Identification and functional analysis of the genes for naphthalenesulfonate catabolism by Sphingomonas xenophaga BN6

Abstract

Sphingomonas xenophaga BN6 degrades various (substituted) naphthalenesulfonates to the corresponding (substituted) salicylates. A gene cluster was identified on the plasmid pBN6 which coded for several enzymes participating in the degradative pathway for naphthalenesulfonates. A DNA fragment of 16 915 bp was sequenced which contained 17 ORFs. The genes encoding the 1,2-dihydroxynaphthalene dioxygenase, 2-hydroxychromene-2-carboxylate isomerase, and 29-hydroxybenzalpyruvate aldolase of the naphthalenesulfonate pathway were identified on the DNA fragment and the encoded proteins heterologously expressed in Escherichia coli. Also, the genes encoding the ferredoxin and ferredoxin reductase of a multi-component, ring-hydroxylating naphthalenesulfonate dioxygenase were identified by insertional inactivation. The identified genes generally demonstrated the highest degree of homology to enzymes encoded by the phenanthrene-degrading organism Sphingomonas sp. P2, or the megaplasmid pNL1 of the naphthalene-and biphenyl-degrading strain Sphingomonas aromaticivorans F199. The genes of S. xenophaga BN6 participating in the degradation of naphthalenesulfonates also shared the same organization in three different transcriptional units as the genes involved in the degradation of naphthalene, biphenyl, and phenanthrene previously found in Sphingomonas sp. P2 and S. aromaticivorans F199. The genes were flanked in S. xenophaga BN6 by ORFs which specify proteins that show the highest homologies to proteins of mobile genetic elements.

Selection of Sphingomonadaceae at the Base of Laccaria proxima and Russula exalbicans Fruiting Bodies

“…Various members of the Sphingomonadaceae family (previously subdivided into the genera Sphingomonas, Sphingopyxis, Novosphingobium, and others) are known for their capability to utilize a wide variety of carbon sources, and in fact, several are renowned degraders of recalcitrant (xenobiotic) molecules (4,17,20,32). Members of the family are ubiquitous, as they are found in different soils (1,7,20), sediments (10), and pelagic aquatic environments (7,36,38).…”

Detecting variants with Metabolic Design, a new software tool to design probes for explorative functional DNA microarray development

“…Many researchers have therefore focused on the biodegradation of these pollutants by microorganisms, especially bacteria. Several enzymes involved in these critical biodegradation steps have been characterized and their sequences deposited in databases [24-28]. …”

Sphingobium sp. HV3 degrades both herbicides and polyaromatic hydrocarbons using ortho- and meta-pathways with differential expression shown by RT-PCR

“…The naphthalene -salicylate -, m-toluate -, phenanthreneand biphenyl -phenotypes of Km187 and Km42 showed that the activity of reductase component of a dioxygenase in the pSKY4 megaplasmid is necessary in catabolism of these aromatics. It is thought that aromatic meta-pathways of Sphingomonas contain only one functional reductase (Keck et al 2006;Romine et al 1999). Disruption of the electron transfer chain of dioxygenases leads to an inactive meta-pathway in the HV3 strain shown by the mutant phenotypes.…”

“…Other types of catabolic plasmids have more recently been characterized from the Alphaproteobacteria; (Fredrickson et al 1995;Basta et al 2004;Keck et al 2006), but large plasmids have not been much studied. They are cumbersome to isolate and often difficult to distinguish from the chromosomal DNA.…”