TABLE 1

Inventory of transcriptional regulators with implications for adaptive metabolism, from complete and draft genomes of Nitrospira

Transcriptional regulatorGenePresence or absence of gene in species or strainaFunction
Comammox organismsNOB
Nitrospira sp. UW-LDO-01Ca. Nitrospira nitrosa”Ca. Nitrospira nitrificans”Ca. Nitrospira inopinata”Nitrospira sp. Ga0074138Nitrospira sp. UW-LDO-02NitrospiramoscoviensisNitrospiradefluviiNitrospira sp. OL23
Formate hydrogen lyase transcriptional activator fhlA +++++++++FhlA binds to formate hydrogen
lyase structural genes (formate dehydrogenase and group 4 hydrogenase complex) to
activate transcription of their promoters (54).
Transcriptional activator protein NhaR nhaR +++++++NhaR regulates nhaA, a pH-dependent sodium-proton antiporter that responds to alkaline and saline conditions (82). It is also responsible for osmC induction
(55), required for resistance to organic peroxides and osmotic conditions and for long-term survival in stationary phase (83, 84). NhaR also stimulates transcription of pga, a set of genes responsible for poly-β-1,6-N-acetyl-d- glucosamine (PGA) synthesis (56). PGA is involved in cell-cell adhesion and attachment, which stabilize biofilm formation (85).
Hydrogen peroxide-inducible gene activator oxyR ++++++++OxyR is required for the induction of a hydrogen peroxide-inducible regulon in response to elevated levels of hydrogen peroxide (57).
Chemotaxis regulator CheZ cheZ ++++++++CheZ is a component of the chemotaxis signal-transduction pathway (86). It controls the phosphorylation of CheY, a protein involved in the cell excitation response. Absence of CheZ results in nonchemotactic cells or long stimulus response latencies, demonstrating its critical importance during response to stimuli (87).
Fumarate and nitrate reductase regulatory protein fnr +++++++Fnr is an oxygen-responsive regulator required for the expression of a number of genes involved in anaerobic metabolism (61, 88, 89), including fumarate reductase, nitrate and nitrite reductase, and cytochrome oxidase genes (90).
  • a Plus and minus signs represent the presence and absence of each gene, respectively.