Chapter 7

Question 1

old vs new methods used for bacterial classification

Answer 1

• Morphology (cell size + shape), biochem (staining, C + N sources, fermentation products), physiology (growth temp. range and optimum, osmotic tolerance) and immunological cross-reactivity (esp. infectious species)
• Before sequencing, hybridization of DNA from two different bacteria was a criterion for similarity – occurred only if base sequence similarity is >80%
• Carl Woese: variations in 16S ribosomal RNA (rRNA) and other sequences
• 16S rRNA sequences differ by 2.5 – 3% implying different species.
• Corresponds to <70% similarity in the overall genome sequence.

Question 2

Taxonomy based on sequences

Answer 2

• All life on Earth has enough general similarities to show that all life forms had a common origin.
   Evident from the universality of basic chemical structures of DNA, RNA, proteins and general biological roles and the near universality of the genetic code
• On the basis of 16S rRNAs, Carl Woese divided living things into bacteria, archaea and eukarya.
   While archaea and bacteria are both unicellular organisms that lack nuclei, at the molecular level archaea are somewhat more closely related to eukarya than to bacteria.
   It is also likely that the archaea are the closest living organisms to the root of the Tree of Life.
• Dating of historical events from sequence differences
   by the suggestion of if sequence divergence occurred at a constant rate, it would provide a ‘molecular clock’ that would allow dating of the splits in lineage between species.
• The importance of horizontal gene transfer (HGT);
   HGT is the acquisition of genetic material by one organism from another by natural rather than laboratory procedures by means other than descent from a parent during replication or mating.
   Several mechanisms of HGT are known, including direct uptake or via viral carriers.
   HGT has affected many genes in prokaryotes and requires a change in our thinking from ordinary ‘clonal’ or parental models of heredity.
   Remember: arrangements of species into phylogenetic trees, in contrast, assume strict ancestor-descendant relationships between different organisms during evolution
   Further, due to HGT, microbes do not easily fit into the structure of the ‘tree’ of life but require a more complex organizational chart.

Question 3

correlations and deviations (with examples) between the complexity of the organism and genetic information (thus, genome size and number of genes)

Answer 3

Yes, correlations exist between organism complexity and the amount of DNA per cell, also, an estimated number of genes per genome. With the former (i.e., amount of DNA per cell), it is generally known that prokaryotes have less DNA per cell than eukaryotes while microbes have fewer genes per genome than metazoan. Also, within eukaryotes, yeast has less DNA per cell and gene numbers than mammals.

Yes, there are deviations from both rules. For example, Amoeba dubia (a single-celled organism) and marbled lungfish have genomes that are respectively 200 and 43 times larger than that of humans. Similarly, pufferfish (while having a significantly smaller genome size than humans) seems to have the same number of genes per genome as humans whereas the nematode C. elegans (100 Mbp) has more genes in its genome than Drosophila melanogaster, the fruit fly (122 Mbp). Regarding plants, clivia has a genome that is 6 times larger than that of humans.

Question 4

What can happen to a gene during evolution?

Answer 4

• May pass to descendants, accumulating favourable (or unfavourable) mutations or drifting neutrally.
• May be lost.
• May be duplicated, followed by divergence or by loss of one of the pair.
• May undergo horizontal transfer to an organism of another species.
• May undergo complex patterns of fusion, fission, or rearrangement, perhaps involving regions encoding individual protein domains.

Question 5

Genomes of chimps and humans

Answer 5

• 96% (±3,101 Gbp) is similar to the human genome with similar regions differing at 1.23% of the positions.
• There is an intraspecies divergence between humans, therefore the true interspecies difference amounts to ~ 1% of the similar sequence.
• Non-similar regions (i.e., 4%, ±116 Mbp) represent ‘indels’.
• Distribution of differences is variable across the genome.
• For all syntenic 1 Mb segments across the genomes, the range in difference is about 0.005–0.025%
• With respect to chromosomes, divergence tends to be higher near the telomeres.
• Divergence was lowest for the X chromosomes, but highest for the Y chromosome.
• Proteins encoded are also very similar in sequence.
• 13,454 orthologous proteins: 29% have identical sequences.
• On average, there are 1 – 2 amino acid differences between corresponding chimp and human protein.
• Though most proteins are very similar, a few shows large Ka/Ks ratios, thus, indicating positive selection.
• Changes in gene expression patterns show that genes active in the brain have changed more rapidly in humans.

Question 6

Genomes of mice and rats vs humans

Answer 6

• Genomes of all three species are approximately the same size. Rat genome ∼5% smaller, mouse genome ∼15% smaller.
• Sequence divergence and chromosome segment rearrangement appear to have been faster in rodent lineage, this may be due to a shorter generation time.
• Human genome shows more duplication.
• All three genomes encode similar numbers of genes. Most proteins have homologues in all three species, with very similar amino acid sequences, thus making these organisms ideal models in transgenic studies.
• Gene duplication diversity: Protein families may be of different sizes in different species. For instance, rodents have more odorant receptors than humans due to their greater dependence on a sense of smell.
• Genomic variation is observable at the chromosome level with mice having 19 chromosomes + X/Y, while rats have 20 chromosomes + X/Y
• Synteny is high between mouse and rat genomes, but variable between mouse and human genomes.
• Most human chromosomes contain many small blocks that correspond separately to regions distributed among several mouse chromosomes.
• There is a large correspondence between the human chromosomes 17, 20 and X and the mouse chromosomes 2, 11 and X, respectively, but with some rearrangement of blocks and some reversals.