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Physiology of Microbes > Stationary phase - stress response L8 > Flashcards

Stationary phase - stress response L8 Flashcards

1
Q

how do bacteria effect protein production

A

Bacteria activate and induce systems to make new proteins to carry out new functions switch off systems don’t need to adapt to environment

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2
Q

how are bacteria grown in a batch culture

A

Cells are inoculated into a sterile broth, incubated under permissive growth conditions

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3
Q

when does cell mass increase in batch culture growth

A

Cell mass increases rapidly as cells enter exponential phase of growth, then reach stationary phase

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4
Q

when does cell mass stop increasing

A

until conditions inside flask limited

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5
Q

why is it important for single cells to monitor nutrients

A

needs to be able to monitor level of nutrients and respond that will run out - no point continually running processes if these processes can’t run to completion, need to start to ‘turn things down’

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6
Q

when do toxic products start to accumulate in batch growth, effect

A

Will get a change in environment, pH tends to drop, oxygen lowers, toxic by-products will start to accumulate– protect against harsh conditions
Cell growth stops, and cells go into a dormant state

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7
Q

what is the stringent response

A

Fast cell growth requires high levels of protein synthesis, so cell needs lots of ribosomes
Under starvation conditions, when amino acids levels are limited, cell reduces number of ribosomes - would use a lot of energy to make all proteins that wouldn’t be used

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8
Q

how is regulation achieved

A

Regulation achieved by stringent factor acts with GTP in synthesis of ppGpp

stringent factor (RelA protein)

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9
Q

how can ppGpp be synthesised

A

Carbon limitation can also cause synthesis of (p)ppGpp

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10
Q

what does ppGpp do

A

down regulates the rRNA synthesis of genes = fewer ribosomes being assembled
- ppGpp down regulated tRNA synthesis
Everything in the cell is being down regulated

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11
Q

ppGpp and protein production

A

signal to RNA polymerase to stop making proteins, needs to switch off transcription – need to turn things down till have nutrients available again

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12
Q

what is ppGpp

A

an alarmone

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13
Q

how is ppGpp an alarmone

A

involved in the stringent response in bacteria, causing the inhibition of RNA synthesis when there is a shortage of amino acids present

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14
Q

what causes increased ppGpp

A

nutritional stress

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15
Q

how does transcription reprogramming occur

A

ppGpp will bind to the RNAP sites, causes “reprogramming” of transcription

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16
Q

what transcription changes occur during reprogramming in E.coli

A

results in changes in ~700 genes now changed in their gene pattern of regulation
- Most of them are down regulated – rRNA (to make ribosomes, fatty acids for membrane synthesis), some specific stress genes are up-regulated

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17
Q

how do bacterial cells in stationary phase differ to those in growing cells

A
  • shorter and rounder (if rod shaped) (spheres would be smaller)
  • altered metabolism (recycle molecules from other things)
  • change in membrane and cell wall structure as defines shape
  • increase resistance to number of different stresses e.g. starvation, osmotic shock – cell prepared self for ‘survival mode’
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18
Q

what are sigma factors like

A

interchangeable, control which sets of genes are expressed (differential expression)

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19
Q

what is core polymerase

A

enzyme that makes RNA in cell carries out transcription, when it binds to a promoter – core polymerase is directed where to start transcription by the sigma factor

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20
Q

where will the sigma factor bind to

A

-10 -35 motif

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21
Q

what are the motifs in bacteria

A

motifs differ in different sigma factors

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22
Q

what must a bacteria have to be expressed all the time

A

sigma 70 motif, can switch on others when they’re needed

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23
Q

how may names does each sigma factor have

A

two as discovered in two ways

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24
Q

what is the primary site of control of prokaryotes

A

transcription

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25
Q

how are prokaryotic genes arranged

A

operons

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26
Q

what is monocistronic

A

1 protein

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27
Q

what us polycistronic

A

more than one protein

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28
Q

what drives the expression of genes

A

promoters

29
Q

are bacteria monocistronic or polycistronic

A

Bacteria have option to go from monocistronic to polycistronic and translated into separate proteins

30
Q

how can genes and operons that are spatially separate on chromosome be controlled

A

by same regulatory mechanism (regulon)

e.g. stress response controlled by RpoS

31
Q

what does RpoS control

A

novel gene expression at onset of stationary phase

32
Q

how many genes are identified that can change pattern of expression

A

> 100 genes identified that change their pattern of expression – form a ‘regulon’ of genes

33
Q

what are many genes needed for

A

stress survival

34
Q

in regulon are genes down or up regualted

A

Some down regulated and others are up regulated – don’t have to go the same way in regulon

35
Q

what molecules are needed for RpoS control of cell shape

A

bolA
dacC
ftsQAZ

36
Q

what does bolA do

A
  • morphogene controlling pattern of peptidoglycan synthesis and determines cell shape
  • over expression causes rounder cells
37
Q

what does dacC do

A
  • transpeptidase in peptidoglycan synthesis
  • crosslinking in peptidoglycan thickens cell wall - stronger
  • over expression causes increased cell wall strength
38
Q

what is dacC

A

penicillin-binding protein 6

39
Q

what does ftsQAZ do

A
  • cell division genes up-regulated
  • increased cell division
  • over expression causes cells to be rounder and shorter as not grown much before divided
40
Q

what molecules does RpoS need for metabolism control

A 
otsAB
arcAB
glg genes
pex
appA
41
Q

what does otsAB do

A
  • synthesis of trehalose (compatible solute) in cytoplasm

- protects cell against thermal and osmotic stress (dehydration) hold proteins in complex, more stabilised

42
Q

what does arcAB do

A
  • adaptation to anaerobiosis
43
Q

what does glg genes do

A
  • synthesis of glycogen (storage granules)
44
Q

what does pex do

A
  • carbon starvation proteins (utilisation of alternative C sources)
45
Q

what does appA do

A
  • uptake of organophosphates (phosphate starvation)
46
Q

what molecules are needed in RpoS resistance control

A

katG
katE
dps

47
Q

what is katG and katE

A

catalase genes

48
Q

what are katG and katE like

A

resistant to oxidising agents

49
Q

what is dps

A

(upregulated) structures the nucleoid

> small DNA binding histone-like protein

50
Q

what does dps do

A

compacts DNA in nucleoid (if not growing, dividing can be compact)
protects DNA from damage

51
Q

when is RpoS induced

A

ANY condition that interrupts cell growth will induce RpoS expression (often at the end of stationary phase)

52
Q

when is RpoS switched off

A

Responding to environment they switch RpoS off again

53
Q

how is it tested if RpoS is needed

A

Transient thing that the cell tests out if RpoS needed - very responsive to environment

e. g. nutrient or physical changes during exponential growth result can also in induction of RpoS regulation
- starvation
- acid shock
- oxidative stress

54
Q

how much RpoS is present when in exponential growth phase

A

RpoS protein barely detectable in exponential phase growth when cells are growing fast and nutrients aren’t limited

55
Q

what are the first two genes in the 2 gene operon

A

first - nlpD (lipoprotein of unknown function)

second - RpoS

56
Q

how many promoters does RpoS have, name

A

Pr1

Pr2

57
Q

what occurs in RpoS operon

A

Always make basal levels of gene expression occur from Pr2
> sigma 70 - dependent expression and NOT growth-phase regulated
Pr1 expression growth-phase induced
> sigma 70 - dependent expression
When things are bad, second promoter- Pr1 (in response to stress)

58
Q

if nplD not present what happens

A

cannot get RpoS

59
Q

how is RpoS gene regulation balanced

A

Lots of different cellular signals act as positive and negative signals to create balanced gene control
- cells don’t want to induce stress response unless condition are becoming extreme

60
Q

what is up regulated in RpoS

A

ppGpp(p), pheromones

61
Q

what is down regulated in RpoS

A

H-NS, cAMP, UDP-glucose

62
Q

what is the effect of RpoS induction

A

regulon induction by any one stress will lead to cross-protection against other stresses
- i.e. stationary phase cells are more resistant to challenge

63
Q

what is an examples of cells inducing genes for survival aid

A

Biofilm formation regulated by rpoS

64
Q

effect of pathogenic bacteria on rpos induction

A

Pathogenic bacteria become primed for infection of hosts

- induction of many virulence genes

65
Q

what are the features of stressed cells that are like spores

A
  • condensed DNA
  • small rounded cell shape
  • synthesis of protective molecules
  • gene expression controlled by alternative sigma factors
66
Q

what is the stress response like in other bacteria - eubacteria

A

RpoS equivalent found in all eubacteria

- Mechanism of control is NOT always the same

67
Q

what is the stress response in gram-positive

A

Equivalent system identified in Gram-positive bacteria = SigB
- Mechanism of control is very different, involving multiple anti-sigma factors

68
Q

what is ppGpp

A

guanosine 5’-diphosphate, 3’-diphosphate

Physiology of Microbes (21 decks)

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