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
2
Q
List the exceptions to the bacterial genome being mostly single, circular chromosomes rule
A
- Burkholderia cenocepacia
- Borrelia burgdorferi
3
Q
Describe Burkholderia cenocepacia
A
- three circular chromosomes
- 3.87, 3.22, 0.88 Mb
4
Q
Describe Borrelia burgdorferi
A
- linear chromosomes
- 0.91Mb
- 12 linear + 9 circular plasmids (60kb)
5
Q
Describe the episomal elements of the bacterial genome
A
- plasmids
- phases
6
Q
Describe the shape of plasmids and phases
A
Circular (very rarely linear)
7
Q
Give examples of exceptions to the episomal element conventions
A
- Rhizobium leguminosarum
- Borrelia burgdorferi
8
Q
Describe Rhizobium leguminosarum
A
- 6 plasmids
- largest 0.87Mb
9
Q
Compare and contrast operons in prokaryotes v eukaryotes
A
Prokaryotes: often have them
Eukaryotes: typically do not
10
Q
What is an operon?
A
A cluster of Co-transcribed genes
11
Q
Compare and contrast introns in eukaryotes v prokaryotes
A
Eukaryotes: preserved
12
Q
Describe the range of introns in eukaryotes
A
- only a handful in smaller protists
- 8 per gene in humans
13
Q
Describe the size of introns in eukaryotes
A
- 20-200nts long
- up to 2kb in larger animals
14
Q
How much larger are eukaryote genomes compared to prokaryote genomes generally?
A
An order of magnitude
15
Q
Bacterial genomes are
A
Highly compact
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
17
Q
Most bacterial genomes contain very little
A
Non-coding DNA
18
Q
ORF
A
- open reading frame
- a sequence of DNA that could be translated to give a gene
19
Q
As genome size increases, so does the
A
- Repertoire of genes encoded
- metabolic capacity
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%
21
Q
Describe the smallest bacterial genome
A
- Candidatus Acintomarina minuta
- 0.0013Mbp
- 800 ORFs
22
Q
Describe the largest virus genome
A
- Pandorravirus
- 2.5Mbp
23
Q
Describe the largest bacterial genome
A
- Sorangium cellulosum
- gliding myxobacteria
- 14.8Mbp
24
Q
What are the mechanisms of prokaryote gene transfer?
A
- Transformation
- Transduction
- Conjugation
- Transposable elements (mobile DNA)
25
What phenomenon does transformation rely on?
Not all cells within a population are competent to take up DNA at the same time
26
What is transformation?
DNA uptake
27
Give examples of naturally high-efficiency transformers
1. Neisseria
2. Acinetobacter
3. Bacillus
4. Streptococcus
5. Haemophilus
28
Give examples of poor transformers
Many Gram negative bacteria and archaea (e.g. E. Coli)
29
How can transformation be induced?
- Electroporation
- Ca2+ ions
30
Describe electroporation
Brief high voltage electrical pulses
31
To transform, cells must be
- competent
- competence inducible
32
How is transformation (in the form of stable incorporation of foreign DNA) achieved?
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
33
What is needed for transduction?
A phage
34
What is generalised transduction?
Any gene can be transferred from donor to recipient
35
How often does generalised transduction occur in phage lytic cycle?
- low frequency
- 1 cell in 10^6/10^8
36
What is specialised transduction?
specific bacterial DNA fragments from chromosomes adjective to phage integration site may be transferred
37
Describe specialised transduction
Selective but efficient
38
Give an example of specialised transduction
Galactose catabolism in E. Coli when phage is in lysogenic cycle
39
How does generalised transduction work?
- 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
40
How does specialised transduction work ?
- 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+
41
a+
Any bacterial gene
42
s+
Special bacterial gene
43
What does conjugation require?
A plasmid
44
Give an example of a conjugation plasmid
E Coli F+ cell (forms pilus which retracts)
45
Describe conjugation
- 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
What is the accessory genome?
Mobile DNA
47
List the two types of movement that MGEs can undergo
1) intercellular
2) intracellular
48
MGEs
Mobile genetic elements
49
List the MGEs that undergo intercellular movement
1. Phages
2. Plasmids
3. ICEs
50
ICE
- Integrative conjugation elements
- derivative of a phage/plasmid
51
List the MGEs that undergo intracellular movement
1. Transposons
2. Insertion sequences
3. Integrons
4. Introns
52
Compare and contrast transposons with insertion sequences
- both require transposase
- insertion sequences are smaller elements
53
What do integrons rely on?
Integrase
54
Describe the general structure of a bacterial composite transposon
Genes for transposition at either end are bracketed by inverted repeats
55
What are intracellular MGEs?
- selfish genetic elements, that can increase their own transmission at the expense of other genes
56
How are MGEs classified?
According to their genetic makeup (core and accessory genes, and inverted repeat regions)
57
What do transposons use transposase enzymes for?
to ‘cut and paste’, ‘copy and paste’ or Co-integrate DNA position
58
Why are MGEs advantageous?
They carry genes which give their host a selective advantage
59
Give examples of advantageous MGE genes
1. Antibiotic resistance
2. Virulence
3. Unusual metabolic pathways
4. Gene expression
60
Describe insertion sequences
- they can rapidly expand in bacterial populations
- can be influenced by host lifestyle
61
Tn
Transposon
62
Gene cassette
A type of MGE that contains a gene and a recombination site
63
What is the consequence of the widespread occurrence of genetic exchange between bacteria?
- bacterial genomes are not closed
- closely related bacteria open genomes
64
Open genomes contain
Very different gene complements
65
The pangenome
- the genes available to a particular bacterium
66
Describe the core genome
- the operating system
- DNA replication, ribosomes, cell envelope, key metabolic pathways
67
Describe the parasitic elements of bacterial genomes
- phages, plasmids
- e.g. toxins, restriction/modification systems
68
Describe the accessory genome in bacteria
alternative metabolic pathways, transport systems
69
Describe the gene pool of bacteria
- e.g. antibiotic rand distance, degradative metabolism
70
Which types of selection may genetic elements be subject to?
- stabilising (negative)
- diversifying (positive)
- neutral (rare in most bacteria)
71
What are the three mechanisms of genetic change?
1. Point mutation
2. Indels
3. Rearrangement
72
At what scale does a point mutation act?
Small
73
At what scale does an indel act?
Small/large
74
At what scale does a rearrangement act?
Small/large
75
Linkage disequilibrium
- 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
Congruence
Phylogenetic tree topologies are similar
77
What have previous models of bacterial phylogeny assumed?
- no loss of diversity
- no recombination
78
Are there are bacteria left in which previous assumptions still hold true?
Yes - genetically monomorphic pathogens
79
Give examples of genetically monomorphic pathogens
- Mycobacterium leprae
- Mycobacterium tuberculosis
- Yersinia pestis
80
Describe the progressive natural of mutational change in bacteria:
- 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
What is Muller’s ratchet?
Reductive evolution
82
Why are small asexual bacterial populations susceptible to Muller’s ratchet?
They are vulnerable to the accumulation of deleterious mutations
83
What are some examples of bacteria especially vulnerable to Muller’s ratchet
- Mycobacterium leprae
- Yersinia pestis
84
Describe the clonal population model
Asexuality (while infrequently facilitating periodic selection), reduces diversity by bottlenecking
85
What are mosaic genes?
Chromosomal genes containing homologously recombined introduced genes
86
What is the impact of recombination on bacterial population structure?
Recombination disrupts clonal structure, disrupting arboreal phylogeny, linkage disequilibrium and congruence
87
Why do we see a spectrum of clonal signal in different bacterial populations?
Differing relative rates of recombination to mutation
88
Prokaryotes generally have
Small, compact, highly structured genomes with a high density of protein-coding genes
89
Prokaryote diversity comprises
Accumulated mutation in the core genome, and lateral transfer of accessory genome
90
What is the effect of the Mobileome?
It creates very large pangenomes
91
HGT/LGT are
‘A major impact on prokaryote population structure’
92
How does the bacterial chromosome replicate?
DNA helicase replicates in two directions (leading and lagging strand) so they don’t overlap, and toxic products don’t interfere
93
Describe the plasmid content of E Coli
- 300 plasmids
- wouldn’t expect to see them all in a cell at one time
94
Describe transposable elements
Shortest DNA that can move between cells
95
Describe the capsule
Smooth
96
Compétence proteins
Shuffling proteins through membranes to incorporate bacterial chromosomes
97
What can electroporation or calcium ions do to cell membranes?
Make them more permeable to take up DNA
98
Why aren’t all cells in a population transformable at the same time?
Group survival mechanism
99
Prophage
Integrated virus
100
How is phage DNA excised?
UV
101
How long does conjugation take?
5 mins
102
Mobile DNA aka
Jumping genes
103
What do transposons provide?
A clue into the history and ecology and bacteria
104
Rearrangement occurs via the
reverse complement
105
Leprosy is
Host-restricted
106
What does HGT allow
Population recovery
107
What is recombination?
- disruption of inheritance
- loci-set transfer
