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Microbiology > Microbe Regulation > Flashcards

Microbe Regulation Flashcards

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Biology 101 flashcards
1
Q

Vibrio Cholera conditions in water and Humans

A

In the water, there is low temperatures, low nutrients, low osmotic strength, pH near neutral, O2 available for repiratory metabolism, free iron available, adhesins needed to bind to rocks. In humans, temperatures are high, there is high osmotic strength, high nutrients, low pH, and high pH, low/no O2 meaning fermentative metabolism is needed, Iron bound to haem, adhesins stick to cells.

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2
Q

Stimulon

A

group of operons that are all transcribed in response to a particular environmental signal, but might be transcribed by different sigma factors.

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3
Q

Antibiotic that selectively binds to the bacteria RNA polymerase and inhibits Transcription initiation

A

Rifamycin B
Blocks exit path for elongating mRNA.

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4
Q

Antibiotic that binds to DNA, inhibiting transcription elongation.

A

Actinomycin D
Intercalates between C and G base pairs, blocking protein synthesis.

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5
Q

Sigma factors

A

Recognise the promoter region (-35 to –10) upstream of the start site, allowing RNA polymerase to bind to the promoter by the start site.

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6
Q

Operon

A

There are multiple open reading frames within the one mRNA, coding for different proteins. Each one has a ribosome binding site (RBS) to allow for translation.

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7
Q

Sigma factor for house keeping genes

A

Sigma-A

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8
Q

Sigma factor for internal (cytoplasmic) stresses

A

Sigma-B

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9
Q

Sigma factor for extracytoplasmic stresses

A

Sigma-24

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10
Q

Sigma factor for stationary phase stress

A

Sigma-S

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11
Q

Sigma factor for nitrogen regulation

A

Sigma-54

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12
Q

Sigma factor for iron transport

A

Sigma-19

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13
Q

Sigma factor for flagella synthesis

A

Sigma-29

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14
Q

Oxidative stress

A

Sigma-R is used for responding to Oxidative stress. Sig-R is bound by the anti-sigma factor, RsrA. RsrA keeps sigR inactive with a zinc molecule that is kept into place via 3 cysteines. During oxidative stress, the cysteines form a disulfide bond, causing the Zinc to be released. This causes a conformational change in RsrA, which releases SigR to go interact with RNA polymerase for oxidative stress genes. Once oxidative stress is alleviated, the disulfide bonds are broken and RsrA returns to a conformation where it can bind SigR.

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15
Q

Heat response sigma factor

A

Sigma-H

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16
Q

Heat stress

A

Sigma-H is encoded in the rpoH coding region. The mRNA has a hairpin structure formed, which hides the ribosome binding site, blocking the translation of the sigH gene. If any of the Sigma-H is translated, chaperones guide the degradation of those proteins. During heat stress, the hairpin structure becomes unstable, opening up, allowing for the mRNA to be translated. The produced Sigma-H overwhelms the degradation chaperones which are not able to degrade all the sigH. SigH can then bind RNA pol and form a holoenzyme for transcribing heat stress response genes.

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17
Q

Sporolation sigma Factor

A

Sigma-F

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18
Q

Bacillus subtilis, spacial separation during spore formation

A

In normal Bacillus subtilus cells, sigF, anti-SigF and anti-anti-sigF are all produced. Anti-SigF binds sigF, repressing its function. Anti-anti-sigF binds and removes anti-sigF and sends it to be degraded.
During spore formation, a pore is formed between the mother cell and the forespore. This pumps a chromosome through, with the origin first. The anti-sigF genes are by the terminus, which is pumped into the forespore last. The proteins from the mother cell are also inherited into the forespore. When the inherited anti-sigF is sent for degradation, the gene is not present for the protein to be translated and replenished. This allows for Sigma-F to bind RNA polymerase and promote sporulation.

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19
Q

Response regulator Dna binding domain

A

winged helix-turn-helix (ompR/PhoB), helix-turn-helix (NarL).

20
Q

Response regulator Enzymatic domain

A

Methylesterase (CheB), Diguanylate cyclase (GGDEF), Protein phosphatase (PP2C).

21
Q

Response regulator stand alone domain

A

Phosphotransferase components (SpoOF), chemotaxis motility control (CheY)

22
Q

Sensor kinase

A

In its active form it forms a dimer. It is modularm meaning the domains can be changed for different functions. The overall structure is conserved, with a variable sensing domain, a transmembrane helicase, a linker domain (variable), a catalytic domain and a DHp domain.

23
Q

MicF RNA

A

non-coding RNA that is complementary to OmpF mRNA, blocking translation

24
Q

sRNA regulation of rpoS mRNA

A

Oxys is a negative regulator, blocking translation by pairing with the RBS.

DsrA is a positive regulator. It promotes translation by pairing with 1 strand of the stem loop. This frees the RBS which was also part of the stem loop, allowing for translation.

25
Q

Nucleotide-based second messengers

A

Relay signal from changes in the environment or intracellular conditions into appropriate cellular responses in all domains of life.

26
Q

cAMP

A

cAMP is a secondary messenger. It is produced in response to extracellular or intracellular conditions. cAMP is produced by adenelyl cyclase and destroyed by phosphodiesterase. Different levels activity from these two dictates the level of cAMP. cAMP allosterically binds CRP. cAMP-CRP bind CRP binding sites in promoters to promote expression of cAMP responsive genes.

27
Q

cAMP produced for alternative carbon source

A

When there is glucose, cAMP is low. When there isnt the preffered carbon source, the cAMP levels rise and promote expression of genes for metabolising alternative carbon sources. In E. coli the glucose is imported via a phosphotransferase system (PTS), which dephosphorylate IIA. When there is no glucose, IIA remains phosphorylated and activates Adenelyl cyclase.

28
Q

Lac Operon and cAMP

A

The lac operon contains genes to promote the use of lactose as an alternative carbon source. This lac operon is repressed by LacI. Allolactose binds LacI, causing it to leave the Lac operon. Then the cAMP-CRP complex can bind the CRP binding site -60 bp upstream of the operon. The CRP interacts with an alpha subunit CTD of RNA polymerase to promote expression.

29
Q

cAMP in virulence

A

Pseudomonas aeruginosa uses cAMP to promote virulence gene expression.

30
Q

ppGpp

A

ppGpp is produced in response to nutrient stress. It is formed from ATP and GTP by SpoT and RelA. SpoT is also able to hydrolise ppGpp incase ppGpp levels get too high. ppGpp regulates RNA polymerase directly and indirectly

31
Q

ppGpp nutrient stress detection

A

SpoT senses a variety of nutrient stress signals.
RelA responds specifically to amino acid starvation by directly monitoring ribosomes. If tRNA lacking AA (uncharged) binds to the ribosome A site, RelA responds to produce ppGpp.

32
Q

ppGpp signalling

A

ppGpp accumulates and binds RNAP to alter expression.
During Amino acid starvation it reduces rRNA expression and tRNA (less AAs used) and promotes AA biosynthesis genes.
ppGpp binds to the beta subunit of RNAP in cooperation with DksA. This reduces the ability of RNA pol to recognise sigma70 promoters, including those for rRNA genes.
ppGpp promotes the use of alternative stress responsive sigma factors.

33
Q

c-di-GMP

A

Synthesised by diguanylate cyclases (DGCs) and broken down by PDEs. Promotes the switch between being virulent and mobile, to sessile/biofilm and growth. c-di-GMP binds to the Pil2 allosteric site on effectors. Binding can affect enzyme activity, expression, proteolysis, flagella.

34
Q

c-di-GMP flagella

A

c-di-GMP binds the YcgR protein, which binds and inhibits the flagella.

35
Q

c-di-GMP biofilm

A

c-di-GMP binds and activates the synthesis of biofilm producing enzymes. It binds and activates cellulose synthase. It activates the pga complex, which produces the biofilm polysaccharide, PGA.

36
Q

c-di-GMP biofilm dispersal.

A

In a biofilm, when phosphate starts getting low, c-di-GMP decreases, causing biofilm dispersal. Decreased c-di-GMP releases LapG and LapD, which cleave the adhesin, LapA.

37
Q

Quorum Sensing

A

This involves bacteria cell to cell communication. They secrete auto inducers that accumulate in areas of high population density. At high enough density a threshold is reached, causing a response throughout the population. Many processes regulated by QS are costly on their own, but as a group they are very effective.

38
Q

QS signalling

A

They can bind to extracellular kinase receptors that signal to a response regulator. They can also enter cells and act as TFs.

39
Q

Auto-inducers

A

In gram (-) bacteria there are AHLs and other small signalling molecules such as AI-2.
In gram (+) bacteria there are AIP (autoinducer peptides) and AI-2.

40
Q

AHL

A

They are synthesised by LuxI family proteins. They are detected by the LuxR transcription regulators that have a CTD AHL binding domain and an N terminal DNA binding domain. At a high concentration, AHL binds LuxR which upregulates LuxI to amplify the signal and other target genes.

41
Q

Auto-inducer peptide (AIP)

A

Precursor peptide is processed during or after secretion. AIPs are detected by extracellular histone receptor kinases or imported and bound to TFs. They regulate virulence factor expression, copetence, conjugation and sporulation.

42
Q

Agr QS system

A

This regulates the expression of virulence genes in Staphylococcus aureus. AgrB secretes and processes AgrD prepeptide to form cyclic AIP. AIP is detected by AgrC which phosphorylateds AgrA which is a TF for RNAIII. RNAIII is expressed and promotes expression of secreted toxins and immune modulators, while suppressing surface adhesins and biofilm formation.

43
Q

PapR/PlcR system of Bacillus cereus

A

AIP is imported by the Opp transporter. AIP binds PlcR and regulates 40+ genes.

44
Q

Autoinducer 2 (AI-2)

A

Set of interconverting molecules derived from DPD. It is a product of LuxS. LuxS is a metabollic enzyme, with DPD being a side product. This AI-2 signalling is widespread in bacteria, possibly allowing for cross-species interactions.

45
Q

AI-2 in Vibrio species

A

3 parallel QS systems converge. HA-1 is species specific. CAI-1 is Vibrio specific. AI-2 is widely produced. The signal is received by histidine kinases. At low cell density, LuxU is phosphorylated and uses sRNA to activate AphA which activates virulence and biofilm formation. At high density LuxU is unphosphorylated. LuxR is no longer inhibited and can promote luminescence and inhibit biofilm formation.

Microbiology (8 decks)

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