Pnpase is stadia a homotrimer of subunits that each contain two rnase ph-type domains, organised in an inverted arrangement similar to the individual subunits of rnase. In addition, each pnpase monomer contains two rna-binding domains in the c-terminus: one S1 type and one kh type, which are similar to those found in the eukaryotic exosome cap proteins. The existence of two similar ring-shaped rna degradation complexes in bacteria (RNase ph and pnpase) suggests that one was derived from the other via gene duplication or lateral gene transfer. However, phylogenetic analysis shows that rnase ph is more closely related to the second catalytic domain of pnpase than the two domains of pnpase are to each other, suggesting that the proteins co-evolved from a common primordial single-domain enzyme ( Leszczyniecka., 2004 ). That enzyme also evolved into two archaeal ( Rrp41 and Rrp42 ) and six eukaryotic genes ( Rrp41, Rrp42, Rrp45, Rrp46, Rrp43 and Mtr3 ). In fact, the eukaryotic genes can be organised into two groups based on their similarity to either archaeal Rrp41 (eukaryotic Rrp41, Rrp46 and Mtr3 ) or Rrp42 (eukaryotic Rrp42, Rrp43 and Rrp45 ) ( Lorentzen., 2005 ). This indicates that the eukaryotic exosome evolved from a single rnase ph-type ancestor by several subsequent gene duplication events, the first of which produced Rrp41 and Rrp42, which later diversified into the six individual proteins. The finding that the cap proteins are present in both eukaryotes and archaea also indicates common ancestry. However, a strict requirement of the cap for stability of the exosome core seems to be a development that is specific to eukaryotes ( Buttner., 2005 ; liu., 2006 ; Lorentzen., 2005 ).
The archaeal exosome is a simplified version of the eukaryotic complex that only consists of two different proteins, Rrp41 and Rrp42, which are arranged as a homotrimer of heterodimers and capped by a combination of Rrp4 or Csl4 proteins (. Buttner., 2005 ; Evguenieva-hackenberg., 2003 ; Lorentzen., 2005 ) fig. The eukaryotic and archaeal ring subunits are related both structurally and by sequence to bacterial rnase ph, an enzyme that uses inorganic phosphate to mediate cleavage of rna (. Deutscher., 1988 ). Rnase ph itself forms a ring of six subunits similar to the exosome, and is essential for the 3 end maturation of transfer rna (tRNA) molecules in bacteria ( deutscher., 1988 ; Ishii., 2003 ). But unlike the exosome, the rnase ph ring is a homo-hexamer, with neighbouring subunits in an inverted orientation with respect to each other ( Fig. Interestingly, a third rna-processing and -degradation complex known as polynucleotide phosphorylase (pnpase) forms a similar ring structure ( Leszczyniecka., 2002 ; Littauer and Kornberg, 1957 ; Shi., 2008 ; Symmons., 2000 ). Pnpase is present both in bacteria and in higher eukaryotes ( Leszczyniecka., 2002 where it is located in the mitochondria ( Piwowarski., 2003 suggesting that the eukaryotic enzyme might have been derived from bacteria through endosymbiosis.
Structures of, eukaryotic, cells and Their Functions
During the course of evolution, some of the exosome components in eukaryotes have become inactive structural subunits. This has resulted in a sophisticated machine that is capable of dealing with a wide range of rna transactions, more of which are continuously being identified. Structural organisation of the exosome core. Structure determination fame of the archaeal and eukaryotic exosomes allowed a detailed analysis of the architecture of the complexes, and showed for the first time that the core forms a ring-shaped structure (. Buttner., 2005 ; liu., 2006 ; Lorentzen., 2005 ). In eukaryotes, the ring consists of three distinct heterodimers built from six different proteins, Rrp41-Rrp45, Rrp46-Rrp43 and Mtr3-Rrp42 (. Hernandez., 2006 ; Lehner and Sanderson, 2004 ; liu., 2006 ) fig.
However, the ring of six proteins is not stable on its own in vitro; it requires three additional proteins Rrp4, Csl4 and Rrp40 as a cap to form a stable core exosome' (. Liu., 2006 ). In addition to stabilising the complex, the cap proteins contain rna-binding domains of either the kh (K-homology domain) (. Grishin, 2001 ) or S1 (ribosomal protein S1) type (. Suryanarayana and Subramanian, 1984 ).
The additional association of the exosome with rna-helicase and poly(A) polymerase activities results in a flexible molecular machine that is capable of dealing with the multitude of cellular rna substrates that are found in eukaryotic cells. Interestingly, the same basic set of enzymatic activities is found in prokaryotic cells, which might therefore illustrate the evolutionary origin of the eukaryotic system. In this Commentary, we compare the structural and functional characteristics of the eukaryotic and prokaryotic rna-degradation systems, with an emphasis on some of the functional networks in which the rna exosome participates in eukaryotes. Introduction, when it was first discovered, the rna exosome was described as an elusive complex consisting of several 3-5 exonucleases (. Allmang., 1999b ; Mitchell., 1997 ).
The idea that many exonucleases could work together in a single functional unit made it very difficult to understand how the regulation of this complex could be achieved. Today, looking back at ten years of combined functional and structural studies, it is clear that the exosome is a highly organised and regulated macromolecular machine that has only a few enzymatically active components. The new insights provide pieces of a puzzle that promises to teach us not only about rna processing and degradation in general, but also about how eukaryotic cells regulate the activity and fidelity of gene expression at a very fundamental level. In this Commentary, we compare multi-subunit rna-degradation complexes in bacteria, archaea and eukaryotes to trace the evolutionary origins of the enzymatic activities of the exosome, the repertoire of which has been expanded by the recent discovery. Saccharomyces cerevisiae that the exosome has an associated endonucleolytic activity (. Lebreton., 2008 ; Schaeffer., 2009 ; Schneider., 2009 ). We describe how the basic nucleolytic functions found in prokaryotes have evolved to participate in the more complex and compartmentalised pathways that are found in eukaryotic cells.
Biology: Animal, cell, structure
Commentary, origins and activities of the eukaryotic exosome. Søren lykke-andersen, ditlev. Brodersen, torben heick jensen. Journal of Cell Science 2009 122: ; doi: 10.1242/jcs.047399. Summary, the exosome is a multi-subunit 3-5 exonucleolytic complex that is conserved in structure and function in all eukaryotes studied to date. The complex is present in both the nucleus and cytoplasm, where it continuously works to ensure adequate quantities and quality of rnas by facilitating normal rna processing and turnover, as well as by participating in more complex rna quality-control mechanisms. Recent progress in the field has convincingly shown that the nucleolytic activity of the exosome is maintained by only two exonuclease co-factors, one of which is also an endonuclease.
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Structure of a cell