To celebrate the week of Biology of Genome conference, we are compiling a list of most interesting genomes. Many of these genomes are being discussed at the conference. Our previous three entries can be seen at the links below.
In 1996, a team led by J. Craig Venter and Carl Woese published the genome of the first archaea and the results surprised the entire biologist community. Instead of nicely resolving questions about the origin of three kingdom, it complicated matters further. The majority of genes related to energy production, cell division, and metabolism in M. jannaschii were found to be related to bacteria, whereas the informational component (transcription, translation, and replication) seemed to have similarity with Eukaryotes.
[Complete Genome Sequence of the Methanogenic Archaeon, Methanococcus jannaschii
The complete 1.66-megabase pair genome sequence of an autotrophic archaeon, Methanococcus jannaschii, and its 58- and 16-kilobase pair extrachromosomal elements have been determined by whole-genome random sequencing. A total of 1738 predicted protein-coding genes were identified; however, only a minority of these (38 percent) could be assigned a putative cellular role with high confidence. Although the majority of genes related to energy production, cell division, and metabolism in M. jannaschii are most similar to those found in Bacteria, most of the genes involved in transcription, translation, and replication in M. jannaschii are more similar to those found in Eukaryotes.
Archaeoglobus fulgidus is the first sulphur-metabolizing organism to have its genome sequence determined. Its genome of 2,178,400 base pairs contains 2,436 open reading frames (ORFs). The information processing systems and the biosynthetic pathways for essential components (nucleotides, amino acids and cofactors) have extensive correlation with their counterparts in the archaeon Methanococcus jannaschii . The genomes of these two Archaea indicate dramatic differences in the way these organisms sense their environment, perform regulatory and transport functions, and gain energy. In contrast to M. jannaschii , A. fulgidus has fewer restrictionmodification systems, and none of its genes appears to contain inteins. A quarter (651 ORFs) of the A. fulgidus genome encodes functionally uncharacterized yet conserved proteins, two-thirds of which are shared with M. jannaschii (428 ORFs). Another quarter of the genome encodes new proteins indicating substantial archaeal gene diversity.
Further sequencing did not help. The origin of Eukaryotes remains to be one of the biggest unresolved mysteries in evolution.
Here is a 2008 paper by T. Martin Embley and collaborators explaining the issues.
The origin of the eukaryotic genetic apparatus is thought to be central to understanding the evolution of the eukaryotic cell. Disagreement about the source of the relevant genes has spawned competing hypotheses for the origins of the eukaryote nuclear lineage. The iconic rooted 3-domains tree of life shows eukaryotes and archaebacteria as separate groups that share a common ancestor to the exclusion of eubacteria. By contrast, the eocyte hypothesis has eukaryotes originating within the archaebacteria and sharing a common ancestor with a particular group called the Crenarchaeota or eocytes. Here, we have investigated the relative support for each hypothesis from analysis of 53 genes spanning the 3 domains, including essential components of the eukaryotic nucleic acid replication, transcription, and translation apparatus. As an important component of our analysis, we investigated the fit between model and data with respect to composition. Compositional heterogeneity is a pervasive problem for reconstruction of ancient relationships, which, if ignored, can produce an incorrect tree with strong support. To mitigate its effects, we used phylogenetic models that allow for changing nucleotide or amino acid compositions over the tree and data. Our analyses favor a topology that supports the eocyte hypothesis rather than archaebacterial monophyly and the 3-domains tree of life.
Readers will also find Dan Graur’s blog post helpful. It is a section from his book on genome evolution.
The origin of the eukaryotic cell is one of the hardest and most interesting puzzles in evolutionary biology (Lake 2007). Any theory attempting to describe the evolution of eukaryotes must be able to explain the following seven eukaryotic characteristics: (1) The eukaryotic cell is considerably more complex than the prokaryotic cell, possessing, among others a nucleus with a contiguous endoplasmic reticulum, Golgi bodies, flagella with a 9+2 pattern of microtubule arrangement, and organelles surrounded by double membranes. (2) Only eukaryotes achieved great size and morphological complexity, whereas prokaryotes have remained small and have not evolved either morphological complexity or multicellularity. (3) The protein-coding genes of eukaryotes are interspersed with introns that need to be removed prior to translation by spliceosomes. (4) The process of transcription is physically and temporally separated from the process of translation. (5) The eukaryote genome consists of components that are archaebacterial and components that are eubacterial. (6) The distribution of the archaebacterial and eubacterial genomic components is not random with respect to function. (7) There are no known precursor structures among prokaryotes from which such attributes could be derived, and no intermediate cell types known that would point to a gradual evolutionary change of a prokaryote into a eukaryote. For all intents and purposes, the eukaryotic cell represents a sudden organizational upgrade or an evolutionary leap. Moreover, any theory on eukaryote evolution must provide a reason why the length of time it took for prokaryotes to evolve out of inanimate matter is so much shorter than the time it took eukaryotes to evolve out of prokaryotes.
Given the importance of evolutionary origin of eukaryotes, Methanococcus jannaschii deserves a place among top ten genomes.