Heaphy 3 Taxonomy genomics genetics Flashcards
TAXONOMY:
• science of classification,
concerned with classification, nomenclature and identification.
• process of organising groups of organisms, defining relationships, identifying boundaries.
Species concept:
- Cardinal principle in taxonomy
- organisms exist as real, separate, identifiable groups; basic taxonomic unit is the species.
- In higher organisms, species readily recognised by morphology and reproductive isolation; members of a species genetically similar, sharing gene pool.
- In bacteria, asexual reproduction gives clones of genetically identical cells. But…..bacteria have mechanisms for genetic exchange, so possibilities for variation and evolution exist.
serotypes or serovars:
subspecies, same species but differ in expression of surface antigens
virotypes:
subspecies, same species but differ in virulence
biotypes or biovars:
subspecies, same species but differ in biological characteristics
Phenetic:
assessing similarities
classification good for identifying organisms (hospitals and medicine)
Phylogenetic:
assessing evolutionary relationships
useful in defining evolutionary relationships (labs and research).
Classical phenetic classification systems based on similarity with respect to selected features, e.g.
- Cell shape
- Cell wall constituents
- Cell size
- Energy sources
- Colonial morphology
- Fermentation products
- Ultrastructural characteristics
- Growth temperature optimum & range
- Staining behaviour
- Osmotic tolerance
- Mechanism of motility
- Oxygen relationships
- Cellular inclusions
- pH optimum & growth range
- Carbon & nitrogen sources
- Sensitivity to metabolic inhibitors & antibiotics
Numerical taxonomy
extends classical phenetic approach, but uses computers to analyse many characters produce indices and matrices of similarity and remove subjectivity.(Peter Sneath).
• Data are converted into dendrograms, similarity indicated by lengths of the horizontal lines.
Chemical and molecular phenetic taxonomic markers
x4
• molecular research increases understanding of micro-organisms, classification schemes change, become more refined, e.g.
·cell wall composition -
·membrane lipid structures characteristic of particular taxonomic groups
·proteins - particular enzymes
·nucleic acid composition
Hybridisation:
extent to which DNA molecules from different species hybridise indicates level of genetic similarity; >70% = same species
Gene sequence similarities :
direct comparison of gene that occurs in all organisms, viz. 16S ribosomal RNA (Carl Woese, early 1970s).
16S rRNA sequences and phylogenetic classification:
- ·polymerase chain reaction permits rapid sequence analysis of genes that encode 16S rRNA
- ·differences represent evolutionary divergence; greater difference longer ago species diverged - evolutionary clock.
GENOMICS
• Whole genome sequencing. 1000+ 2010. All important medical and veterinary pathogens completed?
Mycoplasma genitalium:
Smallest free living bacteria • DNA 580,074 nucleotides • GC content 31.6% • 483 genes • 466 assigned function.
GENETICS
OLD: Most bacterial genes reside on single chromosome; free in cytoplasm, no nucleus, no membrane around chromosome. Linear or circular
Lessons from Genomics
- Prokaryotic cell <500 genes M. genitalium
- Free living prokaryote ~1500 genes Aquifex aeolicus
- Solibacter usitatus 10. Mb genome 10 000 genes (largest)
- Free living eukaryote ~5000genes S. pombe and cerevissae
- 15000 genes multicellular organism Drosphila C.elegans
- Human consciousness 20 000 genes
- Distinction between prokaryote cell and eukaryote cell is one of gene type and organisation and interaction- NOT NUMBER OR GENOME COMPLEXITY
- ‘62’ genes define a eukaryote- 8 classes- e.g.histones, cytoskeleton.
- ‘No’ difference between a uni and multicellular organism.
- Accords with the geological record 2300 Myr to go prokaryote-eukaryote 500Myr multicellular
ADDITIONAL GENETIC ELEMENTS
• plasmids:
heterogeneous group of dsDNA molecules encoding additional features e.g. antibiotic resistance, toxin synthesis. (5 to ~200 genes)
ADDITIONAL GENETIC ELEMENTS
bacteriophages
viruses specific for bacteria, form plaques in lawn of bacterial growth; two types:
• · virulent, lytic cycle, infection with single phage gives burst of >100 new, genetically identical phages in 20- 30 minutes,
• ·temperate, phage genes repressed so virus lives harmlessly inside bacterial cell, chromosome replicating in step with bacterial chromosome
ADDITIONAL GENETIC ELEMENTS
• transposable elements
(‘jumping genes’), DNA able to move within and between DNA molecules:
ADDITIONAL GENETIC ELEMENTS
• simplest are insertion sequences
(IS, 1-2 kb), only known function is transposition, recognised only if ‘jump’ into a gene (insertional inactivation)
• more complex transposons, larger versions of ISs that include genes such as antibiotic resistance (e.g. Tn3 penicillin resistance, Tn10 tetracycline resistance)
Gene exchange in bacteria
Transformation
1 uptake of DNA released into environment by death/degradation of bacteria (i.e. physical sampling of gene pool rather than relying on sex)
Gene exchange in bacteria
Transduction
2 phage-dependent carry over of bacterial DNA from one infected cell to the next
Gene exchange in bacteria
Conjugation
3 plasmid-dependent DNA transfer between bacteria; ‘conjugative’ plasmids specify pilus production, initiate cell-to-cell contact, DNA transferred by ‘rolling circle’ replication
