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

Horisontal / LateralVertical Transfer of genetic material from one genome to another Transfer of a genetic material to the next generation Basic Modes of Genetic Transfer

Basic Modes of Molecular Evolution Gene duplication Gene losses Mutations HGT

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

Gene Duplication 3 mechanisms: 1.Unequal crossing over 2.Retroposition 3.Chromosomal (or genome) duplication Different fates: 1.Pseudo-genization 2.Conservation of gene function 3.Sub-functionalization 4.Neo-functionalization Zhang, 2003

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.

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

DNA Transfer Between Bacterial Cells Transformation Conjugation Transduction Mechanisms:

DNA Transfer Between Bacterial Cells A complicated mechanism

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

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.

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 1.Scenario 1: a single HGT event from bacteria to archea 2.Scenario 2: 10 gene losses after the last common ancestor However, there could be a problem in the phylogenetic tree…

So… how does the biosphere look like?

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

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

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

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

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.

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

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

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 Physiological modules tend to be conserved during evolution 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 Gains of physiologically fully coupled pairs together most likely occurred in 1 step

Conclusions: In the recent period HGT is more frequent than gene duplication In E.coli K-12: 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

Pathway Evolution: 1.Pathways might have evolved spontaneously without adopting existing enzymes 2.“Retro-evolution” of pathways: selective pressure on a pathway targets the successful production of its end-product 3.Evolution from multifunctional enzymes 4.Whole pathways (as a unit) become duplicated 5.“Recruiting” enzymes from existing pathways (a mosaic, or a “patchwork” ) Schmidt et al, 2003

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

There are several highly abundant metabolites (H 2 O or ATP) Pathways evolve and concentrate around these central metabolites They lead to short pathway distances in the network Pathway Evolution:

Oxygen Earth was created ~4.5 billion years ago Between 3.2 and 2.4 billion years ago- the first production of O 2 by an organism Within 100 million years O 2 built up in Earth’s atmosphere O 2 caused major changes on Earth: 1.Many of the reductants that were so abundant were depleted 2.New metabolic pathways were introduced 3.Protective pathways evolved to treat ROS 4.Enabled the Cambrian “baby boom”

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.

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 10 5 highly variable seed conditions. Metabolic Network Expansion

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

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 What does it mean? The Effect of Various Metabolites on the Total Number of Reactions in Ecosystem Level Metabolic Networks

O2O2 Networks simulated in the presence of oxygen are found in a separate group, unreachable under any anoxic conditions Group IV has 10 5 more reactions than anoxic conditions of group III 52% of the additional reactions used O 2 indirectly

The Effect of Oxygen Two representative networks were seeded with / without O 2 The seed included putative prebiotic set of metabolites (NH 3, H 2 S, CO 2, ATP/ADP, NAD + /H, pyridoxal phosphate and tetrahydrofuran) *Without highly abundant metabolites

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

The Effect of Oxygen

Strict anaerobesObligate aerobesFacultative aerobes Adaptation to O 2 occurred after the major prokaryotic divergence on the tree of life (support of geological and molecular evolutionary analyses)

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)

Oxygen – Conclusions Oxygen enabled at least 10 3 more reactions Most of the change was an introduction of new pathways Adaptation to O 2 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!

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 O 2 effect on the evolution process

Thank you!