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Detection and molecular analysis of plant- and insect-associated bacteria harboring aconitate isomerase involved in biosynthesis of trans-aconitic acid as antifeedant in brown planthoppers.

The activity of aconitate isomerase, which is involved in the biosynthesis of trans-aconitic acid as antifeedant in brown planthoppers, was detected in Pseudomonas fluorescens LRB3W1 and Pseudomonas putida MAFF301685 but not in Pseudomonas putida MAFF301684. The enzyme activity was induced in the presence of trans-aconitate, and therefore bacteria showing the enzyme activity were easily detected by their ability to grow on the minimal medium containing trans-aconitate as the sole carbon source (ACO agar medium). Experiments on growth of plant- or insect-associated bacteria on ACO agar medium showed that most of the Gram-negative bacteria displayed the aconitate isomerase activity unlike most of the Gram-positive bacteria isolated mainly from insects. Mini-Tn5 transposon derivatives of P. fluorescens LRB3W1 lacking completely or partially their ability to grow on ACO agar medium were obtained. Southern blot analysis with a mini-Tn5 DNA probe definitely showed that the genes responsible for the biosynthesis of aconitate isomerase present on chromosomal DNA. Thus, it was suggested that genes for aconitate isomerase biosynthesis are commonly present in Gram-negative plant- or insect-associated bacteria, and also the DNA fragments including the genes were detected in P. fluorescens LRB3W1.

Aconitic Acid↗

Stimulation of mutases and isomerases by vanadium.

The effects of vanadate and vanadate complexes on the rates of exchange of phosphoryl groups in the reactions catalyzed by the enzymes phosphoglucomutase and the coupled system formed by phosphoglycerate mutase and enolase, and the effects of vanadyl complexes on the interconversion of aldehyde and keto groups catalyzed by the enzymes phosphomannose isomerase, phosphoribose isomerase, and phosphoglucose isomerase, were measured using one-dimensional 31P nuclear magnetic resonance spectroscopy. Chemical exchange was investigated by observing the transfer of magnetization achieved by selective irradiation of resonances using the DANTE pulse sequence. The presence of vanadium stimulated the catalytic activity of the enzymes in vitro, with the exception of enolase whose activity was not affected. Addition of vanadate also increased the rate constants of the interconversion of glucose 6-phosphate and fructose 6-phosphate in hemolysates. 51V nuclear magnetic resonance spectroscopy and electron paramagnetic resonance spectroscopy were employed to investigate the interactions between ammonium vanadate and sugar phosphates and the formation of vanadium--sugar phosphate complexes that may be involved in the stimulation of the catalytic activity of the isomerases.

Animals↗

Purification, some properties and nucleotide sequence of 5-carboxymethyl-2-hydroxymuconate isomerase of Escherichia coli C.

As part of an investigation into the evolution of catabolic pathway enzymes a cloned gene encoding the Escherichia coli C 5-carboxymethyl-2-hydroxymuconate (CHM) isomerase, an enzyme of the homoprotocatechuate catabolic pathway, was used to produce large amounts of the protein. The isomerase was purified to homogeneity and some of its properties determined. The reaction occurred optimally at pH 7.6 and the specificity constant was 5.8 x 10(5) M-1.s-1 with CHM and 6.0 x 10(2) M-1.s-1 with 2-hydroxyhepta-2,4-diene-1,7-dioate, the substrate of a second isomerase in the pathway. The pure protein showed one type of subunit of Mr 14,000 whilst the molecular mass of the native enzyme was 30,000, suggesting that it was a dimer of identical subunits. The first 19 N-terminal amino acids were sequenced and the data used to confirm that the open reading frame of 378 bp, identified from the nucleotide sequence, encoded the CHM isomerase.

Amino Acid Sequence↗

Cis-trans isomerization is rate-determining in the reactivation of denatured human carbonic anhydrase II as evidenced by proline isomerase.

The refolding of human carbonic anhydrase II is a sequential process. The slowest step involved is the recovery of enzymic activity (t1/2 = 9 min). Kinetic data from 'double-jump' measurements indicate that proline isomerization might be rate determining in the reactivation of the denatured enzyme. Proof of this is provided by the effect of proline isomerase on the reactivation kinetics: the presence of isomerase during reactivation lowers the half-time of the reaction to 4 min, and inhibition of proline isomerase completely abolishes this kinetic effect. A similar acceleration of the refolding process by proline isomerase is also observed for bovine carbonic anhydrase II, in contrast to what has previously been reported. In human carbonic anhydrase II there are two cis-peptidyl-Pro bonds at Pro30 and Pro202. Two asparagine single mutants (P30N and P202N) and a glycine double mutant (P30G/P202G) were constructed to investigate the role of these prolines in the rate limitation of the reactivation process. Both in the presence and absence of PPIase the P202N mutant behaved exactly like the unmutated enzyme. Thus, cis-trans isomerization of the Pro202 cis-peptidyl bond is not rate determining in the reactivation process. The mutations at position 30 led to such extensive destabilization of the protein that the refolding reaction could not be studied.

Amino Acid Isomerases↗

A novel peptidyl-prolyl cis/trans isomerase from Escherichia coli.

A novel peptidyl-prolyl cis/trans isomerase was isolated from Escherichia coli cell extract and characterized partially. Determination of the molecular mass by electrospray mass spectrometry indicated a protein of 10102 +/- 2 Da, smaller than cyclophilins or FK 506 binding proteins currently known. The specificity constant kcat/Km determined with Succinyl-Ala-Xaa-Pro-Phe-4-nitroanilide (Xaa = Leu) had a value comparable to those from cyclophilins from the same organism. However, the pattern of subsite specificity (Xaa = Gly, Ala, Val, Ile, Leu, Phe, Trp, His, Lys and Glu) was reminiscent of FK506 binding peptidyl-prolyl cis/trans isomerases. The enzyme activity was not inhibited by cyclosporin A or FK506 at inhibitor concentrations of < 5 microM, concentrations that affect most bacterial peptidyl-prolyl cis/trans isomerases. Computer-assisted analysis of 21 amino acid residues of the N-terminus determined by Edman degradation revealed no homology to known peptidyl-prolyl cis/trans isomerases.

Amino Acid Isomerases↗

Purification and properties of testicular 3 beta-hydroxy-5-ene-steroid dehydrogenase and 5-ene-4-ene isomerase.

Through the treatment of rat testicular microsomes with sodium cholate, 3 beta-hydroxy-5-ene-steroid dehydrogenase and 5-ene-4-ene isomerase (abbreviated as the 3 beta-hydroxysteroid dehydrogenase and isomerase, respectively) were solubilized, and then purified by DEAE and hydroxylapatite column chromatographies. The findings were as follows: With this purification procedure, the 3 beta-hydroxysteroid dehydrogenase activity could not be separated from the isomerase. For 3-oxo-4-ene-steroid formation from 3 beta-hydroxy-5-ene-steroids, NAD+ was required as a cofactor. While the 3 beta-hydroxysteroid dehydrogenase required NAD+, the isomerase also required NAD+ or its reduced form, in contrast to the microbial enzyme. On treatment of the purified enzyme with 5'-p-fluorosulfonyl-benzoyladenosine (FSBA), both enzyme activities were markedly reduced. The enzyme, affinity labeled with [adenine-8-14C]FSBA, showed a mol. wt of 46.8 K. During 4-androstenedione production from DHA, 5-androstenedione was detected as an intermediate.

3-Hydroxysteroid Dehydrogenases↗

Purification and characterization of rat adrenal 3 beta-hydroxysteroid dehydrogenase with steroid 5-ene-4-ene-isomerase.

After solubilization of rat adrenal microsomes with sodium cholate, 3 beta-hydroxysteroid dehydrogenase with steroid 5-ene-4-ene isomerase (abbreviated as steroid isomerase) activity was purified to a homogeneous state. The following characteristics of the enzyme were obtained: 3 beta-Hydroxysteroid dehydrogenase together with steroid isomerase was detected as a single protein band in SDS-polyacrylamide gel electrophoresis, where its mol. wt was estimated as 46,500. Either NAD+ or NADH was required for demonstration of steroid isomerase activity. Treatment of the enzyme with 5'-p-fluorosulfonylbenzoyladenosine, an affinity labeling reagent for NAD+-dependent enzyme, diminished both the enzyme activities.

3-Hydroxysteroid Dehydrogenases↗

Human placental 3 beta-hydroxy-5-ene-steroid dehydrogenase and steroid 5----4-ene-isomerase: purification from microsomes, substrate kinetics, and inhibition by product steroids.

In human pregnancy, placental 3 beta-hydroxy-5-ene-steroid dehydrogenase and steroid 5----4-ene-isomerase produce progesterone from pregnenolone and metabolize fetal dehydroepiandrosterone sulfate to androstenedione, an estrogen precursor. The enzyme complex was solubilized from human placental microsomes using the anionic detergent, sodium cholate. Purification (500-fold, 3.9% yield) was achieved by ion exchange chromatography (Fractogel-TSK DEAE 650-S) followed by hydroxylapatite chromatography (Bio-Gel HT). The purified enzyme was detected as a single protein band in sodium dodecylsulfate-polyacrylamide gel electrophoresis (monomeric Mr = 19,000). Fractionation by gel filtration chromatography at constant specific enzyme activity supported enzyme homogeneity and determined the molecular mass (Mr = 76,000). The dehydrogenase and isomerase activities copurified. Kinetic constants were determined at pH 7.4, 37 degrees C for the oxidation of pregnenolone (Km = 1.9 microM, Vmax = 32.6 nmol/min/mg) and dehydroepiandrosterone (Km = 2.8 microM, Vmax = 32.0 nmol/min/mg) and for the isomerization of 5-pregnene-3,20-dione (Km = 9.7 microM, Vmax = 618.3 nmol/min/mg) and 5-androstene-3,17-dione (Km = 23.7 microM, Vmax = 625.7 nmol/min/mg). Mixed substrate analyses showed that the dehydrogenase and isomerase reactions use the appropriate pregnene and androstene steroids as alternative, competitive substrates. Dixon analyses demonstrated competitive inhibition of the oxidation of pregnenolone and dehydroepiandrosterone by both product steroids, progesterone and androstenedione. The enzyme has a 3-fold higher affinity for androstenedione than for progesterone as an inhibitor of dehydrogenase activity. Based on these competitive patterns of substrate utilization and product inhibition, the pregnene and androstene activities of 3 beta-hydroxy-5-ene-steroid dehydrogenase and steroid 5----4-ene-isomerase may be expressed at a single catalytic site on one protein in human placenta.

3-Hydroxysteroid Dehydrogenases↗

Human placental 3 beta-hydroxy-5-ene-steroid dehydrogenase and steroid 5----4-ene-isomerase: purification from mitochondria and kinetic profiles, biophysical characterization of the purified mitochondrial and microsomal enzymes.

In human placenta, 3 beta-hydroxy-5-ene-steroid dehydrogenase and steroid 5----4-ene-isomerase, an enzyme complex found in microsomes and mitochondria, synthesizes progesterone from pregnenolone and androstenedione from fetal dehydroepiandrosterone sulfate. The dehydrogenase and isomerase activities of the mitochondrial enzyme were copurified (733-fold) using sequential cholate solubilization, ion exchange chromatography (DEAE-Toyopearl 650S), and hydroxylapatite chromatography (Bio-Gel HT). Enzyme homogeneity was demonstrated by a single protein band in SDS-polyacrylamide gel electrophoresis (monomeric Mr = 41,000), gel filtration at constant specific enzyme activity (Mr = 77,000), and a single NH2-terminal sequence. Kinetic constants were determined for the oxidation of pregnenolone (Km = 1.6 microM, Vmax = 48.6 nmol/min/mg) and dehydroepiandrosterone (Km = 2.4 microM, Vmax = 48.5 nmol/min/mg) and for the isomerization of 5-pregnene-3,20-dione (Km = 9.3 microM, Vmax = 914.2 nmol/min/mg) and 5-androstene-3,17-dione (Km = 27.6 microM, Vmax = 888.4 nmol/min/mg. Mixed substrate studies showed that the dehydrogenase and isomerase activities utilize their respective pregnene and androstene substrates competitively. Dixon analysis demonstrated that the product steroids, progesterone and androstenedione, are competitive inhibitors of the C-21 and C-19 dehydrogenase activities. Enzyme purified from mitochondria and microsomes had similar kinetic profiles with respect to substrate utilization, product inhibition, and cofactor (NAD+) reduction (mean Km +/- SD using C-19 and C-21 dehydrogenase substrates = 26.4 +/- 0.8 microM, mean Vmax = 73.2 +/- 1.3 nmol/min/mg). Pure enzyme from both organelles exhibited identical biophysical properties in terms of molecular weight and subunit composition, pH optima (pH 9.8, dehydrogenase; pH 7.5, isomerase), temperature optimum (37 degrees C), stability in storage and solution, effects of divalent cations, and the single NH2-terminal sequence of 27 amino acids. These results suggest that the mitochondrial and microsomal enzymes are the same protein localized in different organelles.

3-Hydroxysteroid Dehydrogenases↗

Characterization of the complete protein disulfide isomerase gene of Schistosoma mansoni and identification of the tissues of its expression.

cDNA and genomic clones of Schistosoma mansoni containing the complete sequence of a homolog of protein disulfide isomerase have been identified. The protein disulfide isomerase gene in schistosomes is a single copy gene having a genomic structure that is very similar to that of man. The C-terminus of the deduced protein is KDEL which in mammals functions as a signal sequence for retention of luminal proteins in the endoplasmic reticulum. Immunohistology and in situ hybridization identify the gastrodermis of the gut, the wall cells of the protonephridia, and the sustentacular cells of the testes to be the major tissues of protein disulfide isomerase gene expression. The protein disulfide isomerase of schistosomes, produced in an expression vector in Escherichia coli, catalyzes disulfide/sulfhydryl isomerization in vitro.

Amino Acid Sequence↗

Cloning of the gene for delta 5-3-ketosteroid isomerase from Pseudomonas testosteroni.

We have cloned an approx. 5-kb fragment of Pseudomonas testosteroni DNA containing the structural gene of delta 5-3-ketosteroid isomerase into the EcoRI site of the lambda gt11 genome. Escherichia coli infected with these recombinant phages produce a polypeptide which is recognized by antiserum raised against the purified isomerase. Four of the recombinant lambda gt11 clones contain significant levels of isomerase activity and produce an immunopositive polypeptide of the same apparent Mr as the native isomerase obtained from P. testosteroni. The approx. 5-kb fragment hybridizes to synthetic 21-mer and 17-mer oligodeoxynucleotide mixtures corresponding to the 5' and 3' regions, respectively, of the expected nucleotide sequence of the gene.

Base Sequence↗

Cloning, expression, and purification of the functional Delta(3)-Delta(2)-enoyl-CoA isomerase fusion protein.

Delta(3)-Delta(2)-Enoyl-CoA isomerase (EC 5.3.3.8) is a key enzyme for the beta-oxidation of unsaturated fatty acids. The cDNA of the full-length rat liver Delta(3)-Delta(2)-enoyl-CoA isomerase was previously cloned as pAG847. PCR methodologies were used to subclone the gene encoding the functional Delta(3)-Delta(2)-enoyl-CoA isomerase from pAG847 with primers that were designed to add six continuous histidine codon to the 5(') primer. The PCR product was inserted into a pLM1 expression vector and overexpressed in Escherichia coli. The soluble expressed protein was purified with a nickel HiTrap chelating metal affinity column to apparent homogeneity based on Coomassie blue-stained SDS-PAGE and the molecular weight of the protein subunit was 30 kDa. The purified protein had a dimeric structure composed of identical subunits, and the molecular weight of the enzyme determined by gel chromatography was 60 kDa. Kinetic studies have been carried out and K(M) of 81 microM and V(max) of 292 micromol/min/mg were determined. The specific activity of the protein is 201 U/mg, which is significantly higher than that reported before for the same protein isolated from a natural source. The one-step purification of the highly active Delta(3)-Delta(2)-enoyl-CoA isomerase will greatly facilitate the further investigation of this enzyme through site-directed mutagenesis and enzyme catalyzed reactions with substrate analogues.

Animals↗

The N-terminal cyclophilin-homologous domain of a 150-kilodalton tumor recognition molecule exhibits both peptidylprolyl cis-trans-isomerase and chaperone activities.

A cyclophilin-related protein has recently been found to be involved in tumor recognition by natural killer cells. The N-terminal end of this 150-kDa surface molecule (NK-TR) is homologous to cyclophilin/peptidylprolyl cis-trans-isomerase. We have constructed a soluble bacterial fusion protein between the cyclophilin-homologous domain of the NK-TR molecule and glutathione S-transferase (GST) to test for the presence of peptidylprolyl cis-trans-isomerase and chaperone activities and for cyclosporin A binding. The purified NK-cyp-GST fusion protein is shown to accelerate the isomerization of the prolyl peptide bond of the substrate N-succinyl-Ala-Ala-Pro-Phe-p-nitroanilide with a kcat/KM value of 7.4 x 10(5) M-1 s-1. The isomerase activity of the NK-TR cyclophilin homolog has been determined to be relatively insensitive to inhibition by the immunosuppressive drug cyclosporin A, with an IC50 value of 770 nM as compared to 19 nM for human cyclophilin. Furthermore, the NK-cyp-GST fusion protein has been found to participate in the protein folding process as a chaperone by preventing the aggregation of early folding intermediates of carbonic anhydrase. The implications of the finding of both peptidylprolyl cis-trans-isomerase and chaperone activities within the N-terminal domain of a large, cell type-restricted, surface molecule are discussed.

Amino Acid Isomerases↗

Positioning of a spin-labeled substrate analogue into the structure of delta 5-3-ketosteroid isomerase by combined kinetic, magnetic resonance, and X-ray diffraction methods.

We have shown by kinetic and magnetic resonance measurements that a spin-labeled substrate analogue, spiro[doxyl-2,3'-5' alpha-androstan]-17'beta-ol, binds at the substrate site of crystalline delta 5-3-ketosteroid isomerase (steroid delta-isomerase; EC 5.3.3.1) of Pseudomonas testosteroni. The spin-labeled steroid is a linear competitive inhibitor with a Ki value (25 +/- 5 microM) that is consistent with dissociation constants obtained by direct binding measurements based on changes in the electron paramagnetic resonance spectrum of the nitroxide, longitudinal relaxation rates of water protons, and longitudinal and transverse relaxation rates of carbon-bound protons of the isomerase. These binding studies yield a stoichiometry for the nitroxide of 1 per subunit of the enzyme. Measurements of the longitudinal relaxation rates of water protons indicate that the 3-doxyl portion of the spin-label is highly immobilized yet is exposed to solvent. Paramagnetic effects of the nitroxide on T1 defined distances to several previously assigned [Benisek, W. F., & Ogez, J. R. (1982) Biochemistry 21, 5816-5825] and newly assigned protons of the enzyme. These distances were then used to locate (with an accuracy of +/- 2 A) the nitroxide moiety at a unique position in a partially refined 2.5-A resolution X-ray structure of native isomerase. Three of five additional proton resonance peaks, attributed to ring-shielded methyl groups, could be assigned to specific residues on the basis of distances from the spin-label in the X-ray structure. The remaining portion of the spin-labeled steroid was then docked into the X-ray structure in a hydrophobic cavity of the enzyme. This position of the steroid is consistent with the steroid binding site previously proposed [Westbrook, E. M., Piro, O. E., & Sigler, P. B. (1984) J. Biol. Chem. 259, 9096-9103]. However, the rotational orientation of this steroid about its long axis could not be unambiguously established. If we assume that steroid substrates and the spin-labeled inhibitor bind to the same site, but with reversal of the 3- and 17-positions, then the phenolic hydroxyl of Tyr-55 is optimally positioned to function as the general acid that protonates the 3-keto group of the substrate, facilitated by the negative end of the dipole of a 10-residue alpha-helix, the only helix in the molecule.(ABSTRACT TRUNCATED AT 400 WORDS)

Binding Sites↗

In vivo cross-linking of protein disulfide isomerase to immunoglobulins.

To test the proposed role of protein disulfide isomerase in the synthesis of immunoglobulins (Ig), intact lymphocytes were treated with a thiol-cleavable, bifunctional cross-linking agent and lysed, and the lysates were immunoprecipitated with antibodies to either Ig or enzyme. When the immunoprecipitates were analyzed on polyacrylamide-sodium dodecyl sulfate gels, protein disulfide isomerase was found to be cross-linked to immunoglobulins. The extent of cross-linking was dependent upon the concentration of cross-linker added and the class of Ig. For IgMs and high concentrations of cross-linker, approximately one molecule of Ig was coupled per two molecules of enzyme. For IgGs, the extent of cross-linking was less. Finally, depletion of the intracellularly reduced glutathione by diamide was found to also result in the linkage of protein disulfide isomerase to IgM. These results therefore support the hypothesis that protein disulfide isomerase functions in the in vivo synthesis of immunoglobulins.

Animals↗

Isopentenyl-diphosphate isomerase: inactivation of the enzyme with active-site-directed irreversible inhibitors and transition-state analogues.

Seven analogues of isopentenyl diphosphate (1) and dimethylallyl diphosphate (2) containing fluorine, epoxy, and ammonium functional groups irreversibly inhibited isopentenyl-diphosphate:dimethylallyl-diphosphate isomerase (EC 5.3.3.2) from the mold Claviceps purpurea. Inactivation kinetics, substrate protection studies, and labeling experiments demonstrated that the analogues interacted stoichiometrically with the active site of the enzyme. Radioactive enzyme-inactivator complexes were stable to extended dialysis and treatment with chaotropic reagents. The complexes resulting from inactivation of isomerase by 3-(fluoromethyl)-3-buten-1-yl diphosphate (3) and 3,4-epoxy-3-methyl-1-butyl diphosphate (4) were also stable to ion-exchange chromatography and gel electrophoresis. Stoichiometric release of fluoride ion occurred during inactivation of isomerase with 3. This observation is consistent with SN2 or SN2' displacement of fluorine by an active-site nucleophile with concomitant covalent attachment of the inactivator to the enzyme. 2-(Dimethylamino)ethyl diphosphate (9) formed a stable noncovalent complex with isomerase with Kdis less than 1.2 x 10(-10) M. The enzyme-inhibitor complex was stable in 6 M urea, but the inhibitor was partially released upon treatment with SDS and 2-mercaptoethanol at 37 degrees C for 1 h. The results indicate that 9 is a transition-state/reactive intermediate analogue where the positively charged ammonium group mimics a tertiary carbocationic species in the enzyme-catalyzed reaction.

Binding Sites↗

Recruitment of a double bond isomerase to serve as a reductive dehalogenase during biodegradation of pentachlorophenol.

Tetrachlorohydroquinone dehalogenase catalyzes the replacement of chlorine atoms on tetrachlorohydroquinone and trichlorohydroquinone with hydrogen atoms during the biodegradation of pentachlorophenol by Sphingomonas chlorophenolica. The sequence of the active site region of tetrachlorohydroquinone dehalogenase is very similar to those of the corresponding regions of maleylacetoacetate isomerases, enzymes that catalyze the glutathione-dependent isomerization of a cis double bond in maleylacetoacetate to the trans configuration during the catabolism of phenylalanine and tyrosine. Furthermore, tetrachlorohydroquinone dehalogenase catalyzes the isomerization of maleylacetone (an analogue of maleylacetoacetate) at a rate nearly comparable to that of a bona fide bacterial maleylacetoacetate isomerase. Since maleylacetoacetate isomerase is involved in a common and presumably ancient pathway for catabolism of tyrosine, while tetrachlorohydroquinone dehalogenase catalyzes a more specialized reaction, it is likely that tetrachlorohydroquinone dehalogenase arose from a maleylacetoacetate isomerase. The substrates and overall transformations involved in the dehalogenation and isomerization reactions are strikingly different. This enzyme provides a remarkable example of Nature's ability to recruit an enzyme with a useful structural scaffold and elaborate upon its basic catalytic capabilities to generate a catalyst for a newly needed reaction.

Amino Acid Sequence↗

The catalytic mechanism of the hydroxylation reaction of peptidyl proline and lysine does not require protein disulphide-isomerase activity.

Prolyl 4-hydroxylase, an alpha 2 beta 2 tetramer, catalyses the formation of 4-hydroxyproline in collagens. The beta subunit is known to be identical with the enzyme protein disulphide-isomerase and to possess disulphide-isomerase activity even when present in the prolyl 4-hydroxylase tetramer. We here report that lysyl hydroxylase, a homodimer, and algal prolyl 4-hydroxylase, a monomer, do not contain detectable protein disulphide-isomerase activity. Since the hydroxylase reaction mechanisms are similar, the data suggest that the protein disulphide-isomerase activity of the vertebrate prolyl 4-hydroxylase beta subunit is unlikely to be involved in the catalytic mechanism of the hydroxylation reaction.

Animals↗