Showing papers by "Nikos C. Kyrpides published in 1998"
TL;DR: It is demonstrated herein that the "analogous" translation initiation factors IF-1 and eIF-1A are actually related in sequence, and the "eukaryotic" translation factor SUI1 is universal in distribution, which implies that at the universal ancestor stage, a translation initiation mechanism either did not exist or was of a different nature than the extant processes.
Abstract: The process by which translation is initiated has long been considered similar in Bacteria and Eukarya but accomplished by a different unrelated set of factors in the two cases. This not only implies separate evolutionary histories for the two but also implies that at the universal ancestor stage, a translation initiation mechanism either did not exist or was of a different nature than the extant processes. We demonstrate herein that (i) the “analogous” translation initiation factors IF-1 and eIF-1A are actually related in sequence, (ii) the “eukaryotic” translation factor SUI1 is universal in distribution, and (iii) the eukaryotic/archaeal translation factor eIF-5A is homologous to the bacterial translation factor EF-P. Thus, the rudiments of translation initiation would seem to have been present in the universal ancestor stage. However, significant development and refinement subsequently occurred independently on both the bacterial lineage and on the archaeal/eukaryotic line.
229 citations
148 citations
TL;DR: Overall, the data lend further support to the suggestion that the rudiments of translation initiation were present at the Universal Ancestor stage, and the occurrence of bacterial IF-2-like molecules in all Archaea and in some eukaryotes further complicates the picture oftranslation initiation.
Abstract: As the amount of available sequence data increases, it becomes apparent that our understanding of translation initiation is far from comprehensive and that prior conclusions concerning the origin of the process are wrong. Contrary to earlier conclusions, key elements of translation initiation originated at the Universal Ancestor stage, for homologous counterparts exist in all three primary taxa. Herein, we explore the evolutionary relationships among the components of bacterial initiation factor 2 (IF-2) and eukaryotic IF-2 (eIF-2)/eIF-2B, i.e., the initiation factors involved in introducing the initiator tRNA into the translation mechanism and performing the first step in the peptide chain elongation cycle. All Archaea appear to posses a fully functional eIF-2 molecule, but they lack the associated GTP recycling function, eIF-2B (a five-subunit molecule). Yet, the Archaea do posses members of the gene family defined by the (related) eIF-2B subunits α, β, and δ, although these are not specifically related to any of the three eukaryotic subunits. Additional members of this family also occur in some (but by no means all) Bacteria and even in some eukaryotes. The functional significance of the other members of this family is unclear and requires experimental resolution. Similarly, the occurrence of bacterial IF-2-like molecules in all Archaea and in some eukaryotes further complicates the picture of translation initiation. Overall, these data lend further support to the suggestion that the rudiments of translation initiation were present at the Universal Ancestor stage.
102 citations
TL;DR: It is becoming clear that the advent of the genome sequencing era is accompanied by the propagation of erroneous functional annotations in an increasing number of cases.
Abstract: It is becoming clear ([1][1]) that the advent of the genome sequencing era is accompanied by the propagation of erroneous functional annotations in an increasing number of cases. The sudden availability of an enormous amount of information has raised the probability that review articles may contain
21 citations
TL;DR: The authors thank C. Ouzounis for critical reading of the manuscript, and R. Overbeek for expert support during the analysis.
13 citations
9 citations