DNA repair in Corynebacterium model

Resende, Bruno Carvalho; Rebelato, Arnaldo Basso; D’Afonseca, Vívian; Santos, Anderson; Stutzman, T.; Azevedo, Vasco; Santos, Luciana Lara dos; Miyoshi, Anderson; Lopes, Débora de Oliveira

doi:10.1016/j.gene.2011.03.008

Cited by 29 publications

(18 citation statements)

References 36 publications

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“…An up to 1.3-fold increase in recombineering frequency was obtained, demonstrating the importance of sequence context. This is rather low compared with the comparable experiments on E. coli, and it could indicate a difference in the mismatch repair system between these organisms, as indicated by comparisons of the repertoire of DNA-repairing enzymes in Corynebacterium species (32). However, this aspect warrants further studies.…”

Section: Resultsmentioning

confidence: 71%

Recombineering in Corynebacterium glutamicum combined with optical nanosensors: a general strategy for fast producer strain generation

Binder

Siedler

Marienhagen

et al. 2013

Nucleic Acids Research

136

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Recombineering in bacteria is a powerful technique for genome reconstruction, but until now, it was not generally applicable for development of small-molecule producers because of the inconspicuous phenotype of most compounds of biotechnological relevance. Here, we establish recombineering for Corynebacterium glutamicum using RecT of prophage Rac and combine this with our recently developed nanosensor technology, which enables the detection and isolation of productive mutants at the single-cell level via fluorescence-activated cell sorting (FACS). We call this new technology RecFACS, which we use for genomic site-directed saturation mutagenesis without relying on pre-constructed libraries to directly isolate l-lysine-producing cells. A mixture of 19 different oligonucleotides was used targeting codon 81 in murE of the wild-type, at a locus where one single mutation is known to cause l-lysine production. Using RecFACS, productive mutants were screened and isolated. Sequencing revealed 12 different amino acid exchanges in the targeted murE codon, which caused different l-lysine production titers. Apart from introducing a rapid genome construction technology for C. glutamicum, the present work demonstrates that RecFACS is suitable to simply create producers as well as genetic diversity in one single step, thus establishing a new general concept in synthetic biology.

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Section: Resultsmentioning

confidence: 71%

Recombineering in Corynebacterium glutamicum combined with optical nanosensors: a general strategy for fast producer strain generation

Binder

Siedler

Marienhagen

et al. 2013

Nucleic Acids Research

136

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“…DNA lesions are repaired by conserved pathways that have been extensively studied in E. coli (Baharoglu and Mazel, 2014). The simplest system, the direct damage reversal pathway, removes only the base-modifying agent in one single step (Resende et al, 2011) catalyzed by the AlkB demethylase, the Ogt alkyltranferase, and the Phr (photorepairs of pyrimidine) photolyase.…”

Section: Resultsmentioning

confidence: 99%

“…It converts dimers of the chromosome into monomers to permit their segregation during cell division, and it contributes to the segregational stability of plasmids (Resende et al, 2011; Buljubašic 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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“…Nth is a base excision repair enzyme [71] that participates in a pathway preventing the loss of DNA functionality e.g., by spontaneous mutagenic lesion [72] or near-UV radiations [73]. This mechanism is well studied and is conserved in the Corynebacterium species [74]. Trigger factor Tig (Tig) has a DEG homology against Pseudomonas aeruginosa and participates in the protein folding process.…”

Section: Resultsmentioning

confidence: 99%

In silico identification of essential proteins in Corynebacterium pseudotuberculosis based on protein-protein interaction networks

et al. 2016

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Background Corynebacterium pseudotuberculosis (Cp) is a gram-positive bacterium that is classified into equi and ovis serovars. The serovar ovis is the etiological agent of caseous lymphadenitis, a chronic infection affecting sheep and goats, causing economic losses due to carcass condemnation and decreased production of meat, wool, and milk. Current diagnosis or treatment protocols are not fully effective and, thus, require further research of Cp pathogenesis.ResultsHere, we mapped known protein-protein interactions (PPI) from various species to nine Cp strains to reconstruct parts of the potential Cp interactome and to identify potentially essential proteins serving as putative drug targets. On average, we predict 16,669 interactions for each of the nine strains (with 15,495 interactions shared among all strains). An in silico sanity check suggests that the potential networks were not formed by spurious interactions but have a strong biological bias. With the inferred Cp networks we identify 181 essential proteins, among which 41 are non-host homologous.ConclusionsThe list of candidate interactions of the Cp strains lay the basis for developing novel hypotheses and designing according wet-lab studies. The non-host homologous essential proteins are attractive targets for therapeutic and diagnostic proposes. They allow for searching of small molecule inhibitors of binding interactions enabling modern drug discovery. Overall, the predicted Cp PPI networks form a valuable and versatile tool for researchers interested in Corynebacterium pseudotuberculosis.Electronic supplementary materialThe online version of this article (doi:10.1186/s12918-016-0346-4) contains supplementary material, which is available to authorized users.

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DNA repair in Corynebacterium model

Cited by 29 publications

References 36 publications

Recombineering in Corynebacterium glutamicum combined with optical nanosensors: a general strategy for fast producer strain generation

Recombineering in Corynebacterium glutamicum combined with optical nanosensors: a general strategy for fast producer strain generation

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

In silico identification of essential proteins in Corynebacterium pseudotuberculosis based on protein-protein interaction networks

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