Intrastrand triplex DNA repeats in bacteria: a source of genomic instability

Holder, Isabelle T.; Wagner, Stefanie; Peng, Xiong; Sinn, Malte; Frickey, Tancred; Meyer, Axel; Hartig, Jörg S.

doi:10.1093/nar/gkv1017

Cited by 19 publications

(24 citation statements)

References 98 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Genetic instability correlates with the toxicity of the products, and homologous recombination between repeated DNA motifs (Gellert and Nash, 1987; Holder et al, 2015), which are frequent in cyanobacteria (Elhai, 2015). …”

Section: Resultsmentioning

confidence: 99%

Comparative Genomics of DNA Recombination and Repair in Cyanobacteria: Biotechnological Implications

2016

View full text Add to dashboard Cite

Cyanobacteria are fascinating photosynthetic prokaryotes that are regarded as the ancestors of the plant chloroplast; the purveyors of oxygen and biomass for the food chain; and promising cell factories for an environmentally friendly production of chemicals. In colonizing most waters and soils of our planet, cyanobacteria are inevitably challenged by environmental stresses that generate DNA damages. Furthermore, many strains engineered for biotechnological purposes can use DNA recombination to stop synthesizing the biotechnological product. Hence, it is important to study DNA recombination and repair in cyanobacteria for both basic and applied research. This review reports what is known in a few widely studied model cyanobacteria and what can be inferred by mining the sequenced genomes of morphologically and physiologically diverse strains. We show that cyanobacteria possess many E. coli-like DNA recombination and repair genes, and possibly other genes not yet identified. E. coli-homolog genes are unevenly distributed in cyanobacteria, in agreement with their wide genome diversity. Many genes are extremely well conserved in cyanobacteria (mutMS, radA, recA, recFO, recG, recN, ruvABC, ssb, and uvrABCD), even in small genomes, suggesting that they encode the core DNA repair process. In addition to these core genes, the marine Prochlorococcus and Synechococcus strains harbor recBCD (DNA recombination), umuCD (mutational DNA replication), as well as the key SOS genes lexA (regulation of the SOS system) and sulA (postponing of cell division until completion of DNA reparation). Hence, these strains could possess an E. coli-type SOS system. In contrast, several cyanobacteria endowed with larger genomes lack typical SOS genes. For examples, the two studied Gloeobacter strains lack alkB, lexA, and sulA; and Synechococcus PCC7942 has neither lexA nor recCD. Furthermore, the Synechocystis PCC6803 lexA product does not regulate DNA repair genes. Collectively, these findings indicate that not all cyanobacteria have an E. coli-type SOS system. Also interestingly, several cyanobacteria possess multiple copies of E. coli-like DNA repair genes, such as Acaryochloris marina MBIC11017 (2 alkB, 3 ogt, 7 recA, 3 recD, 2 ssb, 3 umuC, 4 umuD, and 8 xerC), Cyanothece ATCC51142 (2 lexA and 4 ruvC), and Nostoc PCC7120 (2 ssb and 3 xerC).

show abstract

Section: Resultsmentioning

confidence: 99%

Comparative Genomics of DNA Recombination and Repair in Cyanobacteria: Biotechnological Implications

2016

View full text Add to dashboard Cite

show abstract

“…Another problem is the extreme difficulty in cloning highly repetitive DNA into plasmid vectors9. Fragments rich in repeats affect the structure of DNA, forming hairpins and other complex structures that induce instability10. Moreover, the superhelical stress induced by the presence of repeats generates secondary structures that become substrates for deletion.…”

mentioning

confidence: 99%

Sequencing of long stretches of repetitive DNA

Bustos

Cuadrado

Jouve

2016

Sci Rep

View full text Add to dashboard Cite

Repetitive DNA is widespread in eukaryotic genomes, in some cases making up more than 80% of the total. SSRs are a type of repetitive DNA formed by short motifs repeated in tandem arrays. In some species, SSRs may be organized into long stretches, usually associated with the constitutive heterochromatin. Variation in repeats can alter the expression of genes, and changes in the number of repeats have been linked to certain human diseases. Unfortunately, the molecular characterization of these repeats has been hampered by technical limitations related to cloning and sequencing. Indeed, most sequenced genomes contain gaps owing to repetitive DNA-related assembly difficulties. This paper reports an alternative method for sequencing of long stretches of repetitive DNA based on the combined use of 1) a linear vector to stabilize the cloning process, and 2) the use of exonuclease III for obtaining progressive deletions of SSR-rich fragments. This strategy allowed the sequencing of a fragment containing a stretch of 6.2 kb of continuous SSRs. To demonstrate that this procedure can sequence other kinds of repetitive DNA, it was used to examine a 4.5 kb fragment containing a cluster of 15 repeats of the 5S rRNA gene of barley.

show abstract

“…Still, although very intriguing, this interaction involves the so-called BOXC, i.e. a GC rich intergenic repeat, likely involved in genome instability (Holder et al, 2015). When we used IntaRNA software (Wright et al, 2014) to predict GraL-mRNA interactions with this region, no possible interactions were found.…”

Section: Discussionmentioning

confidence: 99%

A search for the in trans role of GraL, an Escherichia coli small RNA

2018

View full text Add to dashboard Cite

Small RNA are very important post-transcriptional regulators in both, bacteria and eukaryotes. One of such sRNA is GraL, encoded in the greA leader region and conserved among enteric bacteria. Here, we conducted a bioinformatics search for GraL's targets in trans and validated our findings in vivo by constructing fusions of probable targets with lacZ and measuring their activity when GraL was overexpressed. Only one target's activity (nudE) decreased under those conditions and was thus selected for further analysis. In the absence of GraL and greA, the nudE::lacZ fusion's β-galactosidase activity was increased. However, a similar effect was also visible in the strain deleted only for greA. Furthermore, overproduction of GreA alone increased the nudE::lacZ fusion's activity as well. This suggests existence of complex regulatory loop-like interactions between GreA, GraL and nudE mRNA. To further dissect this relationship, we performed in vitro EMSA experiments employing GraL and nudE mRNA. However, stable GraL-nudE complexes were not detected, even though the detectable amount of unbound GraL decreased as increasing amounts of nudE mRNA were added. Interestingly, GraL is being bound by Hfq, but nudE easily displaces it. We also conducted a search for genes that are synthetic lethal when deleted along with GraL. This revealed 40 genes that are rendered essential by GraL deletion, however, they are involved in many different cellular processes and no clear correlation was found. The obtained data suggest that GraL's mechanism of action is non-canonical, unique and requires further research.

show abstract

Intrastrand triplex DNA repeats in bacteria: a source of genomic instability

Cited by 19 publications

References 98 publications

Comparative Genomics of DNA Recombination and Repair in Cyanobacteria: Biotechnological Implications

Comparative Genomics of DNA Recombination and Repair in Cyanobacteria: Biotechnological Implications

Sequencing of long stretches of repetitive DNA

A search for the in trans role of GraL, an Escherichia coli small RNA

Contact Info

Product

Resources

About