Degradative plasmids from sphingomonads

Abstract

Large plasmids ('megaplasmids') are commonly found in members of the Alphaproteobacterial family Sphingomonadaceae ('sphingomonads'). These plasmids contribute to the extraordinary catabolic flexibility of this group of organisms, which degrade a broad range of recalcitrant xenobiotic compounds. The genomes of several sphingomonads have been sequenced during the last years. In the course of these studies, also the sequences of several plasmids have been determined. The analysis of the published information and the sequences deposited in the public databases allowed a first classification of these plasmids into a restricted number of groups according to the proteins involved in the initiation of replication, plasmid partition and conjugation. The sequence comparisons demonstrated that the plasmids from sphingomonads encode for four main groups of replication initiation (Rep) proteins. These Rep proteins belong to the protein superfamilies RepA_C (Pfam 04796), Rep_3 (Pfam 01051), RPA (Pfam 10134) and HTH-36 (Pfam 13730). The 'degradative megaplasmids' pNL2, pCAR3, pSWIT02, pCHQ1, pISP0, and pISP1, which code for genes involved in the degradation of aromatic hydrocarbons, carbazole, dibenzo-p-dioxin and γ-hexachlorocyclohexane, carry Rep proteins which either belong to the RepA_C- (plasmids pNL2, pCAR3, pSWIT02), Rep-3- (plasmids pCHQ1, pISP0) or RPA-superfamily (pISP1). The classification of these 'degradative megaplasmids' into three groups is also supported by sequence comparisons of the proteins involved in plasmid partition (ParAB) and the organization of the three genes on the respective plasmids. All analysed 'degradative megaplasmids' carry genes, which might allow a conjugative transfer of the plasmids. Sequence comparisons of these genes suggest the presence of at least two types of transfer functions, which either are closer related to the tra- or vir-genes previously described for plasmids from other sources.

Phenanthrene biodegradation by sphingomonads and its application in the contaminated soils and sediments: A review

“…An example is the genes for the upper and lower pathways of naphthalene of several pseudomonads and sphingomonads (Yen et al, 1988), which are borne on iso-functional nah-plasmids, are often found either on different replicons or are at least organized in several transcriptional units (Stolz, 2009). Moreover, after transfer, these plasmids often undergo evident rearrangements between the various sphingomonads (Basta et al, 2005(Basta et al, , 2004Stolz, 2014). The transfer, maintenance, and recombination of these plasmids, therefore, are of great significance for the exceptional degradative capabilities of this group of bacteria in contaminated soils and sediments.…”

“…The occurrence of PAH-degradative genes on mobile genetic elements may be an efficient method of spreading PAH-catabolic abilities among bacteria in polluted soils as a result of conjugative gene transfer. This makes sphingomonads capable hosts in containing several different plasmids in a single cell, an essential feature for the degradation of many organic compounds (Stolz, 2014).…”

Integrated multi-omics analyses reveal the biochemical mechanisms and phylogenetic relevance of anaerobic androgen biodegradation in the environment

“…denitrificans cannot be excluded. The presence of catabolic genes in plasmids has been reported in numerous bacteria (Roselli et al, 2013;Stolz, 2014).…”

Metabolic Pathway Involved in 2-Methyl-6-Ethylaniline Degradation by Sphingobium sp. Strain MEA3-1 and Cloning of the Novel Flavin-Dependent Monooxygenase System meaBA

“…strain KA1 (55). Until this study, Stolz (56) reported that, at most, five plasmids have been isolated from sphingomonads, namely, those found among two plasmids from Sphingomonas aromaticivorans strain F199, Sphingomonas wittichii strain RW1, and Novosphingobium pentaromativorans strain US6-1, three plasmids from S. japonicum strain UT26 and Novosphingobium sp. strain PP1Y, four plasmids from Sphingomonas xenophagum strain BN6 and Sphingobium fuliginis strain ATCC 27551, and five plasmids from Sphingomonas sp.…”

“…strain PP1Y, four plasmids from Sphingomonas xenophagum strain BN6 and Sphingobium fuliginis strain ATCC 27551, and five plasmids from Sphingomonas sp. strain MM-1 (56). The meaBA genes are located on plasmid pMEA02 and are surrounded by a transposable element from the IS6100 family (Fig.…”