Characterization of the IS895 family of insertion sequences from the cyanobacterium Anabaena sp. strain PCC 7120

Alam, Jawed; Vrba, J M; Cai, Yuping; Martin, James A.; Weislo, L. J.; Curtis, S. E.

doi:10.1128/jb.173.18.5778-5783.1991

Cited by 23 publications

(13 citation statements)

References 19 publications

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“…Their genomes differ in size (from 1.44 to 12.07 Mb), ploidy (from two to more than 20 chromosome copies per cell) or GC content (30–60%), probably as a result from gains and losses of genes transferred by plasmids, insertion sequences (Alam et al, 1991; Cassier-Chauvat et al, 1997) and/or cyanophages (Hess, 2011; Shih et al, 2013). Most cyanobacteria possess a single circular chromosome, ranging from 1.44 Mb in size (the marine symbiotic strain UCYN-A) to 12.07 Mb ( Scytonema hofmanni PCC7110) (Dagan et al, 2013).…”

Section: Resultsmentioning

confidence: 99%

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

2016

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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).

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Section: Resultsmentioning

confidence: 99%

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

2016

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“…(i) They are both families of transposases, and proteins of both families have similar sizes (Fig. 2). (ii) IS895 has two long ORFs that overlap for 25 codons (17). Within this overlap, we noted the potentially "slippery" sequence AAAAAAAAAAG.…”

Section: ----K---i---dn---h-srk-r-wlk-----------kv-ll--ps-spdlnpie-hlmentioning

confidence: 90%

A proposed superfamily of transposase genes: transposon-like elements in ciliated protozoa and a common "D35E" motif.

Doak

Doerder

Jahn

et al. 1994

Proc. Natl. Acad. Sci. U.S.A.

305

229

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“…Possible IHF binding sites have been found in IS elements of various origins (12). The presence of a putative IHF binding site near one end of IS892, in IS701 (12), and in IS895 (2) makes it tempting to speculate that an IHF-like protein, although not yet observed in cyanobacteria, could be involved in the transposition of their IS elements.…”

Section: Methodsmentioning

confidence: 99%

“…In addition, genetic elements, collectively denoted the mys family, from the cyanobacterium Anabaena sp. strain PCC 7120 were suggested to be IS on the basis of the structural similarity of their nucleotide sequence to that of typical IS elements (1).…”

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Characterization of insertion sequence IS892 and related elements from the cyanobacterium Anabaena sp. strain PCC 7120

Cai

1991

J Bacteriol

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IS892, one of the several insertion sequence (IS) elements discovered in Anabaena sp. strain PCC 7120 (Y. Cai and C. P. Wolk, J. Bacteriol. 172:3138-3145, 1990), is 1,675 bp with 24-bp near-perfect inverted terminal repeats and has two open reading frames (ORFs) that could code for proteins of 233 and 137 amino acids. Upon insertion into target sites, this IS generates an 8-bp directly repeated target duplication. A 32-bp sequence in the region between ORF1 and ORF2 is similar to the sequence of the inverted ternmini. Similar inverted repeats are found within each of those three segments, and the sequences of these repeats bear some similarity to the 11-bp direct repeats flanking the 11-kb insertion interrupting the nifD gene of this strain (J. W. Golden, S. J. Robinson, and R. Haselkorn, Nature [London] 314:419-423, 1985). A sequence similar to that of a binding site for the Escherichia coli integration host factor is found about 120 bp from the left end of IS892. Partial nucleotide sequences of active IS elements IS892N and IS892T, members of the IS892 family from the same Anabaena strain, were shown to be very similar to the sequence of IS892.Insertion sequences (IS) are transposable elements that are generally smaller than transposons and normally bear only genes related to transposition (for a review, see reference 12). Because IS elements lack selectable markers, they are usually identified by their ability to introduce insertional mutations in marker genes and operons (9, 14). Most IS elements from a variety of prokaryotes are 0.8 to 2.5 kb in size and have a pair of near-perfect inverted terminal repeats ranging from 8 to 41 bp. Almost all bacterial IS elements characterized to date generate directly repeated duplications of their target DNA sequences upon insertion. Many elements make a duplication of a fixed number of base pairs, ranging from 2 to 13 bp, as a characteristic of the element (12).Cyanobacteria (blue-green algae) are prokaryotes that differ physiologically and phylogenetically (43) from other eubacteria. Two active IS elements have been isolated and sequenced from cyanobacteria: IS701 from Calothrix sp. strain PCC 7601 (12, 27) and IS891 from Anabaena sp. strain M-131 (4). IS701 appears to be a typical IS element with inverted terminal repeats and the generation of target duplications (27). By contrast, IS891 lacks inverted terminal repeats and fails to generate a target duplication upon insertion (4). In addition, genetic elements, collectively denoted the mys family, from the cyanobacterium Anabaena sp. strain PCC 7120 were suggested to be IS on the basis of the structural similarity of their nucleotide sequence to that of typical IS elements (1).In a study of spontaneous mutation of the conditionally lethal gene sacB in Anabaena sp. strain PCC 7120, 10 IS elements of five different sizes were detected and one of them, IS892, was restriction mapped (7). I report here a more detailed study of IS892 and of related IS elements in this Anabaena strain. MATERIALS AND METHODSBacterial strains,...

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Characterization of the IS895 family of insertion sequences from the cyanobacterium Anabaena sp. strain PCC 7120

Cited by 23 publications

References 19 publications

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

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

A proposed superfamily of transposase genes: transposon-like elements in ciliated protozoa and a common "D35E" motif.

Characterization of insertion sequence IS892 and related elements from the cyanobacterium Anabaena sp. strain PCC 7120

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