Starvation- and xenobiotic-related transcriptomic responses of the sulfanilic acid-degrading bacterium, Novosphingobium resinovorum SA1

Abstract

Novosphingobium resinovorum SA1 was the first single isolate capable of degrading sulfanilic acid, a widely used representative of sulfonated aromatic compounds. The genome of the strain was recently sequenced, and here, we present whole-cell transcriptome analyses of cells exposed to sulfanilic acid as compared to cells grown on glucose. The comparison of the transcript profiles suggested that the primary impact of sulfanilic acid on the cell transcriptome was a starvation-like effect. The genes of the peripheral, central, and common pathways of sulfanilic acid biodegradation had distinct transcript profiles. The peripheral genes located on a plasmid had very high basal expressions which were hardly upregulated by sulfanilic acid. The genomic context and the codon usage preference of these genes suggested that they were acquired by horizontal gene transfer. The genes of the central pathways were remarkably inducible by sulfanilic acid indicating the presence of a substrate-specific regulatory system in the cells. Surprisingly, the genes of the common part of the metabolic pathway had low and sulfanilic acid-independent transcript levels. The approach applied resulted in the identification of the genes of proteins involved in auxiliary processes such as electron transfer, substrate and iron transports, sulfite oxidases, and sulfite transporters. The whole transcriptome analysis revealed that the cells exposed to xenobiotics had multiple responses including general starvation-like, substrate-specific, and substrate-related effects. From the results, we propose that the genes of the peripheral, central, and common parts of the pathway have been evolved independently.

TonB-Dependent Transporters in Sphingomonads: Unraveling Their Distribution and Function in Environmental Adaptation

“…Transcriptome and proteome analysis was done for certain sphingomonads grown under certain unique physiological conditions. These omics studies showed substrate specific expression patterns of TBDTs [14,16,33,34,36,[38][39][40]. About 32 TBDTs showed differential expression in the presence of heavy metals, xenobiotics, temperature stress, and poor nutrient conditions ( Table 1).…”

“…One of them showed a seven-fold increased expression when the cells were grown in sulfanilic acid. Such an increase in TBDT amounts is believed to facilitate active transport of polar sulfanilic acid across the outer membrane [36]. TonB-dependent transport system appears to be advantageous to bacteria in more than one way.…”

Challenges of unculturable bacteria: environmental perspectives

“…To date, a great variety of physico-chemical treatments have been available for removing these contaminants from the environment (Scullion 2006), but biological approaches are still among the most promising methods. Bioremediation based on natural processes utilizes the metabolic pathways of microorganisms (Laczi et al 2015;Hegedüs et al 2017;Heged} us et al 2017) (or plants) to neutralize pollutants and, thus, can be performed either ex situ or in situ (Vidali 2001;Perei et al 2001;Kang 2014;Kis et al 2015Kis et al , 2017. A decrease in contamination can be achieved by stimulating the indigenous microflora of the polluted site with nutrient addition (i.e.…”

“…By now, many reports have revealed different physiological states in bacteria ( Fig. 1) ranging from unstressed living cells to dead cells (Kell et al 1998;Bergkessel et al 2016;Hegedüs et al 2017); a range which includes VBNC states. VBNC cells maintain their viability but unable to grow on routinely-used laboratory media (Oliver 2005).…”

“…Like other living organisms, microorganisms are able to interact with changing environmental conditions by triggering specific stress responses and survival mechanisms if the environmental parameters become suboptimal (Heimann 2002;Hegedüs et al 2017). Bacteria can survive in extreme environments by forming spores (Hutchison et al 2014) or entering a non-sporulating dormant state (Lennon and Jones 2011;Shoemaker and Lennon 2018).…”