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Michaelmas Term 1 > The Prokaryotes I > Flashcards

The Prokaryotes I Flashcards

1
Q

Describe bacterial genomes

A
  • mostly single, circular chromosomes
  • épisomal elements
  • coding sequences are preferentially located on the leading strand
  • most pronounced in Gram +be with low G+C content
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2
Q

List the exceptions to the bacterial genome being mostly single, circular chromosomes rule

A
  • Burkholderia cenocepacia
  • Borrelia burgdorferi
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3
Q

Describe Burkholderia cenocepacia

A
  • three circular chromosomes
  • 3.87, 3.22, 0.88 Mb
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4
Q

Describe Borrelia burgdorferi

A
  • linear chromosomes
  • 0.91Mb
  • 12 linear + 9 circular plasmids (60kb)
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5
Q

Describe the episomal elements of the bacterial genome

A
  • plasmids
  • phases
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6
Q

Describe the shape of plasmids and phases

A

Circular (very rarely linear)

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7
Q

Give examples of exceptions to the episomal element conventions

A
  1. Rhizobium leguminosarum
  2. Borrelia burgdorferi
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8
Q

Describe Rhizobium leguminosarum

A
  • 6 plasmids
  • largest 0.87Mb
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9
Q

Compare and contrast operons in prokaryotes v eukaryotes

A

Prokaryotes: often have them
Eukaryotes: typically do not

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10
Q

What is an operon?

A

A cluster of Co-transcribed genes

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11
Q

Compare and contrast introns in eukaryotes v prokaryotes

A

Eukaryotes: preserved

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12
Q

Describe the range of introns in eukaryotes

A
  • only a handful in smaller protists
  • 8 per gene in humans
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13
Q

Describe the size of introns in eukaryotes

A
  • 20-200nts long
  • up to 2kb in larger animals
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14
Q

How much larger are eukaryote genomes compared to prokaryote genomes generally?

A

An order of magnitude

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15
Q

Bacterial genomes are

A

Highly compact

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16
Q

Describe the relationship between genome size and number of ORFs in the genome

A

Positive, strong, linear correlation
ORFS: 0-9000
Genome size: 0-10

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17
Q

Most bacterial genomes contain very little

A

Non-coding DNA

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18
Q

ORF

A
  • open reading frame
  • a sequence of DNA that could be translated to give a gene
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19
Q

As genome size increases, so does the

A
  • Repertoire of genes encoded
  • metabolic capacity
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20
Q

Graph depicting % of gene by function against genome size

A
  • as genome size increases, % of genes involved in mesh Leon and transport increases, relative to the other function of translation, replication and repair, as well as regulation
  • from 10.5-17.5%
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21
Q

Describe the smallest bacterial genome

A
  • Candidatus Acintomarina minuta
  • 0.0013Mbp
  • 800 ORFs
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22
Q

Describe the largest virus genome

A
  • Pandorravirus
  • 2.5Mbp
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23
Q

Describe the largest bacterial genome

A
  • Sorangium cellulosum
  • gliding myxobacteria
  • 14.8Mbp
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24
Q

What are the mechanisms of prokaryote gene transfer?

A
  1. Transformation
  2. Transduction
  3. Conjugation
  4. Transposable elements (mobile DNA)
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25
Q

What phenomenon does transformation rely on?

A

Not all cells within a population are competent to take up DNA at the same time

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26
Q

What is transformation?

A

DNA uptake

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27
Q

Give examples of naturally high-efficiency transformers

A
  1. Neisseria
  2. Acinetobacter
  3. Bacillus
  4. Streptococcus
  5. Haemophilus
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28
Q

Give examples of poor transformers

A

Many Gram negative bacteria and archaea (e.g. E. Coli)

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29
Q

How can transformation be induced?

A
  • Electroporation
  • Ca2+ ions
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30
Q

Describe electroporation

A

Brief high voltage electrical pulses

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31
Q

To transform, cells must be

A
  • competent
  • competence inducible
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32
Q

How is transformation (in the form of stable incorporation of foreign DNA) achieved?

A
  1. dsDNA from the environment binds to cell
  2. Exonuclease digests dsDNA to ssDNA
  3. ssDNA (6-8Kbp) associates with competence proteins
  4. Strand replacement by donor DNA
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33
Q

What is needed for transduction?

A

A phage

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34
Q

What is generalised transduction?

A

Any gene can be transferred from donor to recipient

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35
Q

How often does generalised transduction occur in phage lytic cycle?

A
  • low frequency
  • 1 cell in 10^6/10^8
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36
Q

What is specialised transduction?

A

specific bacterial DNA fragments from chromosomes adjective to phage integration site may be transferred

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37
Q

Describe specialised transduction

A

Selective but efficient

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38
Q

Give an example of specialised transduction

A

Galactose catabolism in E. Coli when phage is in lysogenic cycle

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39
Q

How does generalised transduction work?

A
  • bacterial chromosome contains gene (a+) with variant in other bacterial cells (a-)
  • phage infects and replicates, fragmenting bacterial DNA
  • cell lyses
  • rarely, a phage will have accidentally packaged the a+ gene
  • this phage can now transduce a- cells to a+ cells
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40
Q

How does specialised transduction work ?

A
  • a prophage has been integrated into bacterial chromosome
  • if rare, abnormal excision of prophage occurs, prophage might pick adjacent s+ gene
  • on lysis, these phage carry the s+ gene, and can transduce other cells from s- to s+
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41
Q

a+

A

Any bacterial gene

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42
Q

s+

A

Special bacterial gene

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43
Q

What does conjugation require?

A

A plasmid

44
Q

Give an example of a conjugation plasmid

A

E Coli F+ cell (forms pilus which retracts)

45
Q

Describe conjugation

A
  • donor cell attaches pilus to recipient cell
  • DNA polymerase exchange
  • by the relaxasome and the transferasome, the plasmid is replicated
  • the recipient (new donor) now has the plasmid, as well as the old donor
46
Q

What is the accessory genome?

A

Mobile DNA

47
Q

List the two types of movement that MGEs can undergo

A

1) intercellular
2) intracellular

48
Q

MGEs

A

Mobile genetic elements

49
Q

List the MGEs that undergo intercellular movement

A
  1. Phages
  2. Plasmids
  3. ICEs
50
Q

ICE

A
  • Integrative conjugation elements
  • derivative of a phage/plasmid
51
Q

List the MGEs that undergo intracellular movement

A
  1. Transposons
  2. Insertion sequences
  3. Integrons
  4. Introns
52
Q

Compare and contrast transposons with insertion sequences

A
  • both require transposase
  • insertion sequences are smaller elements
53
Q

What do integrons rely on?

A

Integrase

54
Q

Describe the general structure of a bacterial composite transposon

A

Genes for transposition at either end are bracketed by inverted repeats

55
Q

What are intracellular MGEs?

A
  • selfish genetic elements, that can increase their own transmission at the expense of other genes
56
Q

How are MGEs classified?

A

According to their genetic makeup (core and accessory genes, and inverted repeat regions)

57
Q

What do transposons use transposase enzymes for?

A

to ‘cut and paste’, ‘copy and paste’ or Co-integrate DNA position

58
Q

Why are MGEs advantageous?

A

They carry genes which give their host a selective advantage

59
Q

Give examples of advantageous MGE genes

A
  1. Antibiotic resistance
  2. Virulence
  3. Unusual metabolic pathways
  4. Gene expression
60
Q

Describe insertion sequences

A
  • they can rapidly expand in bacterial populations
  • can be influenced by host lifestyle
61
Q

Tn

A

Transposon

62
Q

Gene cassette

A

A type of MGE that contains a gene and a recombination site

63
Q

What is the consequence of the widespread occurrence of genetic exchange between bacteria?

A
  • bacterial genomes are not closed
  • closely related bacteria open genomes
64
Q

Open genomes contain

A

Very different gene complements

65
Q

The pangenome

A
  • the genes available to a particular bacterium
66
Q

Describe the core genome

A
  • the operating system
  • DNA replication, ribosomes, cell envelope, key metabolic pathways
67
Q

Describe the parasitic elements of bacterial genomes

A
  • phages, plasmids
  • e.g. toxins, restriction/modification systems
68
Q

Describe the accessory genome in bacteria

A

alternative metabolic pathways, transport systems

69
Q

Describe the gene pool of bacteria

A
  • e.g. antibiotic rand distance, degradative metabolism
70
Q

Which types of selection may genetic elements be subject to?

A
  • stabilising (negative)
  • diversifying (positive)
  • neutral (rare in most bacteria)
71
Q

What are the three mechanisms of genetic change?

A
  1. Point mutation
  2. Indels
  3. Rearrangement
72
Q

At what scale does a point mutation act?

A

Small

73
Q

At what scale does an indel act?

A

Small/large

74
Q

At what scale does a rearrangement act?

A

Small/large

75
Q

Linkage disequilibrium

A
  • Non-random association of different genes in a population
  • particular patterns of mutational changes accumulating in different lineages, each characteristic by certain patterns of changes
76
Q

Congruence

A

Phylogenetic tree topologies are similar

77
Q

What have previous models of bacterial phylogeny assumed?

A
  • no loss of diversity
  • no recombination
78
Q

Are there are bacteria left in which previous assumptions still hold true?

A

Yes - genetically monomorphic pathogens

79
Q

Give examples of genetically monomorphic pathogens

A
  • Mycobacterium leprae
  • Mycobacterium tuberculosis
  • Yersinia pestis
80
Q

Describe the progressive natural of mutational change in bacteria:

A
  • derived genes will be created by mutation during clonal expansion of ancestral genes
  • mutations occur stochastically - some are lost through selection or drift, but some accumulate
  • results in linkage disequilibrium
81
Q

What is Muller’s ratchet?

A

Reductive evolution

82
Q

Why are small asexual bacterial populations susceptible to Muller’s ratchet?

A

They are vulnerable to the accumulation of deleterious mutations

83
Q

What are some examples of bacteria especially vulnerable to Muller’s ratchet

A
  • Mycobacterium leprae
  • Yersinia pestis
84
Q

Describe the clonal population model

A

Asexuality (while infrequently facilitating periodic selection), reduces diversity by bottlenecking

85
Q

What are mosaic genes?

A

Chromosomal genes containing homologously recombined introduced genes

86
Q

What is the impact of recombination on bacterial population structure?

A

Recombination disrupts clonal structure, disrupting arboreal phylogeny, linkage disequilibrium and congruence

87
Q

Why do we see a spectrum of clonal signal in different bacterial populations?

A

Differing relative rates of recombination to mutation

88
Q

Prokaryotes generally have

A

Small, compact, highly structured genomes with a high density of protein-coding genes

89
Q

Prokaryote diversity comprises

A

Accumulated mutation in the core genome, and lateral transfer of accessory genome

90
Q

What is the effect of the Mobileome?

A

It creates very large pangenomes

91
Q

HGT/LGT are

A

‘A major impact on prokaryote population structure’

92
Q

How does the bacterial chromosome replicate?

A

DNA helicase replicates in two directions (leading and lagging strand) so they don’t overlap, and toxic products don’t interfere

93
Q

Describe the plasmid content of E Coli

A
  • 300 plasmids
  • wouldn’t expect to see them all in a cell at one time
94
Q

Describe transposable elements

A

Shortest DNA that can move between cells

95
Q

Describe the capsule

A

Smooth

96
Q

Compétence proteins

A

Shuffling proteins through membranes to incorporate bacterial chromosomes

97
Q

What can electroporation or calcium ions do to cell membranes?

A

Make them more permeable to take up DNA

98
Q

Why aren’t all cells in a population transformable at the same time?

A

Group survival mechanism

99
Q

Prophage

A

Integrated virus

100
Q

How is phage DNA excised?

A

UV

101
Q

How long does conjugation take?

A

5 mins

102
Q

Mobile DNA aka

A

Jumping genes

103
Q

What do transposons provide?

A

A clue into the history and ecology and bacteria

104
Q

Rearrangement occurs via the

A

reverse complement

105
Q

Leprosy is

A

Host-restricted

106
Q

What does HGT allow

A

Population recovery

107
Q

What is recombination?

A
  • disruption of inheritance
  • loci-set transfer

Michaelmas Term 1 (42 decks)

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