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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Clustering algorithms find the species can be grouped together by site Nature 486: 207-214 (2013)

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: 207-214 (2013)

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

Fungal species are abundant at some sites

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

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

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

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

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?

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

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

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

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

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