Prokaryote evolution

Question 1

What are prokaryotes?

Answer 1

Bacteria and Archaea

Question 2

How long have prokaryotes been evolving for?

Answer 2

~4 billion years

Question 3

T or F: all prokaryotes (and all life) are related

Answer 3

true

Question 4

What significance is it that all prokaryotes, and all life, are related?

Answer 4

because we can use prokaryotes as a baseline to study evolution and population genetics

Question 5

What is allowing new discoveries?

Answer 5

innovations in DNA sequencing technology aka genomics

Question 6

What are the major groups in the tree of life?

Answer 6

Archaea
Bacteria
Eukaryotes
Candidate Phyla Radiation (newly discovered bacteria)

Question 7

What were the new bacteria that have been recently discovered?

Answer 7

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

Question 8

the newly discovered bacteria, Ca. Thiomargarita magnifica, are more similar to prokaryotes or eukaryotes?

Answer 8

they are single-celled prokaryotes, but more similar to eukaryotes because they have membrane bound organelles and vacuoles

Question 9

What are the 3 key features of prokaryotic evolution?

Answer 9

1. good at obtaining and exchanging DNA
2. cells are typically haploid (no dominance or recessive, all genes are expressed)
3. most have very big population sizes

Question 10

Is genetic drift or natural selection a stronger driver of prokaryotic evolution? why?

Answer 10

natural selection because generally population sizes are very large

GD only has strong influence on small population sizes

Question 11

Describe the bacterial genome

Answer 11

mostly coding DNA genes

very little noncoding, intergenic, and pseudogenes

very streamlined genome

Question 12

T or F: typically, free-living bacteria have larger genomes than those that require a host

Answer 12

true

Question 13

What are the 3 major ways DNA can be exchanged in prokaryotes?

Answer 13

conjugation (plasmid-mediated)

transduction (virus/phage or transposable element-mediated)

transformation (uptake from environment)

Question 14

What are the 2 ways DNA is acquired by prokaryotes?

Answer 14

homologous recombination
non-homologous recombination

Question 15

Describe homologous recombination

Answer 15

basically the same as gene flow and sexual recombination seen in eukaryotes

Question 16

Describe non-homologous recombination

Answer 16

lateral/horizontal gene transfer - a way to bring in new genetic material

Question 17

Why are prokaryotes good at acquiring and/or exchanging DNA?

Answer 17

they can use 3 different methods of exchanging DNA
they can do homologous recombination or non-homologous recombination

Question 18

What is horizontal/lateral gene transfer?

Answer 18

a method that prokaryotes use to acquire new genetic material from the environment

huge source of innovation and adaptation for prokaryotes

Question 19

How is horizontal/lateral gene transfer detected?

Answer 19

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

Question 20

What type of genes are horizontally transferred?

Answer 20

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

Question 21

T or F: all genes can be horizontally transferred in prokaryotes

Answer 21

true

Question 22

Describe the sushi gene and its relationship to lateral gene transfer

Answer 22

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

Question 23

If prokaryotes are so good at acquiring new genes, how do they maintain such streamlined genomes?

Answer 23

they are also very good at losing genes

Question 24

Explain how prokaryotic genomes are dynamic

Answer 24

they are always fluctuating - gaining and losing genes

comparing genomes of closely related strains may show different composition of genes

Question 25

How might closely related strains differ in their genome gene content?

Answer 25

they may have shared core genes but different non-core (accessory) genes that have ecological significance

Question 26

What is the most abundant photosynthetic organism on earth?

Answer 26

marine cyanobacterium

Question 27

How many species of marine cyanobacterium is there?

Answer 27

one Prochloroccus marinus

Question 28

How is there just one species of marine cyanobacterium if it's the most abundant photosynthetic organism on the planet?

Answer 28

there's a LOT of variation homologous recombination creates a lot of shared and a lot of differences in nonshared genes

Question 29

What did the comparison study of 2 strains of P. marinus cyanobacteria that are both adapted to high light conditions (ie., same ecology) find?

Answer 29

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

Question 30

What was notable about the strain-specific genes found in the genomes of the two light-adapted strains of P. marinus?

Answer 30

these genes were found in genomic islands and associated with phage genes (horizontal transfer) these genes are ecologically important

Question 31

What does having strain-specific genes even within the same species of P. marinus cyanobacteria tell us?

Answer 31

there are evolutionary differences between ecologically similar strains - evolutionary differences within a single species

Question 32

How do the genomes of the studied P. marinus strains compare to that of E.coli?

Answer 32

their genomes are very small compared to E. coli, even though they're both free-living bacterium

Question 33

What are genomic islands?

Answer 33

part of a genome that was horizontally transferred

Question 34

How do you interpret a graph comparing two genomes? Use the 2 P. marinus strains as an example

Answer 34

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

Question 35

How were the strain-specific genes in the genomic islands of the 2 P. marinus genomes related to the ecology of the strains?

Answer 35

they were related to: obtaining nutrients adaptations for environmental conditions predator defense viral defense

Question 36

How can the evolution of gene loss be studied?

Answer 36

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

Question 37

What did the study of pseudogenes tell us about the evolution of gene loss in bacteria?

Answer 37

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

Question 38

What type of evolutionary force would be acting on a prokaryotic species like P. marinus? why?

Answer 38

natural selection would be strongest force because population is huge, it's the most abundant photosynthetic organism on earth

Question 39

What type of prokaryotic genome is favoured by natural selection? give an example

Answer 39

small, streamlined genomes such as P. marinus are favoured

Question 40

How do we know that natural selection is favouring small, streamlined genomes such as P. marinus?

Answer 40

because it's the most abundant photosynthetic organism on earth = very successful

Question 41

Why are small, streamlined genomes favoured?

Answer 41

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

Question 42

What is one reason why non-free living prokaryotes tend to have very small genomes?

Answer 42

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)

Question 43

How can the idea that non-free living bacteria lose metabolic genes because they steal nutrients from their hosts be tested?

Answer 43

experimental evolution

Question 44

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)

Answer 44

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

Question 45

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)?

Answer 45

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

Question 46

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?

Answer 46

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

Question 47

How do prokaryotes maintain streamlined genomes?

Answer 47

by rapidly removing unnecessary genes and pseudogenes = they're very good at deletions