A group I intron in the SSUrDNA of some Naegleria spp. demonstrated by polymerase chain reaction amplification.

The small subunit ribosomal DNA (SSUrDNA) of all described Naegleria spp. was amplified by polymerase chain reaction with universal primers. In all strains of N. andersoni andersoni, N. andersoni jamiesoni, N. australiensis italica and two related strains, and one out of four clusters of N. gruberi, a band of approximately 3.3 kb was obtained. All other strains displayed a band with the expected DNA length of 2.0 kb. This means the former have a 1.3 kb intron in the SSUrDNA. Restriction analysis demonstrated that the intron is between two conserved Pst I sites at the 5' end of the SSUrDNA. It also suggested the introns might not be identical in each species or subspecies. The Pst I fragment of SSUrDNA containing the 1.3 kb insert in N. andersoni andersoni was cloned and sequenced. The 1,296-nucleotide insert is situated in helix 19 of the SSUrDNA, which is an area of conserved primary and secondary structure. Sequence and secondary structure analyses of the insert revealed it it is a group I intron. This group I intron is very large and contains an open reading frame that could serve to encode a polypeptide of 139 amino acids in size.