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Bacteria resist phage infection through restriction modification systems that degrade foreign DNA, and a system that uses CRISPR sequences to retain fragments of the genomes of phage that the bacteria have come into contact with in the past, which allows them to block virus replication through a form of RNA interference.

This type of working hypothesis cannot be generated using conventional theoretical flux analysis because it requires that the modification systems that control enzyme activity be taken into account.

A significant amount of recombination between CCs has been observed, even though the Nm strains contain restriction modification systems that have been suggested to generate barriers to recombination between clades (Budroni et al. 2011).

Other genetic isolation mechanisms have been recently described in bacteria (Carrolo et al. 2009; Budroni et al. 2011; Corander et al. 2012), which consist on clade-associated recombination modification systems that generate differential barriers to DNA exchange that corresponds to population structure and, interestingly, are themselves subject to horizontal transfer.

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In addition, the advantage of yeast cell surface display over bacterial display is that yeast has a post-translational modification system that resembles the mammalian system for efficient processing and folding of proteins ([Kondo and Ueda,2004]).

CDC123 joins these as a potential protein modification system that was recruited from a bacterial effector.

The IPA-identified network for genes regulated by Hcy revealed strong interactions of those genes with the ubiquitin C (UBC) posttranslational modification system that targets proteins for proteolytic degradation (Fig.  6).

Restriction endonucleases (REases) are components of restriction-modification systems that occur ubiquitously among prokaryotic organisms and are among the basic tools of molecular biology (Roberts, 2005).

The primary function of methylation is DNA self-recognition via restriction-modification systems that protect the organism against invading DNA.

Three GIs of each genome encoded restriction-modification systems that may act as mechanisms of resistance to bacteriophages or foreign DNA.

Recent studies have demonstrated that the common clonal complexes of S. aureus contain unique restriction-modification systems that contribute to the inhibition of genetic exchange between some S. aureus lineages (Waldron and Lindsay 2006).

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