Lecture 25

Question 1

What is the definition of a minimal genome and why?

Answer 1

The minimal genome is the minimal number of genes required to support cellular life independently of a host. (Ones that require a host are getting to much to support to count)

Question 2

What is an essential gene and what are the two potential problems for working them out? What are two approaches?

Answer 2

An essential gene is essential for bacterial growth or survival, hence mutation will mean no growth, these could be conditionally essential (depends on the growth medium), or essential but redundant (some genes can do the same essential function but deletion of either gene is okay). This means how we test the essentiality will vary the outcome, a top down approach (remove gene see if it survives), vs a bottom-up approach will alter perception, e.g top down would lead to essential but redundant genes both being non essential.

Question 3

What is P.ubique?

Answer 3

P. ubique is the smallest known free living bacteria, makes up 25-50% of all bacteria in the ocean and has roughly 1300 genes and no junk (median space between genes of 3 base pairs, believed to be for energy savings during replication as an advantage for its nutrient poor niche).

Question 4

What are the caveats of estimation of minimal genome by genome comparison?

Answer 4

The caveats of estimation of minimal genome by genome comparison are that:

1. some proteins share no sequence or structural similarity but can perform the same function.
2. These will be omitted from the analysis.
3. Hence more than one different methods for achieving something will lead to both being ignored.

Question 5

What are four approaches for estimating the minimal genome?

Answer 5

Approaches to defining the minimal genome include: looking in nature for the minimal genome, an example of which is genome sequencing of many ocean bacteria.

2. Estimation of minimal genome by genome comparison (seeing which genes don’t change, found a minimal genome of 256 genes, found to be zero as more bacteria are compared).
3. Estimation of minimal genome by mutagenesis (took two bacteria with small genomes and did transposon mutagenesis, transposons in essential genes would lead to no growth insertion sites determined by DNA sequencing, this led to a minimal genome of 382 genes).
4. Making a synthetic minimal cell, this would be handy for growing compounds for consumer use (found 473 minimal genes, this is the only bottom up approach).