Genomic Insights in the Metabolism of Aromatic Compounds in Pseudomonas

Jiménez, José I.; Miñambres, Baltasar; Garcı́a, José Luis; Dı́az, Eduardo

doi:10.1007/978-1-4419-9088-4_15

Cited by 52 publications

(57 citation statements)

References 103 publications

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“…2B). However, a gene encoding a muconolactone isomerase (usually clustered in Pseudomonas strains with genes encoding muconate cycloisomerases and catechol 1,2-dioxygenases (16,17) could not be localized in the sequenced region. In contrast, salC was preceded by ORFs with high homology to genes encoding salicylate 1-hydroxylases (salA) and permeases of the major facilitator subfamily (salB).…”

Section: Resultsmentioning

confidence: 99%

“…Aerobic degradation of aromatic compounds usually involves their successive activation and modification such that they are channeled toward a few dihydroxylated intermediates (17,38). Catechol is the common intermediate during the degradation of a significant number of aromatic compounds such as benzoate, benzene, phenol, or salicylate and can be subject to either intradiol cleavage by a catechol 1,2-dioxygenase (C12O) or extradiol cleavage by a catechol 2,3-dioxygenase (17,38).…”

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confidence: 99%

“…Catechol is the common intermediate during the degradation of a significant number of aromatic compounds such as benzoate, benzene, phenol, or salicylate and can be subject to either intradiol cleavage by a catechol 1,2-dioxygenase (C12O) or extradiol cleavage by a catechol 2,3-dioxygenase (17,38). Enzymes for catechol degradation via intradiol cleavage are encoded by the catechol branch of the 3-oxoadipate pathway (15).…”

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confidence: 99%

“…Enzymes for catechol degradation via intradiol cleavage are encoded by the catechol branch of the 3-oxoadipate pathway (15). Pseudomonas strains usually contain a catRBCA gene cluster (16,33,54) comprising genes encoding catechol 1,2-dioxygenase (CatA), muconate cycloisomerase (MCI; CatB), and muconolactone isomerase (CatC), which are controlled by a LysR type regulator (CatR) in response to the inducer muconate (17). However, various permutations with respect to enzyme distribution, regulation, and gene organization have also been observed (15,30,47,55).…”

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A Gene Cluster Involved in Degradation of Substituted Salicylates viaorthoCleavage inPseudomonassp. Strain MT1 Encodes Enzymes Specifically Adapted for Transformation of 4-Methylcatechol and 3-Methylmuconate

et al. 2007

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Pseudomonas sp. strain MT1 has recently been reported to degrade 4-and 5-chlorosalicylate by a pathway assumed to consist of a patchwork of reactions comprising enzymes of the 3-oxoadipate pathway. Genes encoding the initial steps in the degradation of salicylate and substituted derivatives were now localized and sequenced. One of the gene clusters characterized (sal) showed a novel gene arrangement, with salA, encoding a salicylate 1-hydroxylase, being clustered with salCD genes, encoding muconate cycloisomerase and catechol 1,2-dioxygenase, respectively, and was expressed during growth on salicylate and chlorosalicylate. A second gene cluster (cat), exhibiting the typical catRBCA arrangement of genes of the catechol branch of the 3-oxoadipate pathway in Pseudomonas strains, was expressed during growth on salicylate. Despite their high sequence similarities with isoenzymes encoded by the cat gene cluster, the catechol 1,2-dioxygenase and muconate cycloisomerase encoded by the sal cluster showed unusual kinetic properties. Enzymes were adapted for turnover of 4-chlorocatechol and 3-chloromuconate; however, 4-methylcatechol and 3-methylmuconate were identified as the preferred substrates. Investigation of the substrate spectrum identified 4-and 5-methylsalicylate as growth substrates, which were effectively converted by enzymes of the sal cluster into 4-methylmuconolactone, followed by isomerization to 3-methylmuconolactone. The function of the sal gene cluster is therefore to channel both chlorosubstituted and methylsubstituted salicylates into a catechol ortho cleavage pathway, followed by dismantling of the formed substituted muconolactones through specific pathways.

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Section: Resultsmentioning

confidence: 99%

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confidence: 99%

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A Gene Cluster Involved in Degradation of Substituted Salicylates viaorthoCleavage inPseudomonassp. Strain MT1 Encodes Enzymes Specifically Adapted for Transformation of 4-Methylcatechol and 3-Methylmuconate

et al. 2007

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“…Other sequenced aromatic compound-degrading bacteria, such as the aerobic P. putida KT2440 (39), Rhodococcus RHA1 (31), and anaerobic strain EbN1 (40), have six, eight, and five central aromatic pathways, respectively. Nine such pathways were found in the combined genomes of all fully or partially sequenced Pseudomonas strains (41). In addition, the LB400 genome contains twenty ''peripheral aromatic'' catabolic pathways (Fig.…”

Section: Genetic Factors Indicating the Ecological Niche Of B Xenovomentioning

confidence: 99%

Burkholderia xenovorans LB400 harbors a multi-replicon, 9.73-Mbp genome shaped for versatility

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et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

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Burkholderia xenovorans LB400 (LB400), a well studied, effective polychlorinated biphenyl-degrader, has one of the two largest known bacterial genomes and is the first nonpathogenic Burkholderia isolate sequenced. From an evolutionary perspective, we find significant differences in functional specialization between the three replicons of LB400, as well as a more relaxed selective pressure for genes located on the two smaller vs. the largest replicon. High genomic plasticity, diversity, and specialization within the Burkholderia genus are exemplified by the conservation of only 44% of the genes between LB400 and Burkholderia cepacia complex strain 383. Even among four B. xenovorans strains, genome size varies from 7.4 to 9.73 Mbp. The latter is largely explained by our findings that >20% of the LB400 sequence was recently acquired by means of lateral gene transfer. Although a range of genetic factors associated with in vivo survival and intercellular interactions are present, these genetic factors are likely related to niche breadth rather than determinants of pathogenicity. The presence of at least eleven ''central aromatic'' and twenty ''peripheral aromatic'' pathways in LB400, among the highest in any sequenced bacterial genome, supports this hypothesis. Finally, in addition to the experimentally observed redundancy in benzoate degradation and formaldehyde oxidation pathways, the fact that 17.6% of proteins have a better LB400 paralog than an ortholog in a different genome highlights the importance of gene duplication and repeated acquirement, which, coupled with their divergence, raises questions regarding the role of paralogs and potential functional redundancies in large-genome microbes.genomics ͉ niche adaptation ͉ evolution ͉ biodegradation ͉ redundancy

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