oxygen regulation Flashcards
which two systems does E. coli use to sense oxygen
two component ArcAB and one component FNR
how do bacteria sense oxygen
directly eg binding to haem group or indirectly eg different electron transport products (Q/QH2) or binding of metals (Fe)
when is quinone abundant
oxidised quinone (Q) is abundant in aerobic conditions. reduced quinone (QH2) is abundant in anaerobic conditions as there isn’t enough oxygen present to remove the hydrogen and form an H2O product
how does the electron transfer chain work at low oxygen
the terminal cytochrome c is replaced by cytochrome d which has a higher oxygen affinity
how does the TCA cycle affect oxygen sensing
in anaerobic condition the TCA cycle can’t be completed and there is a build up of intermediates eg formate, d-lactate, acetate, which can be an indicator or low oxygen
which sensor systems detect low and no O2 in E.coli
ArcAB senses low oxygen in the upper gut whereas FNR senses low/ no oxygen in the lower gut
how is ArcAB phosphorylated
H1 is autophosphorylated. if d-lactate (sign of low O2) binds to D1 then Pi moves to D1, then H2 and then D2 on the response regulator
how does quinone inhibit ArcAB
oxidised quinone (sign of high O2) interacts with Cys in the sensory domain and oxidises SH to form S-S bonds. this conformationally changes the sensory domain and inhibits Pi transfer from H1 to D1
how is ArcA phosphorylated
it collides with ArcB and is phosphorylated then dimerises head to head. only one monomer needs to be phosphorylated
how does ArcAB repress genes
it binds to the same site as RNAP or attracted RNAP to different genes. it repressed genes for TCA enzymes as these are not needed anaerobically
how does ArcAB induce genes
it recruits RNAP to the promoter site. it induces genes needed anaerobically eg for fermentation or cytochrome d (only when there is some O2!)
what types of system to sino/bradyrhizobium and rhodobacter use
rhyzobium use FixLJ when going to deeper soil and roots and rhodobacter use RegAB when going to deeper water to use a photosynthetic reaction instead of respiration
what genes does FixLJ regulate
genes for nitrogenase which is needed in anaerobic conditions and is inhibited by O2
how does FixL detect oxygen
O2 binds directly to haem (bound partially by His 194) if oxygen is bound it has an inactive conformation and it regains an active conformation if the oxygen dissociates. His285 is autophosphorylated, then FixJ
how does FixJ regulate transcription
it is phosphorylated by FixL then dimerises and binds to nitrogenase promoter to recruit RNAP and activate transcription
what are the two methods by which rhodobacter can produce ATP energy
through a respiratory or photosynthetic electron transport chain. they can’t operate at the same time due to them both using quinone and cytochrome bc1
how does RegB sense oxygen
direct binding of Q in aerobic conditions which inactivates it and respiration is used instead. if anaerobic QH2 can’t bind so RegB is active and autophosphorylation occurs
what is the second regulator level of RegB
there is a Cys 265 on the kinase domain of the sensor kinase. when oxygen is present it forms sulfenic acid which inhibits the kinase function
which genes does RegAB regulate
it controls the expression of Puf/Poc genes which synthesise proteins needed for the photosynthetic electron transport chain eg the reaction centre, light harvesting proteins
what is FNR
a one- component, dimerised sensor regulator which regulates in very low/ no O2. it is active in low O2 but in higher O2 the dimer dissociates and is proteolytically degraded
how is FNR activated
in anaerobic conditions 4x Fe bind each monomer at Cys residues in the N terminus regions. this allows dimerisation
how does FNR cause activation
if it binds at -41.5 and -61.5/-71.5 it causes RNAP binding and transcription of the anaerobic genes. RNAP interacts with 5’ and 3’ faces of the FNR respectively
how does FNR cause repression
if it binds at -50.5 and -94.5 FNR blocks RNAP and prevents transcription of aerobic genes because the sequences overlap
what happens in terms of activation and repression at low O2, not none
FNR may bind only one repression region. there is a small amount of transcription of aerobic genes
what are fnrS
small RNA molecules which are activated by ArcA and FNR. they bind mRNA of around 30 aerobic genes and prevent their expression in aerobic conditions
