Download BIME, ERIC, REP, RIME, and Other Short Bacterial Repeated

BIME, ERIC, REP, RIME, and Other Short Bacterial Repeated Elements
DJ SenGupta, University of Washington Medical Center, Seattle, WA, USA
© 2013 Elsevier Inc. All rights reserved.
This article is a revision of the previous edition article by X Perret, volume 1, pp 214–215, © 2001, Elsevier Inc.
Glossary
DNA element A specific DNA sequence of defined length.
Genome Complete genetic material of an organism.
The presence of repeated DNA sequence was first suggested in
eukaryotic genomes in 1968 by a faster than expected rate of
DNA–DNA self-hybridization. Repeated DNA has since been
discovered not only in eukaryotes but also in bacteria such as
Escherichia coli. Understanding the evolution and biological
role of these repeated elements have been a vigorous area of
study in E. coli and other bacteria. These studies have revealed
that DNA repeat elements vary considerably in size and the
function of genes they are associated with.
Repetitive extragenic palindrome (REP) or palindromic unit
(PU) was the first short repetitive sequence reported initially
discovered in E. coli and Salmonella typhimurium. REP elements
are 21–65 bp imperfect palindromic sequences with potential
to form stem-loop structures. Another short repeat element
discovered among enterobacteria is known as the enterobacterial repetitive intergenic consensus (ERIC) that varies between
69 and 127 bp in length and harbor large palindromic
sequences. Genome sequencing revealed 314 REP elements
and 19 ERIC elements in the E. coli genome.
BIME or bacterial interspersed mosaic elements are
40–500 bp in length and the sequence is characterized by a
mosaic combination of REP separated by other sequence elements. BIMEs have been suggested to play a role in
transcription termination, mRNA stabilization, control of
translation, and genomic rearrangements. These elements also
act as binding site for DNA-modifying enzymes such as DNA
polymerase, integration host factor, and DNA gyrase. Similar
modular repeats found in Rhizobium were called
rhizopus-specific interspersed mosaic elements (RIMEs).
In addition to REP, ERIC, BIME, and RIME, another
noncoding repeat element called the clustered regularly interspersed short palindromic repeats (CRISPRs) is widely
distributed in bacteria and archae. CRISPR elements contain
direct repeats between 24 and 47 bp in length and they are
repeated up to 250 times. These elements are positioned
330
RNAi (RNA interference) A mechanism for degrading
specific mRNAs.
adjacent to cas (CRISPR-associated genes). Recent studies have
suggested that CRISPR elements are involved in conferring
acquired resistance against foreign DNA such as bacteriophages. The spacers between repeats in CRISPR are highly
similar to sequences of phages that could allow an RNA interference (RNAi)-like mechanism to degrade mRNA transcribed
by phage DNA.
While the biological function of these repeat elements continues to be elucidated, their ubiquitous presence and ability to
move within the genome helped develop simple polymerase
chain reaction (PCR)-based methods for differentiating strains
within the same species of bacteria. These methods are commonly called REP-PCR or ERIC-PCR depending on the target
element. Due to the variation in length and position of these
repeat elements among different strains of same species, these
PCR products when analyzed on agarose gels result in a fingerprint pattern that is unique to a strain. These methods are now
being used for differentiating among strains as a part of epidemiological investigation during an outbreak of bacterial
infection.
Since many bacterial genomes have been completely
sequenced, computational approaches have been developed
to identify repeated DNA sequences, and also publicly available databases of various repeat elements have been
established. These developments will further help understand
biological role of these repeats in different species of bacteria.
See also: Direct Repeats; Inverted Repeats; Tandem Repeats.
Further Reading
Snyder L and Champness W (2007) Molecular Genetics of Bacteria. Washington, DC:
ASM Press.
Brenner’s Encyclopedia of Genetics, 2nd edition, Volume 1
doi:10.1016/B978-0-12-374984-0.00151-0