Degradation of 3-O-methylgallate in Sphingomonas paucimobilis SYK-6 by pathways involving protocatechuate 4,5-dioxygenase

Sphingomonas paucimobilis SYK-6 converts vanillate and syringate to protocatechuate and 3-O-methylgallate (3MGA), respectively. 3MGA is metabolized via multiple pathways involving 3MGA 3,4-dioxygenase, protocatechuate 4,5-dioxygenase (LigAB), and gallate dioxygenase whereas protocatechuate is degraded via the protocatechuate 4,5-cleavage pathway. Here the secondary role of LigAB in syringate metabolism is investigated. The reaction product of 3MGA catalyzed by His-tagged LigAB was identified as 4-carboxy-2-hydroxy-6-methoxy-6-oxohexa-2,4-dienoate (CHMOD) and 2-pyrone-4,6-dicarboxylate (PDC), indicating that 3MGA is transformed to CHMOD and PDC by both reactions catalyzed by DesZ and LigAB. Mutant analysis revealed that the 3MGA catabolic pathways involving LigAB are functional in SYK-6.     

Mineralization of 4-aminobenzenesulfonate (4-ABS) by Agrobacterium sp. strain PNS-1

A bacterial strain, PNS-1, isolated from activated sludge, could utilize sulphanilic acid (4-ABS) as the sole organic carbon and energy source under aerobic conditions. Determination and comparison of 16S r DNA sequences showed that the strain PNS-1 is closely related to the species of Agrobacterium genus. Growth on 4-ABS was accompanied with ammonia and sulfate release. TOC results showed complete mineralization of sulphanilic acid. This strain was highly specific for 4-ABS as none of the sulphonated aromatics used in the present study including other ABS isomers were utilized. Strain PNS-1 could, however, utilize all the tested monocyclic aromatic compounds devoid of a sulfonate group. No intermediates could be detected either in the growth phase or with dense cell suspensions. Presence of chloramphenicol completely inhibited 4-ABS degradation by cells pregrown on succinate, indicating that degradation enzymes are inducible. No plasmid could be detected in the Agrobacterium sp. Strain PNS-1 suggesting that 4-ABS degradative genes may be chromosomal encoded.     

Crystal structure of 3-chlorocatechol 1,2-dioxygenase key enzyme of a new modified ortho-pathway from the Gram-positive Rhodococcus opacus 1CP grown on 2-chlorophenol

The crystal structure of the 3-chlorocatechol 1,2-dioxygenase from the Gram-positive bacterium Rhodococcus opacus (erythropolis) 1CP, a Fe(III) ion-containing enzyme specialized in the aerobic biodegradation of 3-chloro- and methyl-substituted catechols, has been solved by molecular replacement techniques using the coordinates of 4-chlorocatechol 1,2-dioxygenase from the same organism (PDB code 1S9A) as a starting model and refined at 1.9 A resolution (R(free) 21.9%; R-factor 17.4%). The analysis of the structure and of the kinetic parameters for a series of different substrates, and the comparison with the corresponding data for the 4-chlorocatechol 1,2-dioxygenase isolated from the same bacterial strain, provides evidence of which active site residues are responsible for the observed differences in substrate specificity. Among the amino acid residues expected to interact with substrates, only three are altered Val53(Ala53), Tyr78(Phe78) and Ala221(Cys224) (3-chlorocatechol 1,2-dioxygenase(4-chlorocatechol 1,2-dioxygenase)), clearly identifying the substitutions influencing substrate selectivity in these enzymes. The crystallographic asymmetric unit contains eight subunits (corresponding to four dimers) that show heterogeneity in the conformation of a co-crystallized molecule bound to the catalytic non-heme iron(III) ion resembling a benzohydroxamate moiety, probably a result of the breakdown of recently discovered siderophores synthesized by Gram-positive bacteria. Several different modes of binding benzohydroxamate into the active site induce distinct conformations of the interacting protein ligands Tyr167 and Arg188, illustrating the plasticity of the active site origin of the more promiscuous substrate preferences of the present enzyme.     

深渊沉积物中盐单胞菌(Halomonas sp.)NyZ771菌株的分离培养及其降解芳香酸的研究

【背景】海洋是地球上最大的碳库,也是地球生物最大的栖息地。在这个庞大的生态系统中拥有多种多样的微生物,它们在全球碳循环中扮演了重要的角色。海斗深渊(海平面6 000 m以下的海域)由于高静水压和表层沉积汇集了大量有机质,形成了包含丰富生物资源的特殊生境。【目的】从马里亚纳海沟海斗深渊沉积物样品中分离培养能够以芳香酸为唯一碳源和能源生长的微生物,并研究其降解特性。【方法】通过模拟原位高压环境富集培养和常压条件下芳香酸选择性分离培养获得深渊来源的纯培养细菌,并根据形态学观察和16S rRNA基因序列系统发育分析进行种属鉴定,利用不同芳香酸进行培养和生物转化,通过HPLC和LC/MS鉴定芳香酸代谢中间产物。【结果】从马里亚纳海沟6 300 m沉积物样本中分离获得了一株盐单胞菌(Halomonas sp.)NyZ771。该菌株能够利用苯甲酸和4-羟基苯甲酸作为唯一碳源生长。其代谢4-羟基苯甲酸的中间产物鉴定为原儿茶酸。【结论】从深渊沉积物样本分离得到一株能降解苯甲酸和4-羟基苯甲酸的盐单胞菌NyZ771,丰富了深渊来源的微生物资源,为今后研究深渊中微生物的芳香酸降解及海洋微生物驱动的碳循环提供了一定的理论基础。     

Aromatic metabolism in Rhizobium trifolii —protocatechuate 3,4-dioxygenase

Protocatechuate 3,4-dioxygenase (EC 1.13.11.3) has been purified 42-fold from 4-hydroxybenzoate-grown cells of Rhizobium trifolii TA1, where it constitutes about 2% of the cell protein. The dioxygenase has a molecular weight of 220,000, with two dissimilar sub-units of molecular weights 29,000 and 26,500, corresponding to an 44 composition. The enzyme is specific for protocatechuate, with a Km of 1.75×10^-5 M and maximum activity at pH 9.2. Metal removal and replacement studies indicate that the enzyme contains complexed Fe³⁺ which is required for activity. Direct atomic absorption analysis gave 1.3–1.5 g atoms Fe³⁺ per mole of isolated enzyme, but correction for metal-deficient proteins suggests that the value is close to 2.     

The Ins and Outs of Ring-Cleaving Dioxygenases

ABSTRACT

Ring-cleaving dioxygenases catalyze the oxygenolytic fission of catecholic compounds, a critical step in the aerobic degradation of aromatic compounds by bacteria. Two classes of these enzymes have been identified, based on the mode of ring cleavage: intradiol dioxygenases utilize non-heme Fe(III) to cleave the aromatic nucleus ortho to the hydroxyl substituents; and extradiol dioxygenases utilize non-heme Fe(II) or other divalent metal ions to cleave the aromatic nucleus meta to the hydroxyl substituents. Recent genomic, structural, spectroscopic, and kinetic studies have increased our understanding of the distribution, evolution, and mechanisms of these enzymes. Overall, extradiol dioxygenases appear to be more versatile than their intradiol counterparts. Thus, the former cleave a wider variety of substrates, have evolved on a larger number of structural scaffolds, and occur in a wider variety of pathways, including biosynthetic pathways and pathways that degrade non-aromatic compounds. The catalytic mechanisms of the two enzymes proceed via similar iron-alkylperoxo intermediates. The ability of extradiol enzymes to act on a variety of non-catecholic compounds is consistent with proposed differences in the breakdown of this iron-alkylperoxo intermediate in the two enzymes, involving alkenyl migration in extradiol enzymes and acyl migration in intradiol enzymes. Nevertheless, despite recent advances in our understanding of these fascinating enzymes, the major determinant of the mode of ring cleavage remains unknown.     

In vitro reconstitution of the catabolic reactions catalyzed by PcaHG,PcaB, and PcaL: the protocatechuate branch of the β-ketoadipate pathway in Rhodococcus jostii RHA1

The β-ketoadipate pathway is a major pathway involved in the catabolism of the aromatic compounds in microbes. The recent progress in genome sequencing has led to a rapid accumulation of genes from the β-ketoadipate pathway in the available genetic database, yet the functions of these genes remain uncharacterized. In this study, the protocatechuate branch of the β-ketoadipate pathway of Rhodococcus jostii was reconstituted in vitro. Analysis of the reaction products of PcaHG, PcaB, and PcaL was achieved by high-performance liquid chromatography. These reaction products, β-ketoadipate enol-lactone, 3-carboxy-cis,cis-muconate, γ-carboxymuconolactone, muconolactone, and β-ketoadipate, were further characterized using LC-MS and nuclear magnetic resonance. In addition, the in vitro reaction of PcaL, a bidomain protein consisting of γ-carboxy-muconolactone decarboxylase and β-ketoadipate enol-lactone hydrolase activities, was demonstrated for the first time. This work provides a basis for analyzing the catalytic properties of enzymes involved in the growing number of β-ketoadipate pathways deposited in the genetic database.     

Cloning,Sequencing, and Expression of the Gene Encoding 4-Hydroxy-4-methyl-2-oxoglutarate Aldolase from Pseudomonas ochraceae NGJ1

A DNA fragment that carried the gene (proA) encoding 4-hydroxy-4-methyl-2-oxoglutarate aldolase was cloned from the chromosomal DNA of Pseudomonas ochraceae NGJ1, and the coding region was assigned to the nucleotide sequence based on the N-terminal amino acid sequence of the enzyme purified from the organism. The proA gene was 684 bp long, corresponding to a protein of 227 amino acid residues with a calculated molecular mass of 24,067 Da. The genes encoding a putative transporter and a 4-oxalomesaconate hydratase were upstream, and a 3'-truncated gene encoding 2-pyrone-4,6-dicarboxylate lactonase was downstream from the proA gene in the same orientation on the DNA fragment. The proA gene product was overproduced in Escherichia coli and briefly purified to homogeneity from the crude extract by a two-step purification. The molecular and catalytic properties of the gene product were similar to those of the P. ochraceae enzyme.     

Key enzymes of the protocatechuate branch of the β-ketoadipate pathway for aromatic degradation inCorynebacterium glutamicum

Although the protocatechuate branch of the β-ketoadipate pathway in Gram⁻ bacteria has been well studied, this branch is less understood in Gram⁺ bacteria. In this study,Corynebacterium glutamicum was cultivated with protocatechuate,p-cresol, vanillate and 4-hydroxybenzoate as sole carbon and energy sources for growth. Enzymatic assays indicated that growing cells on these aromatic compounds exhibited protocatechuate 3,4-dioxygenase activities. Data-mining of the genome of this bacterium revealed that the genetic locusncg12314-ncg12315 encoded a putative protocatechuate 3,4-dioxygenase. The genes,ncg12314 andncg12315, were amplified by PCR technique and were cloned into plasmid (pET21aP34D). RecombinantEscherichia coli strain harboring this plasmid actively expressed protocatechuate 3,4-dioxygenase activity. Further, when this locus was disrupted inC. glutamicum, the ability to degrade and assimilate protocatechuate,p-cresol, vanillate or 4-hydroxybenzoate was lost and protocatechuate 3,4-dioxygenase activity was disappeared. The ability to grow with these aromatic compounds and protocatechuate 3,4-dioxygenase activity ofC. glutamicum mutant could be restored by gene complementation. Thus, it is clear that the key enzyme for ring-cleavage, protocatechuate 3,4-dioxygenase, was encoded byncg12314 andncg12315. The additional genes involved in the protocatechuate branch of the β-ketoadipate pathway were identified by mining the genome data publically available in the Gen Bank. The functional identification of genes and their unique organization inC. glutamicum provided new insight into the genetic diversity of aromatic compound degradation.     

深渊来源Citricoccus sp.strain NyZ702的分离培养及其降解4-羟基苯甲酸的特性

【背景】深渊沉积物中存在丰富的微生物细胞和活跃的微生物碳周转,因此,分离培养微生物资源对于认识深渊中的物质循环、能量代谢具有重要意义。芳香化合物在环境中广泛存在,基于组学分析揭示了深渊中具有潜在的芳香化合物代谢菌株,然而深渊来源的芳香化合物降解微生物纯培养和相关的代谢机理研究仍然缺乏。【目的】从马里亚纳海沟沉积物样本中分离培养具有降解芳香化合物能力的微生物,对其代谢途径、中间产物和降解酶活力进行初步鉴定。【方法】以4-羟基苯甲酸为唯一碳源对马里亚纳海沟沉积物样本中的降解菌株进行分离培养,结合形态观察、16S rRNA基因扩增与序列分析对菌株进行鉴定,通过底物生长实验验证其降解能力,通过高效液相色谱和超高效液相色谱-飞行时间质谱联用仪初步鉴定全细胞生物转化中间产物,利用紫外分光光度计测定其粗酶液催化4-羟基苯甲酸的活力,进而推测菌株降解4-羟基苯甲酸的代谢途径。【结果】从深渊沉积物中分离培养获得一株好氧细菌,16SrRNA基因序列分析显示该菌株隶属于柠檬球菌属(Citricoccus),命名为Citricoccus sp. strain NyZ702。该菌株在LB固体培养基上经30°C培养4 d后呈柠檬黄色、不透明、表面光滑、边缘整齐、凸出于培养基表面、直径约为1-2 mm的圆形菌落。扫描电镜表明菌体呈球形,直径为0.4-0.6μm,无鞭毛结构。该菌株为耐盐菌,最适生长盐浓度范围为2%-8%(质量体积分数)。该菌株可利用4-羟基苯甲酸为唯一碳源进行生长,可转化4-羟基苯甲酸至中间产物原儿茶酸,推测该菌株通过原儿茶酸途径降解4-羟基苯甲酸。菌株NyZ702的粗酶液具有4-羟基苯甲酸单加氧酶活力,对4-羟基苯甲酸的催化反应需要还原型烟酰胺腺嘌呤二核苷酸磷酸(NADPH)作为辅因子。【结论】从深渊沉积物样本分离得到一株4-羟基苯甲酸降解菌Citricoccus sp. strain NyZ702,该菌株以原儿茶酸为中间代谢产物降解4-羟基苯甲酸,丰富了深渊来源的微生物菌种资源,为深渊中的芳香化合物降解研究提供了一定的理论基础。