RecR-mediated Modulation of RecF Dimer Specificity for Single- and Double-stranded DNA

Makharashvili, Nodar; Tian, Ming; Королева, О. В.; Korolev, Sergey

doi:10.1074/jbc.m806378200

Cited by 26 publications

(25 citation statements)

References 62 publications

(74 reference statements)

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“…In addition, our RecF protein stock may not be 100% active, also contributing to an overestimated value. NMR and gel filtration analysis of Thermus thermophilus RecF and RecR protein suggested formation of a 4:2 (RecR/RecF) heterohexamer (36), a stoichiometry confirmed for the proteins from Deinococcus radiodurans (37). Therefore, in conjunction with our results, one or two protomers of such a heterohexameric complex would be sufficient to promote the loading of RecA protein onto gDNA.…”

Section: Discussionsupporting

confidence: 73%

RecFOR Proteins Target RecA Protein to a DNA Gap with Either DNA or RNA at the 5′ Terminus

Morimatsu

Wu²,

Kowalczykowski

2012

Journal of Biological Chemistry

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Background: Mediator proteins regulate assembly of RecA onto single-stranded DNA complexed with SSB protein.Results: RecFOR targets RecA to the 5Ј-end of DNA gaps, regardless whether terminated by DNA or RNA. Conclusion: RecFOR loads RecA onto RNA-DNA substrates that mimic unfinished lagging strand replication gaps. Significance: This work provides biochemical evidence for recognition by RecF of gaps created when DNA replication halts.

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Section: Discussionsupporting

confidence: 73%

RecFOR Proteins Target RecA Protein to a DNA Gap with Either DNA or RNA at the 5′ Terminus

Morimatsu

Wu²,

Kowalczykowski

2012

Journal of Biological Chemistry

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“…7, steps 3 and 4). Overall, the loading of RecA at the processed DSB site is mediated by RecR interactions with RecO, which binds SSB-coated ssDNA, and with RecF, which in turn recognizes the ssDNA-dsDNA junctions (386).…”

Section: Recombinational Processes In D Radiodurans Dna Repairmentioning

confidence: 99%

Oxidative Stress Resistance inDeinococcus radiodurans

Slade

Radman

2011

Microbiol Mol Biol Rev

660

639

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SUMMARY Deinococcus radiodurans is a robust bacterium best known for its capacity to repair massive DNA damage efficiently and accurately. It is extremely resistant to many DNA-damaging agents, including ionizing radiation and UV radiation (100 to 295 nm), desiccation, and mitomycin C, which induce oxidative damage not only to DNA but also to all cellular macromolecules via the production of reactive oxygen species. The extreme resilience of D. radiodurans to oxidative stress is imparted synergistically by an efficient protection of proteins against oxidative stress and an efficient DNA repair mechanism, enhanced by functional redundancies in both systems. D. radiodurans assets for the prevention of and recovery from oxidative stress are extensively reviewed here. Radiation- and desiccation-resistant bacteria such as D. radiodurans have substantially lower protein oxidation levels than do sensitive bacteria but have similar yields of DNA double-strand breaks. These findings challenge the concept of DNA as the primary target of radiation toxicity while advancing protein damage, and the protection of proteins against oxidative damage, as a new paradigm of radiation toxicity and survival. The protection of DNA repair and other proteins against oxidative damage is imparted by enzymatic and nonenzymatic antioxidant defense systems dominated by divalent manganese complexes. Given that oxidative stress caused by the accumulation of reactive oxygen species is associated with aging and cancer, a comprehensive outlook on D. radiodurans strategies of combating oxidative stress may open new avenues for antiaging and anticancer treatments. The study of the antioxidation protection in D. radiodurans is therefore of considerable potential interest for medicine and public health.

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“…A LAMP reaction of Salmonella-specific sequences requires the identification of DNA primers that recognize a region of the Salmonella genome that is sufficiently conserved-such that a single set of LAMP primers amplifies the region in a large subset of pathogenic Salmonella serovars-yet divergent enough that internal sequences within the amplicon can readily discriminate closely related serovars (60)(61)(62). To this end, we employed PrimerExplorer v4 software to design a primer set for the amplification of a region in the recF gene, a well-conserved gene encoding the RecF gap repair protein (63,64). These LAMP primers consist of two outer (F3 and B3) and two inner (FIP and BIP) primers that should amplify the recF gene in Salmonella serovars, producing barbell-shaped DNA molecules possessing target-containing, single-stranded loops varying by 4 bases between S. Typhimurium and S. Choleraesuis ( Fig.…”

Section: Resultsmentioning

confidence: 99%

Microfluidic Chip-Based Detection and Intraspecies Strain Discrimination of Salmonella Serovars Derived from Whole Blood of Septic Mice

Patterson

Heithoff

Ferguson

et al. 2013

Appl Environ Microbiol

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Salmonella is a zoonotic pathogen that poses a considerable public health and economic burden in the United States and worldwide. Resultant human diseases range from enterocolitis to bacteremia to sepsis and are acutely dependent on the particular serovar of Salmonella enterica subsp. enterica, which comprises over 99% of human-pathogenic S. enterica isolates. Point-of-care methods for detection and strain discrimination of Salmonella serovars would thus have considerable benefit to medical, veterinary, and field applications that safeguard public health and reduce industry-associated losses. Here we describe a single, disposable microfluidic chip that supports isothermal amplification and sequence-specific detection and discrimination of Salmonella serovars derived from whole blood of septic mice. The integrated microfluidic electrochemical DNA (IMED) chip consists of an amplification chamber that supports loop-mediated isothermal amplification (LAMP), a rapid, single-temperature amplification method as an alternative to PCR that offers advantages in terms of sensitivity, reaction speed, and amplicon yield. The amplification chamber is connected via a microchannel to a detection chamber containing a reagentless, multiplexed (here biplex) sensing array for sequence-specific electrochemical DNA (E-DNA) detection of the LAMP products. Validation of the IMED device was assessed by the detection and discrimination of S. enterica subsp. enterica serovars Typhimurium and Choleraesuis, the causative agents of enterocolitis and sepsis in humans, respectively. IMED chips conferred rapid (under 2 h) detection and discrimination of these strains at clinically relevant levels (<1,000 CFU/ml) from whole, unprocessed blood collected from septic animals. The IMED-based chip assay shows considerable promise as a rapid, inexpensive, and portable point-of-care diagnostic platform for the detection and strain-specific discrimination of microbial pathogens.

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RecR-mediated Modulation of RecF Dimer Specificity for Single- and Double-stranded DNA

Cited by 26 publications

References 62 publications

RecFOR Proteins Target RecA Protein to a DNA Gap with Either DNA or RNA at the 5′ Terminus

RecFOR Proteins Target RecA Protein to a DNA Gap with Either DNA or RNA at the 5′ Terminus

Oxidative Stress Resistance inDeinococcus radiodurans

Microfluidic Chip-Based Detection and Intraspecies Strain Discrimination of Salmonella Serovars Derived from Whole Blood of Septic Mice

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