Metablome and Evolution

1. Metablome and Evolution “Nothing in biology makes sense except in the light of Evolution” (Theodosius Dobzhansky)

2. Basic Modes of Genetic Transfer Horisontal / Lateral Vertical Transfer of genetic material from one genome to another Transfer of a genetic material to the next generation

3. Basic Modes of Molecular Evolution Gene duplication Gene losses Mutations HGT

4. Gene Duplication Prevalence of gene duplications Gene duplications occurs in all 3 kingdoms of life Often referred as paralogous Zhang, 2003

5. Different fates: Pseudo-genization Conservation of gene function Sub-functionalization Neo-functionalization Gene Duplication 3 mechanisms: Unequal crossing over Retroposition Chromosomal (or genome) duplication Zhang, 2003

6. Gene Loss Sometimes less is more Frequent in all 3 kingdoms of life Gene loss can provide an opportunity for adaptation Gene loss can be a cause of species-specific phenotype An example: pseudo-genization of MYH16 (a sacromeric myosin gene) at the time of emergence of the genus homo is thought to be responsible for size reduction of masticatory muscles, which may allowed the expansion of our brain.

7. Horizontal (Lateral) Gene Transfer Transfer of a gene from one genome to another. An outcome, not a specific genetic mechanism. Inter-domain or intra-domain transfer

8. DNA Transfer Between Bacterial Cells Mechanisms: Transformation Conjugation Transduction

9. DNA Transfer Between Bacterial Cells A complicated mechanism

10. HGT in Eukaryotes Probably less frequent than in prokaryotes Endosymbiont-origin 2 types of gene transfer in eukaryotes: Species Most of the gene transfers are in the prokaryoteeukaryote direction High variation in the frequency of HGT in different eukaryotes

11. Detecting HGT • Unexpected ranking of sequence similarity among homologs (BLAST) • Unexpected phylogenetic tree topology • Unusual phyletic patterns (phyletic pattern = the pattern of species present or missing in the given cluster of orthologs) • Conservation of gene order between distant taxa (HGT of operons) • Anomalous nucleotide composition (such as codon usage or GC content). Applicable only to recent HGT events.

12. HGT Vs. Gene Duplication Problem: any putative HGT event can be explained by a series of gene losses and duplications An example: evolution of the anaerobic glycerol-3-phosphate dehydrogenase • Scenario 1: a single HGT event from bacteria to archea • Scenario 2: 10 gene losses after the last common ancestor However, there could be a problem in the phylogenetic tree…

13. So… how does the biosphere look like?

14. Adaptive evolution of bacterial metabolic networks by horizontal gene transfer Pal, C., Papp, B. and Lercher, M.J Nature Genetics 37, 1372-1375 E.Coli K-12 931 unique biochemical reactions and 904 genes

15. HGT Vs. Gene Duplication Is there any difference between eukaryotes and prokaryotes? E.Coli – 107 proteins S.cerevisiae – 285 proteins

16. Lawrence et al. 1991 Construction of a phylogenetic tree (51 proteobacteria species) Identification of the most parsimonious scenarios for HGT and gene losses HGT Vs. Gene Duplication: E.coli K-12 In the last 100 million years: 1 – gene duplication (out of 451) 15-32 – HGT HGT is more frequent in E.coli K-12 in the recent period

17. Why is HGT More Frequent? The most difficult thing in gene duplication is retaining the duplicated gene until they develop distinct functions The initial preservation of the two copies depends on the effect of enhance gene dosage There are number of mechanisms that facilitate gene transfer

18. What are the Selective Pressures Driving the Acquisition of Foreign Genes? Flux balance analysis of the metabolic network Only 7% of the HGT genes are essential under nutrient-rich conditions. The genes that were frequently gained or lost were environment-specific.

19. The Topological Effect of HGT on the Network Supplementary table 2: The number of independent HGT events was highly variable across different enzymatic pathways Genes in central pathways of the network had undergone few transfer events

20. HGT – At Which Stage of the Metabolic Network? Transport √ First reaction Intermediate Biomass Production

21. Physiological modules tend to be conserved during evolution Gains of physiologically fully coupled pairs together most likely occurred in 1 step Gene Loss and Gain: 1 at a Time or As a Set of Genes? • Physiologically coupled genes were identified (flux coupling analysis) • Two cases: - fully coupled enzyme pairs - directionally coupled enzyme pairs • Both fully and directional coupled enzymes were much more often gained or lost together than would be expected by chance 30% of the fully coupled pairs are encoded in the same operon 75% of the fully coupled pairs that were gained together are encoded in the same operon

22. Conclusions: In E.coli K-12: In the recent period HGT is more frequent than gene duplication HGT is involved in transfer of environment-specific genes • HGT occurs mainly in the peripheral reactions of the metabolic pathway HGT frequently takes place in a set of genes

23. Pathway Evolution: Pathways might have evolved spontaneously without adopting existing enzymes “Retro-evolution” of pathways: selective pressure on a pathway targets the successful production of its end-product Evolution from multifunctional enzymes Whole pathways (as a unit) become duplicated “Recruiting” enzymes from existing pathways (a mosaic, or a “patchwork” ) Schmidt et al, 2003

24. Pathway Evolution: Another factor for pathway evolution: metabolites Several possibilities: • Early stages of metabolic evolution occurred by enzyme-driven evolution, whereas more recent pathways are metabolite-driven • Constraints by structural and chemical properties of highly represented metabolites might have already biased the evolutionary space explored in the early days of pathway evolution

25. Pathway Evolution: There are several highly abundant metabolites (H2O or ATP) Pathways evolve and concentrate around these central metabolites They lead to short pathway distances in the network

27. Oxygen Earth was created ~4.5 billion years ago Between 3.2 and 2.4 billion years ago- the first production of O2 by an organism Within 100 million years O2 built up in Earth’s atmosphere O2 caused major changes on Earth: • Many of the reductants that were so abundant were depleted • New metabolic pathways were introduced • Protective pathways evolved to treat ROS • Enabled the Cambrian “baby boom”

28. Metabolic Network Expansion Based on the fact that there is a hierarchical ordering of metabolic reactions The procedure starts with one or more initial compounds = seed Reactions take place, which form new compounds. The new compounds can be used as substrates in subsequent steps The process ends when no new products are generated, and no new reactions are possible.

29. Metabolic Network Expansion The reactions are taken from a base set of biochemically feasible reactions (KEGG). The reactions are from a collective, not from one organism. Currently, there are 6836 reactions in KEGG across 70 genomes and involving 5057 distinct compounds Sampling of 105 highly variable seed conditions.

30. Metabolic Network Expansion

31. The Effect of Various Metabolites on the Total Number of Reactions in Ecosystem Level Metabolic Networks

32. The Effect of Various Metabolites on the Total Number of Reactions in Ecosystem Level Metabolic Networks What does it mean? There is a convergence into 4 groups Each group shares >95% identical reactions and metabolites. The networks in smaller groups are nested within those in larger group Transitions between smaller groups and between subgroups are determined by the availability of biomolecules involved in the assimilation and cycling of key elements

33. The Effect of Various Metabolites on the Total Number of Reactions in Ecosystem Level Metabolic Networks O2 Networks simulated in the presence of oxygen are found in a separate group, unreachable under any anoxic conditions Group IV has 105 more reactions than anoxic conditions of group III 52% of the additional reactions used O2 indirectly

34. *Without highly abundant metabolites http://prelude.bu.edu/O2/networks.html The Effect of Oxygen Two representative networks were seeded with / without O2 The seed included putative prebiotic set of metabolites (NH3, H2S, CO2, ATP/ADP, NAD+/H, pyridoxal phosphate and tetrahydrofuran)

35. Oxic Conditions Anoxic Conditions 2162 reactions 3283 reactions 1672 metabolites 2317 metabolites Consistent with group III Consistent with group IV The Effect of Oxygen

36. The Effect of Oxygen

37. Facultative aerobes Strict anaerobes Obligate aerobes The Effect of Oxygen Adaptation to O2occurred after the major prokaryotic divergence on the tree of life (support of geological and molecular evolutionary analyses)

38. The Effect of Oxygen Oxic network expansion was most profilic in eukaryotes and aerobic prokaryotes Eukaryote-specific reactions make up ~50% of the oxic network (Vs. 21% of the anoxic network)

39. Oxygen – Conclusions Oxygen enabled at least 103 more reactions Most of the change was an introduction of new pathways Adaptation to O2 occurred after the major prokaryotic divergence on the tree of life Oxygen contributed mostly to eukaryotes So relax and breathe- it’s good for evolution!

40. Final Conclusions There are two major mechanisms for evolution: Horizontal and vertical gene transfer We saw an extensive research of E.coli K-12 genome evolution Metabolites can influence the evolution process We saw an example of O2 effect on the evolution process

41. Thank you!