Bacterial Phylogeny Flashcards
Morphological characters of bacteria
Gram strain
Motility
Biochemical (phenetic characters used for classification)
Functional genes
Use single carbon sources for growth - Biolog
Ability to grow at a range of pH and temperature
Tests (phonetic characters)
Tests that provide large amounts of data are suitable
FAME - fatty acid fingerprint
GC/MS - compositional fingerprint
DNA sequence - DNA fingerprint
Define artificial classification
A group of organisms that look similar to each other and distinct from other groups
Define natural classification
A reproductively isolated group, genes do not combine with those of outsiders - are able to combine by sexual reproduction within the group
Why are similar organisms similar?
Shared a recent common ancestor and therefore have more closely related genes
What are the implications of no sexual reproduction?
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?
What does strain designation reflect?
When mutations occur in reproductively isolated clones - therefore new phenotype cannot spread back into the parental population
What are the three mechanisms of gene transfer?
Transformation
Conjugation
Transduction
What is horizontal or lateral gene transfer?
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
Outline the Griffith experiment that demonstrates transformation
…
Transformation in Streptococcus sp
Stable incorporation of foreign DNA
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
What is conjugation in bacteria
A form of horizontal gene transfer that requires cell to cell contact. Plasmid encoded mechanism (can transfer copies of themselves)
What is transformation
Free DNA is incorporated into a recipient cell
What is transduction
A bacteriophage transfers DNA from one cell to another (host genes).
What is the problem with using a phenetic character classification scheme for bacteria?
(results in unstable classification schemes if based on single character states)
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
What are the three different models of lateral gene transfer?
Common and promiscuous
Very uncommon and confined to intra-species exchange
Common but confined to intra-species exchange
If common and promiscuous
All bacteria share a common gene pool and belong to the same species
If uncommon and confined to intra-species exchange
Very little mixing of gene pools and the taxonomic unit could be the individual cell or clone
If common and confined to intra-species exchange
Reproductive isolation and mixing of species pools would give the equivalent of Biological Species Concept
What is the consequence of lateral gene transfer for bacterial systematics?
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)
Consequences of gene transfer for bacterial systematics
- 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
Whats the damn solution then? Since no bacterial phylogeny existed?
The ribosomal RNA sequence analysis
What are three sub units of the RNA component of the ribosome?
Bacterial 70s has: 7S + 16S + 23S
different parts have different functions e.g. holding mRNA and tRNA, reading mRNA, forming peptide bonds etc
