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Haloalkane-utilizing Rhodococcus strains isolated from geographically distinct locations possess a highly conserved gene cluster encoding haloalkane catabolism.

The sequences of the 16S rRNA and haloalkane dehalogenase (dhaA) genes of five gram-positive haloalkane-utilizing bacteria isolated from contaminated sites in Europe, Japan, and the United States and of the archetypal haloalkane-degrading bacterium Rhodococcus sp. strain NCIMB13064 were compared. The 16S rRNA gene sequences showed less than 1% sequence divergence, and all haloalkane degraders clearly belonged to the genus Rhodococcus. All strains shared a completely conserved dhaA gene, suggesting that the dhaA genes were recently derived from a common ancestor. The genetic organization of the dhaA gene region in each of the haloalkane degraders was examined by hybridization analysis and DNA sequencing. Three different groups could be defined on the basis of the extent of the conserved dhaA segment. The minimal structure present in all strains consisted of a conserved region of 12.5 kb, which included the haloalkane-degradative gene cluster that was previously found in strain NCIMB13064. Plasmids of different sizes were found in all strains. Southern hybridization analysis with a dhaA gene probe suggested that all haloalkane degraders carry the dhaA gene region both on the chromosome and on a plasmid (70 to 100 kb). This suggests that an ancestral plasmid was transferred between these Rhodococcus strains and subsequently has undergone insertions or deletions. In addition, transposition events and/or plasmid integration may be responsible for positioning the dhaA gene region on the chromosome. The data suggest that the haloalkane dehalogenase gene regions of these gram-positive haloalkane-utilizing bacteria are composed of a single catabolic gene cluster that was recently distributed worldwide.

Alkanes↗

Haloalkane hydrolysis with an immobilized haloalkane dehalogenase.

Haloalkane dehalogenase from Rhodococcus rhodochrous was covalently immobilized onto a polyethyleneimine impregnated gamma-alumina support. The dehalogenating enzyme was found to retain greater than 40% of its original activity after immobilization, displaying an optimal loading (max. activity/supported protein) of 70 to 75 mg/g with an apparent maximum (max. protein/support) of 156 mg/g. The substrate, 1,2,3-trichloropropane, was found to favorably partition (adsorb) onto the inorganic alumina carrier (10 to 20 mg/g), thereby increasing the local reactant concentration with respect to the catalyst's environment, whereas the product, 2,3-dichloropropan-1-ol, demonstrated no affinity. Additionally, the inorganic alumina support exhibited no adverse effects because of solvent/component incompatibilities or deterioration due to pH variance (pH 7.0 to 10.5). As a result of the large surface area to volume ratio of the support matrix and the accessibility of the bound protein, the immobilized biocatalyst was not subject to internal mass transfer limitations. External diffusional restrictions could be eliminated with simple agitation (mixing speed: 50 rpm; flux: 4.22 cm/min). The pH-dependence of the immobilized dehalogenase was essentially the same as that for the native enzyme. Finally, both the thermostability and resistance toward inactivation by organic solvent were improved by more than an order of magnitude after immobilization.

Aluminum Oxide↗

Analysis of the reaction mechanism and substrate specificity of haloalkane dehalogenases by sequential and structural comparisons.

Haloalkane dehalogenases catalyse environmentally important dehalogenation reactions. These microbial enzymes represent objects of interest for protein engineering studies, attempting to improve their catalytic efficiency or broaden their substrate specificity towards environmental pollutants. This paper presents the results of a comparative study of haloalkane dehalogenases originating from different organisms. Protein sequences and the models of tertiary structures of haloalkane dehalogenases were compared to investigate the protein fold, reaction mechanism and substrate specificity of these enzymes. Haloalkane dehalogenases contain the structural motifs of alpha/beta-hydrolases and epoxidases within their sequences. They contain a catalytic triad with two different topological arrangements. The presence of a structurally conserved oxyanion hole suggests the two-step reaction mechanism previously described for haloalkane dehalogenase from Xanthobacter autotrophicus GJ10. The differences in substrate specificity of haloalkane dehalogenases originating from different species might be related to the size and geometry of an active site and its entrance and the efficiency of the transition state and halide ion stabilization by active site residues. Structurally conserved motifs identified within the sequences can be used for the design of specific primers for the experimental screening of haloalkane dehalogenases. Those amino acids which were predicted to be functionally important represent possible targets for future site-directed mutagenesis experiments.

Amino Acid Sequence↗

Cloning, biochemical properties, and distribution of mycobacterial haloalkane dehalogenases.

Haloalkane dehalogenases are enzymes that catalyze the cleavage of the carbon-halogen bond by a hydrolytic mechanism. Genomes of Mycobacterium tuberculosis and M. bovis contain at least two open reading frames coding for the polypeptides showing a high sequence similarity with biochemically characterized haloalkane dehalogenases. We describe here the cloning of the haloalkane dehalogenase genes dmbA and dmbB from M. bovis 5033/66 and demonstrate the dehalogenase activity of their translation products. Both of these genes are widely distributed among species of the M. tuberculosis complex, including M. bovis, M. bovis BCG, M. africanum, M. caprae, M. microti, and M. pinnipedii, as shown by the PCR screening of 48 isolates from various hosts. DmbA and DmbB proteins were heterologously expressed in Escherichia coli and purified to homogeneity. The DmbB protein had to be expressed in a fusion with thioredoxin to obtain a soluble protein sample. The temperature optimum of DmbA and DmbB proteins determined with 1,2-dibromoethane is 45 degrees C. The melting temperature assessed by circular dichroism spectroscopy of DmbA is 47 degrees C and DmbB is 57 degrees C. The pH optimum of DmbA depends on composition of a buffer with maximal activity at 9.0. DmbB had a single pH optimum at pH 6.5. Mycobacteria are currently the only genus known to carry more than one haloalkane dehalogenase gene, although putative haloalkane dehalogenases can be inferred in more then 20 different bacterial species by comparative genomics. The evolution and distribution of haloalkane dehalogenases among mycobacteria is discussed.

Animals↗

On the role of lipid peroxidation and protein-bound aldehydes in the haloalkane-induced inactivation of microsomal glucose 6 phosphatase.

The inactivation of liver microsomal glucose 6 phosphatase induced either by Fe2+ or by haloalkanes (CCl4, CBrCl3) was investigated in NADPH-microsomes systems. In the case of haloalkanes, EDTA was included in the incubation mixtures, so to exclude participation of free Fe2+ in the ensuing lipid peroxidation. Microsomal glucose 6 phosphatase activity was measured along with the release of malonic dialdehyde and the appearance of carbonyl products bound to microsomal protein, taken as indices of the peroxidative process. Fe2+ was added to NADPH-microsomes at different concentrations, one (6 microM) resulting in an extent of lipid peroxidation comparable with that induced by haloalkanes, the other (60 microM) representing a situation of excess Fe2+, leading to massive lipid peroxidation. Inhibition of glucose 6 phosphatase caused by 6 microM Fe2+ was comparable to that induced by haloalkanes in EDTA-microsomes systems, which supports the view that lipid peroxidation--rather than covalent binding of free radical metabolites--represents the main event leading to the inactivation of glucose 6 phosphatase caused by haloalkanes. The production of 4-hydroxynonenal--the known toxic product of lipid peroxidation--was also studied. A remarkable accumulation of 4-hydroxynonenal was observed in the microsomal membranes after peroxidation induced by 6 microM Fe2+ or haloalkanes, as compared to the incubation medium. In addition, experiments carried out with CCl4 and CBrCl3 in vivo suggested the possible existence of a cytosolic detoxification system able to remove lipid-derived carbonyls bound to microsomal protein.

Aldehydes↗

Experimental evaluation of haloalkanes and liver injury.

Potentiation of haloalkane-induced hepatotoxicity by ketones and ketogenic substances is used to illustrate questions that are raised when considering biological interactions involving toxicants. The following characteristics are considered: The effect of the potentiator (ketone or ketogenic agent) on the dose-response characteristics of the haloalkane toxicant; the recovery process of the potentiated tissue injury; dose-response characteristics of the potentiators (minimally effective dosages); correlation of the potentiation with blood levels of the potentiator (threshold concentrations). The relative specificity of the haloalkanes for interaction are discussed, as well as the potentiation of various forms of hepatic injury (acute, chronic, necrogenic, and cholestatic). Enhanced bioactivation of the haloalkane toxicant is a major mechanism of action for the potentiator; other possible contributing mechanisms, however, require consideration. Mixtures of haloalkanes, leading to enhanced liver injury, can also be potentiated by ketones.

Animals↗

Dehalogenation of haloalkanes by Mycobacterium tuberculosis H37Rv and other mycobacteria.

Haloalkane dehalogenases convert haloalkanes to their corresponding alcohols by a hydrolytic mechanism. To date, various haloalkane dehalogenases have been isolated from bacteria colonizing environments that are contaminated with halogenated compounds. A search of current databases with the sequences of these known haloalkane dehalogenases revealed the presence of three different genes encoding putative haloalkane dehalogenases in the genome of the human parasite Mycobacterium tuberculosis H37Rv. The ability of M. tuberculosis and several other mycobacterial strains to dehalogenate haloaliphatic compounds was therefore studied. Intact cells of M. tuberculosis H37Rv were found to dehalogenate 1-chlorobutane, 1-chlorodecane, 1-bromobutane, and 1,2-dibromoethane. Nine isolates of mycobacteria from clinical material and four strains from a collection of microorganisms were found to be capable of dehalogenating 1,2-dibromoethane. Crude extracts prepared from two of these strains, Mycobacterium avium MU1 and Mycobacterium smegmatis CCM 4622, showed broad substrate specificity toward a number of halogenated substrates. Dehalogenase activity in the absence of oxygen and the identification of primary alcohols as the products of the reaction suggest a hydrolytic dehalogenation mechanism. The presence of dehalogenases in bacterial isolates from clinical material, including the species colonizing both animal tissues and free environment, indicates a possible role of parasitic microorganisms in the distribution of degradation genes in the environment.

Alkanes↗

Enzymatic dehalogenation of gas phase substrates with haloalkane dehalogenase.

Haloalkane dehalogenase is an enzyme capable of catalyzing the conversion of short-chained (C(2)-C(8)) aliphatic halogenated hydrocarbons to a corresponding primary alcohol. Because of its broad substrate specificity for mono-, di-, and trisubstituted halogenated hydrocarbons and cofactor independence, haloalkane dehalogenases are attractive biocatalysts for gas-phase bioremediation of pollutant halogenated vapor emissions. A solid preparation of haloalkane dehalogenase from Rhodococcus rhodochrous was used to catalyze the dehalogenation reaction of 1-chlorobutane or 1,3-dichloropropane delivered in the gas phase. For optimal gas-phase dehalogenase activity, a relative humidity of 100%, a(w) = 1, was desired. With a 50% reduction in the vapor-phase hydration level, an 80% decrease in enzymatic activity was observed. The enzyme kinetics for the gas-phase substrates obeyed an Arrhenius-"like" behavior and the solid haloalkane dehalogenase preparation was more thermally stable than its water-soluble equivalent. Triethylamine was added to the gaseous reaction environment in efforts to increase the rate of reaction. A tenfold increase in the dehalogenase activity for the vapor-phase substrates was observed with the addition of triethylamine. Triethylamine altered the electrostatic environment of haloalkane dehalogenase via a basic shift in local pH, thereby minimizing the effect of the pH-reducing reaction product on enzyme activity. Both organic phase and solid-state buffers were used to confirm the activating role of the altered ionization state.

Air Pollutants↗

Influence of two haloalkanes on the redox behavior of hepatic microsomal cytochrome b-5 and its possible relationship to stearate desaturase.

The possible interaction of two haloalkanes - bromotrichloromethane and 1,2-dibromo-1,2-dichlorethane - with stearate desaturase was assessed in hepatic microsomes from rats fed a high carbohydrate diet which elevates the levels of stearate desaturase. Both compounds shifted the redox steady state of NADPH reduced hepatic microsomal cytochrome b-5 towards ferricytochrome b-5 and enhanced the re-oxidation of NADH reduced hepatic microsomal cytochrome b-5. The equilibrium constants for the enhancement of microsomal electron transfer by the haloalkanes in these preparations were 2.2 +/- 0.3 mM and 0.46 +/- 0.1 mM for bromotrichloromethane and 1,2-dibromo-1,2-dichlorethane, respectively. The haloalkane mediated enhancement of the oxidation of cytochrome b-5 in hepatic microsomes from rats fed a high carbohydrate diet was diminished by KCN and the inhibitors of cytochrome P-450, CO and/or metyrapone, as well as by fasting of the experimental animals. The I50 values for KCN inhibition of the effects of the haloalkanes on the re-oxidation of cytochrome b-5 (01 mM) were identical to the I50 for KCN inhibition of stearate desaturase (Oshino et al., 1966). The haloalkanes did not affect the activity of hepatic microsomal NADH- or NADPH-cytochrome c reductase, the autoxidation of purified trypsin-cleaved ferrocytochrome b-5 or the conversion of stearoyl CoA to oleate. It is concluded that bromotrichloromethane and 1,2-dibromo-1,2-dichloroethane stimulate hepatic microsomal electron transfer from NADH via cytochrome b-5 by interacting with cytochrome P-450 and with stearate desaturase.

Animals↗

Functional Characterization of Luciferase in a Brittle Star Indicates Parallel Evolution Influenced by Genomic Availability of Haloalkane Dehalogenase.

Determining why convergent traits use distinct versus shared genetic components is crucial for understanding how evolutionary processes generate and sustain biodiversity. However, the factors dictating the genetic underpinnings of convergent traits remain incompletely understood. Here, we use heterologous protein expression, biochemical assays, and phylogenetic analyses to confirm the origin of a luciferase gene from haloalkane dehalogenases in the brittle star Amphiura filiformis. Through database searches and gene tree analyses, we also show a complex pattern of the presence and absence of haloalkane dehalogenases across organismal genomes. These results first confirm parallel evolution across a vast phylogenetic distance, because octocorals like Renilla also use luciferase derived from haloalkane dehalogenases. This parallel evolution is surprising, even though previously hypothesized, because many organisms that also use coelenterazine as the bioluminescence substrate evolved completely distinct luciferases. The inability to detect haloalkane dehalogenases in the genomes of several bioluminescent groups suggests that the distribution of this gene family influences its recruitment as a luciferase. Together, our findings highlight how biochemical function and genomic availability help determine whether distinct or shared genetic components are used during the convergent evolution of traits like bioluminescence.

Echinodermata↗

Construction of an expression and site-directed mutagenesis system of haloalkane dehalogenase in Escherichia coli.

Haloalkane dehalogenase from Xanthobacter autotrophicus was efficiently expressed in Escherichia coli BL21 (DE3) and E. coli JM101. After introduction of restriction sites by PCR the haloalkane dehalogenase gene (dhlA) was translationally fused behind the T7 (phi 10), trc, and tac promoters. This resulted in expression at 30 degrees C up to 38 and 18% of the total soluble cellular protein with the T7 and trc promoters, respectively. Dehalogenase expression under control of the tac promoter was below 1% of the soluble cell protein, however. Aggregation of haloalkane dehalogenase into inclusion bodies was found during growth at 37 degrees C but not at 30 degrees C. Aggregates were also formed from intact enzyme upon incubation at 37 degrees C of cells or crude extracts containing active mature dehalogenase. The high level of expression resulted in a short purification procedure in which 30-35 mg highly enriched haloalkane dehalogenase was obtained from an 0.51 culture. For the production of single-stranded DNA an f1(+) origin was introduced in the T7 expression system.

Amino Acid Sequence↗

Correlations of in vitro and in vivo hepatotoxicity for five haloalkanes.

Five haloalkanes--CBrCl3, CCl4, CHCl3, and 1,1,1-and 1,1,2-trichloroethane (TCE)--were ranked for their relative hepatotoxicity in an in vitro system of isolated hepatocyte suspensions and in vivo by po administration of the test chemical to fasted rats of the same strain and sex as used for the hepatocytes. Cytotoxic parameters used for ranking in the in vitro system were GOT and LDH release, and the results were expressed in terms of EC50 values (the dissolved haloalkane concentration required to release 50% of the cell content of each enzyme after 2 hr of exposure) for rank determination. Cytotoxic parameters measured in vivo were SGOT and SGPT, and the ranking was based on ED50 values (the haloalkane dose that produced an above normal serum transaminase level in 50% of the test animals). With these parameters, the potency rankings in each system were the same except that of 1,1,1-TCE, which was more cytotoxic in the in vitro system than would have been expected from the animal experiments. Purification of the 1,1,1-TCE to remove stabilizers, use of phenobarbital-induced hepatocytes or hepatocytes from starved rats, and administration of the haloalkanes ip instead of po failed to improve the correlation. The discrepancy could be resolved, however, by factoring air: medium partition coefficient data into the EC50 values to take into account differences in the volatility and aqueous and lipid solubility of the chemicals, and hence their retention in vivo. These observations encourage the belief that isolated hepatocyte systems have value for ranking structurally related chemicals as to their cytotoxic potential, even though their mechanisms of action may differ.

Alanine Transaminase↗

Exploring the structure and activity of haloalkane dehalogenase from Sphingomonas paucimobilis UT26: evidence for product- and water-mediated inhibition.

The hydrolysis of haloalkanes to their corresponding alcohols and inorganic halides is catalyzed by alpha/beta-hydrolases called haloalkane dehalogenases. The study of haloalkane dehalogenases is vital for the development of these enzymes if they are to be utilized for bioremediation of organohalide-contaminated industrial waste. We report the kinetic and structural analysis of the haloalkane dehalogenase from Sphingomonas paucimobilis UT26 (LinB) in complex with each of 1,2-dichloroethane and 1,2-dichloropropane and the reaction product of 1-chlorobutane turnover. Activity studies showed very weak but detectable activity of LinB with 1,2-dichloroethane [0.012 nmol s(-1) (mg of enzyme)(-1)] and 1,2-dichloropropane [0.027 nmol s(-1) (mg of enzyme)(-1)]. These activities are much weaker compared, for example, to the activity of LinB with 1-chlorobutane [68.2 nmol s(-1) (mg of enzyme)(-1)]. Inhibition analysis reveals that both 1,2-dichloroethane and 1,2-dichloropropane act as simple competitive inhibitors of the substrate 1-chlorobutane and that 1,2-dichloroethane binds to LinB with lower affinity than 1,2-dichloropropane. Docking calculations on the enzyme in the absence of active site water molecules and halide ions confirm that these compounds could bind productively. However, when these moieties were included in the calculations, they bound in a manner similar to that observed in the crystal structure. These data provide an explanation for the low activity of LinB with small, chlorinated alkanes and show the importance of active site water molecules and reaction products in molecular docking.

Amino Acid Sequence↗

Halide-stabilizing residues of haloalkane dehalogenases studied by quantum mechanic calculations and site-directed mutagenesis.

Haloalkane dehalogenases catalyze cleavage of the carbon-halogen bond in halogenated aliphatic compounds, resulting in the formation of an alcohol, a halide, and a proton as the reaction products. Three structural features of haloalkane dehalogenases are essential for their catalytic performance: (i) a catalytic triad, (ii) an oxyanion hole, and (iii) the halide-stabilizing residues. Halide-stabilizing residues are not structurally conserved among different haloalkane dehalogenases. The level of stabilization of the transition state structure of S(N)2 reaction and halide ion provided by each of the active site residues in the enzymes DhlA, LinB, and DhaA was quantified by quantum mechanic calculations. The residues that significantly stabilize the halide ion were assigned as the primary (essential) or the secondary (less important) halide-stabilizing residues. Site-directed mutagenesis was conducted with LinB enzyme to confirm location of its primary halide-stabilizing residues. Asn38Asp, Asn38Glu, Asn38Phe, Asn38Gln, Trp109Leu, Phe151Leu, Phe151Trp, Phe151Tyr, and Phe169Leu mutants of LinB were constructed, purified, and kinetically characterized. The following active site residues were classified as the primary halide-stabilizing residues: Trp125 and Trp175 of DhlA; Asn38 and Trp109 of LinB; and Asn41 and Trp107 of DhaA. All these residues make a hydrogen bond with the halide ion released from the substrate molecule, and their substitution results in enzymes with significantly modified catalytic properties. The following active site residues were classified as the secondary halide-stabilizing residues: Phe172, Pro223, and Val226 of DhlA; Trp207, Pro208, and Ile211 of LinB; and Phe205, Pro206, and Ile209 of DhaA. The differences in the halide stabilizing residues of three haloalkane dehalogenases are discussed in the light of molecular adaptation of these enzymes to their substrates.

Amino Acids↗

Modification of activity and specificity of haloalkane dehalogenase from Sphingomonas paucimobilis UT26 by engineering of its entrance tunnel.

Structural comparison of three different haloalkane dehalogenases suggested that substrate specificity of these bacterial enzymes could be significantly influenced by the size and shape of their entrance tunnels. The surface residue leucine 177 positioned at the tunnel opening of the haloalkane dehalogenase from Sphingomonas paucimobilis UT26 was selected for modification based on structural and phylogenetic analysis; the residue partially blocks the entrance tunnel, and it is the most variable pocket residue in haloalkane dehalogenase-like proteins with nine substitutions in 14 proteins. Mutant genes coding for proteins carrying all possible substitutions in position 177 were constructed by site-directed mutagenesis and heterologously expressed in Escherichia coli. In total, 15 active protein variants were obtained, suggesting a relatively high tolerance of the site for the introduction of mutations. Purified protein variants were kinetically characterized by determination of specific activities with 12 halogenated substrates and steady-state kinetic parameters with two substrates. The effect of mutation on the enzyme activities varied dramatically with the structure of the substrates, suggesting that extrapolation of one substrate to another may be misleading and that a systematic characterization of the protein variants with a number of substrates is essential. Multivariate analysis of activity data revealed that catalytic activity of mutant enzymes generally increased with the introduction of small and nonpolar amino acid in position 177. This result is consistent with the phylogenetic analysis showing that glycine and alanine are the most commonly occurring amino acids in this position among haloalkane dehalogenases. The study demonstrates the advantages of using rational engineering to develop enzymes with modified catalytic properties and substrate specificities. The strategy of using site-directed mutagenesis to modify a specific entrance tunnel residue identified by structural and phylogenetic analyses, rather than combinatorial screening, generated a high percentage of viable mutants.

Alanine↗

Isolation and characterization of a haloalkane halidohydrolase from Rhodococcus erythropolis Y2.

Rhodococcus erythropolis strain Y2, isolated from soil by enrichment culture using 1-chlorobutane, was able to utilize a range of halogenated aliphatic compounds as sole sources of carbon and energy. The ability to utilize 1-chlorobutane was conferred by a single halidohydrolase-type haloalkane dehalogenase. The presence of the single enzyme in cell-free extracts was demonstrated by activity strain polyacrylamide gel electrophoresis. The purified enzyme was a monomeric protein with a relative molecular mass of 34 kDa and demonstrated activity against a broad range of haloalkanes, haloalcohols and haloethers. The highest activity was found towards alpha, omega disubstituted chloro- and bromo- C2-C6 alkanes and 4-chlorobutanol. The Km value of the enzyme for 1-chlorobutane was 0.26 mM. A comparison of the R. erythropolis Y2 haloalkane halidohydrolase with other haloalkane dehalogenases is discussed on the basis of biochemical properties and N-terminal amino acid sequence data.

Chemical Phenomena↗

Utilization of trihalogenated propanes by Agrobacterium radiobacter AD1 through heterologous expression of the haloalkane dehalogenase from Rhodococcus sp. strain M15-3.

Trihalogenated propanes are toxic and recalcitrant organic compounds. Attempts to obtain pure bacterial cultures able to use these compounds as sole carbon and energy sources were unsuccessful. Both the haloalkane dehalogenase from Xanthobacter autotrophicus GJ10 (DhlA) and that from Rhodococcus sp. strain m15-3 (DhaA) were found to dehalogenate trihalopropanes to 2,3-dihalogenated propanols, but the kinetic properties of the latter enzyme are much better. Broad-host-range dehalogenase expression plasmids, based on RSF1010 derivatives, were constructed with the haloalkane dehalogenase from Rhodococcus sp. strain m15-3 under the control of the heterologous promoters P(lac), P(dhlA), and P(trc). The resulting plasmids yielded functional expression in several gram-negative bacteria. A catabolic pathway for trihalopropanes was designed by introducing these broad-host-range dehalogenase expression plasmids into Agrobacterium radiobacter AD1, which has the ability to utilize dihalogenated propanols for growth. The recombinant strain AD1(pTB3), expressing the haloalkane dehalogenase gene under the control of the dhlA promoter, was able to utilize both 1,2,3-tribromopropane and 1,2-dibromo-3-chloropropane as sole carbon sources. Moreover, increased expression of the haloalkane dehalogenase resulted in elevated resistance to trihalopropanes.

Hydrolases↗