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Cells to Organisms - Lectures > Lecture 5. Cell-Cell Communication and Development in Bacteria > Flashcards

Lecture 5. Cell-Cell Communication and Development in Bacteria Flashcards

1
Q

What is quorum sensing ?

A

A process that allows microbes to control behaviors as a function of signal molecule concentration

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2
Q

What is another name for the quorum sensing molecule ?

A

Autoinducer

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3
Q

Can a single bacterium make enough of the quorum sensing molecule to affect behavior ?

A

No

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4
Q

What can make enough of the quorum sensing molecule to exceed the concentration threshold for a behavioral change ?

A

A group of bacteria

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5
Q

What is the variable in the quorum sensing molecule system ?

A

The concentration of the signalling molecule

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6
Q

What does the concentration of the signalling molecule act as ?

A

A proxy for microbes in an effective range

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7
Q

Does the autoinducer have to be produced by bacteria of the same species ?

A

No

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8
Q

What is the advantage of the autoinducer not being produced by bacteria of the same species ?

A

Allows complex community structures

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9
Q

What must bacteria possess to participate in quorum sensing ?

A

The means to detect the signals and alter cellular function

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10
Q

What is a disadvantage of bacteria making its own signal ?

A

Leads to cheating

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11
Q

What are the four examples of behaviors controlled by quorum sensing ?

A
  1. Bioluminescence
  2. Biofilm formation
  3. Conjugation
  4. Virulence
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12
Q

What is the bioluminescence behavior controlled by quorum sensing and give an example ?

A
  1. Some bacteria generate light

2. Aliivibrio fischeri

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13
Q

What is the behavior surrounding biofilm formation that is controlled by quorum sensing ?

A

The transition from plankton (free swimming) to a community based lifestyle

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14
Q

What is the conjugation behavior controlled by quorum sensing and give an example?

A
  1. DNA transfer from one bacterium to another in the gram-positive organism
  2. Enterococcus
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15
Q

What is the virulence behavior controlled by quorum sensing ?

A

The expression of a virulent phenotype by a pathogenic bacteria

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16
Q

When may virulence behavior controlled by quorum sensing occur ?

A

When a large number of bacteria is needed to establish a successful infection

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17
Q

Are quorum sensing reaction limited to just bacteria ?

A

No - they can be between organisms of completely different kingdoms

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18
Q

Give an example of quorum sensing behaviour between organisms of different kingdoms ?

A

The symbiotic relationship between the Hawaiian Bobtail squid and the Aliivibrio fischeri

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19
Q

What does the Alviibrio fischeri do to the Hawaiian bobtail squid ?

A

Colonise the squids light producing organ

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20
Q

What are the two states that the Alviibrio fischeri can exist in ?

A
  1. Naturally, free living, planktonic state

2. Symbiont of certain luminescent squid or fish

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21
Q

What are the advantages of bioluminescence to the squid ?

A
  1. Attraction of prey
  2. Camoflague
  3. During nocturnal feeding, prevents a shadow of squid on sea floor by mimicing moonlight
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22
Q

What is the source of luminesce in the Hawaiian bobtail squid and Aliivibrio fischeri ?

A

The bacteria themselves

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23
Q

In the marine environment, when do the bacteria only luminesce ?

A

When colonising the light organs and they do not emit light in the free living state

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24
Q

Why does it make good evolutionary sense for bacteria to tightly regulate bioluminescence as the mechanism by which the light is produced ?

A

It is a very energy intensive process

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25
Q

How did the research carried out to show that the Aliivibrio fischeri regulate bioluminescence lead to the discovery of bacterial quorum sensing ?

A

Via acyl homoserine lactones

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26
Q

What does the quorum sensing rely on ?

A

The synthesis, accumulation and the subsequent sensing of the signal molecule

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27
Q

In the Aliivibrio fischeri, what is the acyl homoserine lactone synthesised by ?

A

LuxI enzyme

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28
Q

In the Aliivibrio fischeri, what is the acyl homoserine lactone sensed by ?

A

The luxR regulatory protein

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29
Q

At low cell densities how is the acyl homoserine lactone signal produced ?

A

Bacteria produces it at low levels

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30
Q

When the acyl homoserine lactone signal is produced at low levels in the Aliivibrio fischeri what state is it in ?

A

Free living

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31
Q

What happens to the acyl homoserine lactone when the Aliivibrio fischeri is in the free state ?

A

The acyl homoserine lactone diffuses into the surrounding environment

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32
Q

What happens when the bacterial cell density increases ?

A

The acyl homoserine lactone signal accumulates in the areas surrounding the bacteria.

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33
Q

When does cell density increase in the Aliivibrio cholerae ?

A

Colonising an organism

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34
Q

What happens when the acyl homoserine lactone signal reaches a critical threshold concentration ?

A

The signal is able to interact with the LuxR protein

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35
Q

Where dos the LuxR AHL complex bind to ?

A

Lux box

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36
Q

What is the Lux box made up of ?

A

A region of DNA

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37
Q

What is the function of the Lux box ?

A

Causes the luminescence genes to switch on

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38
Q

What else does the LuxR AHL complex also cause ?

A

The acyl homoserine lactone via Lux to be produced at higher levels.

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39
Q

What is the acyl homoserine lactone said to do ?

A

To autoinduce its own synthesis

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40
Q

What can quorum sensing explain ?

A

Why the bacteria is dark in free living and light in the light organ

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41
Q

How do bacteria measure their cell density ?

A

By measuring the amount of the signal present

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42
Q

What are some other examples of bacteria which use the acyl homoserine lactone quorum sensing ?

A
  1. The AI2 molecule from the fibrio harveyi and fibrio cholerae
  2. The AIP1 molecule from the stephylcoccus aureus
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43
Q

What is the problem with quorum sensing for gram positive organisms ?

A

They need to actively transport out of the cell using ATP binding casette? transporter system (ABC transporter)

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44
Q

What happens as biofilm begins to mature ?

A

Accumulation of quorum sensing signalling molecules causes the bacteria to display co-operative behavior

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45
Q

When do bacteria turn on their virulence genes ?

A

When they have sufficient numbers

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46
Q

What happens to biofilm formation when virulence is high ?

A

Biofilm formation is shut down as well as virulence

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47
Q

How can bacteria share information ?

A

Horizontal gene transfer

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48
Q

What is the process of conjugation ?

A

The sharing of mobile genetic elements such as plasmids between neighbouring bacteria

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49
Q

What else can bacteria do to take in genetic material ?

A

They can have sample genetic material floating around the environment freely. They plug these newly acquired genes into their own genome in the hope they find something useful

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50
Q

What is the name of the plasmid used in the Enterococcus ?

A

Pcf10

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51
Q

Where is PCF10 plasmid contained ?

A

Donor cell

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52
Q

What is the first step of the plasmid transfer process in Enterococcus ?

A

The recipient cell secreted high amount of the pheromone CCF10 which is encoded in its genome

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53
Q

What is the second step in plasmid transfer in Enterococcus ?

A

The pheromone CCF10 diffuses into the environment. If a donor cell is close enough for he pheromone to be in sufficient concentration, it initiates conjugation and transfers the plasma to the recipient resulting in both cells containing the plasmid

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54
Q

Where does the vibrio cholerae attack ?

A

Gut/small intestine

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55
Q

Where do the vibrio cholerae move from ?

A

The lumen of the small intestine to the surface of the microvilli

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56
Q

What secretion system do vibrio cholerae use ?

A

Type 6 secretion system

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57
Q

What is the function of the type 6 secretion system ?

A

To target and kill gut commensal bacteria on the surface of the microvilli

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58
Q

What is the main reason for the killing of bacteria by vibrio cholerae ?

A

To reduce competition for resources and make space for themselves on the surface of microvilli

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59
Q

What do signals from the microvillus environment do in bacterial virulence in vibrio cholerae ?

A

Induces expression of toxin co-regulated pili

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60
Q

What do vibrio cholerae do to cholera toxin ?

A

Produce and export cholera toxin

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61
Q

What does toxin co-regulated pili do to vibrio cholerae ?

A

Toxin co-regulated pili anchor the vibrio cholerae cells to host surface and a biofilm begins to form

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62
Q

What does cholera toxin do ?

A

Disrupts the metabolism of the human cells, causing increased production of cAMP

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63
Q

What does the rise in cAMP concentration signify in bacterial virulence in vibrio cholerae ?

A

Triggers the loss of water and electrolytes from the gut cells

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64
Q

Vibrio Cholerae, low cell density: What is low at the start of biofilm production ?

A

The concentration of autoinducer-2

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65
Q

What is autoinducer-2 synthesised by ?

A

LuxS protein and cholera autoinducer(CAI1)

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66
Q

Vibrio Cholerae, low cell density: What happens when the autoinducer levels are low ?

A

The AI receptor LuxP functions as a kinase

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67
Q

Vibrio Cholerae, low cell density: What is the function of the AI receptor LuxP ?

A

Funnels phosphate to the response regulator LuxO through a phospho-relay using LuxQ and LuxU

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68
Q

Vibrio Cholerae, low cell density: What does phosphorylated LuxO activate ?

A

The expression of four genes encoding the QRR sRNAs

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69
Q

Vibrio Cholerae, low cell density: What aids the expression of four genes encoding the QRR sRNAs ?

A

The nucleoid associative protein (FIS)

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70
Q

What is FIS associated with ?

A

Early exponential growth

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71
Q

Vibrio Cholerae, low cell density: What does the production of the sRNAs require ?

A

The stress sigma factor RponN

72
Q

What are sRNAs ?

A

Non-coding RNAs that dont produce proteins

73
Q

What is the function of sRNAs ?

A

They regulate the translation of mRNA. Thye can either be positive where they aid in the translation or they can destabilise the mRNA to prevent its translation

74
Q

Vibrio Cholerae, low cell density: What do sRNAs and mRNAs require to keep them in correct topological state ?

A

The aid of specialist chaperone

75
Q

Vibrio Cholerae, low cell density: What does the QRR sRNA do and what helps it achieve it ?

A
  1. Destabilises the mRNA encoding HapR

2. The HFQ chaperone

76
Q

What is HapR ?

A

The major regulator of quorum sensing and repression of biofilm formation and virulence gene expression in vibrio cholerae

77
Q

What is the function of HapR ?

A

Controls the transcription of 14 genes encoding a group of proteins that synthesise and degrade C di GMP

78
Q

Vibrio Cholerae, high cell density: What is the net affect of the transcriptional program ?

A

A reduction in the C di GMP levels at high cell density and consequently a decrease in biofilm formation and virulence gene activation

79
Q

Vibrio Cholerae,: What is activated and acts directly on and degrades the biofilm ?

A

The HA protease

80
Q

Vibrio Cholerae, low cell density: What actually happens ?

A

No HapR present, no repression of the biofilm forming systems or virulence gene expression and conversely no production of the HA protease and so no biofilm escape

81
Q

Vibrio Cholerae, high cell density: What happens to the autoinducers ?

A

They accumulate

82
Q

Vibrio Cholerae, high cell density: What does the accumulation of autoinducers result in ?

A

The binding of cognitive receptors

83
Q

Vibrio Cholerae, high cell density: What does the binding of cognitive receptors result in ?

A

Switching the receptors to being phosphatases

84
Q

Vibrio Cholerae, high cell density: What is high cell density associated with ?

A

The stationary phase

85
Q

Vibrio Cholerae, high cell density: What happens as a result of the stationary phase ?

A

There in no FIS present

86
Q

Vibrio Cholerae, high cell density: What does phosphatase activity lead to ?

A

The dephosphorylation of LuxO along with the absence of FIS, the termination of QRR expression

87
Q

Vibrio Cholerae, high cell density: What happens to the mRNA encoded by HapR ?

A
  1. It is stabilised and the HapR protein is produced, shutting down biofilm formation and virulence gene expression.
  2. Thee production of the HA protease which aids a return to planktonic lifestyle
88
Q

What does vibrio cholerae make decisions in relation to ?

A

The environmental signals

89
Q

What does vibrio cholerae associate with ?

A

Chitinous marine organisms

90
Q

What is chitin ?

A

An important molecular signal in the life cycle of the bacterium

91
Q

What controls bacteria behavior ?

A

The combination of the chitin signal and the bacterial cell density by the quorum sensing system

92
Q

What is chitins role in the cell ?

A

To enhance the cells ability to take up foreign DNA

93
Q

What are competent cells ?

A

Cells which can take up foreign DNA naturally

94
Q

What happens when HapR is present ?

A

It represses the dns gene

95
Q

What is the function of the dns gene ?

A

Encodes the dns protein

96
Q

What is the dns protein ?

A

The dns enzyme

97
Q

What is the function of the dns enzyme ?

A

Responsible for the degradation of oncoming DNA

98
Q

What does HapR activate ?

A

The expression of the quorum sensing secondary activator qstR

99
Q

What happens when qstR is present ?

A
  1. The protein activates the gene for vibrio cholerae type 6 secretion system
  2. The genes responsible for competence are activated
100
Q

What is the function of the pilus structure ?

A

The physical structure for importing DNA into the cell

101
Q

What are the genes responsible for the pilus structure activated by ?

A

A regulatory cascade by chitin

102
Q

What happens when there is no chitin present ?

A

The chitin binding protein represses the activity of the ChiS activator

103
Q

What happens when chitin is present ?

A

The repression of ChiS is removed and is free to activate the expression of tfoX

104
Q

What can tfoX not do on its own ?

A

TfoX mRNA cannot be translated on its own, it requires help from an sRNA

105
Q

What does the presence of chitin increase the activity of ?

A

TfoS

106
Q

What is the function of tfoS ?

A

Activates the expression of TfoR

107
Q

What is TfoR ?

A

It is the sRNA responsible for TfoS translation

108
Q

What is the sRNA responsible for TfoS translation aided by ?

A

The chaperon HFQ

109
Q

What drives the transcription of the genes involved in the construction and operation of the pilus ?

A

TfoX in conjugation with chitin and the cAMP-CRP transcriptional activator complex

110
Q

What does the type 6 secretion system not do ?

A

Transport things out of the cell

111
Q

What is the function of type 6 secretion system ?

A

To fire the vgrG spike with great force through the cell envelope of the neighboring bacteria

112
Q

How does the type 6 secretion system work ?

A

Using a spring loaded mechanism

113
Q

What does the TssB and TssC sheath complex house ?

A

The HCP tube

114
Q

What is the HCP tube held in place by ?

A

The YSS and GLM complex

115
Q

What happens when the type 6 secretion system fires ?

A

The sheath complex contracts forcing the HCP tube through the center of the complex, which in turn extrudes the spike through its own outer membrane and into its target. Resulting in lysis and loss of cellular contents

116
Q

What is the first step in DNA uptake by naturally competent vibrio cholerae ?

A

Double stranded DNA being taken across the outer membrane of the cell through the periplasmic space, through the pilQ apparatus

117
Q

What happens to the double stranded DNA as it is been taken up naturally by competent vibrio cholerae ?

A

The strands are separated into single strands by the ComEA complex

118
Q

What is passed through the inner membrane through the ComEC complex during DNA uptake by naturally competent vibrio cholerae ?

A

A single strand of DNA

119
Q

What keeps the single strand of DNA in single stranded conformation during DNA uptake by naturally competent vibrio cholerae ?

A

Binding of the incoming DNA by single stranded binded protein monomers

120
Q

Where is the single stranded DNA passed to ?

A

The homologous recombinant DNA binding protein RecA by the protein DprA

121
Q

What does RecA integrate ?

A

The DNA into the bacterial genomee

122
Q

What does horizontal gene transfer allow ?

A

Bacteria to acquire new traits through a single event, potentially accelerating the rate of genome evolution

123
Q

What are the three processes that horizontal gene transfer occurs through ?

A
  1. Transduction
  2. Transformation
  3. Conjugation
124
Q

What is transduction ?

A

A bacteriophage mediates the transfer process following the attachment to the bacterial surface

125
Q

What is transformation ?

A

Naked DNA is taken up from the external environment by bacteria that are competent for transformation

126
Q

What is conjugation ?

A

A plasmid mediates its own transfer between bacterial cells, encoding the machinery for transfer in its own genome

127
Q

What are the two types of transduction ?

A
  1. Generalised and specialised
128
Q

What is generalised transduction ?

A

The bacteriophage injects its genetic material into the cell, which it then undergoes replication and in the process destroys the host genome

129
Q

In generalised transduction, how is the DNA packaged ?

A

Randomly occuring DNA is packed into the newly formed phage heads (headful packaging)

130
Q

In generalised transduction, what are the three things that can happen once another bacterial cell is infected ?

A
  1. The DNA is recycled for spare parts
  2. If the DNA was originally a plasmid it may circularise inside the new cell and become a plasmid again.
  3. If the new DNA matches with a homologous region of the recipient cells chromosome it may exchange DNA materials similar to the actions in bacterial recombination
131
Q

What is specialised transduction ?

A

The bacteriophage injects its genetic material into the cell, and gets inserted into sites within the genome which possess some homology to the viral genetic material

132
Q

What does specialised transduction not do ?

A

Destroy the bacterial genome

133
Q

What may happen in rare circumstances in specialised transduction ?

A

The genetic material can become excised from the genome along with some bacterial DNA and will be packed into phage heads so the cycle can repeat

134
Q

What does transformation use ?

A

Direct repeats

135
Q

What do direct repeats result in ?

A

The excision of material in the direct repeat region

136
Q

What does transformation involve ?

A

The transferring of naked DNA into a bacterial cell

137
Q

What are the two ways transformation can occur ?

A
  1. Linear DNA fragments

2. Plasmid

138
Q

What is transformation by linear DNA fragments ?

A

After DNA has been taken up, it can become a stable transformation or an unsuccessful one

139
Q

What is transformation using the plasmid ?

A

The closed circle of the plasmid is more stable and can reside on its own within the cell and does not have to become part of the cells genome

140
Q

What is an example of a plasmid that integrates into the genome ?

A

Fertility F plasmid from E. coli

141
Q

What plasmids are degraded ?

A

If they are non-self DNA

142
Q

What does plasmid transfer by conjugation involve ?

A

The transmission of self-transmissible plasmids

143
Q

In plasmid transfer by conjugation, what does the plasmid code for ?

A

All the machinery necessary for its transmission

144
Q

What does the plasmid transfer by conjugation process have ?

A

A donor cell contains the plasmid and a recipient cell that will receive a copy of the plasmid

145
Q

What does the plasmid transfer by conjugation process begin with ?

A

The formation of the pilus which connects the donor and recipient cells

146
Q

In the plasmid transfer by conjugation process what is transferred to the recipient cell ?

A

A single strand of the plasmid is peeled off and transferred to the recipient cell.

147
Q

What size is the fertility factor a conjugative plasmid from E. coli ?

A

99.2 kb

148
Q

What does the fertility factor, a conjugative plasmid from E. coli contain ?

A

The genes for the machinery necessary for transfer by conjugation

149
Q

Where are the genes for the fertility factor from E. coli from ?

A

Tra region

150
Q

What else does the plasmid with the fertility factor from E. coli contain ?

A
  1. Origin of replication

2. Origin of transfer

151
Q

What is the origin of replication ?

A

This is the region replication begins in during normal plasmid replication

152
Q

What is the origin of transfer ?

A

This is a short sequence that is necessary for the transfer of DNA

153
Q

What else can the fertility factor plasmid contain ?

A

A number of insertion sequences and a transposon TN1000

154
Q

Where is the type 4 secretion system ?

A

Tra region

155
Q

What is the type 4 secretion system responsible for ?

A

The physical transfer of material between cells

156
Q

What does the type 4 secretion system span ?

A

The inner and outer membrane

157
Q

What does the type 4 secretion system require ?

A

The formation of the relaxosome

158
Q

What is the relaxosome composed of ?

A

traY and traM accessory proteins

159
Q

What is the function of the TraM and traY responsible for ?

A

With the help of the nucleative associative protein IHF hold the protein in a tight bend close to the origin of transfer

160
Q

What does the association between traM and traY and IHF do ?

A

Allows the traI relaxase dimer to nick a single strand

161
Q

What happens in a type 4 secretion system once the strand has been nicked ?

A

The free end of the nicked strand gets passed to the virB4

162
Q

What is virB4 ?

A

A type coupling protein which mediates the single strands passage through the center of the type 4 secretion system and into the recipient cell

163
Q

Are all plasmids mobilizable ?

A

Yes

164
Q

Are all plasmids conjugative on their own ?

A

No

165
Q

What is a plasmid containing an origin of transfer and a relaxase ?

A

Its mobilisible but not conjugative

166
Q

What is needed for recombination and integration ?

A

Homologous sequences in the genome

167
Q

What is horizontal gene transfer offset by ?

A

The ability of bacteria to distinguish between self and non -self at the DNA level and to eliminate non-self DNA

168
Q

What does an example of a restriction modification system contain ?

A

A methyltransferase and a restriction endonuclease

169
Q

What is a restriction endonuclease ?

A

Cut at very specific sites

170
Q

Why cant restriction modification systems destroy the bacterial genome itself ?

A

The methyltransferase methylates the genomic DNA in very specific patterns, protecting it from degradation by the restriction system, the incoming foreign DNA will always be degradative, it it contains the specific genetic sequences recognised by the endonuclease if it does not have the approved methylation pattern

171
Q

How does the CRISPR-cas system act ?

A

By recognising invading DNA, sends the system off with the cas proteins which hunt and destroy proteins in the same sequenc

172
Q

How would you describe the CRISPR-cas system ?

A

Dynamic

173
Q

What is the first step in the CRISPR-cas system ?

A

The invading DNA is recognised and integrated into the adaption module

174
Q

What does the second step in the CRISPR-cas system involve ?

A

Transcribing foreign DNA held within the adaption module into crRNAs

175
Q

What are crRNAs also known as ?

A

Guide RNAs

176
Q

What is the function of the guide RNAs ?

A

These guide RNAs direct the system towards complementary sequences of other invading bacteriophage or plasmids which are then cleaved by the cas nuclease

177
Q

What is the third step in the CRISPR-cas system ?

A

When the cell incorporates foreign DNA, it immediately stops its expression

Cells to Organisms - Lectures (36 decks)

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