Mutation and Recombination Rates Vary Across Bacterial Chromosome

Kivisaar, Maia

doi:10.3390/microorganisms8010025

Cited by 18 publications

(19 citation statements)

References 96 publications

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“…Given the variety of the functions overseen by NAPs, it is unsurprising that their expression pattern differs during growth (see Figure 1; Ali Azam et al, 1999;Dillon and Dorman, 2010;Verma et al, 2019). During the exponential phase of growth, the most abundant NAPs in E. coli include HU and Fis (Wold et al, 1996;Ryan et al, 2002;Kivisaar, 2020). Cells in the stationary phase produce NAPs that can most effectively condense the chromosome (e.g., Dps) (Calhoun and Kwon, 2011;Sato et al, 2013).…”

Section: Nucleoid Dynamics Are Orchestrated By Napsmentioning

confidence: 99%

“…Interestingly, expression of the M. tuberculosis napM gene increases upon stress; the NapM protein binds DnaA (a replication initiation protein) to inhibit chromosome replication, which in turn ensures that mycobacteria transition to the dormant state to survive inside host macrophages (Liu et al, 2019). Almost all processes involving spatial transitions of DNA strands, such as DNA repair and recombination and the topoisomerasemediated maintenance of topological homeostasis, are based on cooperation with NAPs (e.g., HU interacts directly with topoisomerase A to alter its DNA-relaxing activity) (Shanado et al, 1998;Kamashev and Rouviere-Yaniv, 2000;Ghosh et al, 2014;Kivisaar, 2020). Overall, the low DNAbinding specificity and relatively high copy number of NAPs make them readily available and able to assist with complex cellular processes.…”

Section: Naps Alter Basic Cellular Processes In Response To Stressmentioning

confidence: 99%

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Nucleoid Associated Proteins: The Small Organizers That Help to Cope With Stress

Hołówka

Zakrzewska‐Czerwińska

2020

Front. Microbiol.

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The bacterial chromosome must be efficiently compacted to fit inside the small and crowded cell while remaining accessible for the protein complexes involved in replication, transcription, and DNA repair. The dynamic organization of the nucleoid is a consequence of both intracellular factors (i.e., simultaneously occurring cell processes) and extracellular factors (e.g., environmental conditions, stress agents). Recent studies have revealed that the bacterial chromosome undergoes profound topological changes under stress. Among the many DNA-binding proteins that shape the bacterial chromosome structure in response to various signals, NAPs (nucleoid associated proteins) are the most abundant. These small, basic proteins bind DNA with low specificity and can influence chromosome organization under changing environmental conditions (i.e., by coating the chromosome in response to stress) or regulate the transcription of specific genes (e.g., those involved in virulence).

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Section: Nucleoid Dynamics Are Orchestrated By Napsmentioning

confidence: 99%

Section: Naps Alter Basic Cellular Processes In Response To Stressmentioning

confidence: 99%

Nucleoid Associated Proteins: The Small Organizers That Help to Cope With Stress

Hołówka

Zakrzewska‐Czerwińska

2020

Front. Microbiol.

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“…counting the occurrence of Rif R or Str R clones). On the one hand, mutation frequencies and the actual spectrum of mutations have been shown to vary at different chromosomal positions in several bacterial species, including P. putida 67-69 . Other genetic factors, such as the orientation of the target gene in the replication fork, its level of transcription and/or the immediately flanking nucleotides can also influence the mutation frequency 67-68 .…”

Section: Resultsmentioning

confidence: 99%

Spatiotemporal manipulation of the mismatch repair system ofPseudomonas putidaaccelerates phenotype emergence

Fernández-Cabezón

Cros

Nikel

2021

Preprint

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Developing complex phenotypes in industrially-relevant bacteria is a major goal of metabolic engineering, which encompasses the implementation of both rational and random approaches. In the latter case, several tools have been developed towards increasing mutation frequencies—yet the precise spatiotemporal control of mutagenesis processes continues to represent a significant technical challenge. Pseudomonas species are endowed with one of the most efficient DNA mismatch repair (MMR) systems found in bacteria. Here, we investigated if the endogenous MMR system could be manipulated as a general strategy to artificially alter mutation rates in Pseudomonas species. To bestow a conditional mutator phenotype in the platform bacterium Pseudomonas putida, we constructed inducible mutator devices to modulate the expression of the dominant-negative mutLE36K allele. Regulatable overexpression of mutLE36K in a broad-host-range, easy-to-cure plasmid format resulted in a transitory inhibition of the MMR machinery, leading to a significant increase (up to 438-fold) in mutation frequencies and a heritable fixation of genome mutations. Following such accelerated mutagenesis-followed-by selection approach, three phenotypes were successfully evolved: resistance to antibiotics streptomycin and rifampicin and reversion of a synthetic uracil auxotrophy. Thus, these mutator devices could be applied to accelerate evolution of metabolic pathways in long-term evolutionary experiments, alternating cycles of (inducible) mutagenesis coupled to selection schemes.

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“…Xenogeneic silencers belong to a larger group of nucleoid-associated proteins (NAPs), each of which may affect the rates of both mutation and recombination, two key processes for the evolution of bacterial genomes ( Tavita et al 2012 ; Warnecke et al 2012 ; Kivisaar 2019 ). NAPs were found to have a significant growth phase-specific effect on mutation dynamics in E. coli , as they can not only shield DNA from certain mutagenesis processes during the stationary phase but also interfere with efficient DNA repair during the exponential phase ( Warnecke et al 2012 ).…”

Section: Introductionmentioning

confidence: 99%

Xenogeneic Silencing and Bacterial Genome Evolution: Mechanisms for DNA Recognition Imply Multifaceted Roles of Xenogeneic Silencers

Duan

Ding

Navarre

et al. 2021

Molecular Biology and Evolution

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Horizontal gene transfer (HGT) is a major driving force for bacterial evolution. To avoid the deleterious effects due to the unregulated expression of newly-acquired foreign genes, bacteria have evolved specific proteins named xenogeneic silencers to recognize foreign DNA sequences and suppress their transcription. As there is considerable diversity in genomic base compositions among bacteria, how xenogeneic silencers distinguish self- from non-self DNA in different bacteria remains poorly understood. This review summarizes the progress in studying the DNA binding preferences and the underlying molecular mechanisms of known xenogeneic silencer families, represented by H-NS of Escherichia coli, Lsr2 of Mycobacterium, MvaT of Pseudomonas, and Rok of Bacillus. Comparative analyses of the published data indicate that the differences in DNA recognition mechanisms enable these xenogeneic silencers to have clear characteristics in DNA sequence preferences, which are further correlated with different host genomic features. These correlations provide insights into the mechanisms of how these xenogeneic silencers selectively target foreign DNA in different genomic backgrounds. Furthermore, it is revealed that the genomic AT contents of bacterial species with the same xenogeneic silencer family proteins are distributed in a limited range, and are generally lower than those species without any known xenogeneic silencers in the same phylum/class/genus, indicating that xenogeneic silencers have multifaceted roles on bacterial genome evolution. In addition to regulating horizontal gene transfer, xenogeneic silencers also act as a selective force against the GC to AT mutational bias found in bacterial genomes and help the host genomic AT contents maintained at relatively low levels.

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Mutation and Recombination Rates Vary Across Bacterial Chromosome

Cited by 18 publications

References 96 publications

Nucleoid Associated Proteins: The Small Organizers That Help to Cope With Stress

Nucleoid Associated Proteins: The Small Organizers That Help to Cope With Stress

Spatiotemporal manipulation of the mismatch repair system ofPseudomonas putidaaccelerates phenotype emergence

Xenogeneic Silencing and Bacterial Genome Evolution: Mechanisms for DNA Recognition Imply Multifaceted Roles of Xenogeneic Silencers

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