1. Prokaryotes capture solar energy
Primitive eukaryotes
Atmospheric oxygen levels begin to rise ~2.3 Mya
Photosynthetic bacteria generate oxygen

2. 4 3 2 1 Billions of years ago (Bya) Eukaryotes appear Now!
photosynthesis
Origin of the earth
Cyanobacteria
produce O2
First prokaryotes 4 3 2 1
Now!
Billions of years ago (Bya)
~1 billion years to first cell
additional ~1.5-2 billion years to first eukaryotic cell

3. Endosymbiont hypothesis
Uptake of prokaryotes capable of respiration and photosynthesis was critical to the evolution of multicellular eukaryotes

4. Mitochondria: our batteries
Human cells have hundreds of mitochondria inherited from the egg
Inner membrane of mitochondria contains proteins involved in energy production – many in-foldings increase surface area for energy production
Mitochondrial DNA (mtDNA)
circular genome with 37 genes
small and large rDNA
22 tRNA genes
small number inner membrane proteins
protein synthesis is more similar to prokaryotes
Mitochondrial DNA: A closer look from DNA Learning Center

5. Consensus tree is consistent with sequences of ribosomal RNA
eukaryotic evolution involved the symbiosis of bacteria that gave rise to mitochondria and chloroplasts
LUCA

6. Changes in rDNA sequences used to predict evolutionary relationships
What is the smallest number of sequence changes that can account for the data?

7. LUCA What happened to disturb this nice tree?
sequences of other genes did not produce the same tree structure
both archaeal and bacterial sequences could be found in the same genome
LUCA

8. LUCA is replaced with a community of cells
Genome projects suggest complex microbial communities at the root of the tree
Data with individual genes varies
Lateral transfer of DNA has occurred many times, particularly in prokaryotes
LUCA is replaced with a community of cells

9. Proximity is important in horizontal gene transfer
Photo by Yellowstone NPS
Archaea and thermophilic bacteria in environments like this one have exchanged many genes.

10. What do we know about horizontal (lateral) gene transfer?
Multiple mechanisms are involved in gene transfer
Gene transfer is infrequent
Selection is required to maintain transferred genes
Common among unicellular organisms; rare in multicellular organisms

11. Japanese get more nutrients from sushi than the average American because of their gut bacteria
Horizontal gene transfer from ocean microbe, Zobellia galactanivorans, to gut bacteria

12. The Microbiome Our extra organ? Bacteria outnumber human cells 10:1
Bacterial genes outnumber human genes 100:1
Majority of the microbiota cannot be cultured in the lab with traditional techniques
Our knowledge of the microbiome has been obtained by metagenomics

13. Metagenomics – a shotgun approach
Collect environmental sample
Separate microbes (small)
Isolate DNA*
Clone the DNA into plasmids (makes it possible to obtain many copies of the sequences)
Obtain the DNA sequences of individual clones
Align the DNA sequences to reconstruct the complete genome sequences
random fragments of DNA

14. Goal of the Human Microbiome Project was to characterize the microbial communities at defined sites in the body
standardized data collection
samples from 242 HEALTHY individuals over two years

15. Who’s there? The microbiome includes:
Bacteria – DOMINANT – represent >99% cells
Archaea
Eukaryotes: fungi and others
Viruses: bacteriophages and human viruses (non-cellular)

16. Conclusions:
No two people are alike
Diversity highest in gut and teeth
Sites have characteristic taxonomic signatures (species present)
Species vary greatly in their abundance
Number of species
Number of genes

17. Clustering algorithms find the species can be grouped together by site
Nature 486: (2013)

18. Balance between species is important for health
Bacteria from different phyla predominate at each site
Often multiple members of same genus coexist
Opportunistic pathogens are also present
Balance between species is important for health
Nature 486: (2013)

19. Billions of years separate the bacterial phyla
Line length is proportional to time

20. Fungal species are abundant at some sites

21. Mouth is dominated by Streptococcus, a firmacute
Firmicutes
(Gram positive)
Proteobacteria
Yeast (fungus)

22. Gut is dominated by Bacteroides
Proteobacteria
H. pylori affects stomach acid, appetite
Firmacutes
Lactobacilli are commonly found in probiotics
boosts anti-inflammatory T cells
digestion of complex carbohydrates

23. opportunisitic fungus can cause dermatitis
Firmacutes
Actinobacteria
(gram positive)
Basidomycota fungus

24. Hijackers!
Viruses are infectious agents that replicate within the cytoplasm of a living cell
Viruses are host-specific
Bacteriophage infecting a bacterium
Viruses are categorized according to their type of genome:
double-stranded DNA
single-stranded DNA
double-stranded RNA
single-stranded RNA

25. The diameter of an influenza virus is ~100 nm.
The diameter of a eukaryotic cell is ~10 µm (10,000 nm)
How many influenza viruses would fit in a eukaryotic cell?

26. single stranded RNA negative-sense
Influenza viruses
single stranded RNA negative-sense
(genome is copied into DNA in the host)
1918 virus reconstructed in the lab
What kinds of genes do viruses generally need to carry with them?
coat proteins, including some that bind receptors on the host cell
RNA or DNA polymerase
proteins required to hijack the cell’s RNA and protein synthesis

27. Viral replication consists of several “stages”
Initial engagement
virus binds to a receptor on the host cell
virus penetrates the cell
virus is uncoated
Host range: viruses can only attach to cells that have the right receptors

28. Viruses use the host machinery for replication and information transfer
Multiple copies of viral genome are made
Synthesis of viral mRNAs

29. New viruses are released
Virus particles assemble in the cytoplasm
Viruses are released from the cell
Newly synthesized viruses will attack other targets

30. Much harder to identify viruses in metagenomics (no ribosomal RNA)
MANY bacteriophage are present
Potential pathogens (flu, etc.) are also present
Stay tuned!