Lecture 8

Question 1

What is a ribosome?

Answer 1

• made up of many proteins plus 3 rRNAs
• Function: translation of mRNA => protein
• Contain large (LSU) and small (SSU) subunits
• SSU contains one rRNA referred to as the 16S rRNA in bacteria and archea or the 18S rRNA in eucarya
• LSU contains 2 rRNAs

Question 2

What is a progenote?

Answer 2

are hypothetical organisms in which cellular information would have been encoded on DNA maintained as unlinked genes
- unlinked genes=> before a genome!

• genes would not have been linked in chromosomes as they are in modern organisms, as the domains
• genetic rather than genomic system
• genomes evolved after domain splits

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Question 3

What is a specie?

Answer 3

• In animals and plants:

- 2 individuals that can breed and produce fertile offspring

Question 4

What is a bacterial or archeal species?

Answer 4

• No firm or completely accepted definition
• Individual cells are clones
  
  • Not the products of sexual reproduction
• Bacterial reproduction involves transfer of pieces of DNA via : Trnasformation (naked DNA) , transduction (virus), conjugation (sex pilus)
• not limited to members of the same species, and not for the direct purpose of producing offsprings
• not as much is known about archaeal genetics

Question 5

What are some bacterial and archeal species systematic?

Answer 5

1. Classical bacterial taxonomy
2. DNA-DNA hybridization (DDH)
3. 16S rRNA sequence comparisons
4. Polyphasic taxonomy and new species
5. Whole genome sequence comparison

Question 6

What is classical bacterial taxonomy

Answer 6

• Physiological and cytological tests for classfication purposes
  (gram stain, various biochemical tests)
• Pathogen and symbiont host range
• serological (antibod) and phage typing

Question 7

What is DNA-DNA hybridization (DDH) and what is it good for?

Answer 7

• calculate % homology between 2 genomes via comparison of melting temp profiles of pure vs mixed genomic DNA samples
• for 2 organisms to be considered to be possibly of the same species their genomesmust have minimum 70% homology via DDH
• a very seful standard for sorting out some taxonomic problems
• DDH cannot be used as the sole criterion for determination of species

Question 8

What is 16S rRNA sequence comparisons?

Answer 8

• For 2 bacterial strains to be considered the same species they must have at least 98,7% 16S rRNA gene sequence identity
• Cannot be used as the sole criterion for species determination
• Better for higher levels (genus, kingdom, domains) comparisons
• pther gene sequence comparisons may be more useful for distinguising between species, subspecies
• species cannot be named solel on the basis of 16S rRNA gene sequences obtained from an environmental sample
  - need evidence that the sequence is from a real cell1
  - could be artificial chimera
  - ususally requires isolation as a pure culture, but there are exceptions

Question 9

What is the Adékambi study?

Answer 9

• Interspecies and INTRAspecies comparisons are presented for 16SrRNA sequence and DDH
• some interspecies comparisons score at 100%for both criteria, so >98,7 16S rRNA gene sequence identiy and 70% DDH are not sufficient to determine species

Question 10

What is polyphasic taxonomy?

Answer 10

• combination of molecular (16S rRNA gene sequences, %DDH) and classical determinative taxonomy data used to characterize strains that have been isolated as pure cultures
• Used for Bergey’s manual of systematic bacteriology
• organisms that cannot be cultured may be characterize via other molecular techniques, but will not be accepted as species (nor will they be given names) until they can be cultured otherwise isolated, such as via cell sorting
• new species are accepted by internation union of microbiological societies (IUMS or international commitee on systematics of prokaryotes (ICSP) and reported via the International Journal of Systematic and Evolutionary Microbiology

Question 11

What is whole genome sequence comparison?

Answer 11

• Similar to multi-locus-sequence typing (MLST)
• compare genomes (min 50- >500 genes) via a.a. identity (AAI) and/or average nucleotide identity (ANI)
• Compare 16S sequences and AAI identities
• general, but not perfect correlation

Question 12

What is the concept of habitat vs culturability?

Answer 12

• The vast majority of bacteria and archea cannot be grown in culture
• Some may be viable-but-not-culturable
• direct microscopic counts can exceed viable counts by several orders of magnitude

Question 13

Go see habitat vs culturability slide p.81

Answer 13

go