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(termed the introns-late hypothesis).
I argue that several lines of evidence now suggest a coherent solution to the introns-early versus introns-late debate, and the emerging picture of intron evolution integrates aspects of both views although, formally, there seems to be no support for the original version of introns-early. Firstly, there is growing evidence that spliceosomal introns evolved from group II self-splicing introns which are present, usually, in small numbers, in many bacteria, and probably, moved into the evolving eukaryotic genome from the α-proteobacterial progenitor of the mitochondria. Secondly, the concept of a primordial pool of 'virus-like' genetic elements implies that self-splicing introns are among the most ancient genetic entities. Thirdly, reconstructions of the ancestral state of eukaryotic genes suggest that the last common ancestor of extant eukaryotes had an intron-rich genome. Thus, it appears that ancestors of spliceosomal introns, indeed, have existed since the earliest stages of life's evolution, in a formal agreement with the introns-early scenario. However, there is no evidence that these ancient introns ever became widespread before the emergence of eukaryotes, hence, the central tenet of introns-early, the role of introns in early evolution of proteins, has no support. However, the demonstration that numerous introns invaded eukaryotic genes at the outset of eukaryotic evolution and that subsequent intron gain has been limited in many eukaryotic lineages implicates introns as an ancestral feature of eukaryotic genomes and refutes radical versions of introns-late. Perhaps, most importantly, I argue that the intron invasion triggered other pivotal events of eukaryogenesis, including the emergence of the spliceosome, the nucleus, the linear chromosomes, the telomerase, and the ubiquitin signaling system. This concept of eukaryogenesis, in a sense, revives some tenets of the exon hypothesis, by assigning to introns crucial roles in eukaryotic evolutionary innovation.
Author response: If I understand the idea correctly, it is suggested that there was a stage of evolution of the hypothetical ancestral eukaryotes when Group II introns interrupted many genes. There is nothing inherently impossible about that. Moreover, there is a clear parallel with our (with Bill Martin) scenario under which such a stage was a transient one triggered by endosymbiosis. I believe, though, that the latter version has distinct advantages in terms of compatibility with the available data and explanatory power. Firstly, organisms with numerous Group II introns in protein-coding genes (to be concrete, with a density comparable to the density of spliceosomal introns in eukaryotes) are not known (some organelles come the closest but still fall short of comparable density), so it is, at least, less of a stretch to postulate that condition as a transient one. Secondly, I believe there is a very good reason why such an organism has never been discovered: it never existed because having those multiple (even if self-splicing) introns under the transcriptional-translational coupling mode of expression would be too much of a disadvantage. If so, one would think that such an organism would already have transcription and translation uncoupled. Again, we are unaware of such organisms – other than eukaryotes, of course. I think the hypothesis that we proposed with Bill Martin (ref. 59) and that I expand somewhat in the present paper offers a plausible chain of causation to tie it all together.
(termed the introns-early hypothesis), ..
So the absence of introns in prokaryotes was not as Koonin asserts "a potentially embarrassing complication" needing to be "explained away" but rather an important element in the development of the theory! In the context of the unrooted three-domain tree, introns early was no more "a decidedly unparsimonious scenario" than was introns late. Indeed, if introns played the role in gene assembly first envisioned or later integrated into the RNA World hypothesis by Darnell and me (PNAS 83: 1271–1275) and by Gilbert in his "Exon Theory of Genes", their presence in the progenote and before may even have been a precondition for the rapid evolution of complex proteins. Really we know nothing about how genes arose, and to suppose that they sprang full blown and full length from noncoding polynucleotides seems to me more of a stretch than to imagine that they were cobbled together from smaller oligopeptide-encoding modules. Parsimony is often in the eye of the beholder, and its relevance in reconstructing evolution is in any case questionable. Surely we do not require of real historians that a primary criterion for constructing narratives about the human cultural or political past be that they invoke only the minimum possible number of historical forces and events! Yet what are we biological evolutionists but historians of Life?
So, what are the assumptions we must accept? The first is that group II introns are related to the spliceosomal snRNAs and spliceosomal introns, and that the evolution of the these from group II introns is established, as per the mitochondrial seed hypothesis (Logsdon 1998 Curr Opin Genet Dev 8:637). The assumption of common ancestry is not really debated, since both introns-early and introns-late proponents accept this as given, albeit in different forms. In the former case, it has been argued that group II introns are relics of the RNA world (Gilbert & de Souza 1999 In: Gesteland et al The RNA World) and interrupted RNA genes, and that excision of the group II intron was required for production of functional RNAs. Group II introns would thus be early parasites, and, contrary to the historical situation Koonin alludes to where introns-early and the exon theory of genes were one and the same, this is not so in the revised introns-early scenario. However, in this scenario a satisfactory explanation for how group II introns could have evolved into a trans-splicing system comprising 5 snRNAs is not given, though, aside from an issue of timing, the problem is one and the same as for introns-late: the origin of the spliceosome.
23/03/2015 · Theories on the origin of introns
Fig. 1. Possible products of alternative splicing of a hypothetical gene
Structure of a three-exon, two-intron gene. Exons are illustrated in dark green and introns in light green. Two alternative promoters, one upstream of the coding region (Pwt) and one in the first exon (Palt), are shown as black arrows. Two alternative polyadenylation sites are shown as green downward arrows and indicated as poly(A)wt for the most frequently used polyadenylation site and poly(A)alt for an alternative polyadenylation site in intron 2.
Some examples of possible mRNAs that could arise from transcription using alternative promoters and using alternative splicing and polyadenylation. The 3’-untranslated region is shown as a black line.
To investigate the evolutionary history of AST intron structure, (intron early versus intron late hypothesis), all available Arthropoda FGLamide AST gene sequences were examined from genome databases with reference to intron presence and position/phase.
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24/09/2009 · An Overview of the Introns-First Theory
In addition to all these innovations, the intron invasion, obviously, created the potential for controlled alternative splicing, a mechanism that came to prominence at a later stage of eukaryotic evolution and made a crucial contribution to the evolution of complexity in multicellular organisms. In a sense, the (potential) contributions of introns to eukaryogenesis that are outlined here recapitulate aspects of the exon theory of gene evolution. Indeed, although there seems to be no support for a role of introns in the emergence of the original genes, their roles in eukaryogenesis might have been multiple and crucial, in line with the gist of the exon hypothesis – the evolutionary importance of the "junky" intron sequences.
Introns: a Mystery. by Brig Klyce
Mechanistically, support for introns-late rests on the observation that group II introns-in-pieces are found (admittedly in a chloroplast genome – that of Chlamydomonas reinhardtii), and this three-piece self-splicing intron does at least provide a plausible intermediate in an organelle of bacterial endosymbiotic origin (see Stoltzfus 1999 J Mol Evol 49:169 for a model). The importance of this observation in the context of the mitochondrial seed hypothesis cannot be denied; other RNA genes in pieces are found in mitochondria (e.g. tmRNA – Keiler et al 2000 PNAS 97:7778), even if no split group II introns have thus far been found in this type of organelle.
Introns: a Mystery What'sNEW A ..
Taken together, these independent lines of evidence seem to refute introns-early, even in its modified form, which allows some late insertion of introns: there is no indication that the genes of LUCA contained numerous introns, that prokaryotes underwent genome streamlining, or that exon shuffling had any role in the emergence of the first genes. However, the introns-early hypothesis incorporated too many good ideas to just go out with a whimper; in the rest of this article, we shall see that things are not quite easy for introns-late either and that the latest results of comparative genomics converge with general, conceptual thinking to stage a partial, modest but tangible renaissance of "introns-early".
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