#FEMSmicroBlog: Micrococcus luteus closes the gap with insertion sequences

03-10-2022

Bacteria can respond to environmental challenges or newly available resources rapidly thanks to their genomic plasticity. One process to facilitate genomic rearrangements and thus speed up bacterial adaption is mediated by insertion sequences (IS). The article “A synergistic arrangement of two unrelated IS elements facilitates adjacent deletion in Micrococcus luteus ATCC49732” in FEMS Microbiology Letters describes how insertion sequences promote a previously unrecognized DNA rearrangement mechanism. David Barker explains for the #FEMSmicroBlog why the following site-specific genomic deletion events help Micrococcus luteus adapt to the ever-changing environment. #FascinatingMicrobes

 

Why do bacteria contain insertion sequences in their genomes?

Bacterial genomes are generally quite compact with protein-coding sequences, transcription signals and genes for tRNA and rRNA packed closely together. All these sequences are often separated by gaps of just a few base pairs (bp) or are even slightly overlapping.

With such high DNA information density, it is surprising that most bacterial genomes contain non-beneficial or even harmful insertion sequence (IS) elements of about 1000-2000 bp length. These include short segments (~50 bp) of highly similar DNA sequences at each end that flank the coding sequence of a transposase. Once expressed, this enzyme enables the IS to move from one DNA site to another – the so-called transposition.

The transposition of any IS within the genome is potentially harmful if the new insertion inactivates a functionally essential gene. Yet, ISs can also facilitate large-scale genomic modifications that open evolutionary avenues not readily accessible otherwise.

Insertion sequences can facilitate large-scale genomic modifications that open evolutionary avenues not readily accessible otherwise.

Interestingly, bacterial genomes often include various ISs from different families and in multiple copies. IS elements are classified into 29 families according to their distinct mechanisms of transposition, which is determined by the specific terminal sequences and the type of encoded transposase.

Best described so far is the transposition mechanism of two homologous IS that are inserted at different sites. Recombination between these ISs can result in integration, deletion or inversion of genomic segments depending on their location and relative orientation. Additionally, composite transposons include two homologous IS copies flanking one or more genes. These then become mobilized in the same manner as the IS so that they can spread within a bacterial population.

 

A novel insertion sequence structure detected in Micrococcus luteus

The study “A synergistic arrangement of two unrelated IS elements facilitates adjacent deletion in Micrococcus luteus ATCC49732” in FEMS Microbiology Letters finds that two unrelated and non-homologous IS elements interact to enhance genomic plasticity in Micrococcus luteus.

Most previous studies of IS-mediated plasticity have utilized the Proteobacteria Escherichia coli and its close relatives. In comparison, Micrococcus luteus from the phylum Actinobacteria has a distinctively small genome of ~2 MB with a large IS component. Hence, insights into this bacterium’s IS organization offer a new perspective.

Work began, though, with the fortuitous observation of white colony mutants that carried deletions of the crt operon encoding the biosynthetic genes for the yellow pigment sarcinaxanthin. The study identified 11 deletion mutants with unique arrangements of two unrelated IS elements: ISMlu2 and ISMu8.

The mutants all share one terminal point at which two ISMlu2 copies are inserted into two adjacent ISMlu9 copies. This results in a fragment of two intact ISMlu2 copies flanking a short segment containing an ISMlu8-terminus.

The study observed that within this region all deletion endpoints occurred. Interestingly, the ISMlu8 transposase is specific for the DNA sequence CTAG and all of the deletions extended from the ISMlu8-terminus to adjacent CTAG-containing sites. Such an arrangement implies that deletion formation requires the ISMlu8 transposase.

Arrangement of the insertion sequence in Micrococcus luteus
New insertion sequences in Micrococcus luteus. From Barker (2022).

No deletion occurs at a nearby ISMlu8-terminus showing that the positioning of the flanking ISMlu2 is also essential for deletion facilitation. In this case, the inverted flanking ISMlu2 forms a “stem and loop” structure together with the ISMlu8-terminal segment. This exposes a loop that becomes more susceptible to the binding of the ISMlu8 transposase triggering the DNA deletion formation at nearby CTAG sites. Remarkably, with the flanking ISMlu2 elements, this structure emulates a transposon possibly able to mobilize to other locations in the Micrococcus luteus genome.

This previously undetected and unanticipated genomic deletion mechanism expands our insights into the potential evolutionary role of IS elements. Such fascinating findings again illustrate the elusiveness of any complete comprehension of bacterial genome dynamics.

 

About the author of this story

David F. Barker, Ph.D., is now mostly retired after nearly 50 years of active laboratory benchwork. He has done research in a wide range of areas including bacterial gene regulation, human disease gene mapping, mutation detection and population genetics. His interest in bacterial insertion sequences dates from when he was fortunate as an undergraduate to participate in early studies of the transposable element Tn10. His favourite analogue activities include gardening and spoiling his two cats.

About this blog section

The section #FascinatingMicrobes for the #FEMSmicroBlog explains the science behind a paper and highlights the significance and broader context of a recent finding. One of the main goals is to share the fascinating spectrum of microbes across all fields of microbiology.

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