8392 8396 PNAS July 18 2000 vol 97

8392– 8396 | PNAS | July 18, 2000 | vol. 97 | no. 15 Interpreting the universal phylogenetic tree Carl R. Woese* Department of Microbiology, University of Illinois at Urbana-Champaign, B 103 Chemical and Life Sciences Laboratory, MC-110, 601 South Goodwin Avenue, Urbana, IL 61801 -3709 Archaea | Bacteria | Eucarya | universal ancestor | horizontal gene transfer 2009/03/06 KORDI, MMG Jeong, Da Geum

The universal phylogenetic tree Extant life Vertically derived & Horizontally acquired variation Ancestor

* The Grand Challenge • A New Era, a New Perspective * A Lesson from Some Wanderers. • Horizontal Gene Transfer * The Evolutionary Roles of Horizontally Acquired and Vertically Generated Variation Transfer. * How the organization of the Cell Shapes Horizontal Gene • Organismal History, Genealogy, and the Concept of Organismal Lineage • What is the Universal Phylogenetic Tree Tell us? • Cellular Evolution • Summary and Conclusion

The Grand Challenge Darwin’s Vision Molecular Biology (1960 s’~) - Molecular sequencing ⇒ Gene histories + Organismal genealogies - Genome sequencing ⇒ Full history of cellular life New molecular approach vs. Old classical ones: Molecules ancestral to a group, whose phenotypes are invariant within the group(ex: Plesiomorphies) Huxley Darwin www. aca 2000. com blog. chosun. com =>Phylogenetic relationships Comparing the sequence of molecules Þ Genealogicla trees for Darwin’s great kingdoms Þ Universal phylogenetic tree (united all of the kingdoms) ”Empire” Plesiomorphy: An ancestral or primitive character Apomorphy: A derived or specialized character

The Grand Challenge http: //mic. sgmjournals. org/cgi/content-nw/full/146/5/1045/F 1 Ribosomal RNA • Molecule ubiquitous • Functional constancy • Changes slowly • Tractable • Highly Complex <-> Horizontal gene transfer so, a bona fide organismal trace * The universal Tree -> Microbiology Side -> center Most important impact of the universal phylogenetic tree A new and powerful perspective An image that unifies all life (histories and common origin) Life’s incredible diversity The Overwhelming importance of the microbial world

A New Era, a New Perspective 1990 s Genomic era. Sequences of many molecules, whose distriburtions are phylogenetically broad -> not agree with the r. RNA-based universal phylogenetic tree The cause of this incongruity • Reticulate Evolution • Horizontal gene flow ÞThat is what is now beginning to happen. Confusion of trees * r. RNA tree is not the true organismal tree. * Archaea and Bacteria are specifically related than with eukaryotes -> the most basic systems(genome replication, expression system) of the cell -clearly suggest a specific relationship between the Archaea and the Eukrayotes. • Horizontal gene transfer as having completely erased any record of the deepest branchings in the universal phylogenetic tree -> root and earliest branchings of the tree are not knowable.

I interpret them from a classical biologist’s perspective instead of asking, tabula rasa, what the r. RNA(or any other) tree means, what it is telling us about the evolutionary process and about the origin and organization of modern cells.

A Lesson from Some Wanderers * Aminoacyl-t. RNA synthetases (aa. RS) =Subject to extensive horizontal gene transfer(HGT) From the species level to transfers between organismal domains =generally be translated independently journals. prous. com *From these twenty enzymes => Universal phylogenetic trees -Unexpected taxonomic juxtaposition. ex) rickettsias & mycobacteria= ostensible sister relationship (2 -I, M aa. RS) -But, same basic branching pattern -Same major taxonomic grouping within each domain as does the r. RNA tree Consequently, aa. RS trees cannot itself be the result of HGT An organismal gene trace is preserved in certain of the cell’s componentry -a trace that extends back to the stage of the universal ancestor of all extant lifeis unavoidable

Horizontal Gene Transfer – HGT Horizontal gene transfer (HGT), also known as lateral gene transfer, refers to the movement of genetic information across normal mating barriers, between more or less distantly related organisms, and thus stands in distinction to the standard vertical transmission of genes from parent to offspring. Ex) plastid, mitochondria nature reviews | genetics volume 9 | august 2008 | 605 -618

Horizontal Gene Transfer – HGT * Selectively driven - evolutionary impact * Selectively neutral - simpler to interpret • The universality of the genetic code attests to the evolutionary importance of the process Þmechanisms: exclude, destroy, counteract foreign DNA(deleterious) none seems to use the strongest defense against alien protein coding genes. => Alien genes would be of no value =>HGT is an avoidable consequence of a universal genetic code But rather the reverse, HGT selectively maintains the universality of the genetic code

Horizontal Gene Transfer – HGT The evolutionary Roles of Horizontally Acquired and Vertically Generated Variation The yin and the yang ( - , +) Without their interplay, evolutions as we know it seems impossible. Vertically generated variation: necessarily highly restricted in character Variations on a lineage’s existing cellular themes Horizontal transfer: on the diversity of the entire biosphere, molecules and systems in a great variety of different cellular environments. => major, * Evolutionary source of true innovation ÞNovel enzymatic pathways, Þnovel membrane transporter capacities, Þnovel energetics, etc

Horizontal Gene Transfer – HGT The evolutionary Roles of Horizontally Acquired and Vertically Generated Variation What is special about vertically generated variation(VGV)? VGV may hold the key to the evolution of biological complexity and specificity. Ex) simple cyclic process, homodimeric molecule -> tandem duplication Homodimer -> Heterodimer, something potentially more sophisticated functionally than the original homodimer A small, simple molecule ÞLarge, functionally complex one ÞHave a higher biological specificity Vertically generated variation ÞThe principal way in which biological complexity, specificity, and cellular integration evolve True novelty (HGT) + complexity, functional differentiation & integration(VGV) => Two forces whose interplay propel the evolution of the cell

Horizontal Gene Transfer – HGT The evolutionary Roles of Horizontally Acquired and Vertically Generated Variation Organism B Real! HGT Organism A Organism B Organism A Investigator! VGV Organism A A vs. B Phylogenetically close enough Proteins(circle) differ very little in sequence And not at all in function Neutral horizontal gene transfers of cellular Components should predominantly involve Closely related species

Horizontal Gene Transfer – HGT How the Organization of the Cell Shapes Horizontal Gene Transfer Cellular organization in particular strongly affects the quality of HGT The degree and nature of coupling among the various cellular components 1. Loosely coupled to the cellular fabric. *Structure: modular component=> independent *Function: self-defined and minimally connected to other cellular functions *Ex) The aminoacyl-t. RNA synthetases, *Easy to get HGT, easily involve phylogenetically remote donors. On the other hand, 2. Tightly coupled into the cellular fabric, strongly integrated with others *Structurally and/or functionally : make large complexes or complex network *Tend not to be (fully) functional in their own right. *ex) Ribosomal proteins *HGT: relatively small extent, only donors closely related to the recipient.

Organismal History, Geneaology, and the Concept of Organismal Lineage *Genomics Evolutionary history of an organismal lineage ≠ Organismal geneaology A cell’s evolutionary history From the highly modular to the tightly integrated *Organismal lineage Reticular wanderings of modular elements, in which the steady, predictable vertical descent of the tightly integrated element is lost *Organismal genealogy Be central to, integrated into, and so, defining of the fabric of the cell(organism)

Organismal History, Geneaology, and the Concept of Organismal Lineage Organismal genealogical trace: The trace of population to which the individuals organism belongs A subtle but useful change in general and the HGT 1) All sexually reproducing species ->HGT with every generation -Strictly confined to the gene pool 2)Asexually reproducing species (microorganisms) -Hard to define a comparable gene pool *Closely related microoragnisms Extensive genetic transfer(whole chromosomes, large sections) * Individuals genes: various vector(phages, plasmids, naked DNA) -> need not be phylogenetically close, between donar and recipient organisms ex) transfer of antibiotic resistance

Organismal History, Geneaology, and the Concept of Organismal Lineage Metaphorically speaking, Organismal genealogies are fuzzy lines, fuzzier at some junctures than at others. HGT from closely related donors need not significantly blur Blurring is a function of taxonomic level the organismal genealogical trace in the limit becoming indistinguishable Ex) Proteobacteria : E. coli and Proteus Same gene transfer would be of no significance Different taxonomic level-> different degrees of “phylogenetic resolution” Organismal genealogy: ill-defined, context dependent, not homogeneously mixed Organismal lineages HGT is basically confined to a natural taxonomic grouping(gene pool) Their “fuzziness” does not significantly overlap that of other lineages.

What Is the Universal Phylogenetic Tree Telling Us? 1. The nature of the entity represented by its root 2. How this entity gave rise to the primary organismal lineage We cannot blithely assume that the universal ancestor is just a typical ancestor, a modern, fully evolved and complex type of cell. What the universal ancestor was and how it gave rise to the first lineages are pivotal biological questions.

What Is the Universal Phylogenetic Tree Telling Us? 1. : The amount of evolutionary change occurring during earlier, > during latter Different quality of the rate of evolution rapid in the earlier one. Lack of homology (aa. RA) Genome replication mechanism Strongly resemble 3 billion yrs Ancestors of the Bacteria Universal ancestor stage 1. 5 Billion yrs 1. Relatively short period Prebiotic chemical stage

What Is the Universal Phylogenetic Tree Telling Us? Transcription apparatus -underwent radical change, major refinement Bacteria vs. Archaea vs. Eucarya Genome replication mechanism No resemblance Resemblance Transcription apparatus on the modern cells Lack of homology Closely related Translation apparatus No counterpart Closely related The root and earliest branchings of the universal phylogenetic tree were not modern cells, but primitive types of cellular entities in the process of becoming modern cells. The universal phylogenetic tree is not confined to what we can call the “modern evolutionary era” The deepest branchings of this tree take us into uncharted evolutionary waters;

Cellular Evolution Modern cells: Fully evolved entities, Be sufficiently complex, integrated, “individualized” 3 distinct celluar design: the bacteria, the archaeal, and the eukaryotic The stage when cells are simple enough, HGT totally dominates the evolutionary scene, and all life becomes a single, diverse gene pool; all of the cell’s componentry can be subject to horizontal gene flow. -> radical novelty need to progressively boot-strap primitive cellular entities into modern cells can occur. At such a stage, evolution was in effect communal: there was a progressive evolution of the whole, not an evolution of individual organismal lineages per se. From the universal gene pool (the communal ancestor), there will emerge “individual” pools, characterized by the fact that HGT continuous to occur in a more or less, but HGT becomes progressively restricted in character

Cellular Evolution Primary organimsal Lineages will be of “fuzzy” variety Active HGT No HGT Because immunity to displacement extends to the specific pools themselves will these subsystems become fully locked-in Stable cellular lineage Vertical inheritance True organismal geneaology can arise. The balance between horizontally acquired and vertically generated variation will continue to change until the evolution of the cell is complete, until the complex(finalized) modern cell types emerge

Summary and Conclusion The universal phylogenetic tree based on r. RNA is a valid representation of organismal genealogy, ≠ any other phylogenetic tree. It transcends the era of modern cells; its deepest branchings extends back in time to an era when cellular entities were considerably more primitive than cells are today The primary bifurcation of the universal phylogenetic tree presents the first evolutionary stage at which cellular design became sufficiently stable that horizontal gene transfer could not completely was away a collective (organismal) trace, and true organismal lineages then gradually began to consolidate

Summary and Conclusion At the first organismal trace resided in a few molecular species only. Those that had become sufficiently complex (tightly coupled) and Woven into the emerging cellular fabric that they were largely refractory to global horizontal gene displacement -> RNA component – integrated entities - other functions Exception: aminoacyl-t. RNA synthetases, etc. : modular components of the translation apparatus that are subject to widespread HGT…

Summary and Conclusion The high, pervasive levels of HGT created an evolutionarily communal state of living systems in the sense that the aboriginal organismal community evolved With the enevitable emergence of complexity in early cellular entities, a stage was reached where distinct subpopulations emerged from the universal ancestral communal state HGT continued to abate wihin and between these pools- three of which would refine into the ancestors of the three extant organimsal domains- until the evolution of the cell (in each) attained a (modern) fully evolved stage. This stage was probably reached as the major lineages in each organismal domain emerged