Long Simple Sequence Repeats in Host-Adapted Pathogens Localize Near Genes Encoding Antigens, Housekeeping Genes, and Pseudogenes

Abstract

Simple sequence repeats (SSRs) in DNA sequences are tandem iterations of a single nucleotide or a short oligonucleotide. SSRs are subject to slipped-strand mutations and a common source of phase variation in bacteria and antigenic variation in pathogens. Significantly long SSRs are generally rare in prokaryotic genomes, and long SSRs composed of iterations of mono-, di-, tri-, and tetranucleotides are mostly restricted to host-adapted pathogens. We present new results concerning associations between long SSRs and genes related to different cellular functions in genomes of host-adapted pathogens. We found that in the majority of the analyzed genomes, at least some of the genes associated with SSRs encode potential antigens, which is expected if the primary function of SSRs is their contribution to antigenic variation. However, we also found a number of long SSRs associated with housekeeping genes, including rRNA and tRNA genes, genes encoding ribosomal proteins, amino acyl-tRNA synthetases, chaperones, and important metabolic enzymes. Many of these genes are probably essential and it is unlikely that they are phase-variable. Few statistically significant associations between SSRs and gene functional classifications were detected, suggesting that most long SSRs are not related to a particular cellular function or process. Long SSRs in Mycobacterium leprae are mostly associated with pseudogenes and may be contributing to gene loss following the adaptation to an obligate pathogenic lifestyle. We speculate that LSSRs may have played a similar role in genome reduction of other host-adapted pathogens.

Spatial Genetic Structure in Natural Populations of Phragmites australis in a Mosaic of Saline Habitats in the Yellow River Delta, China

“…Therefore, genetic divergence among reed populations in the YRD is unlikely to be driven by strictly neutral processes. The correspondence between ecological and genetic landscapes may be indicative of the potential role of environmental variables in driving population divergence [82], [83], [84], [85].…”

The role of variable DNA tandem repeats in bacterial adaptation

“…Streptococcus ) pathogens, SSR‐associated genes frequently encode virulence factors, cell surface components, and restriction–modification enzymes (van Belkum, ; Moxon et al ., ; Guo & Mrázek, ; Power et al ., ; Janulczyk et al ., ). On the other hand, several intragenic SSRs with numerous repeat copies and a unit size that is not a multiple of three are also found in housekeeping genes whose products are essential for important cellular processes, such as cell division, energy production, and DNA replication and repair (Guo & Mrázek, ). Obviously, corresponding TR rearrangements leading to reading frame disruption are anticipated to be detrimental or even lethal for the cell, and it remains unclear why such TRs have been maintained during evolution.…”

The pseudogenes of Mycobacterium leprae reveal the functional relevance of gene order within operons

“…Moreover, the presence of simple sequence repeats nearby Ml pseudogenes has been observed (18) and this can be taken as an indication that Mls pseudogenes are being actively removed as they disrupt RNA and DNA stability (19). …”