Sphingomonas wittichii Strain RW1 Genome-Wide Gene Expression Shifts in Response to Dioxins and Clay.
Sphingomonas wittichii strain RW1 (RW1) is one of the few strains that can grow on dibenzo-p-dioxin (DD). We conducted a transcriptomic study of RW1 using RNA-Seq to outline transcriptional responses to DD, dibenzofuran (DF), and the smectite clay mineral saponite with succinate as carbon source. The ability to grow on DD is rare compared to growth on the chemically similar DF even though the same initial dioxygenase may be involved in oxidation of both substrates. Therefore, we hypothesized the reason for this lies beyond catabolic pathways and may concern genes involved in processes for cell-substrate interactions such as substrate recognition, transport, and detoxification. Compared to succinate (SUC) as control carbon source, DF caused over 240 protein-coding genes to be differentially expressed, whereas more than 300 were differentially expressed with DD. Stress response genes were up-regulated in response to both DD and DF. This effect was stronger with DD than DF, suggesting a higher toxicity of DD compared to DF. Both DD and DF caused changes in expression of genes involved in active cross-membrane transport such as TonB-dependent receptor proteins, but the patterns of change differed between the two substrates. Multiple transcription factor genes also displayed expression patterns distinct to DD and DF growth. DD and DF induced the catechol ortho- and the salicylate/gentisate pathways, respectively. Both DD and DF induced the shared down-stream aliphatic intermediate compound pathway. Clay caused category-wide down-regulation of genes for cell motility and chemotaxis, particularly those involved in the synthesis, assembly and functioning of flagella. This is an environmentally important finding because clay is a major component of soil microbes' microenvironment influencing local chemistry and may serve as a geosorbent for toxic pollutants. Similar to clay, DD and DF also affected expression of genes involved in motility and chemotaxis.
Center for Microbial Ecology, Michigan State University, East Lansing, MI, United States of America.
Benli
http://orcid.org/0000-0003-4140-4530
B
Chai
Center for Microbial Ecology, Michigan State University, East Lansing, MI, United States of America.
Tamara V
TV
Tsoi
Center for Microbial Ecology, Michigan State University, East Lansing, MI, United States of America.
Shoko
S
Iwai
Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States of America.
Cun
C
Liu
Center for Microbial Ecology, Michigan State University, East Lansing, MI, United States of America.
Jordan A
JA
Fish
School of the Environment, Nanjing University, Nanjing, China.
Cheng
C
Gu
Center for Microbial Ecology, Michigan State University, East Lansing, MI, United States of America.|Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States of America.
Timothy A
TA
Johnson
Department of Biochemistry & Microbiology, Rutgers University, New Brunswick, NJ, United States of America.
Gerben
G
Zylstra
Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States of America.
Brian J
BJ
Teppen
Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States of America.
Hui
H
Li
Civil and Environmental Engineering, Michigan State University, East Lansing, MI, United States of America.
Syed A
SA
Hashsham
Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States of America.
Stephen A
SA
Boyd
Center for Microbial Ecology, Michigan State University, East Lansing, MI, United States of America.
James R
JR
Cole
Center for Microbial Ecology, Michigan State University, East Lansing, MI, United States of America.
James M
JM
Tiedje
D000538:Aluminum Silicates / Q000737:chemistry / Q000378:metabolism; D001673:Biodegradation, Environmental; D002465:Cell Movement / Q000187:drug effects; D002633:Chemotaxis / Q000187:drug effects; D000077215:Clay; D004147:Dioxins / Q000737:chemistry* / Q000378:metabolism; D015964:Gene Expression Regulation, Bacterial / Q000187:drug effects; D010105:Oxygenases / Q000235:genetics; D012988:Soil Microbiology; D020578:Sphingomonas / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D059467:Transcriptome / Q000235:genetics*
D000538:Aluminum Silicates; D004147:Dioxins; D010105:Oxygenases; C020887:dibenzo(1,4)dioxin; D000077215:Clay