The Whole Genome Sequence of Sphingobium chlorophenolicum L-1: Insights into the Evolution of the Pentachlorophenol Degradation Pathway

Abstract

Sphingobium chlorophenolicum Strain L-1 can mineralize the toxic pesticide pentachlorophenol (PCP). We have sequenced the genome of S. chlorophenolicum Strain L-1. The genome consists of a primary chromosome that encodes most of the genes for core processes, a secondary chromosome that encodes primarily genes that appear to be involved in environmental adaptation, and a small plasmid. The genes responsible for degradation of PCP are found on chromosome 2. We have compared the genomes of S. chlorophenolicum Strain L-1 and Sphingobium japonicum, a closely related Sphingomonad that degrades lindane. Our analysis suggests that the genes encoding the first three enzymes in the PCP degradation pathway were acquired via two different horizontal gene transfer events, and the genes encoding the final two enzymes in the pathway were acquired from the most recent common ancestor of these two bacteria.

Comparison of 26 Sphingomonad Genomes Reveals Diverse Environmental Adaptations and Biodegradative Capabilities

“…strain PP1Y, more GHs were encoded on the megaplasmid than the chromosome (41 versus 36), and the plasmids of Sphingomonas wittichii RW1 and Novosphingobium aromaticivorans DSM 12444 contain several dioxygenases. Moreover, the smaller of the two chromosomes in Sphingobium chlorophenolicum L-1 has been shown to encode the genes necessary to degrade the aromatic pesticide pentachlorophenol, and evidence suggests that three genes involved have arisen through multiple horizontal gene transfer events (38). Together with the high incidence of chromosomal rearrangements and plasmid-mediated gene transfers observed, this is consistent with the assertion that plasmids and other selfish genetic elements are likely responsible for frequent exchange of biodegradative capabilities in sphingomonads (14).…”

“…S1 in the supplemental material). As noted previously (38), a small degree of shared gene order is present between Sphingobium japonicum UT26S and Sphingobium chlorophenolicum L-1. These genomes appear to have undergone multiple chromosomal rearrangements since their divergence, and neither shares identifiable synteny with strain SYK-6.…”

Selection for Growth on 3-Nitrotoluene by 2-Nitrotoluene-Utilizing Acidovorax sp. Strain JS42 Identifies Nitroarene Dioxygenases with Altered Specificities

“…Moreover, bacteria exposed to toxic synthetic chemicals in the environment evolve to take advantage of these potential sources of carbon and energy by developing new catabolic pathways (19,(56)(57)(58)(59). This and similar studies (52,(60)(61)(62) highlight the rapid evolution of bacteria to utilize toxic human-made carbon and energy sources in laboratory time scales, allowing evolution to be studied in real time rather than being reconstructed from history.…”

Sequestration of a highly reactive intermediate in an evolving pathway for degradation of pentachlorophenol

“…strain NyZ215 (15), respectively. However, despite the similarities in reaction sequences and genetic organization, the reductase genes in these microbes are not necessarily homologous to each other or to pcpD (12). The reductases in the degradation of TriCP (TcpB) and p-nitrophenol (PnpB) belong to the nitroreductase-like family 5 and NADPH-dependent FMN reductase superfamilies, respectively.…”

“…The gene encoding the reductase is located immediately downstream of the gene encoding the hydroxylase (12). Examples are found in the pathways for degradation of 2,4,6-trichlorophenol (TriCP), p-nitrophenol and o-nitrophenol in Cupriavidus necator JMP134 (13), Pseudomonas sp.…”