A Phylogenetic Approach to Structural Variation in Organization of Nuclear Group I Introns and Their Ribozymes

Abstract

Nuclear group I introns are restricted to the ribosomal DNA locus where they interrupt genes for small subunit and large subunit ribosomal RNAs at conserved sites in some eukaryotic microorganisms. Here, the myxomycete protists are a frequent source of nuclear group I introns due to their unique life strategy and a billion years of separate evolution. The ribosomal DNA of the myxomycete Mucilago crustacea was investigated and found to contain seven group I introns, including a direct repeat-containing intron at insertion site S1389 in the small subunit ribosomal RNA gene. We collected, analyzed, and compared 72 S1389 group IC1 introns representing diverse myxomycete taxa. The consensus secondary structure revealed a conserved ribozyme core, but with surprising sequence variations in the guanosine binding site in segment P7. Some S1389 introns harbored large extension sequences in the peripheral region of segment P9 containing direct repeat arrays. These repeats contained up to 52 copies of a putative internal guide sequence motif. Other S1389 introns harbored homing endonuclease genes in segment P1 encoding His-Cys proteins. Homing endonuclease genes were further interrupted by small spliceosomal introns that have to be removed in order to generate the open reading frames. Phylogenetic analyses of S1389 intron and host gene indicated both vertical and horizontal intron transfer during evolution, and revealed sporadic appearances of direct repeats, homing endonuclease genes, and guanosine binding site variants among the myxomycete taxa.

Structural Organization of S516 Group I Introns in Myxomycetes

“…The SSU rDNA dataset 1 (1524 nt) and dataset 2 (1784 nt) alignments were manually adjusted according to published information about myxomycete SSU rDNA genes [ 42 , 43 ], excluding parts of variable regions that were not confidently aligned. Group I intron core sequences (143 bp) were manually aligned and strictly based on secondary structure features as described previously [ 6 , 8 , 11 ] using the Geneious prime ® software program.…”

“…Most nucleolar group I introns interrupt functionally important sequences in the small subunit (SSU) and large subunit (LSU) rRNAs corresponding to the peptidyl transferase center and decoding center [ 4 , 5 ]. Intriguingly, a given insertion site harbors related intron sequences with a common evolutionary history even in distantly related taxa [ 6 , 7 , 8 , 9 , 10 , 11 ]. An rDNA group I intron nomenclature has been established based on species name abbreviation, insertion site, and the E. coli rRNA gene numbering system [ 12 ].…”

“…Several structural features appear to facilitate the cellular expression of nuclear HEGs embedded in ribosomal DNA [ 25 ]. Some homing endonuclease mRNAs have a unique lariat cap at their 5′ ends catalyzed by a separate intron-encoded ribozyme [ 26 , 27 , 28 ], and most appear polyadenylated at their 3′ ends [ 11 , 29 , 30 ]. Interestingly, several HEGs also carry small spliceosomal introns of about 50 nt that have to be removed in order to generate a functional open reading frame [ 11 , 29 , 30 , 31 ] and thus may facilitate the expression.…”

“…Several examples of direct repeat (DR) arrays within nuclear group I introns have been reported [ 7 , 9 , 11 , 32 , 33 ]. These arrays appear to have a similar location in the intron RNA structure as HEGs, but their biological role remains unknown.…”

“…Variations in sequence motifs, number of copies, and size of arrays are generally observed, but a common feature appears that arrays do not interfere with ribozyme functions due to their locations in peripheral segments. Recently, we reported a complex pattern of DR array within the S1389 group I intron in the myxomycete Mucilago crustacea that contained 34 copies of the intron internal guide sequence [ 11 ], which may suggest a functional role in splicing.…”