The phage T4 DNA ligase mediates bacterial chromosome DSBs repair as single component non-homologous end joining

Su, Tianyuan; Liu, Fapeng; Chang, Yen‐Chiang; Guo, Qi; Wang, Junshu; Wang, Qian; Qi, Qingsheng

doi:10.1016/j.synbio.2019.04.001

Cited by 24 publications

(21 citation statements)

References 37 publications

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“…Recent works have shown that NHEJ-like activity could occur even in the absence of Ku, e.g. it was found to recombine non-homologous DNA in E. coli (45) and the T4 ligase performs NHEJ-like functions with high efficiency in the absence of Ku (46, 47). The poor understanding of these Ku-independent processes precludes assessing their role in phage recombination, but they could contribute to explain gene flux between unrelated phages.…”

Section: Discussionmentioning

confidence: 99%

Causes and consequences of bacteriophage diversification via genetic exchanges across lifestyles and bacterial taxa

Sousa

Pfeifer

Touchon

et al. 2020

Preprint

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11 12Bacteriophages (henceforth phages) evolve by mutation and recombination. Temperate 13 phages are known to evolve rapidly by genetic exchanges. In contrast, recombination events 14 between virulent and between temperate and virulent phages have rarely been reported. A 15 gene flow barrier between these two large distinct groups of phages could affect the ability of 16 phages to acquire novel functions. Here, we show that genomes of temperate and virulent 17 phages are very distinct but often have a few almost identical genes. These cases are due to 18 recent genetic exchanges of both phage-like and bacterial-like genes. These exchanges were 19 probably mediated by phage recombinases with low homology requirements and mechanisms 20 of non-homologous end joining, since both were over-represented in recombinant phages and 21 their hosts. When assessing the impact of gene flow across the two populations of phages we 22 realized that temperate phages have narrower host ranges than virulent phages. This 23 suggests, and we find some evidence, that gene flow between temperate phages infecting 24 distant bacterial hosts might be mediated by recombination with the broader host virulent 25 phages. Hence, gene flow across phages with distinct lifestyles could drastically increase the 26 gene repertoire available for phage evolution, including the transfer of functional innovations 27 across taxa. These results also have implications for bacterial evolution because of the impact 28 of phage predation in bacterial population dynamics and the contribution of temperate phages 29 to the evolution of bacterial gene repertoires. 31 SIGNIFICANCE STATEMENT 33Many microbial communities are intensely predated by temperate and virulent 34 bacteriophages. The former also contribute to bacterial gene repertoires. Gene transfers 35 between bacteriophages favor their rapid adaptation, but are thought to occur rarely between 36 virulent and temperate bacteriophages because their genomes are very different in terms of 37 gene repertoires and genetic organization. We found that genetic exchanges occur frequently 38 3 between these types of bacteriophages, involve different phage and bacterial functions, and 39 are likely due to multiple DNA repair processes. Since we show that virulent bacteriophages 40 have broader host ranges, they can shuttle genes between temperate bacteriophages present 41 in taxa that are beyond the typical range of the latter. This enhances phages diversification 42 and has multiple impacts on bacterial evolution. 43 65 accretion in virulent phages, even if some families of virulent phages have remarkable 66 diversity in their genomes' size, suggesting the existence of mechanisms of gene exchange 67 (12). The genomic plasticity of temperate lambdoid phages has been much more extensively 68 studied (9, 13, 14). Their analyses reveal that pairs of phages tend to have patches of regions 69 of very similar sequences within genomes that are often very dissimilar. This genome 70 mosaicism is facilitated by the modular or...

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Section: Discussionmentioning

confidence: 99%

Causes and consequences of bacteriophage diversification via genetic exchanges across lifestyles and bacterial taxa

Sousa

Pfeifer

Touchon

et al. 2020

Preprint

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“…Some prokaryotes possess relatively unsophisticated NHEJ machinery compared to eukaryotes, typically comprised of the complexes Ku and LigD (Aravind and Koonin, 2001;Weller et al, 2002;Gong et al, 2005;Bowater and Doherty, 2006;Shuman and Glickman, 2007;Tong et al, 2015). Some bacteria such as E. coli lacking Ku and LigD can utilize phage ligases to mediate NHEJ-like repair of CRISPR-Cas induced DSBs (Su et al, 2019). While NHEJ efficiently repairs DNA cleaved by some CRISPR nucleases in eukaryotic cells, some CRISPR-Cas induced DNA damage in prokaryotes is still highly cytotoxic when NHEJ is active (Xu et al, 2015;Bernheim et al, 2017).…”

Section: Surviving Self-targeting By Crispr-cas Systemsmentioning

confidence: 99%

CRISPR-Cas Systems and the Paradox of Self-Targeting Spacers

Wimmer

Beisel

2020

Front. Microbiol.

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CRISPR-Cas immune systems in bacteria and archaea record prior infections as spacers within each system's CRISPR arrays. Spacers are normally derived from invasive genetic material and direct the immune system to complementary targets as part of future infections. However, not all spacers appear to be derived from foreign genetic material and instead can originate from the host genome. Their presence poses a paradox, as self-targeting spacers would be expected to induce an autoimmune response and cell death. In this review, we discuss the known frequency of self-targeting spacers in natural CRISPR-Cas systems, how these spacers can be incorporated into CRISPR arrays, and how the host can evade lethal attack. We also discuss how self-targeting spacers can become the basis for alternative functions performed by CRISPR-Cas systems that extend beyond adaptive immunity. Overall, the acquisition of genome-targeting spacers poses a substantial risk but can aid in the host's evolution and potentially lead to or support new functionalities.

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“…In most eukaryote, however, NHEJ is the dominant mechanism for DNA repairing. It is recently reported that expression of T4 DNA ligase provides efficient in vivo NHEJ repairing pathway in bacteria (Su et al, 2019). Donors also vary between organisms.…”

Section: Adaption Of Crispr/cas System To Non-model Microorganismsmentioning

confidence: 99%

Development and Application of CRISPR/Cas in Microbial Biotechnology

Ding

Yang

Shi

2020

Front. Bioeng. Biotechnol.

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The clustered regularly interspaced short palindromic repeats (CRISPR)-associated (Cas) system has been rapidly developed as versatile genomic engineering tools with high efficiency, accuracy and flexibility, and has revolutionized traditional methods for applications in microbial biotechnology. Here, key points of building reliable CRISPR/Cas system for genome engineering are discussed, including the Cas protein, the guide RNA and the donor DNA. Following an overview of various CRISPR/Cas tools for genome engineering, including gene activation, gene interference, orthogonal CRISPR systems and precise single base editing, we highlighted the application of CRISPR/Cas toolbox for multiplexed engineering and high throughput screening. We then summarize recent applications of CRISPR/Cas systems in metabolic engineering toward production of chemicals and natural compounds, and end with perspectives of future advancements.

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The phage T4 DNA ligase mediates bacterial chromosome DSBs repair as single component non-homologous end joining

Cited by 24 publications

References 37 publications

Causes and consequences of bacteriophage diversification via genetic exchanges across lifestyles and bacterial taxa

Causes and consequences of bacteriophage diversification via genetic exchanges across lifestyles and bacterial taxa

CRISPR-Cas Systems and the Paradox of Self-Targeting Spacers

Development and Application of CRISPR/Cas in Microbial Biotechnology

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