Bacterial Phylogeny

Question 1

Morphological characters of bacteria

Answer 1

Gram strain

Motility

Question 2

Biochemical (phenetic characters used for classification)

Answer 2

Functional genes
Use single carbon sources for growth - Biolog

Ability to grow at a range of pH and temperature

Question 3

Tests (phonetic characters)

Answer 3

Tests that provide large amounts of data are suitable
FAME - fatty acid fingerprint
GC/MS - compositional fingerprint
DNA sequence - DNA fingerprint

Question 4

Define artificial classification

Answer 4

A group of organisms that look similar to each other and distinct from other groups

Question 5

Define natural classification

Answer 5

A reproductively isolated group, genes do not combine with those of outsiders - are able to combine by sexual reproduction within the group

Question 6

Why are similar organisms similar?

Answer 6

Shared a recent common ancestor and therefore have more closely related genes

Question 7

What are the implications of no sexual reproduction?

Answer 7

No mixing of the gene pool so the Biological Species Concept cannot apply

Mutations during division introduce new phenetic characters so no constraints on phonetic divergence?

Question 8

What does strain designation reflect?

Answer 8

When mutations occur in reproductively isolated clones - therefore new phenotype cannot spread back into the parental population

Question 9

What are the three mechanisms of gene transfer?

Answer 9

Transformation
Conjugation
Transduction

Question 10

What is horizontal or lateral gene transfer?

Answer 10

Transfer part/all of a copy of the donor genome to the recipient – then stable incorporation of the copy into recipient genome
Unidirectional
Recipient genetically modified
No reproduction involved

Question 11

Outline the Griffith experiment that demonstrates transformation

Answer 11

…

Question 12

Transformation in Streptococcus sp

Stable incorporation of foreign DNA

Answer 12

Cells must be competent
1 ds DNA binding, 2, exonuclease disgusts Ds DNA to ss DNA, 3, ssDNA associated with competence proteins
4 strand replacement by donor DNA

Question 13

What is conjugation in bacteria

Answer 13

A form of horizontal gene transfer that requires cell to cell contact. Plasmid encoded mechanism (can transfer copies of themselves)

Question 14

What is transformation

Answer 14

Free DNA is incorporated into a recipient cell

Question 15

What is transduction

Answer 15

A bacteriophage transfers DNA from one cell to another (host genes).

Question 16

What is the problem with using a phenetic character classification scheme for bacteria?

(results in unstable classification schemes if based on single character states)

Answer 16

Donor and recipient can be taxonomically unrelated – therefore any phenetic character used for classification could have been acquired simply by gene transfer very recently

Similarity then, does not indicate relatedness

Question 17

What are the three different models of lateral gene transfer?

Answer 17

Common and promiscuous

Very uncommon and confined to intra-species exchange

Common but confined to intra-species exchange

Question 18

If common and promiscuous

Answer 18

All bacteria share a common gene pool and belong to the same species

Question 19

If uncommon and confined to intra-species exchange

Answer 19

Very little mixing of gene pools and the taxonomic unit could be the individual cell or clone

Question 20

If common and confined to intra-species exchange

Answer 20

Reproductive isolation and mixing of species pools would give the equivalent of Biological Species Concept

Question 21

What is the consequence of lateral gene transfer for bacterial systematics?

Answer 21

Different bacterial groups conform to different models.- no single model fits all bacteria (e.g. 10-15% of e.coli genome is derived from lateral gene transfer)

Question 22

Consequences of gene transfer for bacterial systematics

Answer 22

• Tempo of evolution is likely to be affected by integration of entire genes/pathways as well as variation by mutation
• Impossible to deduce bacterial lineages by examination of present phenetic character - lateral gene flow would confuse the phylogeny
• Paleo-bacteriology- useless because cannot identify the fossil record

Question 23

Whats the damn solution then? Since no bacterial phylogeny existed?

Answer 23

The ribosomal RNA sequence analysis

Question 24

What are three sub units of the RNA component of the ribosome?

Answer 24

Bacterial 70s has: 7S + 16S + 23S

different parts have different functions e.g. holding mRNA and tRNA, reading mRNA, forming peptide bonds etc

Question 25

Why is the ribosome a good candidate?

Answer 25

Failure or degradation of any ribosomal function is lethal therefore strong purifying selection

Ribosomal functions derive from structure of ribosome

Structure of ribosome is derived from sequence

Question 26

What is meant by saying ribosomal DNA is assumed to be monophyletic?

Answer 26

Assumed to have never participated in lateral gene transfer

Question 27

Why is ribosomal DNA assumed to be monophyletic?

Answer 27

Large size of rDNA therefore difficulty of homologous recombination successfully integrating the sequence

e.g. 23S has 3000bp - high informational content

Question 28

What if the assumption is true?

Changes in rRNA can be used to infer phylogeny

Answer 28

1. Universal chronometer suitable for all organisms
2. suitable for long and short evolutionary times
3. Suitable for phylogeny of bacteria regardless of how sexy they have been :0

Question 29

How has rRNA revolutionised bacteriology?

Answer 29

Providing sequences that are unique to species, genera etc/

Signature sequences allow unequivocal assignment of an unknown organism to a clade regardless of genes and properties derived from gene transfer

Question 30

What has remained problematic from rRNA based relatedness

Answer 30

Inferences about other genetic properties

Question 31

Why has only a relatively small number of bacterial species been described?

Answer 31

Must be able to generate large amounts to observe phenetic characteristics (based on biochemical properties) hard to do with many bacteria (e.g. extreme conditions cannot be reproduced in the lab)

Question 32

How has PCR helped?

Answer 32

Any fragment of environmental DNA can be artificially amplified to give enough material to sequence

Question 33

How to discover new species?

Answer 33

Recover DNA - sequence the variable region inside and compare the sequences with a web based database.

Question 34

FISHing for biodiversity

Answer 34

Fluorescent in situ hybridisation

Question 35

Bacterial species concepts remain controversial

Answer 35

Molecular species are now widely described as simply rRNA sequence – individuals share this species if they share a degree of similarity of sequence.

Question 36

What processes give rise to bacterial species in the sense of the evolving unit?

Answer 36

Ectotypes differ in requirements and do not compete. Niche provides strong selection pressure - adaptive mutation and strong selection give fixation (maintain coherence)