Lecture 2 - Organisation of genomes Flashcards
How are bacterial genomes often arranged?
in operons allowing coordinated expression
- operons are often polycistronic, meaning that a single mRNA transcribed from a single promoter may contain multiple genes (terminated by transcriptional terminator)
- genes within an operon usually have a related function e.g. all the genes required for histadine biosynthesis are found in one operon
What are the features of gene organisation on the E.coli genome?
- as is common for bacterial genomes, only one DNA strand is used at any location in the genome
- forward strand = 3’ to 5’
- genes encoded within operons have related functions
- short intergenic distances between the genes in operons
- sometimes, they are organised so that the stop codon (GTA) of one gene overlaps with the start codon of the next (ATG)
- estimatied 2758 different transcription unis, 795 of which are operons
- high gene density (88% DNA encodes proteins)
What is a prophage?
- some temperate phage can integrate into the bacterial genome to create inactive lysogenic bacteria (prophage)
- the prophage can now potentially excise itself and start the lytic cycle whenever it wants, generally under times of stress
Why are prophage elements important for bacterial physiology?
-phage often carry other genes that are not important for their own replication
-often vir factors e.g. protein toxins
-Example:
-Infection and integration of a phage like Sp-15 (lambdoid phage) can confer large phenotypic changes on the bacteria
-infection of harmless strains of S.pyogenes by a phage containing the diptheria toxin converts them to bacteria that cause scarlet fever, excises under periods of stress e.g.
take antibiotics -> inducing stress -> sublethal dosage of antibiotics causes it to turn on the transcription of all its genes very quickly ->symptoms get worse before the get better
What is the size range of the bacterial genomes?
- streptomyces avermitilis MA-4680 - 9.1mb
- mycoplasma genitalium G37G-37 - 0.58mb
What are the features of the Streptomyces coelicolor genome, what does it use its large genome for?
large, ~9mb
- large GC rich domains
- linear chromosome
For:
Multicellular development
-colonies can develop so that they can form arial hyphae and some cells can differentiate into spores
-contain over 20 large gene clusters for making antibiotics and other secondary metabolites
Soil dwelling
-Soil - nutritionally, biologyically and physically complex and variable environment
-expansion of the genome for regulation to sense and adapt to the environment- e.g. 65 sigma factors and over 50 two-componant systems
-degradation of extracellular nutrients
What are the life and genomic features of Buchnera aphidicola?
- obligate intracellular symbiont of the pea aphid
- cells localised within specialised insect cells called mycetoctyes or bacteriocytes in the aphid body cavity
- small low GC chromosome of around 640,000bp and 600 genes
- has evolved genome reduction through its intracellular lifestyle (reductive evolution) - common ancestor with e.coli (4.6mb) 200 Mya (3.5Mb)
How can the Buchnera aphidicola survive with so few genes?
Lives in a stable environment
- bacteria are alomost totally protected from environmental stresses by living inside the insect cell
- passed vertically from generation to generation, not been in the ‘outside world’ for 200mYa
- genomes have NO transcriptional regulation
- genome contains elements mainly for its symbiotic function ,which is nutritional
- bacteria provides essential amino acids to the aphid which it cannot get from its diet of plant phloem sap
How does reductive evolution occur?
-by a series of deletion and inactivation of existing genes
-initial large deletions remove large regions of the genome
-followed by smaller deletions and gene inactivation
-meaning that genomes are still relatively co-linear
E.g. Buchnera aphidicola genome is a subset of the e.coli k-12 genome, although smaller, genomes are relatively co linear
Over shorter evolutionary time what does reductive evolution result in?
-accumulation of pseudogenes
Give two examples of bacteria where selective gene loss is essential for movement into certain new niches
Salmonella typhimurium verses typhi
Escherichia coli verses Shigella flexneri
- in both cases the later organisms have many pseudogenes, (typhi and shigella)
-it appears that inactivation of certain genes has allowed these human pathogens to exploit new niches inside the human at the expense of the host range
-inactivation of some genes may be necessary to exploit new niches e.g. Shigella and typhi human pathogens
What is the smallest number of genes required to grow in the lab?
-must first define the growth conditions for growth
Scarab genomics engineered ‘Clean genome E.coli’ by deleteing 15% of the E.coli K-12 genome, all phage elements removed and it still grows fine on a minimal medium
Smallest free-living bacterium (Mycoplasma genitalium)
- 0.58Mb genome, 482 genes
- genetic studies have revealed that 100 of these genes can be mutated and still produce a viable cell
- minimal set of 382 genes
Theoretical studies suggest numbers around 250-300 genes
How are prophage elements formed?
-bacterial viruses
-usually infect bacteria, copy themselves and then kill the bacteria (lytic bacteria)
HOWEVER
-some temperate phage can integrate into the bacterial genome to create lysogenic bacteria (prophage)
-the prophage can now potentially excise itself and starty the lytic cycle whenever it wants
What is a cryptic prophage?
if a prophage stays in a genome for a long time it will accumulate mutations and may become inactive, ‘junk DNA’
