6/7 - Prokaryotic Genomes

Question 1

What is the criticism for the name prokaryotes?

Answer 1

• Archaea and eukarya are more closely related to each other than either is to bacteria
• Prokaryotes is a negative definition (nu nucleus), it would be better to call them bacteria and/or define prokaryotes as having coupled transcription and translation (a positive character)

Question 2

What is the great plate count anomaly?

Answer 2

The cultured cells the we observe and classify are essentially weeds, easy to isolate and easy to grow. Don’t necessarily represent the diversity of nature.

True diversity is better revealed by PCR amplification and analysis of rDNA. The more you look, the more diversity there is.

Medically/industrially relevant species are analyzed first

Question 3

Describe chromosome features of prokaryotes

Answer 3

Nucleoid

Circular/linear/circular and linear/megaplasmid

Some bacteria have a single copy of the chromosome, some have upwards of 200

Question 4

Describe gene density vs. genome size for the three domains of life

Answer 4

Bacteria: Very linear (highly uniform gene density)
Archaea: Very linear
Eukaryotes: Not so linear…

Question 5

How does degree of sequence divergence effect rate of recombination?

Answer 5

More recombination when more related

Homologous recombination needs homology among species/population to generate novelty

Question 6

What is the clonal model of novelty in prokaryotic genomes?

Answer 6

Novelty comes from mutations arising within asexual populations (eg. tree of life)

This is in contrast to homologous recombination and lateral gene transfer

Question 7

What are insertion sequences?

Answer 7

Particular to prokaryotes

Small DNA segments that are capable of transposition (movement in the genome) and mediating recombination (within and between genomes, even to archaea)

They can be embedded in genes, but don’t have to be. Code a protein that facilitates the transposition (transposase).

Characterized by a pair of inverted repeats which are needed to signal for recognition by the transposase and for the DNA cleavage needed for IS displacement

Often found on plasmids where they can mediate recombination with chromosomal DNA

Question 8

What are non-replicative and replicative IS elements?

Answer 8

Non-replicative: IS element is excised from donor site and inserted into a new site

Replicative: IS element is excised and inserted into multiple sites at the time of DNA replication.

Question 9

What are genomic islands?

Answer 9

Prokaryotic regions of chromosomal DNA that are anomalous, they have been acquired by lateral gene transfer. Usually pretty big, unique and interesting.

Often in one organism, but not another of an equal strain (patchy distribution among a population)

Originally called pathogenicity islands, often contain functionally related genes. Often enriched in mobile genetic elements, transposases, integrases, IS elements, tRNA genes and repetitive sequences.

Question 10

Describe tRNA in genomic islands

Answer 10

It turns out that tRNAs are in spots where recombination events seem to happen. They are recombinogenic.

Question 11

Give three ways for detecting foreign genes in a genome (from LGT)

Answer 11

• Gene presence/absence
• Compositional anomalies/genomic landscape
• Phylogenetic incongruence.

Question 12

Give three methods for LGT

Answer 12

• Bacterial transformation (release and acquisition of DNA through environment)
• Bacterial transduction (virus mediated genetic exchange)
• Bacterial conjugation (pillus formation)

Question 13

What are integrative and conjugative elements (ICEs)? How are these related to genomic islands?

Answer 13

Bacterial mobile genetic elements that primarily reside in the host chromosome but can excise and be transferred to other cells by conjugation.

Integration often occurs at tRNA genes

Conjugative transfer typically occurs via assembly of type IV secretion system where DNA passes by ‘rolling circle replication’

Many genomic islands are ICEs that have lost the ability to mediate excision and/or conjugation

Question 14

What is amelioration?

Answer 14

A change in the nucleotide composition of a laterally transferred gene (or group of genes) towards that of its current genomic context.

Acquired genes resemble their donor genomes in G+C content and codon bias at the time of transfer, but over time they come to resemble their recipient genome.

Question 15

List four factors influencing frequency of successful transfer between organisms

Answer 15

• Physical proximity
• Gene-transfer mechanisms (often eating another)
• Metabolic compatibility (will the gene just be destroyed)
• Gene expression systems (proper cis elements, presence of introns etc.)

Question 16

What is a pan genome?

Answer 16

The collection of genes shared among members of the same ‘species’

The core genome is gene families shared by all genomes

Question 17

Describe core genes and variable genes in prokaryotes

Answer 17

Prokaryotic genomes are highly dynamic entities comprised of

(i) a relatively stable (albeit unexpectedly small) ‘core’ of genes and
(ii) variable ‘accessory’ genes, which come and go via LGT, facilitating rapid adaptation of the organism to new environments.

Pan genome increasing, core genome decreasing as more genomes are sequenced.