Genome structures: the Bacteria and the Archaea Flashcards
Genome structures: the Bacteria and Archaea
- DNA is circular.
- divided into true genomic DNA (chromosomes, usually 1-3 at most) and replicon DNA (plasmids, megaplasmids, chromids).
- no protein associated to the DNA per the Eukarya really but there are some histones in the Archaea.
- genome sizes are very variable.
- introns/exons are very rare – only a few proteins in a few taxa.
- inteins are fairly common, usually in DNA-attacking enzymes. Used as safety cap to stop it attacking DNA. It cuts the intein region from itself and spits it out for the enzyme to then become active.
- horizontal gene transfer is commonplace.
- prophage (viruses) are often present
Genome structures: reality versus sequences
- in theory, all the DNA in a given organism can be sequenced.
- this results in nice, closed-circle genome images.
- reality is that to save costs, the final gaps (5 % of the genome or less) are seldom closed nowadays
– leaves a series of contigs and scaffolds instead. - “completed” versus “permanent draft” quality
Genome plots – largely useless
- circular plots are too hard to interpret so useless
in this example (Thiomicrorhabdus heinhorstii, a member of the Thiotrichales from a marine freshwater interface in Florida), the inner ring is the G+C content and you can see an above average region
(olive) – in this case, this is a prophage (bacteriophage genomes integrated into the host genome)
Origins of replication
Name origin of replication in bacteria and in eukarya
- traditionally “12 o’clock” is the origin of replication. Don’t confuse with origin of transfer (oriT) in plasmids etc.
- point at which DNA replication commences.
- in the Bacteria, this is a single site:
the oriC gene (0.25-2.5 kbp). - in the Archaea, 1-4 copies (oriC1, oriC2, oriC3 and oriC4) are spaced around the genome – the map is oriented to oriC1 usually
oriC in the Bacteria
Messer (2002) FEMS Microbiol. Rev. 26: 355-375 will give you work done last century in a good review and you can bring it up to date with more recent work.
Size Range: 0.25 – 2.50 kbp segment of DNA.
Initiator Protein DnaA:
Binds to a specific dsDNA DnaA-box site.
Recognizes a DNA Unwinding Element (DUE) within oriC (origin of replication).
DUE Characteristics:
AT-rich and primarily single-stranded DNA.
DnaA Binding Elements:
Helix-turn-helix element binds the DnaA-box.
AAA+ ATPase domain binds the DUE.
Critical Spacing:
Proper spacing between DnaA-box site and DUE is crucial for function.
Significance:
DnaA initiates DNA replication by binding to specific DNA sequences and promoting unwinding of DNA strands.
Structural elements like helix-turn-helix and AAA+ ATPase domains play key roles.
oriC in the Archaea
best studied in Saccharolobus solfataricus (used to be “Sulfolobus solfataricus” before 2018).
Wu et al. (2014) Frontiers Microbiol. 5: 179
- same kind of size, but 3-4 around genome.
- origin of replication boxes (ORBs) or mini-ORBs are found in each oriCxcopy (x = 1 to 3 or 4).
- extremely diverse even within a single species.
- Orc1/Cdc6 initiator protein binds oriCx – there are multiple paralogs with different binding-affinities e.g. one Orc1 might bind strongly to oriC1 but weakly to oriC3 or oriC2.
- WHiP (Werner helicase interacting proteins) can also act as initiators.
- initiators oligomerise at their binding site.
- generally same principles as in the Bacteria but more complex with more structures formed.
Replicons and things that sound like them!
Replicons are genetic units or entities that can replicate independently within a cell. They serve as the basic functional and structural units of replication
Chromosomes in Bacteria and Archaea:
Both Bacteria and Archaea typically have one chromosome, and it is always the largest replicon.
The chromosome serves as the main genetic material and is crucial for the organism’s viability.
Separation of Replicons:
In addition to the chromosome, there are other replicons such as plasmids, chromids, and megaplasmids.
These replicons are maintained and replicated separately from the main chromosome.
Characteristics of Plasmids:
Plasmids are the smallest replicons and have distinct features.
G+C fraction is >1 mol% below that of the chromosome.
Plasmids typically lack core genes and are seldom shared beyond species.
They are often used as cloning vectors in vitro.
Megaplasmids:
Megaplasmids are somewhat vague and may function as secondary chromosomes.
They are relatively rare in occurrence.
Chromids:
Chromids are plasmid-chromosome hybrids and are second in size to the main chromosome.
Their G+C fraction is within ±0.6 mol% of that of the chromosome.
Chromids typically have a size >0.25 Mbp, with most being >0.5 Mbp.
They contain some core genes, and genes on chromids are often found across the entire genus.
Cloning Vectors and Anthropogenic Replicons:
Fosmids, cosmids, and phasmids are anthropogenic cloning vectors not naturally found in organisms.
Fosmids are based on the F-plasmid from bacteria (Escherichia coli) and can hold a 40 kb insert DNA.
Cosmids are based on the cos operon from the Lambda phage (Escherichia virus lambda) and can hold 37-52 kb insert DNA. They can be used in mammalian tissue culture cell lines.
Phasmids are also anthropogenic and based on the f1 phage DNA (Inovirus Escherichia virus M13). It’s important not to confuse them with “M13 primers” used on pUC plasmids in cloning.
Prophage (sleeping viruses)
- viral DNA from bacteriophages, now incorporated into the host DNA.
- under the right conditions (e.g. change in Ca(II) or Mg(II) ionic strength) the prophage will be translated and become a mass of phage virons that leave (and kill) the cell.
- detected using tools like PHASTER that scan genome sequences for known prophage motifs (Arndt et al. (2016) Nuc. Acids Res. 44: W16-W21)
- 1-10 prophage are not uncommon per genome.
- often mis-annotated
Horizontal gene transfer (HGT)
- transfer of DNA from species to species or strain to strain, usually by temperate (lysogenic) phage or plasmids. Integrons and other mobile genetic elements are also
a source of HGT. - major route of antibiotic resistance transfer.
- also a route of metal resistance transfer.
- if the environmental conditions are right, transformation can occur – a piece of genomic DNA from bacterium A can transfer to bacterium B – the latter must be competent (electrocompetent, chemically competent etc) first.
- conjugation (bacterial sex, basically) occurs between an F+ cell (has a sex pilus, used to be called a ‘male cell’) and an F- cell (does not, used to be called a ‘female cell’).
Sex pilus holds the cells together and plasmid DNA is transferred from F+ to F-. If the plasmid being transferred has the F genes on it, the recipient will become F+
(“transgender Bacteria” as some people call it). - Archaea also conjugate, though stress is often needed to get them to form pili.
Genomes of the Bacteria and the Archaea
Summary
You should be able to:
* Describe the properties of genomic DNA in both Domains.
* Describe the origin of replication in the Bacteria versus the Archaea and discuss in detail the differences in structure and function.
* Describe the properties and roles of all the various replicons that have been described.
* Describe different methods of horizontal gene transfer including transformation and conjugation but could also include phage transfection etc.
* (eventually, after Dr Boschetti’s lecture!) Understand the differences between genomic and secondary DNA in the Bacteria and Archaea and Eukarya
Name the size order of the products we get when sequencing genomes
Genome
reads
contigs
scaffolds
