oxygen regulation

Question 1

which two systems does E. coli use to sense oxygen

Answer 1

two component ArcAB and one component FNR

Question 2

how do bacteria sense oxygen

Answer 2

directly eg binding to haem group or indirectly eg different electron transport products (Q/QH2) or binding of metals (Fe)

Question 3

when is quinone abundant

Answer 3

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

Question 4

how does the electron transfer chain work at low oxygen

Answer 4

the terminal cytochrome c is replaced by cytochrome d which has a higher oxygen affinity

Question 5

how does the TCA cycle affect oxygen sensing

Answer 5

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

Question 6

which sensor systems detect low and no O2 in E.coli

Answer 6

ArcAB senses low oxygen in the upper gut whereas FNR senses low/ no oxygen in the lower gut

Question 7

how is ArcAB phosphorylated

Answer 7

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

Question 8

how does quinone inhibit ArcAB

Answer 8

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

Question 9

how is ArcA phosphorylated

Answer 9

it collides with ArcB and is phosphorylated then dimerises head to head. only one monomer needs to be phosphorylated

Question 10

how does ArcAB repress genes

Answer 10

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

Question 11

how does ArcAB induce genes

Answer 11

it recruits RNAP to the promoter site. it induces genes needed anaerobically eg for fermentation or cytochrome d (only when there is some O2!)

Question 12

what types of system to sino/bradyrhizobium and rhodobacter use

Answer 12

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

Question 13

what genes does FixLJ regulate

Answer 13

genes for nitrogenase which is needed in anaerobic conditions and is inhibited by O2

Question 14

how does FixL detect oxygen

Answer 14

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

Question 15

how does FixJ regulate transcription

Answer 15

it is phosphorylated by FixL then dimerises and binds to nitrogenase promoter to recruit RNAP and activate transcription

Question 16

what are the two methods by which rhodobacter can produce ATP energy

Answer 16

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

Question 17

how does RegB sense oxygen

Answer 17

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

Question 18

what is the second regulator level of RegB

Answer 18

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

Question 19

which genes does RegAB regulate

Answer 19

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

Question 20

what is FNR

Answer 20

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

Question 21

how is FNR activated

Answer 21

in anaerobic conditions 4x Fe bind each monomer at Cys residues in the N terminus regions. this allows dimerisation

Question 22

how does FNR cause activation

Answer 22

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

Question 23

how does FNR cause repression

Answer 23

if it binds at -50.5 and -94.5 FNR blocks RNAP and prevents transcription of aerobic genes because the sequences overlap

Question 24

what happens in terms of activation and repression at low O2, not none

Answer 24

FNR may bind only one repression region. there is a small amount of transcription of aerobic genes

Question 25

what are fnrS

Answer 25

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