Current Bacterial Gene Encoding Capsule Biosynthesis Protein CapI Contains Nucleotides Derived from Exonization

Abstract

Since the proposition of introns-early hypothesis, although many studies have shown that most eukaryotic ancestors possessed intron-rich genomes, evidence of intron existence in genomes of ancestral bacteria has still been absent. While not a single intron has been found in all protein-coding genes of current bacteria, analyses on bacterial genes horizontally transferred into eukaryotes at ancient time may provide evidence of intron existence in bacterial ancestors. In this study, a bacterial gene encoding capsule biosynthesis protein CapI was found in the genome of sea anemone, Nematostella vectensis. This horizontally transferred gene contains a phase 1 intron of 40 base pairs. The nucleotides of this intron have high sequence identity with those encoding amino acids in current bacterial CapI gene, indicating that the intron and the amino acid-coding nucleotides are originated from the same ancestor sequence. Moreover, 5′-splice site of this intron is located in a GT-poor region associated with a closely following AG-rich region, suggesting that deletion mutation at 5′-splice site has been employed to remove this intron and the intron-like amino acid-coding nucleotides in current bacterial CapI gene are derived from exonization. These data suggest that bacterial CapI gene contained intron(s) at ancient time. This is the first report providing the result of sequence analysis to suggest possible existence of spliceosomal introns in ancestral bacterial genes. The methodology employed in this study may be used to identify more such evidence that would aid in settlement of the dispute between introns-early and introns-late theories.

The Coevolution of Fungal Mitochondrial Introns and Their Homing Endonucleases (GIY-YIG and LAGLIDADG)

“…Ancestral bacterial introns were common, according to the “intron-early” theory ( Koonin 2006 ; Wang et al. 2016 ) and rapidly proliferated to multiple genomic sites after their endosymbiotic transformation to mitochondrion ( López-García and Moreira 2006 ; Koonin 2016 ).…”

Simulation of Chordate Intron Evolution Using Randomly Generated and Mutated Base Sequences

“…Using this approach, we have found an intron-containing bacterial gene harbored in sea anemone, which suggests possible existence of introns in ancestral bacterial genes. 15 Second, the lengths and base sequences of introns vary greatly across various organisms. With a group of introns having different lengths, currently there is no measure to find out whether they are evolved from a longer ancestral sequence through gradual reduction in length or from a shorter ancestral sequence through gradual increase in length.…”

An Intron of Invertebrate Microphthalmia Transcription Factor Gene Is Evolved from a Longer Ancestral Sequence

“…Intron variability results from multiple evolutionary events including intron gain, intron loss, intron slippage, DNA recombination, DNA transposition, and horizontal gene transfer. 15,[37][38][39][40] While reduction in intron number has been observed during genome evolution in many eukaryotic lineages, [17][18][19][20][21][22][23][24][25][26] reduction of intron size has only been observed during genome evolution of organisms from different families/genera [27][28][29][30][31][32] and from different classes. 33 Our present work extends the study on intron size variation in organisms from different metazoan phyla.…”