Identification of two fnr genes and characterisation of their role in the anaerobic switch in Sphingopyxis granuli strain TFA

Yolanda Elisabet González-Flores,Francisca Reyes-Ramírez,Rubén De Dios,Eduardo Santero

doi:10.1038/s41598-020-77927-w

Yolanda Elisabet González-Flores, Francisca Reyes-Ramírez + Show 2 more

Open Access

https://doi.org/10.1038/s41598-020-77927-w

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Abstract

Sphingopyxis granuli strain TFA is able to grow on the organic solvent tetralin as the only carbon and energy source. The aerobic catabolic pathway for tetralin, the genes involved and their regulation have been fully characterised. Unlike most of the bacteria belonging to the sphingomonads group, this strain is able to grow in anoxic conditions by respiring nitrate, though not nitrite, as the alternative electron acceptor. In this work, two fnr-like genes, fnrN and fixK, have been identified in strain TFA. Both genes are functional in E. coli and Sphingopyxis granuli although fixK, whose expression is apparently activated by FnrN, seems to be much less effective than fnrN in supporting anaerobic growth. Global transcriptomic analysis of a ΔfnrN ΔfixK double mutant and identification of Fnr boxes have defined a minimal Fnr regulon in this bacterium. However, expression of a substantial number of anaerobically regulated genes was not affected in the double mutant. Additional regulators such regBA, whose expression is also activated by Fnr, might also be involved in the anaerobic response. Anaerobically induced stress response genes were not regulated by Fnr but apparently induced by stress conditions inherent to anaerobic growth, probably due to accumulation of nitrite and nitric oxide.

Highlights

A great number of bacteria show a nutritional versatility that allow them to use multiple molecules as substrates including a wide variety of organic pollutants of natural or anthropogenic origin, many of which are recalcitrant
The genome sequence of Sphingopyxis granuli strain TFA revealed features typical of oligotrophic bacteria, biodegradation genes in addition to the ones involved in tetralin biodegradation-which might confer additional uncharacterised biodegrading capabilities to this strain
In this work we show that both fnr-like genes are functional in both Sphingopyxis granuli and E. coli, fixK is less efficient in activating transcription and is not required for anaerobic growth in Sphingopyxis granuli

Summary

Introduction

A great number of bacteria show a nutritional versatility that allow them to use multiple molecules as substrates including a wide variety of organic pollutants of natural or anthropogenic origin, many of which are recalcitrant The reason for this extraordinary flexibility mainly lies in the variety of metabolic genes coded in their genomes and in the way their regulation networks detect environmental conditions and adjust their cellular physiology to the constant changes in them. Ubiquity is reflected in that they are found in most of the environments, they play a important role in nutrient cycling in marine environments[4] due to its excellent adaptation to oligotrophic e nvironments[5] Their metabolic versatility includes the ability of many of them to degrade different recalcitrant molecules such as polycyclic aromatic h ydrocarbons[6] or xenobiotic compounds such as lindane[7], frequently harbouring this biodegradative capacity in p lasmids[8]. This last feature that allows this bacterium to colonise anoxic environments, is relevant since Sphingopyxis was considered a strictly aerobic genus[1], and no anaerobic growth of other Sphingopyxis strains has been demostrated so far, nitrate reduction to nitrite has been reported in two other Sphingopyxis strains[15,16]

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