chapter 3 genomes

what is a genome?

complete set of DNA in an organism
all of the genes found within the cell

bacterial species chromosome characteristics

single circular
some species have 2+ circular chromosomes
few have linear chromosomes- easier to use for analysis
some have both
dna is actually present as a closed circle in the cell

plasmid characteristics

small, circular extrachromosomal dna
no essential genes- can be lost (transient)
specialty genes (antibiotic resistance, virulence, symbiosis)
own self-interest in mind

what does it mean by the plasmid have their own self-interest in mind

sometimes the genes encoded on a plasmid are beneficial to the bacterial cell and therefore retained

other times, a plasmid contains a toxin/antitoxin module that forces the cell to retain the plasmid or be killed

how does toxin/antitoxin module work?

doesnt like the idea of bacteria getting rid of them

toxin- long lived and makes a bunch

antitoxin- inactivates the toxin (short lived)

when both are expressed, the cell lives
without plasmid- antitoxin is destroyed bc toxin is still present

defining feature of plasmid vs chromosome

plasmid doesnt have essential genes- cell can live without it

chromosomes have essential genes- cell needs to survive

bacteriophage

viruses that infect bacteria
can integrate into the bacterial chromosome and become a prophage

how does bacteriophage become a prophage

lysogenic- injects the dna into the bacterial cell
these add to the bacterial genome
some encode virulence genes and toxins
number and size of prophage can be substantial

sizes of bacterial genomes are characteristics of bacterial species

within a single bacterial species , there are many strains
each strain has a unique genome
total genome size does not vary much within a species

core genome

includes all of the genetic features that are included in all strains of a particular species

accessory genome

each genome will, also, have other genetic features that contribute to it

pan-genome

all genes that exist within a species

how are genomes packed for bacteria

little space, very few base pairs, between genetic features
very little dna is junk
even non-coding sequences often have regulatory roles

how do dna base composition differ between species

proportion of A, T, C, G is relatively constant across a genome

but some species differs

the proportion is measured as GC content
the proportion of genome comprised of G and C
known to range from 14% in some species to 75% in others

how can genomic architecture impact gene expression

dosage effect
replication- genes that are near to the origin of replication are copied first
this creates two copies of these genes in the cell, increasing the gene dose

dosage effect

the location of a gene within the chromosome can impact upon its expression

synteny

the order of genes in a genome (location with respect to one another) is conserved across bacterial species

how does conservation of the order of genetic features between bacterial species work

division and cell wall synthesis clusters of genes for diff bacterial species

mutations in the bacterial genome

each time a genome is replicated, errors can be made and left uncorrected
DNA damage can also lead to incorrect nucleotides being placed within the genome

point mutations

caused by dna damage and replication errors that are left uncorrected

ex: deamination of cytosine to uracil, which gets read as thymine during DNA replication

indels

small insertions or deletions
caused by slipping of the dna polymerase during replication

SNP- variant when its unclear which version is the wildtype and which is the mutation

recombination

joining of dna molecules (crossing over)

homology (sequence similarity) facilitates recombination

non-homologous recombination can also occur but at a lower frequency

mediated by bacterial enzymes

translocation

movement of dna from one place to another
can be within the same dna molecule or into a new dna molecule

inversion

a dna sequence is inverted at its original location
gene is now on the opposite strand

what can result in a change in gene expression

translocation and inversions

some inversion are intentional- way for the cell to toggle between expression levels (on/off based on orientation in respect to promoter)

mobile genetics elements

pieces of dna capable of moving around the genome at high frequency
transposons and insertion sequence elements

transposons and IS element

capable of self-excision and reintergration into the chromosome

they carry within their sequences all of the genes needed for mobilization to new parts of the bacterial genome

transposons carry extra genes, IS elements do not

can be replicative or non replicative

how does mobile genetic elements moving around affect genes and proteins

MGE can disrupt genes and render their proteins non-functional