Identification, variation and transcription of pneumococcal repeat sequences

Area of Science:

• Microbiology
• Genomics
• Molecular Biology

Background:

• Small interspersed repeats are prevalent in bacterial chromosomes.
• Two repeat families, BOX and RUP, are known in Streptococcus pneumoniae.
• The function of these repeats in pneumococcal genetics is largely unknown.

Purpose of the Study:

• To identify and characterize novel repeat families in Streptococcus pneumoniae.
• To investigate the distribution and potential role of these repeats in pneumococcal and related species.
• To understand the evolutionary dynamics and functional implications of these repeats.

Main Methods:

• Genome analysis of Streptococcus pneumoniae ATCC 700669.
• Comparative analysis of repeat distribution across related streptococcal species.
• Identification of open reading frames and RNA structures within repeat elements.
• Experimental validation using directional RNA-seq and RT-PCR.

Main Results:

• A third repeat family, SPRITE, was discovered in S. pneumoniae.
• BOX, RUP, and SPRITE repeats are less abundant in S. mitis and largely absent in other streptococci, except for BOX-related elements in S. suis.
• These repeats are likely parasitic elements with low transposition rates compared to IS elements.
• Some BOX elements encode open reading frames and form complex RNA structures, including T box riboswitches, and are expressed.

Conclusions:

• BOX, RUP, and SPRITE repeats have significantly expanded in the pneumococcal genome historically, with slow recent insertion rates.
• The extensive secondary structures of these repeats suggest they influence the expression of co-transcribed genes.
• Annotation software for these repeats is publicly available.