Lecture 19 - Metagenomics and HGT

Question 1

What is metagenomics?

Answer 1

The study of genetic material recovered directly from environmental samples.

Question 2

What can metagenomics be used for?

Answer 2

To study organisms that cannot be grown in the lab.

Question 3

What is used to analyse the diversity of a sample in metagenomics?

Answer 3

rDNA sequencing, using universal primers

Question 4

How can you estimate the position of an an organism on a phylogenetic tree from metagenomics?

Answer 4

By comparing ribosomal DNA from sample to cultured organisms

Question 5

Give the steps of shotgun sequencing.

Answer 5

1) Extract DNA.
2) Sonicate it - break into tiny fragments.
3) Separate by electrophoresis.
4) Pick out bands of a particular size, best for sequencing.
5) Purify DNA from the gel.
6) Try to reconstruct genome within a plasmid that allows them to be amplified.

Question 6

What are Environmental Gene Tags?

Answer 6

Short sequences from the DNA of microbial communities that contain fragments of functional genes.

Question 7

If a gene is found in two different environments, what is it likely to be?

Answer 7

An essential gene

Question 8

If a gene is only found in one environment, what is it likely to be?

Answer 8

An adaptive gene

Question 9

What are the three types of horizontal gene transfer in prokaryotes?

Answer 9

• Conjugation
• Transduction
• Natural transformation

Question 10

What is conjugation?

Answer 10

A plasmid is transferred from a donor strain to a recipient without the plasmid.
The recipient gains the plasmid.

Question 11

Which horizontal gene transfer type is the mechanism by which prokaryotes gain antibiotic resistance?

Answer 11

Conjugation

Question 12

What is transduction?

Answer 12

Genes are carried by an infected organism to a new bacteria.

Question 13

What is natural transformation?

Answer 13

A bacteria dies and releases its free DNA , which can be taken up by another bacterial cell und§er certain circumstances.

Question 14

Give an example of Horizontal Gene Transfer from a prokaryote to a eukaryote.

Answer 14

Agrobacterium tumefaciens - causes crown gall in trees (tumours).
Causes disease by transferring part of the plasmid, T-DNA, into the plant cell, which integrates into the genome of the plant.

Question 15

What is a retrovirus?

Answer 15

A class of simple viruses with an RNA genome.

Question 16

What is Rous Sarcoma Virus?

Answer 16

A type of retrovirus that causes disease in chicken cells, inducing cancerous growths.

Question 17

Give the four genes of Rous Sarcoma Virus.

Answer 17

• gag; encodes the capsid protein.
• pol; encodes the reverse transcriptase.
• env; encodes the envelope protein
• src; encodes a tyrosine kinase

Question 18

What does the ability to induce a cancerous growth depend on in Rous Sarcoma Virus?

Answer 18

An oncogene known as c-src.

Question 19

Give an example of gene capture in Rous Sarcoma Virus.

Answer 19

At some point landed next to a normal src gene and captured it.

Question 20

Who showed that transposable elements jumped between different species of plants?

Answer 20

El Baidouri (et al)

Question 21

What are Helitrons?

Answer 21

A class of transposable elements that replicate through ‘rolling circle’.

Question 22

What are heterokaryons?

Answer 22

A cell that has more than one nucleus

Question 23

What happens in anastomosis?

Answer 23

Branches from two different hyphae fuse together, leading to a cell with two different nuclei.

Question 24

Give an example of horizontal gene transfer allowing a species to exploit new ecological niches.

Answer 24

Bacterial cellulase gene transferred from bacteria in the rumen to rumen fungi.
Enabled fungi to exist within the rumen, enabling it to break down plant material.