Prokaryote evolution Flashcards
What are prokaryotes?
Bacteria and Archaea
How long have prokaryotes been evolving for?
~4 billion years
T or F: all prokaryotes (and all life) are related
true
What significance is it that all prokaryotes, and all life, are related?
because we can use prokaryotes as a baseline to study evolution and population genetics
What is allowing new discoveries?
innovations in DNA sequencing technology aka genomics
What are the major groups in the tree of life?
Archaea
Bacteria
Eukaryotes
Candidate Phyla Radiation (newly discovered bacteria)
What were the new bacteria that have been recently discovered?
a very large (cm long) bacterium with membrane bound organelles
sulfur-oxidizing bacteria
Ca. Thiomargarita magnifica
- largest single cell organism discovered yet
found in Caribbean mangroves
the newly discovered bacteria, Ca. Thiomargarita magnifica, are more similar to prokaryotes or eukaryotes?
they are single-celled prokaryotes, but more similar to eukaryotes because they have membrane bound organelles and vacuoles
What are the 3 key features of prokaryotic evolution?
- good at obtaining and exchanging DNA
- cells are typically haploid (no dominance or recessive, all genes are expressed)
- most have very big population sizes
Is genetic drift or natural selection a stronger driver of prokaryotic evolution? why?
natural selection because generally population sizes are very large
GD only has strong influence on small population sizes
Describe the bacterial genome
mostly coding DNA genes
very little noncoding, intergenic, and pseudogenes
very streamlined genome
T or F: typically, free-living bacteria have larger genomes than those that require a host
true
What are the 3 major ways DNA can be exchanged in prokaryotes?
conjugation (plasmid-mediated)
transduction (virus/phage or transposable element-mediated)
transformation (uptake from environment)
What are the 2 ways DNA is acquired by prokaryotes?
homologous recombination
non-homologous recombination
Describe homologous recombination
basically the same as gene flow and sexual recombination seen in eukaryotes
Describe non-homologous recombination
lateral/horizontal gene transfer - a way to bring in new genetic material
Why are prokaryotes good at acquiring and/or exchanging DNA?
they can use 3 different methods of exchanging DNA
they can do homologous recombination or non-homologous recombination
What is horizontal/lateral gene transfer?
a method that prokaryotes use to acquire new genetic material from the environment
huge source of innovation and adaptation for prokaryotes
How is horizontal/lateral gene transfer detected?
phylogeny can be used to compare the evolutionary history of the gene
assess sequence features (ex. % GC content) - looking at genome properties
look at neighbours of virus genes
What type of genes are horizontally transferred?
antibiotic resistance is plasmid-mediated = genes evolve in exposure to antibiotics will evolve resistance to them
all genes CAN be horizontally transferred in evolutionary time
virulence genes
T or F: all genes can be horizontally transferred in prokaryotes
true
Describe the sushi gene and its relationship to lateral gene transfer
new enzyme (porphyranase - PorA and PorB) that are capable of breaking down the complex carbohydrates in seaweed
these enzymes are found in the marine bacteria, Zobellia galactovorans
Bacteriodes plebeius (Bp), a gut microbiome in Japanese people has acquired the PorA and PorB enzymes by lateral gene transfer from marine bacteria found in the seaweed used in sushi rolls
If prokaryotes are so good at acquiring new genes, how do they maintain such streamlined genomes?
they are also very good at losing genes
Explain how prokaryotic genomes are dynamic
they are always fluctuating - gaining and losing genes
comparing genomes of closely related strains may show different composition of genes
How might closely related strains differ in their genome gene content?
they may have
shared core genes
but different non-core (accessory) genes that have ecological significance
What is the most abundant photosynthetic organism on earth?
marine cyanobacterium
How many species of marine cyanobacterium is there?
one
Prochloroccus marinus
How is there just one species of marine cyanobacterium if it’s the most abundant photosynthetic organism on the planet?
there’s a LOT of variation
homologous recombination creates a lot of shared and a lot of differences in nonshared genes
What did the comparison study of 2 strains of P. marinus cyanobacteria that are both adapted to high light conditions (ie., same ecology) find?
they both had very small genomes
most of which were shared
139-236 were not shared (still a large amount of genome) and were unique to the strain
What was notable about the strain-specific genes found in the genomes of the two light-adapted strains of P. marinus?
these genes were found in genomic islands and associated with phage genes (horizontal transfer)
these genes are ecologically important
What does having strain-specific genes even within the same species of P. marinus cyanobacteria tell us?
there are evolutionary differences between ecologically similar strains - evolutionary differences within a single species
How do the genomes of the studied P. marinus strains compare to that of E.coli?
their genomes are very small compared to E. coli, even though they’re both free-living bacterium
What are genomic islands?
part of a genome that was horizontally transferred
How do you interpret a graph comparing two genomes? Use the 2 P. marinus strains as an example
looked at two strain-specific genes, one from one strain (MED4) and one from the other strain (MIT9312)
the strain-specific genes from the genomes are the axes
genomic islands are shaded
1:1 line shows shared genes in mostly the same order within the genome
the break in the 1:1 line shows where there’s shared genes but in a different order within the genome
the 1:1 and the break show the CONSERVED genes
everything deviating from the 1:1 line is a strain specific gene
How were the strain-specific genes in the genomic islands of the 2 P. marinus genomes related to the ecology of the strains?
they were related to:
obtaining nutrients
adaptations for environmental conditions
predator defense
viral defense
How can the evolution of gene loss be studied?
counting the number of inactivating mutations on pseudogenes tells us how long a pseudogene has been present in the genome - can compare 2 genomes
an accumulation of inactivating mutations means the pseudogenes must be older because they have persisted long enough to acquire more mutations
What did the study of pseudogenes tell us about the evolution of gene loss in bacteria?
most pseudogenes were young and had just one inactivating mutation, which means they are being removed = at the population level, pseudogenes are not persisting very long
What type of evolutionary force would be acting on a prokaryotic species like P. marinus? why?
natural selection would be strongest force because population is huge, it’s the most abundant photosynthetic organism on earth
What type of prokaryotic genome is favoured by natural selection? give an example
small, streamlined genomes such as P. marinus are favoured
How do we know that natural selection is favouring small, streamlined genomes such as P. marinus?
because it’s the most abundant photosynthetic organism on earth = very successful
Why are small, streamlined genomes favoured?
it’s costly to maintain unnecessary genes
- gene products may be expensive to produce
- pseudogene products may be damaging
cells with smaller genomes may replicate faster
if nutrients are available from other organisms (ex. hosts), metabolic genes can be lost
What is one reason why non-free living prokaryotes tend to have very small genomes?
they are able to acquire nutrients from their host so they don’t need, and can get rid of, metabolic genes (cannot survive without their hosts)
How can the idea that non-free living bacteria lose metabolic genes because they steal nutrients from their hosts be tested?
experimental evolution
Discuss the set up of the study that looked at the metabolic dependency of E. coli (the loss of metabolic genes from the E. coli genome)
E. coli have relatively large genomes
they are not free-living
they have lost the metabolic genes to produce amino acids on their own and instead rely on stealing from hosts
experimental evolution study looked at two groups: control vs. E. coli treated with amino acids
study: conducted the study 8 times with E. coli strands that have not evolved to uptake amino acids from the environment and were treated with amino acid solution
What were the results of the study that looked at the metabolic dependency of E. coli (the loss of metabolic genes from the E. coli genome)?
in the amino acid treatment, E. coli strands that have not evolved to uptake amino acids from the environment, repeatedly and rapidly (over short generation time) lost the ability to make amino acids and instead took up amino acids from their environment
this was seen in 7/8 replicates = evolution of loss of the metabolic genes responsible for synthesizing amino acids occurred over and over again
fitness of bacteria that can’t synthesize AA on their own measured:
highest when reintroduced to control WT bacteria because they were getting AA from environment and their WT neighbours
What does the increased fitness (and the repeated evolution) of the bacteria that cannot produce amino acids on their own tell us about genome size and natural selection?
natural selection is favouring the loss of the genes that synthesize amino acids when there are amino acids present in the bacteria’s environment = streamlined genomes are favourable
How do prokaryotes maintain streamlined genomes?
by rapidly removing unnecessary genes and pseudogenes = they’re very good at deletions
