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Phys Pro Section 3 > Adaptive and environmental challenges > Flashcards

Adaptive and environmental challenges Flashcards

1
Q

What are the 3 components of a 2C regulatory system?

A

Histadine kinase, response regulator, and a regulating phosphatase

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2
Q

Where are the HK and RR phosphorylated?

A

hk: autophosphorylates at a histadine

RR: phosphorylated by HK as an aspartate residue

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3
Q

What domain of the HK senses the signal? what part transmits the signal to the RR?

A

the N terminal part senses the signal and the conserved C-terminal domain transmits the signal

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4
Q

What is the composition of the conserved C terminal domain?

A

conserved sequence of ~200 aa that contains the autophosphorylation (histadine) site

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5
Q

Most HKs are transmembrane, what is one exception that is cytoplasmic?

A

CheA in the chemotaxis system

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6
Q

What is the structure of RR like?

A

Cytoplasmic proteins

Have a conserved N-terminal domain of about 100 aa, which interacts with the C-terminus of HK.
- aspartate residue in this domain is what gets phosphorylated

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7
Q

What can RR-P do?

A

either activate or repress transcription of target genes directly or indirectly.

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8
Q

What is the C- terminus of the RR regulator thought to do?

A

Interact with target

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9
Q

What is catabolite repression?

A

the preferential use of one carbon source for growth over another when both carbon sources are present

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10
Q

What 3 systems mediate catabolite repression? Which are cAMP dependent/independent?

A
  1. PTS (cAMP dependent)
  2. Cra (cAMP independent)
  3. CcpA (cAMP independent)
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11
Q

What does the Cra system stand for?

A

catabolite repressor/activator system

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12
Q

What is Cra?

A

A transcriptional regulator

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13
Q

What does Cra do?

A

represses genes coding for enzymes of the glycolytic pathway and induces genes encoding enzymes required for growth on organic acids and amino acids

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14
Q

What does the pykF gene code for? when is the product used?

A

Pyruvate kinase F which converts PEP to pyruvate during glycolysis

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15
Q

What does pckA code for? when is the product used?

A

PEP carboxykinase which converts oxaloacetate to PEP during gluconeogenesis

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16
Q

Under glucose rich conditions, what happens to Cra?

A

in the presence of a PTS sugar, the Cra complexes with the catabolite.

It can’t repress pykF (pyruvate kinase) or enhance pckA (PEP carboxykinase A)

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17
Q

Under glucose limiting conditions, what does Cra do?

A

Binds upstream of both the pykF and pckA genes

  • inhibits transcription of pykF –> prevents pyruvate kinase F being made for glycolysis
  • enhances transcription of pckA –> more PEP carboxykinase A made for gluconeogenesis
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18
Q

What kind of bacteria posses a CcpA system?

A

low %G+C Gram-positive bacteria

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19
Q

What does CcpA stand for?

A

Catabolite control protein A

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20
Q

What is CcpA?

A

transcriptional inhibitor of genes that are catabolite repressed by glucose

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21
Q

What is another role of CcpA in Streptoccoci?

A

plays a role in controlling virulence of pathogenic streptococci
- acts as a transcriptional activator in this case

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22
Q

Explain how glucose can confer catabolite repression via CcpA

A
  1. When glucose is present, it is metabolized. One of the intermediates F-1,6-BP activates an ATP dependent Hpr kinase
  2. Hpr is phosphorylated
  3. Hpr-P binds to CcpA and F-1,6-BP to form a ternary complex
  4. Ternary complex then binds to CRE: Catabolite-responsive element, a conserved DNA sequence
  5. prevents gene expression of catabolite repressible genes
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23
Q

What are the two kinda of nitrogen sources bacteria can use?

A

inorganic (NH4+, NO3-, N2) and organic (amino acids, urea, peptides)

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24
Q

What are all nitrogen sources ultimately converted to?

A

Ammonia

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25
Q

What is ammonia then assimilated into?

A

Glutamate or glutamine

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26
Q

What does Glutamate dehydrogenase catalyze?

A

assimilation of ammonia into glutamate

- used NADPH and alpha ketoglutarate as the starting materials

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27
Q

Explain the Glutamine synthetase/GOGAT system. What does each enzyme do?

A
  1. Glutamine synthetase converts glutamate to glutamine by adding an NH2 group from ammonia
  2. That glutamine is then converted back glutamate as the amino group is transferred to alpha ketoglutarate
  3. End result is 2 molecules of glutamate
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28
Q

What does GOGAT stand for?

A

glutamine oxoglutarate aminotransferase

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29
Q

When does glutamine synthetase become more active?

A

Under nitrogen limiting conditions

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30
Q

What regulon contains the genes regulated by ammonia supply?

A

Ntr regulon

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31
Q

Which operon in the Ntr regulon encodes glutamine synthetase, NRII (histidine kinase), and NRI (response regulator).

A

glnALG

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32
Q

How many promoters are there in the glnALG operon? What are they called?

A

3.

Ap1, Ap2, and Lp

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33
Q

What sigma factors bind to each promoter in the glnALG operon? which are high affinity and which are lower

A

sigma 70 ( low affinity housekeeping sigma) binds to Ap1 and Lp

Sigma 54 is the high affinity factor and binds to Ap2

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34
Q

Describe what happens under ammonia limiting conditions in terms of NRI and NRII

A

When ammonia is limiting, NRII acts as a kinase
- stimulated by PII-UMP?

it phosphorylates NRI (RR)

NRI-P levels increase which stimulates higher transcription rate of Ap2 (with help from sigma 54)

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35
Q

Describe what happens under excess ammonia conditions in terms of NRI and NRII

A

When ammonia is in excess, NRII acts as a phosphatase
-stimulated by PII

NRII dephosphorylates NRI-P and transcription rates from Ap2 decrease

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36
Q

What is the product of transcription from the Ap2 promoter

A

glutamine synthetase

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37
Q

What increases the levels of PII vs PII-UMP?

A

as glutamine levels increase in the cell, PII levels increase

as levels of alpha ketoglutarate incease in the cell, PII-UMP levels increase

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38
Q

What enzyme controls the switch between PII vs PII-UMP?

A

uridylyl transferase/uridydyl removal (UT/UR)

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39
Q

When is inhibition of the Ntr regulon relieved?

A

when ammonia conc falls below 1 mM.

40
Q

What factor is required for activation of some NRI dependent promoters in the Ntr regulon?

A

Integration host factor (IHF)

- Job is to bind the DNA together and bring the promoter close

41
Q

What example was given in class for the action of IHF?

A

NifA : positive regulator of the nif (nitrogen-fixation) genes

IHF binds a region of DNA between NiFA binding site and promoter. The binding bends the DNA allowing NiFA to interact with RNA polymerase

42
Q

What is the effect of the PII/PII-UMP ratio on the enzyme activity of glutamine synthetase? what other enzyme is involved in this?

A

Under limiting-ammonia conditions, PII-UMP stimulates the adenylyl removal activity of the enzyme adenylyl removal/adenylyl transferase (AR/AT), resulting in GS in the active form.

Under excess ammonia conditions, PII activates the adenylyl transferase activity of AR/AT, resulting the GS as inactive GS-AMP.

43
Q

How is Pi transported into the cell under excess conditions? What is the transporter and what is it driven by?

A

it is transported by a low-affinity transporter called Pit. Pit consists of a single transmembrane protein and the transport is driven by the ∆P

44
Q

What happens when Pi becomes limiting?

A

least 38 genes involved in Pi assimilation are transcribed (in E. coli).

45
Q

What is formed by the transcription of the Pi limiting genes?

A

the PHO regulon

46
Q

What is PhoA

A

alkaline phosphatase

47
Q

What is PhoBR?

A

2 component system

PhoR is the histadine kinase
PhoB is the response regulator

48
Q

What is PhoE?

A

outer membrane protein

49
Q

What is Pst

A

high affinity Pi uptake system

50
Q

How is Pi transported in a saturated state?

A

By an osmotic shock sensitive transport system

  • uses an ABC transporter
  • sensing by PhoR
51
Q

How does signalling occur when Pi is limiting?

A

PhoR autophosphorylates and dimerizes

This causes PhoB to dimerize

PhoB dimer can then translocate to the nucleus and activate the PHO regulon

52
Q

What are the 4 key changes that occur when a facultative anaerobe goes from aerobic to anaerobic conditions?

A
  1. final electron acceptor is not O2 but others (e.g. nitrate, fumarate or DMSO).
  2. replacement of fumarase A and succinate dehydrogenase (SDH) by fumarase B and fumarate reductase (FRD).
  3. repression of alpa-ketoglutarate dehydrogenase (ODHG) synthesis.
  4. acetyl-CoA is made by pyruvate-formate lyase (PFL) instead of pyruvate dehydrogenase (PDHG).
53
Q

What happens to the TCA cycle under anaerobic conditions? Why?

A

becomes non-cyclic and reductive

- b/c alpha ketoglutarate dehydrogenase is absent

54
Q

What are the 4 systems (briefly) in E-coli that bring about the aerobic–>anaerobic switches

A
  1. Arc system
  2. FNR system
  3. Nar system
  4. FhlA system/formate regulon
55
Q

What are the 2 components of the Arc system? what are their roles?

A

ArcB is the sensor, ArcA is the response regulator

56
Q

What is different about ArcB

A

an “unorthodox” HK

- has 3 histadine residues that are used to pass the phosphate through

57
Q

What kinds/how many genes does the Arc system regulate

A

up to 30

Mainly repression of: 
Cytochrome o and d oxidases
TCA cycle enzymes
Glyoxylate cycle enzymes
Several dehydrogenases for aerobic growth (e.g. pyruvate dehydrogenase)
Fatty acid oxidation enzymes
58
Q

What is the end result of the Arc system?

A

Induction of pyruvate formate lyase (PFL)

59
Q

What does the Fnr system stand for?

A

Fumarate, nitrate, reductase regulation

60
Q

how many genes does the Fnr system contol?

A

over 100

61
Q

What does Fnr repress?

A

cytochrome o, cytochrome d, and nar operon

62
Q

What does Fnr activate?

A

formate dehydrogenase, fumarate reductase, DMSO reductase, and nitrate reductase

63
Q

How does FNR sense O2 or no O2?

A

via an oxygen-sensitive (4Fe-4S) center

64
Q

What happens to FNR is there is oxygen?

A

The 4Fe-4S centre becomes oxidized and disassembles into 2x 2Fe-S centres
- without the dimer, FNR can no loner bind to to DNA and therefore no activation or repression occurs

65
Q

What happens to FNR if there is no oxygen?

A

The 4Fe-4S centre remains reduced and the dimer binds to the DNA to control anaerobic gene expression

66
Q

What is the acid tolerance response? why does it occur?

A

exposure of bacteria to non-lethal acidic pH results in the induction of sets of genes whose products can protect the cell when exposed to lethal pH conditions

67
Q

what kind of proteins are produced by the ATR? what response do they have some crossover with?

A

Acid shock proteins, some of which are also heat shock induced

68
Q

What are the 3 mechanisms of the ATR (briefly)

A
  1. Production of glutamate decarboxylase + specific antiporter
  2. Production of arginine deaminase
  3. Production of urease
69
Q

How does glutamate decarboxylase/antiporter help with the ATR? How does it work?

A

It is unclear how it helps.

specific antiporter exports g-amino butyric acid (the decarboxylation product of glutamate) and imports more glutamate

70
Q

How does arginine deaminase help with the ATR?

A
  1. converts arginine to ammonia and citrulline.
  2. Citrulline is further converted to ammonia and CO2.
  3. The ammonia generated can alkalinize the environment
71
Q

How does urease help with the ATR?

A

converts urea to ammonia and CO2

- ammonia alkalizes

72
Q

What increases the rate of heat shock protein synthesis?

A

increase stability and translation of sigma factor 32 (also called RpoH)

73
Q

How does increased temperature affect stability and translation of sigma 32?

A
  1. melts secondary structures in the 5’ region of rpoH mRNA resulting in increased translation
  2. at lower temps, sigma 32 is bound by a bunch of chaperones and easily degraded by proteases. When temperatures increase, the chaperones leave sigma 2 to help other proteins fold and leave it free
74
Q

What causes envelope stress?

A

accumulation of misfolded proteins in the periplasm
- result of altered pH, osmolarity, increases in temperature, over-production of recombinant proteins, or even carbon/energy starvation

75
Q

What are the two response pathways to deal with envelope stress?

A
  1. extracytoplasmic function (ECF) sigma factor

2. CpxRA two-component regulatory system

76
Q

What are the two proteins involved in the ECF system?

A

RseA and RseB

77
Q

How does the ECF system work when there is no envelope stress ?

A
  1. RseA is bound by RseB from the periplasm.
  2. The C-terminus of RseA binds sigma factor E and sequesters it from RNA pol.
  3. Thus, RseA is acting as an anti-sigma factor
78
Q

How does the ECF system work when envelope stress occurs?

A
  1. RseB leaves RseA to bind to misfolded proteins in the periplasm
  2. RseA is now vulnerable to degradation by proteases
  3. sigma factor E is then released from RseA and can bind with RNA polymerase
79
Q

How does the CpxRA system work? what does it activate that links it to the ECF system?

A
  1. CpxA is the sensor, autophosphorylates when it senses envelope stress
  2. transfers P to CpxR
  3. CprR-P activates expression of dsbA (disulfide oxidoreductase) and ppi (peptidyl-prolyl-isomerase) - enzymes needed to refold misfolded proteins
  4. also activates periplasmic protease DegP which requires sigma E
    - links it to ECF
80
Q

What are 3 oxygen reduction products that cause oxidative stress?

A

Superoxide radical (O2-), hydrogen peroxide (H2O2), and hydroxyl radical (OH-)

81
Q

What does superoxide dismutase do?

A

superoxide radical to O2 and H2O2

82
Q

What does catalase do?

A

H2O2 to O2 and H2O

83
Q

What do organic reductants (like glutathione and ascorbic acid), and peroxidases do?

A

H2O2 to H2O

84
Q

superoxide dismutase, catalase, and organic reductants/peroxidases are used by..?

A

aerobic bacteria

85
Q

What 2 methods do anaerobic bacteria use to protect themselves from oxygen radicals

A

NADH oxidase and superoxide reductase system

86
Q

What does NADH oxidase do?

A

the direct reduction of O2 to H2O

87
Q

What does the superoxide reductase system accomplish?

A

converting superoxide to H2O2 then to H2O

88
Q

What are the two oxidative stress regulons in E. coli?

A

OxyR and SoxRS

89
Q

How many proteins are produced by the OxyR regulon? what induces it?

A

9 proteins, induced by H2O2

90
Q

is OxyR a positive or negative regulator

A

Positive

91
Q

How does OxyR exert its effect (what does it bind to? )

A

binds to target DNA and interacts with the C-terminal domain of RNA polymerase to activate gene expression

92
Q

What activates OxyR?

A

oxidation, which results in the formation of a disulfide bond between two cysteine residues in OxyR
- only this form can bind DNA

93
Q

How many proteins are comprised in the SoxRS regulon and what is it induced by?

A

9 proteins induced by superoxide (O2-)

94
Q

how does the SoxRS system work?

A
  1. SoxR senses oxidative stress from O2-
  2. and triggers expression of soxS
  3. SoxS then activates the expression of genes in the regulon
95
Q

How does SoxR sense oxidative stress?

A

uses two (2Fe-2S) centers to sense oxidative stress. Under normal physiological conditions, the Fe-S centers remain reduced and become oxidized when superoxide is present

The oxidized active conformation is what allows it to interact with RNA polymerase

Phys Pro Section 3 (5 decks)

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