodegradable, have been shown to react with natural enzymes. The known limits of enzyme catalysis, and hence biodegradation, are continuing to expand.

Genomic Aromatic Compound Degradation Potential of Novel Paraburkholderia Species: Paraburkholderia domus sp. nov., Paraburkholderia haematera sp. nov. and Paraburkholderia nemoris sp. nov.

We performed a taxonomic and comparative genomics analysis of 67 novel Paraburkholderia isolates from forest soil. Phylogenetic analysis of the recA gene revealed that these isolates formed a coherent lineage within the genus Paraburkholderia that also included Paraburkholderiaaspalathi, Paraburkholderiamadseniana, Paraburkholderiasediminicola, Paraburkholderiacaffeinilytica, Paraburkholderiasolitsugae and Paraburkholderiaelongata and four unidentified soil isolates from earlier studies. A phylogenomic analysis, along with orthoANIu and digital DNA-DNA hybridization calculations revealed that they represented four different species including three novel species and P. aspalathi. Functional genome annotation of the strains revealed several pathways for aromatic compound degradation and the presence of mono- and dioxygenases involved in the degradation of the lignin-derived compounds ferulic acid and p-coumaric acid. This co-occurrence of multiple Paraburkholderia strains and species with the capacity to degrade aromatic compounds in pristine forest soil is likely caused by the abundant presence of aromatic compounds in decomposing plant litter and may highlight a diversity in micro-habitats or be indicative of synergistic relationships. We propose to classify the isolates representing novel species as Paraburkholderia domus with LMG 31832T (=CECT 30334) as the type strain, Paraburkholderia nemoris with LMG 31836T (=CECT 30335) as the type strain and Paraburkholderia haematera with LMG 31837T (=CECT 30336) as the type strain and provide an emended description of Paraburkholderia sediminicola Lim et al. 2008.

Construction of recombinant Escherichia coli for production of L-phenylalanine-derived compounds.

L-phenylalanine is an important amino acid that is widely used in the fields of food flavors and pharmaceuticals. Apart from L-phenylalanine itself, various commercially valuable chemical compounds can also be generated via the L-phenylalanine biosynthesis pathway. Compared with direct extraction from plants or synthesis by chemical reaction, microbial production of L-phenylalanine -derived compounds can overcome the drawbacks of environmental pollution, low yield, and mixtures of stereoisomeric products. Accordingly, increasing intracellular levels of precursors, deregulating feedback inhibition and transcription repression, engineering global regulators and other effective strategies have been implemented to produce different L-phenylalanine -derived compounds in the excellent chassis host Escherichia coli. Finally, this review highlights principal strategies for improving the production of L-phenylalanine and/or its derivatives in E. coli, and discusses the future outlook for further enhancing the titer and yields of these compounds.

Biodegradation of binary mixtures of octane with benzene, toluene, ethylbenzene or xylene (BTEX): insights on the potential of Burkholderia, Pseudomonas and Cupriavidus isolates.

The contamination of the environment by crude oil and its by-products, mainly composed of aliphatic and aromatic hydrocarbons, is a widespread problem. Biodegradation by bacteria is one of the processes responsible for the removal of these pollutants. This study was conducted to determine the abilities of Burkholderia sp. B5, Cupriavidus sp. B1, Pseudomonas sp. T1, and another Cupriavidus sp. X5 to degrade binary mixtures of octane (representing aliphatic hydrocarbons) with benzene, toluene, ethylbenzene, or xylene (BTEX as aromatic hydrocarbons) at a final concentration of 100 ppm under aerobic conditions. These strains were isolated from an enriched bacterial consortium (Yabase or Y consortium) that prefer to degrade aromatic hydrocarbon over aliphatic hydrocarbons. We found that B5 degraded all BTEX compounds more rapidly than octane. In contrast, B1, T1 and X5 utilized more of octane over BTX compounds. B5 also preferred to use benzene over octane with varying concentrations of up to 200 mg/l. B5 possesses alkane hydroxylase (alkB) and catechol 2,3-dioxygenase (C23D) genes, which are responsible for the degradation of alkanes and aromatic hydrocarbons, respectively. This study strongly supports our notion that Burkholderia played a key role in the preferential degradation of aromatic hydrocarbons over aliphatic hydrocarbons in the previously characterized Y consortium. The preferential degradation of more toxic aromatic hydrocarbons over aliphatics is crucial in risk-based bioremediation.

Distinct Crystalline Aromatic Structural Motifs: Identification, Classification, and Implications.

Spatial noncovalent helical organization of nucleobases in DNA and radial organization of chromophores in natural light-harvesting systems are fascinating yet enigmatic. Understanding the numerous weak interactions that drive the formation of elegant supramolecular architectures in native natural systems and developing bioinspired design strategies have seen a surge of interest in recent decades. Self-assembly of functional chromophores in the crystalline phase is a definitive strategy to identify novel molecule-molecule interactions, in particular, atom-atom interactions, and to understand the synergistic nature of noncovalent interactions that stabilizes the supramolecular organization. This Account narrates our recent efforts in developing desirable supramolecular motifs employing weak interaction-based strategies and our observation of deviations from the common motifs chartered in aromatic systems. Modulation of long-range aromatic interactions through chemical modifications (acylation, benzoylation, haloacylation, and alkylation of chromophores) to attain a preferred stacking (herringbone, lamellar, or columnar) is presented. Particular attention has been given to attaining lamellar or columnar packing possessing potential interchromophoric electronic coupling mediated high charge mobility. Supramolecular arrangements of noncovalently or covalently associated donor-acceptor systems that open up additional possibilities of packing modes (segregated, mixed etc.) are explored. Our persistent efforts yielded distinct twisted-segregated and alternate distichous stacks for the nonparallel covalently linked donor-acceptor systems that favor a long-lived photoinduced charge-separated state. We further move on to discuss the unconventional packing motifs that were identified recently. The highly sought-after Greek cross (+) stacking of chromophores in crystalline phase and an elegant crystalline radial arrangement of chromophores are examined. The Greek cross (+) stacked architecture exhibits monomer-like emission characteristics owing to the absence of exciton coupling across the orthogonally stacked chromophores. Crystalline helical chromophore assembly is yet another emerging motif with far-reaching applications in domains ranging from asymmetric catalysis to chiral smart materials and has been accounted here by citing certain phenomenal examples from literature. Thus, this Account demonstrates that identifying and classifying new structural motifs based on topological aspects, such as interchromophoric orientation (cross) and extended chromophore arrangement in the crystal lattice (radial, helical, etc.), are crucial since such fundamental characteristics dictate the properties emerging out of the corresponding motifs. Encouraged from ours and others' works, we propose the addition of new aromatic supramolecular structural motifs, namely, cross-stacked, helical, and radial arrangements, in order to expand the classification. We believe that identifying new emergent property-based supramolecular motifs and investigating the methods to achieve the desired motif will eventually have implications in fundamental crystal engineering, supramolecular chemistry, and biomimetic design of functional materials.

Complete genome sequence of the aromatic-hydrocarbon-degrading bacterium Achromobacter xylosoxidans DN002.

Achromobacter xylosoxidans DN002 is capable of utilizing numerous aromatic hydrocarbons as sole carbon and energy resource. In this study, the whole genome of strain DN002 was sequenced and analyzed, which consisted of one circular chromosome of 5,943,204 bp and a 278,917 bp plasmid with an average GC content of 65.46 mol%, 5694 protein-coding genes, 13 rRNA genes and 57 tRNA genes. Analysis of cluster of orthologous group (COG) demonstrated that strain DN002 had remarkable gene abundance foramino acid transport and metabolism, transcription, inorganic ion transport and metabolism, energy production and conversion, and carbohydrate transport and metabolism. Genes related to biodegradation of aromatic hydrocarbons, chemotaxis and flagella were identified from the genome, which will advance our fundamental understanding the molecular mechanism for degradation and metabolizing of aromatic hydrocarbons.

Degradation strategies and associated regulatory mechanisms/features for aromatic compound metabolism in bacteria.

As a result of anthropogenic activity, large number of recalcitrant aromatic compounds have been released into the environment. Consequently, microbial communities have adapted and evolved to utilize these compounds as sole carbon source, under both aerobic and anaerobic conditions. The constitutive expression of enzymes necessary for metabolism imposes a heavy energy load on the microbe which is overcome by arrangement of degradative genes as operons which are induced by specific inducers. The segmentation of pathways into upper, middle and/or lower operons has allowed microbes to funnel multiple compounds into common key aromatic intermediates which are further metabolized through central carbon pathway. Various proteins belonging to diverse families have evolved to regulate the transcription of individual operons participating in aromatic catabolism. These proteins, complemented with global regulatory mechanisms, carry out the regulation of aromatic compound metabolic pathways in a concerted manner. Additionally, characteristics like chemotaxis, preferential utilization, pathway compartmentalization and biosurfactant production confer an advantage to the microbe, thus making bioremediation of the aromatic pollutants more efficient and effective.