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MOLBIO OFFSEM MIDTERM > MAJOR SHIFTS IN BACTERIAL TRANSCRIPTION > Flashcards

MAJOR SHIFTS IN BACTERIAL TRANSCRIPTION Flashcards

1
Q

(SIGMA FACTOR SWITCHING)

___________ of bacterium - subverts the host’s into transcription machinery

A

Phage infection

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2
Q

(SIGMA FACTOR SWITCHING)

In process, it establishes a time-independent or temporal or program of transcription:
- First early phage genes are _______
- followed by the later _____
- Reaches the late in the infectious cycle - there’s no longer transcription of the host genes, only phage genes

Changes in the genes that are transcribed - is caused by a change in transcription machinery; in RNA polymerase itself

A

Transcribed ; genes

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3
Q

(PHAGE INFECTION)

  • Ɐ σ - ( For all & sigma) is the key factor in determining specificity of T4 DNA
    transcription
  • σ - is a candidate for the shift of the transcription process
  • Study of the process done in B. subtilis and its phage, SPO1
  • Like T4 – SPO1 has a large genome
  • ______ – has a temporal program of transcription
A

SPO1

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4
Q

(TEMPORAL CONTROL OF TRANSCRIPTION
IN SPO1)

Temporal transcription program:
o First 5 mins:
▪ Expression of _____
o After 5 – 10mins:
▪ Expression of ______
o After 10mins to end:
▪ ______ expressed

A

early genes ; middle genes ; Late genes

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5
Q

(TRANSCRIPTION SWITCHING)

___________ – is directed by a set of phages – encoded σ-factors that associate with
the host core RNA polymerase

A

Switching

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6
Q

(TRANSCRIPTION SWITCHING)

________ – change the host polymerase specificity of promoter recognition from
early to middle to late

o ________ – is specific for the phage early genes
o _________ – switches the specificity to the middle genes
o _____________ – switch the specificity to late genes

A

σ-factors ; Host σ-factors ; Phage gp28 protein ; Phage gp33 and gp34 proteins

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7
Q

(SPORULATION)

During infection, ______ – changes specificity of host RNA polymerase

Same type of mechanism applies to changes in gene expression during ________

A

phage SPO1 ; sporulation

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8
Q

(SPORULATION)

_______ – can exist indefinitely in vegetative state if nutrients are available

A

Bacteria

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9
Q

(SPORULATION)

Under starvation conditions, B. subtilis forms endospores

______________ - tough, dormant bodies that can survive for years until favourable conditions return

A

Endospores

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10
Q

(TRANSCRIPTION SWITCHING)

During sporulation:
o Whole new set of genes - is turned ____
o Many vegetative genes - are turned ____
o _____ – occurs largely at the level of transcription
o ________ - displace the vegetative σ-factors from the polymerase core and direct the transcription of sporulation genes
o _______ - has its own preferred promoter sequence

A

ON ; OFF ; Switch ; Several new σ-factors ; Each σ-factors

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11
Q

(GENES WITH MULTIPLE PROMOTERS)

____________ – must be expressed during 2 or more phases of sporulation when different σ-factors predominate

A

Sporulation genes

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12
Q

(GENES WITH MULTIPLE PROMOTERS)

Genes transcribed under different conditions – are equipped with two
different promoters

o _______ – is recognized by one of two different σ-factors
o Ensures their expression no matter which factor is present
o Allows for differential control under different conditions

A

Each promoter

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13
Q

(BACTERIAL HEAT SHOCK)

_____________ - is a defense by cells to minimize damage in response to increased temperatures

___________ – are proteins that bind to proteins partially unfolded by heating and help them to fold properly again

___________ – genes encoding proteins that help cells survive heat

A

Heat shock response ; Molecular chaperones ; Heat shock genes

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14
Q

THE OTHER σ-SWITCHES

______________ – is controlled by an alternative σ-factor, σ32 or
σH (H stands for heat shock)

A

Heat shock response in E. coli

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15
Q

(THE OTHER σ-SWITCHES)

  • Directs RNA polymerase to the heat shock gene promoters
  • Accumulation of σH with high temperature is due to:
    ▪ ____________- of σH
    ▪ Enhanced translation of the mRNA
    encoding ___
A

Stabilization ; σH

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16
Q

(THE OTHER σ-SWITCHES)

Responses to low _____ and _________ – depends on genes
recognized by other σ-factors

A

nitrogen ; starvation stress

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17
Q

(ANTI σ-FACTORS)

These proteins – do not compete with σ-factors for binding to a core polymerase, they bind directly to σ and inhibit its function.

Example: product of the E.coli rsd gene
▪ Regulates the activitiy of the major
____________ – the product of the rpoD gene

A

vegetative σ, σ70 (σD)

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18
Q

(ANTI σ-FACTORS)

Some of the anti - σ-factors – are controlled by ___________ that bind to the complexes between a σ and an anti - σ-factors and release the anti σ-factors

A

anti - σ-factors

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19
Q

(THE RNA POLYMERASE ENCODED IN PHAGE T7)

__________– has a small genome and many fewer genes than SPO1.

Has 3 phases of transcription:
1.
2.
3.

A

Phage T7

  1. Class I
  2. Class II
  3. Class III
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20
Q

(THE RNA POLYMERASE ENCODED IN PHAGE T7)

_______ – is necessary for Class II and III gene expression

If gene 1 is mutated – only _______ are transcribed
o Codes for a phage – specific RNA polymerase that transcribes the ______ class II and III specifically

A

Gene 1 ; class 1 genes ; T7 phage

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21
Q

(TEMPORAL CONTROL OF TRANSCRIPTION)

________ – transcribes the Class I genes

______ of class I genes – is the phage polymerase

_________ – transcribes the class II and III genes

A

Host polymerase ; Gene 1 ; Phage polymerase

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22
Q

(INFECTION OF E. COLI BY PHAGE A)

____________ – replicate and kill their host by lysing or breaking it open

A

Virulent phage

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23
Q

(INFECTION OF E. COLI BY PHAGE A)

Temperate phage such as ___ – infects cells but don’t necessarily kill

o Have 2 paths of reproduction:
▪ ________ – infection progresses as in a virulent phage
▪ __________ – phage DNA is integrated into the host genome

A

λ ; Lytic mode ; Lysogenic mode

24
Q

(LYSOGENIC MODE)

27 – kD phage protein (λ (lambda) repressor, CI) – appears and binds to 2 phage operator regions

____ – shuts down transcription of all genes except for cI, gene for λ repressor itself

A

CI

25
Q

(LYSOGENIC MODE)

When lysogeny is established – the phage DNA integrates into the ________

_______ - bacterium harbouring integrated phageDNA

A

bacterial genome ; Lysogen

26
Q

(LYSOGENIC MODE)

_______ – integrated DNA

Phage DNA in the lysogen – replicates along with the _______

A

Prophage ; host DNA

27
Q

(LYTIC REPRODUCTION OF PHAGE A)

Lytic reproduction cycle of phage λ – has 3 phases of transcription:

A

o Immediate early
o Delayed early
o Late

28
Q

(LYTIC REPRODUCTION OF PHAGE A)

Genes of these phases – are arranged ________ on the phage DNA

A

sequentially

29
Q

(GENETIC MAP OF PHAGE A)

______ – exists in linear form in the phage

A

DNA

30
Q

(GENETIC MAP OF PHAGE A)

After infection of host begins the phage DNA circularizes

_____________ – is controlled by transcriptional switches

A

Gene transcription

31
Q

(ANTITERMINATION)

__________ – is a type of transcriptional switch used by phage λ

____________ – transcribes the immediate early genes first

A

Antitermination ; Host RNA polymerase

32
Q

(ANTITERMINATION)

____________ – serves as antiterminator that permits RNA polymerase to ignore terminators at the end of
the immediate early genes

__________ – are used for both immediate early and delayed earlytranscription

___________ – are transcribed when another antiterminator permits transcription of the late genes from the
late promoter to continue without premature termination

A

Gene product ; Same promoters ; Late genes

33
Q

(ANTITERMINATION AND TRANSCRIPTION)

One of 2 immediate early genes is cro

o ____ – codes for a repressor of cI gene that allows lytic cycle to
continue
o Other immediate early gene is N coding for __, an antiterminator

A

cro ; N

34
Q

(N TERMINATION FUNCTION)

Genetic sites – surrounding the N gene include:

A

o Left promoter (PL)
o Operator (OL)
o Transcription terminator

35
Q

(N TERMINATION FUNCTION)

When N is present:

o ___ – binds transcript of N utilization site (nut site)
o Interacts with protein complex bound to polymerase
o ____ – ignores normal transcription terminator, continues into delayed early genes

A

N ; Polymerase

36
Q

(PROTEINS INVOLVED IN N- DIRECTED
ANTITERMINATION)

Five proteins – collaborate in antitermination at the λ immediate early terminators

o __________ – bind RNA polymerase

o __________ – bind to the box B and box A regions of the nut site

o __________ – bind to NusA and S10 probably tethering the transcript to the polymerase

o ____ – stimulates termination at intrinsic terminator by interfering with binding between upstream part of terminator hairpin and core polymerase

A

NusA and S10 ; N and NusB ; N and NusB ; NusA

37
Q

(ANTITERMINATION AND Q)

Antitermination in the λ late region – requires ___ (discharge)

Q – binds to the Q - binding region of the qut site as RNA polymerase is stalled just downstream of late promoter

Binding of Q to the polymerase – appears to alter the enzyme so it can ignore the terminator and transcribe
the late genes

A

Q

38
Q

(ESTABLISHING LYSOGENY)

Phage establish _______ by:
o Causing production of repressor to bind to early operators
o Preventing further early RNA synthesis

A

lysogeny

39
Q

(ESTABLISHING LYSOGENY)

Delayed early gene products are used
o Integration into the host genome
o Products of _______ – allow transcription of the cI gene and production of λ repressor

A

cII and cIII

40
Q

(ESTABLISHING LYSOGENY)

____ – promoter to establish lysogen

Delayed early transcription from PR – produces cII mRNA translated to cII

___ – allows RNA polymerase to bind to PRE and transcribe the cI gene, resulting in repressor

A

PRE ; cII

41
Q

(AUTOREGULATION OF cI GENE DURING LYSOGENY)

As λ repressor appears, binds as a dimer to λ operators, OR and OL results in:

o Repressor turns off further early transcription
▪ Interrupts lytic cycle
▪ Turnoff of cro – very important as product cro acts to counter repressor activity
o Stimulates own synthesis by activating PRM

A

YES

42
Q

(REPRESSOR PROTEIN)

Repressor protein – a dimer of 2
identical subunits

o each subunit has 2 domains with
distinct roles:
▪ ___________ – is the DNA –binding end of molecule
▪ ___________ – is site of
repressor – repressor interaction that makes
dimerization and cooperative binding
possible

A

amino – terminal ; Carboxyl – terminal

43
Q

(INVOLVEMENT OF OL IN REPRESSION)

_____ – binds to OR1 and OR2, but leaves OR3

RNA polymerase to PRM which overlaps OR3 in sucha way it contacts repressor bound to OR2

________________ – is required for
promoter to work efficiently

_________ – can repress transcription
from PRM
o Process may involve interaction of repressor dimers bound to OR1 and OR2 and OR3
o _________ – bound to OL1 and OL2 and OL3 via DNA looping

A

Repressor ; Protein – protein interaction ; High levels of repressor ; Repressor dimers

44
Q

(SELECTION OF INTERGENIC SUPPRESSOR)

_________ - used bacteria with the chromosome illustrated (in small part) at
bottom.

A

Susskind and colleagues

45
Q

(SELECTION OF INTERGENIC SUPPRESSOR)

A
46
Q

(SELECTION OF INTERGENIC SUPPRESSOR)

The chromosome included two prophages:

  1. a P22 prophage with a _________ (orange) driven by a l PRM promoter with adjacent l OR
  2. a l prophage containing the ______ (light green) driven by a weak lac promoter.
A

kanamycin resistance gene ; l cI gene

47
Q

(SELECTION OF INTERGENIC SUPPRESSOR)

______________- - placed plasmids bearing mutagenized rpoD (s-factor) genes (lighT blue) driven by the lac UV5 promoter.

o Then they challenged the transformed cells with medium containing kanamycin.
o Cells transformed with a wild-type rpoD gene, or with rpoD genes bearing irrelevant
mutations - could not grow in kanamycin.
o Cells transformed with rpoD genes having a mutation (red X) thatcompensated for the
mutation (black X) in the cI gene - could grow.

A

Susskind and colleagues

48
Q

(SELECTION OF INTERGENIC SUPPRESSOR)

This mutation suppression is illustrated by the interaction between the _______ (s*, blue) and the ______r (green), which permits transcription of the kanamycin- resistance gene from PRM.

A

mutant s-factor ; mutant repressor

49
Q

(RNA POLYMERASE/REPRESSOR INTERACTION)

_________________ – studies
show that crucial interaction between
suppressor and RNA polymerase involves region 4 of the σ-subunit of the polymerase

_____________ – binds near the weak -35 box of PRM placing the σ-region 4 close to the
repressor bound to OR2

_________ – can interact with σ – factor helping to compensate for weak promoter

______ – serves as an activator site
Repressor I – is an activator of transcription from
PRM

A

Intergenic suppressor mutation ; Polypeptide ; Repressor ; OR2

50
Q

(ACTIVATION VIA SIGMA)

_______ – subject to polymerase – repressor activation have weak – 35 boxes
o These boxes are poorly recognized by sigma

__________ – overlaps – 35 box, places activator in position to interact with region 4

A

Promoters ; Activator site

51
Q

(DETERMINING THE FATE OF A λ INFECTION)

Balance between lysis or lysogeny is delicate

Place phage particles on bacterial lawn
o If lytic infection occurs:
▪ ______ – spread and infect other cells
▪ ______ – circular hole seen in lawn

Some infected cells – suffer the lytic cycle, others are lysogenized

A

Progeny ; Plaque

52
Q

(BATTLE BETWEEN cI and cro)

_____ – codes for repressor
o blocks _____, ____, ____, ______ – turning off early transcription; leads to lysogeny

_____ – codes for cro
o blocks _____ and ____ – turning off transcription; leads to lytic infection

Gene product in high concentration – first determines cell fate

A

cI gene ; OR1 , OR2, OL1 and OL2

cro gene ; OR3 and OL3

53
Q

(LYSOGEN INDUCTION)

When lysogen suffers, _____ damage – SOS response is induced

_________ – is seen in a coprotease activity in RecA protein

A

DNA ; Initial event

54
Q

(LYSOGEN INDUCTION)

_________ – are caused to cut in half, removing them from λ operators

o _______ – is induced

A

Repressors ; Lytic cycle

55
Q

(LYSOGEN INDUCTION)

_____________ – can escape potentially lethal damage occurring in host

A

Progeny phage

MOLBIO OFFSEM MIDTERM (9 decks)

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