Impact of Small Repeat Sequences on Bacterial Genome Evolution

Abstract

Intergenic regions of prokaryotic genomes carry multiple copies of terminal inverted repeat (TIR) sequences, the nonautonomous miniature inverted-repeat transposable element (MITE). In addition, there are the repetitive extragenic palindromic (REP) sequences that fold into a small stem loop rich in G–C bonding. And the clustered regularly interspaced short palindromic repeats (CRISPRs) display similar small stem loops but are an integral part of a complex genetic element. Other classes of repeats such as the REP2 element do not have TIRs but show other signatures. With the current availability of a large number of whole-genome sequences, many new repeat elements have been discovered. These sequences display diverse properties. Some show an intimate linkage to integrons, and at least one encodes a small RNA. Many repeats are found fused with chromosomal open reading frames, and some are located within protein coding sequences. Small repeat units appear to work hand in hand with the transcriptional and/or post-transcriptional apparatus of the cell. Functionally, they are multifaceted, and this can range from the control of gene expression, the facilitation of host/pathogen interactions, or stimulation of the mammalian immune system. The CRISPR complex displays dramatic functions such as an acquired immune system that defends against invading viruses and plasmids. Evolutionarily, mobile repeat elements may have influenced a cycle of active versus inactive genes in ancestral organisms, and some repeats are concentrated in regions of the chromosome where there is significant genomic plasticity. Changes in the abundance of genomic repeats during the evolution of an organism may have resulted in a benefit to the cell or posed a disadvantage, and some present day species may reflect a purification process. The diverse structure, eclectic functions, and evolutionary aspects of repeat elements are described.

Bacterial Genome Instability

“…MITEs are small, AT-rich DNA sequences (0.1 to 0.5 kb) containing terminal inverted repeats, often displaying a TA dinucleotide motif at their extremities and being surrounded by target-site duplications (Fig. 1B) (4,34,35). They often possess the recognition sequences necessary for their mobility but do not encode a transposase.…”

“…These new junctions have the potential to alter the function or expression of proteins. Finally, rearrangements can influence the structure of the chromosome, with indirect effects on phenotype (4). For example, a large inversion in the chromosome of Escherichia coli can have dramatic effects on cell viability (5,6).…”

Trichodesmium genome maintains abundant, widespread noncoding DNA in situ, despite oligotrophic lifestyle

“…It has been shown in numerous systems that repeating elements (repeats and/or IS; Dataset S8) can be mediators of genomic plasticity (61,62,78); however, the direct impacts of these repeats are not always so clear. For example, high IS density in the genome of Lactobacillus acidophilus has been described (79), and despite the propensity of these elements to inactivate genes and facilitate recombination of genomic structure (61), the genome of this isolate still displays high levels of synteny with other sequenced Lactobacilli.…”

“…For example, high IS density in the genome of Lactobacillus acidophilus has been described (79), and despite the propensity of these elements to inactivate genes and facilitate recombination of genomic structure (61), the genome of this isolate still displays high levels of synteny with other sequenced Lactobacilli. Because it has also been shown that partial IS sequences can inhibit transposition (78,80), it is possible that these repeats/pseudogenes have not been deleted because they are controlling transposition in the transposase-heavy IMS101. Others have hypothesized that the conserved repeat structures observed in some bacteria could function as recombinationdependent "promoter banks" for adaptation to new conditions, thereby allowing relatively quick "rewiring" of metabolism in subpopulations (59,62,81).…”

BengaSaVex: A new computational genetic sequence extraction tool for DNA repeats

“…Variability in DNA repeats could help provide information about functional and evolutionary information on genetic diversity of such organisms (van Belkum, 1999a). Van Belkum as well as Delihas (van Belkum et al, 1999;Delihas, 2011), discovered and revealed the vital role sequence repeats play with the regulation of microbial gene expression. The significance of sequence repeats in epidemiologic typing cannot be underestimated (van Belkum, 1999b).…”