The Emergence of a Synthetic Theory of Intron Evolution

  title={The Emergence of a Synthetic Theory of Intron Evolution},
  author={Sandro Jos{\'e} de Souza},
The debate on the origin and evolution of the intron/exon structure of eukaryotic genes has witnessed profound changes in the last 10 years. Concepts from both the introns-early and introns-late theories have merged into a new synthetic theory of intron evolution. Here I review the debate and discuss the perspectives for the future. 
Origins and evolution of spliceosomal introns.
Research into the origins of introns is at a critical juncture in the resolution of theories on the evolution of early life (which came first, RNA or DNA?), the identity of LUCA (the last universal
The evolution of spliceosomal introns: patterns, puzzles and progress
Patterns of intron-position correspondence between widely diverged eukaryotic species have provided insights into the origins of the vast differences in intron number between eukARYotic species, and studies of specific cases of introns loss and gain have led to progress in understanding the underlying molecular mechanisms and the forces that control intron evolution.
The biology of intron gain and loss.
Evolutionary dynamics of spliceosomal intron revealed by in silico analyses of the P-Type ATPase superfamily genes
There seems to be no intron that arose from before the diversification of the P-Type ATPase superfamily, and the present introns were inserted after the separation of eukaryotes and prokaryotes.
Intron position conservation across eukaryotic lineages in tubulin genes.
A compilation of intron positions obtained from a large number of eukaryotic genomes across orthologous tubulins indicates that the putative ancestral tubulin gene contained at least 19, 33, and 52 introns positions distributed at different sites in the coding regions for alpha, beta, and gamma tubulin, respectively.
Phylogenetic and Exon–Intron Structure Analysis of Fungal Subtilisins: Support for a Mixed Model of Intron Evolution
Phylogenetic and exon–intron structure analyses of intra- and interspecific fungal subtilisins in this study provided support for a mixed model of intron evolution: a synthetic theory of
Origin and evolution of spliceosomal introns
There is no indication that any prokaryote has ever possessed a spliceosome or introns in protein-coding genes, other than relatively rare mobile self-splicing introns, and introns were a major factor of evolution throughout the history of eukaryotes.
Exon size distribution and the origin of introns
This paper examines distributions of exon lengths for six different organisms and finds that they offer empirical evidence that both theories may in part be correct.
Signs of Ancient and Modern Exon-Shuffling Are Correlated to the Distribution of Ancient and Modern Domains Along Proteins
There is a significant correlation between symmetric units of shuffling and the age of protein domains and a model in which shuffling of ancient domains mainly flanked by phase 0 introns was important in the ancestor of eukaryotes and prokaryotes, during the creation of the central part of proteins.
Coevolution Theory of the Genetic Code at Age Forty: Pathway to Translation and Synthetic Life
Coevolution of the genetic code with amino acid biosynthesis generated tRNA paralogs that identify a last universal common ancestor (LUCA) of extant life close to Methanopyrus, which in turn points to archaeal tRNA introns as the most primitive introns and the anticodon usage of Methanipyrus as an ancient mode of wobble.


The recent origins of introns.
Evolution of the intron-exon structure of eukaryotic genes.
Evidence that introns arose at proto‐splice sites.
It is concluded that the tubulin and actin introns are less ancient than the coding sequence and so could not have been involved in the primary evolution of the Tubulin andActin genes.
Intron phase correlations and the evolution of the intron/exon structure of genes.
Using a large data base of eukaryotic intron-containing genes, it is found that there are correlations between intron phases leading to an excess of symmetric exons and asymmetric exon sets, which supports the concept that some of the introns were ancient, the exon theory of genes.
Evolution of novel genes.
  • M. Long
  • Biology
    Current opinion in genetics & development
  • 2001
Toward a resolution of the introns early/late debate: only phase zero introns are correlated with the structure of ancient proteins.
It is suggested that 30-40% of present day intron positions in ancient genes correspond to phase zero introns originally present in the progenote, while almost all of the remaining introns positions correspond to introns added, or moved, appearing equally in all three intron phases.
Five identical intron positions in ancient duplicated genes of eubacterial origin
The discovery of five spliceosomal introns at positions that are precisely conserved between nuclear genes for this chloroplast/cytosol enzyme pair provides strong evidence in favour of the 'introns early' hypothesis, which proposes that introns were present in the earliest cells, consistent with the idea that intron facilitated the assembly of primordial genes by accelerating the rate of exon shuffling.
A novel intron site in the triosephosphate isomerase gene from the mosquito Culex tarsalis
The TPI gene from the mosquito, Culex tarsalis, contains an intron in a unique position that was predicted by W. Gilbert2 and the exon shuffling hypothesis, and is found to be consistent with the 'introns late' view.
Testing the exon theory of genes: the evidence from protein structure.
A tendency for exons to correspond to discrete units of protein structure in protein-coding genes of ancient origin would provide clear evidence in favor of the exon theory of genes, which proposes