Oh my. LECA was really complex.

Earlier I showed you that the last eukaryotic common ancestor (LECA) was quite modern-like in terms of its nuclear pore complex, mechanisms of transport through this complex, and the entire endomembranous system.  Yet the modern-like features do not stop there.

Introns and Spliceosome

I have already provided some evidence that indicates LECA had introns in their protein-coding genes and a complex spliceosome. .

Consider also:

The spliceosome, a sophisticated molecular machine involved in the removal of intervening sequences from the coding sections of eukaryotic genes, appeared and subsequently evolved rapidly during the early stages of eukaryotic evolution. The last eukaryotic common ancestor (LECA) had both complex spliceosomal machinery and some spliceosomal introns [1]

And

Evolutionary reconstructions using maximum likelihood methods point to unexpectedly high densities of introns in protein-coding genes of ancestral eukaryotic forms including the last common ancestor of all extant eukaryotes. [2]

Sterol synthesis

The availability of complete genomes from a wide sampling of eukaryotic diversity has allowed the application of phylogenomics approaches to study the origin and evolution of unique eukaryotic cellular structures, but these are still poorly applied to study unique eukaryotic metabolic pathways. Sterols are a good example because they are an essential feature of eukaryotic membranes. The sterol pathway has been well dissected in vertebrates, fungi, and land plants. However, although different types of sterols have been identified in other eukaryotic lineages, their pathways have not been fully characterized. We have carried out an extensive analysis of the taxonomic distribution and phylogeny of the enzymes of the sterol pathway in a large sampling of eukaryotic lineages. This allowed us to tentatively indicate features of the sterol pathway in organisms where this has not been characterized and to point out a number of steps for which yet-to-discover enzymes may be at work. We also inferred that the last eukaryotic common ancestor already harbored a large panel of enzymes for sterol synthesis and that subsequent evolution over the eukaryotic tree occurred by tinkering, mainly by gene losses. [3]

And

Sterols are ubiquitous features of eukaryotic membranes, and it appears likely that the initial steps in sterol biosynthesis were present in their modern form in the last common ancestor of eukaryotes. [4]

Proteasome and ubiquitin protein degradation system

Eukaryotic proteins can be modified through attachment to various small molecules and proteins. One such modification is conjugation to ubiquitin and ubiquitin-like proteins (UBLs), which controls an enormous range of physiological processes. Bound UBLs mainly regulate the interactions of proteins with other macromolecules, for example binding to the proteasome or recruitment to chromatin. The various UBL systems use related enzymes to attach specific UBLs to proteins (or other molecules), and most of these attachments are transient. There is increasing evidence suggesting that such UBL-protein modification evolved from prokaryotic sulphurtransferase systems or related enzymes. Moreover, proteins similar to UBL-conjugating enzymes and UBL-deconjugating enzymes seem to have already been widespread at the time of the last common ancestor of eukaryotes, suggesting that UBL-protein conjugation did not first evolve in eukaryotes. [5]

Eukaryotic chromosomal replication proteins

Yeast and animal cells require six mini-chromosome maintenance proteins (Mcm2-7) for pre-replication complex formation, DNA replication initiation and DNA synthesis. These six individual MCM proteins form distinct heterogeneous subunits within a hexamer which is believed to form the replicative helicase and which associates with the essential but non-homologous Mcm10 protein during DNA replication…… We used comparative genomics and phylogenetics to reconstruct the diversification of the eukaryotic Mcm2-9 gene family, demonstrating that Mcm2-9 were formed by seven gene duplication events before the last common ancestor of the eukaryotes. Mcm2-7 protein paralogues were present in all eukaryote genomes studied suggesting that no gene loss or functional replacements have been tolerated during the evolutionary diversification of eukaryotes……A multifaceted and heterogeneous Mcm2-7 hexamer evolved during the early evolution of the eukaryote cell in parallel with numerous other acquisitions in cell complexity and prior to the diversification of extant eukaryotes. [6]

Cytoskeleton

LECA not only had a tubulin and actin based cytoskeleton, but also had a complex array of motor proteins that associated with it:

We show that a minimum of 11 kinesin families and 3 protein domain architectures were present in the LCEA. This demonstrates that the microtubule-based cytoskeleton of the LCEA was surprisingly highly developed in terms of kinesin motor types, but that domain architectures have been extensively modified during the diversification of the eukaryotes. Our analysis provides molecular evidence for the existence of several key cellular functions in the LCEA, and shows that a large proportion of motor family diversity and cellular complexity had already arisen in this ancient cell. [7]

Flagellum

Recent progress in understanding phylogenetic relationships among present day eukaryotes and in sequence analysis of flagellar proteins have begun to provide a clearer picture of the origins of doublet and triplet microtubules, flagellar dynein motors, and the 9+2 microtubule architecture common to these organelles. We summarize evidence that the last common ancestor of all eukaryotic organisms possessed a 9+2 flagellum that was used for gliding motility along surfaces, beating motility to generate fluid flow, and localized distribution of sensory receptors, and trace possible earlier stages in the evolution of these characteristics. [8]

And

The microtubule-based flagellum, or basal body/axoneme, is ancestral: it is a so-called “derived character” defining the extant eukaryote branch, present at the apparition of the early eukaryotic cell. It is a genuine cell compartment. Its structural conservation throughout evolution is remarkable, as well as the molecular conservation of the intraflagellar transport genes. From the start, it links cell sensation and cell locomotion, two properties which require integrated wiring at the cell level. The cell division machinery has been also tightly coupled with this organelle throughout evolution, possibly to ensure the continuity of this cellular polarized organization through division. [9]

Mitochondrial Ribosomes

Here, we have reconstructed the composition of the ancestral mitochondrial ribosome in the Last Eukaryotic Common Ancestor (LECA) and investigated its subsequent evolution in six major eukaryotic supergroups. We infer that LECA possessed a mitochondrial ribosome that was already much larger than its bacterial ancestor, with 19 additional specific proteins [10]

So what did the last common ancestral cell of all eukaryotes look like?  A lot like this:

 Cites

  1. Veretnik S, Wills C, Youkharibache P, Valas RE, Bourne PE. 2009. Sm/Lsm genes provide a glimpse into the early evolution of the spliceosome.  PLoS Comput Biol. 5(3):e1000315.

2. Koonin EV. 2009. Intron-dominated genomes of early ancestors of eukaryotes. J Hered. 100(5):618-23. Epub 2009 Jul 17.

3. Desmond E, Gribaldo S. 2009. Phylogenomics of sterol synthesis: insights into the origin, evolution, and diversity of a key eukaryotic feature. Genome Biol Evol. 1:364-81.

  1. Summons RE, Bradley AS, Jahnke LL, Waldbauer JR. 2006. Steroids, triterpenoids and molecular oxygen. Philos Trans R Soc Lond B Biol Sci. 361(1470):951-68.
  1. Hochstrasser M. 2009. Origin and function of ubiquitin-like proteins. Nature. 458(7237):422-9.
  1. Liu Y, Richards TA, Aves SJ. 2009. Ancient diversification of eukaryotic MCM DNA replication proteins.  BMC Evol Biol. 17;9:60.
  1. Wickstead B, Gull K, Richards TA. 2010. Patterns of kinesin evolution reveal a complex ancestral eukaryote with a multifunctional cytoskeleton. BMC Evol Biol. 2010 Apr 27;10:110.
  1. Mitchell DR. 2007. The evolution of eukaryotic cilia and flagella as motile and sensory organelles. Adv Exp Med Biol. 607:130-40.
  1. Bornens M. 2011. The evolutionary fates of the flagellum from the unicellular ancestral eukaryote Biol Aujourdhui. 205(1):1-4.
  1.  Desmond E, Brochier-Armanet C, Forterre P, Gribaldo S. 2011. On the last common ancestor and early evolution of eukaryotes: reconstructing the history of mitochondrial ribosomes.  Res Microbiol. 162(1):53-70.
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6 responses to “Oh my. LECA was really complex.

  1. Let me guess. Eukaryotes are so complex that they could not have evolved, right?

  2. This is getting good!

  3. Thanos,

    Er, no. Try again.

  4. Pingback: Last eukaryotic common ancestor had many “modern-like features” | Uncommon Descent

  5. From the comments section of the above link:

    DrREC
    07/13/2011
    8:45 pm
    This is almost a tautology. The last Eukaryotic common ancestor had the defining features of a Eukaryote….which happen to be more complex than prokaryotic life.
    Therefore design?
    Curious also to invoke LECA, which assumes common ancestry of all Eukarya. This is a technique of using modern sequences to peer back and infer what was.
    Using this assumes there are not multiple origins of Eukarya, and could even be interpreted as ruling out design, as those lines of descent are unbroken and unperturbed (otherwise, we can’t infer what was in LECA-a more modern insertion of a common design kind of rules out inferring what was commonly present in an ancient organism).
    I grant this isn’t mutually exclusive with some versions of ID, but it nearly reduces it to theistic evolution.

  6. Me thinks I should reply.

    Curious also to invoke LECA, which assumes common ancestry of all Eukarya. This is a technique of using modern sequences to peer back and infer what was.

    Using this assumes there are not multiple origins of Eukarya, and could even be interpreted as ruling out design, as those lines of descent are unbroken and unperturbed (otherwise, we can’t infer what was in LECA-a more modern insertion of a common design kind of rules out inferring what was commonly present in an ancient organism).

    He’s making the mistake of conflating design with anti-evolutionism. The common ancestry of all eukaryotes does not rule out design.

    I grant this isn’t mutually exclusive with some versions of ID, but it nearly reduces it to theistic evolution.

    You would think that something that “rules out design” would be mutually exclusive with all versions of ID. Nothing is being “reduced,” as it is about front-loading the process of evolution. Y’know – the design of evolution.

    Replying to the first part deserves its own blog entry.

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