The Prokaryotes I Flashcards
Describe bacterial genomes
- 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
List the exceptions to the bacterial genome being mostly single, circular chromosomes rule
- Burkholderia cenocepacia
- Borrelia burgdorferi
Describe Burkholderia cenocepacia
- three circular chromosomes
- 3.87, 3.22, 0.88 Mb
Describe Borrelia burgdorferi
- linear chromosomes
- 0.91Mb
- 12 linear + 9 circular plasmids (60kb)
Describe the episomal elements of the bacterial genome
- plasmids
- phases
Describe the shape of plasmids and phases
Circular (very rarely linear)
Give examples of exceptions to the episomal element conventions
- Rhizobium leguminosarum
- Borrelia burgdorferi
Describe Rhizobium leguminosarum
- 6 plasmids
- largest 0.87Mb
Compare and contrast operons in prokaryotes v eukaryotes
Prokaryotes: often have them
Eukaryotes: typically do not
What is an operon?
A cluster of Co-transcribed genes
Compare and contrast introns in eukaryotes v prokaryotes
Eukaryotes: preserved
Describe the range of introns in eukaryotes
- only a handful in smaller protists
- 8 per gene in humans
Describe the size of introns in eukaryotes
- 20-200nts long
- up to 2kb in larger animals
How much larger are eukaryote genomes compared to prokaryote genomes generally?
An order of magnitude
Bacterial genomes are
Highly compact
Describe the relationship between genome size and number of ORFs in the genome
Positive, strong, linear correlation
ORFS: 0-9000
Genome size: 0-10
Most bacterial genomes contain very little
Non-coding DNA
ORF
- open reading frame
- a sequence of DNA that could be translated to give a gene
As genome size increases, so does the
- Repertoire of genes encoded
- metabolic capacity
Graph depicting % of gene by function against genome size
- 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%
Describe the smallest bacterial genome
- Candidatus Acintomarina minuta
- 0.0013Mbp
- 800 ORFs
Describe the largest virus genome
- Pandorravirus
- 2.5Mbp
Describe the largest bacterial genome
- Sorangium cellulosum
- gliding myxobacteria
- 14.8Mbp
What are the mechanisms of prokaryote gene transfer?
- Transformation
- Transduction
- Conjugation
- Transposable elements (mobile DNA)
What phenomenon does transformation rely on?
Not all cells within a population are competent to take up DNA at the same time
What is transformation?
DNA uptake
Give examples of naturally high-efficiency transformers
- Neisseria
- Acinetobacter
- Bacillus
- Streptococcus
- Haemophilus
Give examples of poor transformers
Many Gram negative bacteria and archaea (e.g. E. Coli)
How can transformation be induced?
- Electroporation
- Ca2+ ions
Describe electroporation
Brief high voltage electrical pulses
To transform, cells must be
- competent
- competence inducible
How is transformation (in the form of stable incorporation of foreign DNA) achieved?
- dsDNA from the environment binds to cell
- Exonuclease digests dsDNA to ssDNA
- ssDNA (6-8Kbp) associates with competence proteins
- Strand replacement by donor DNA
What is needed for transduction?
A phage
What is generalised transduction?
Any gene can be transferred from donor to recipient
How often does generalised transduction occur in phage lytic cycle?
- low frequency
- 1 cell in 10^6/10^8
What is specialised transduction?
specific bacterial DNA fragments from chromosomes adjective to phage integration site may be transferred
Describe specialised transduction
Selective but efficient
Give an example of specialised transduction
Galactose catabolism in E. Coli when phage is in lysogenic cycle
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
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+
a+
Any bacterial gene
s+
Special bacterial gene
What does conjugation require?
A plasmid
Give an example of a conjugation plasmid
E Coli F+ cell (forms pilus which retracts)
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
What is the accessory genome?
Mobile DNA
List the two types of movement that MGEs can undergo
1) intercellular
2) intracellular
MGEs
Mobile genetic elements
List the MGEs that undergo intercellular movement
- Phages
- Plasmids
- ICEs
ICE
- Integrative conjugation elements
- derivative of a phage/plasmid
List the MGEs that undergo intracellular movement
- Transposons
- Insertion sequences
- Integrons
- Introns
Compare and contrast transposons with insertion sequences
- both require transposase
- insertion sequences are smaller elements
What do integrons rely on?
Integrase
Describe the general structure of a bacterial composite transposon
Genes for transposition at either end are bracketed by inverted repeats
What are intracellular MGEs?
- selfish genetic elements, that can increase their own transmission at the expense of other genes
How are MGEs classified?
According to their genetic makeup (core and accessory genes, and inverted repeat regions)
What do transposons use transposase enzymes for?
to ‘cut and paste’, ‘copy and paste’ or Co-integrate DNA position
Why are MGEs advantageous?
They carry genes which give their host a selective advantage
Give examples of advantageous MGE genes
- Antibiotic resistance
- Virulence
- Unusual metabolic pathways
- Gene expression
Describe insertion sequences
- they can rapidly expand in bacterial populations
- can be influenced by host lifestyle
Tn
Transposon
Gene cassette
A type of MGE that contains a gene and a recombination site
What is the consequence of the widespread occurrence of genetic exchange between bacteria?
- bacterial genomes are not closed
- closely related bacteria open genomes
Open genomes contain
Very different gene complements
The pangenome
- the genes available to a particular bacterium
Describe the core genome
- the operating system
- DNA replication, ribosomes, cell envelope, key metabolic pathways
Describe the parasitic elements of bacterial genomes
- phages, plasmids
- e.g. toxins, restriction/modification systems
Describe the accessory genome in bacteria
alternative metabolic pathways, transport systems
Describe the gene pool of bacteria
- e.g. antibiotic rand distance, degradative metabolism
Which types of selection may genetic elements be subject to?
- stabilising (negative)
- diversifying (positive)
- neutral (rare in most bacteria)
What are the three mechanisms of genetic change?
- Point mutation
- Indels
- Rearrangement
At what scale does a point mutation act?
Small
At what scale does an indel act?
Small/large
At what scale does a rearrangement act?
Small/large
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
Congruence
Phylogenetic tree topologies are similar
What have previous models of bacterial phylogeny assumed?
- no loss of diversity
- no recombination
Are there are bacteria left in which previous assumptions still hold true?
Yes - genetically monomorphic pathogens
Give examples of genetically monomorphic pathogens
- Mycobacterium leprae
- Mycobacterium tuberculosis
- Yersinia pestis
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
What is Muller’s ratchet?
Reductive evolution
Why are small asexual bacterial populations susceptible to Muller’s ratchet?
They are vulnerable to the accumulation of deleterious mutations
What are some examples of bacteria especially vulnerable to Muller’s ratchet
- Mycobacterium leprae
- Yersinia pestis
Describe the clonal population model
Asexuality (while infrequently facilitating periodic selection), reduces diversity by bottlenecking
What are mosaic genes?
Chromosomal genes containing homologously recombined introduced genes
What is the impact of recombination on bacterial population structure?
Recombination disrupts clonal structure, disrupting arboreal phylogeny, linkage disequilibrium and congruence
Why do we see a spectrum of clonal signal in different bacterial populations?
Differing relative rates of recombination to mutation
Prokaryotes generally have
Small, compact, highly structured genomes with a high density of protein-coding genes
Prokaryote diversity comprises
Accumulated mutation in the core genome, and lateral transfer of accessory genome
What is the effect of the Mobileome?
It creates very large pangenomes
HGT/LGT are
‘A major impact on prokaryote population structure’
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
Describe the plasmid content of E Coli
- 300 plasmids
- wouldn’t expect to see them all in a cell at one time
Describe transposable elements
Shortest DNA that can move between cells
Describe the capsule
Smooth
Compétence proteins
Shuffling proteins through membranes to incorporate bacterial chromosomes
What can electroporation or calcium ions do to cell membranes?
Make them more permeable to take up DNA
Why aren’t all cells in a population transformable at the same time?
Group survival mechanism
Prophage
Integrated virus
How is phage DNA excised?
UV
How long does conjugation take?
5 mins
Mobile DNA aka
Jumping genes
What do transposons provide?
A clue into the history and ecology and bacteria
Rearrangement occurs via the
reverse complement
Leprosy is
Host-restricted
What does HGT allow
Population recovery
What is recombination?
- disruption of inheritance
- loci-set transfer
