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

2021 ◽  
Author(s):  
Jorge A Moura de Sousa ◽  
Eugen Pfeifer ◽  
Marie Touchon ◽  
Eduardo P C Rocha
Keyword(s):  
Gene Flow ◽  
Host Range ◽  
Dna Packaging ◽  
Nucleotide Metabolism ◽  
Gene Exchange ◽  
End Joining ◽  
Virion Assembly ◽  
Narrow Host Range ◽  
Genes Encoding ◽  
Non Homologous End Joining

Abstract Bacteriophages (phages) evolve rapidly by acquiring genes from other phages leading to mosaic genomes. Here, we identify numerous genetic transfers between distantly related phages and aim at understanding their frequency, consequences and the conditions favoring them. Gene flow tends to occur between phages that are enriched for recombinases, transposases and non-homologous end joining, suggesting that both homologous and illegitimate recombination contribute to gene flow. Phage family and host phyla are strong barriers to gene exchange, but phage lifestyle is not. Even if we observe four times more recent transfers between temperate phages than between other pairs, there is extensive gene flow between temperate and virulent phages, and between the latter. These predominantly involve virulent phages with large genomes previously classed as low gene flux, and lead to the preferential transfer of genes encoding functions involved in cell energetics, nucleotide metabolism, DNA packaging and injection, and virion assembly. Such exchanges may contribute to the observed twice larger genomes of virulent phages. We used genetic transfers, which occur upon co-infection of a host, to compare phage host range. We found that virulent phages have broader host ranges and can mediate genetic exchanges between narrow host range temperate phages infecting distant bacterial hosts, thus contributing to gene flow between virulent phages, as well as between temperate phages. This gene flow drastically expands the gene repertoires available for phage and bacterial evolution, including the transfer of functional innovations across taxa.

scholarly journals Mono-homologous linear DNA recombination by the non-homologous end-joining pathway as a novel and simple gene inactivation method: a proof of concept study inDietziasp. DQ12-45-1b

2018 ◽  
Author(s):  
Shelian Lu ◽  
Yong Nie ◽  
Meng Wang ◽  
Hong-Xiu Xu ◽  
Dong-Ling Ma ◽  
...  
Keyword(s):  
Genetic Manipulation ◽  
Dna Recombination ◽  
Proof Of Concept ◽  
End Joining ◽  
Circular Dna ◽  
Linear Dna ◽  
Genes Encoding ◽  
Non Homologous End Joining ◽  
Nhej Activity

ABSTRACTNon-homologous end-joining (NHEJ) is critical for genome stability because of its roles in double-strand break repair. Ku and ligase D (LigD) are the crucial proteins in this process, and strains expressing Ku and LigD can cyclize linear DNAin vivo.Herein, we established a proof-of-concept mono-homologous linear DNA recombination for gene inactivation or genome editing by which cyclization of linear DNAin vivoby NHEJ could be used to generate non-replicable circular DNA and could allow allelic exchanges between the circular DNA and the chromosome. We achieved this approach inDietziasp. DQ12-45-1b, which expresses Ku and LigD homologs and presents NHEJ activity. By transforming the strain with a linear DNA mono homolog to the sequence in chromosome, we mutated the genome. This method did not require the screening of suitable plasmids and was easy and time-effective. Bioinformatic analysis showed that more than 20% prokaryotic organisms contain Ku and LigD, suggesting the wide distribution of NHEJ activities. Moreover, theEscherichia colistrain also showed NHEJ activity when the Ku and LigD ofDietziasp. DQ12-45-1b were introduced and expressed in it. Therefore, this method may be a widely applicable genome editing tool for diverse prokaryotic organisms, especially for non-model microorganisms.IMPORTANCEThe non-model gram-positive bacteria lack efficient genetic manipulation systems, but they express genes encoding Ku and LigD. The NHEJ pathway inDietziasp. DQ12-45-1b was evaluated and was used to successfully knockout eleven genes in the genome. Since bioinformatic studies revealed that the putative genes encoding Ku and LigD ubiquitously exist in phylogenetically diverse bacteria and archaea, the mono-homologous linear DNA recombination by the NHEJ pathway could be a potentially applicable genetic manipulation method for diverse non-model prokaryotic organisms.

scholarly journals Genome diversification via genetic exchanges between temperate and virulent bacteriophages

2020 ◽  
Author(s):  
Jorge A. Moura de Sousa ◽  
Eugen Pfeifer ◽  
Marie Touchon ◽  
Eduardo P.C. Rocha
Keyword(s):  
Gene Flow ◽  
Bacterial Population ◽  
Gene Repertoire ◽  
Bacterial Evolution ◽  
End Joining ◽  
Bacterial Gene ◽  
Non Homologous End Joining ◽  
The Impact ◽  
Typical Range ◽  
Two Populations

ABSTRACTBacteriophages (henceforth phages) evolve by mutation and recombination. Temperate phages are known to evolve rapidly by genetic exchanges. In contrast, recombination events between virulent and between temperate and virulent phages have rarely been reported. A gene flow barrier between these two large distinct groups of phages could affect the ability of phages to acquire novel functions. Here, we show that genomes of temperate and virulent phages are very distinct but often have a few almost identical genes. These cases are due to recent genetic exchanges of both phage-like and bacterial-like genes. These exchanges were probably mediated by phage recombinases with low homology requirements and mechanisms of non-homologous end joining, since both were over-represented in recombinant phages and their hosts. When assessing the impact of gene flow across the two populations of phages we realized that temperate phages have narrower host ranges than virulent phages. This suggests, and we find some evidence, that gene flow between temperate phages infecting distant bacterial hosts might be mediated by recombination with the broader host virulent phages. Hence, gene flow across phages with distinct lifestyles could drastically increase the gene repertoire available for phage evolution, including the transfer of functional innovations across taxa. These results also have implications for bacterial evolution because of the impact of phage predation in bacterial population dynamics and the contribution of temperate phages to the evolution of bacterial gene repertoires.SIGNIFICANCE STATEMENTMany microbial communities are intensely predated by temperate and virulent bacteriophages. The former also contribute to bacterial gene repertoires. Gene transfers between bacteriophages favor their rapid adaptation, but are thought to occur rarely between virulent and temperate bacteriophages because their genomes are very different in terms of gene repertoires and genetic organization. We found that genetic exchanges occur frequently between these types of bacteriophages, involve different phage and bacterial functions, and are likely due to multiple DNA repair processes. Since we show that virulent bacteriophages have broader host ranges, they can shuttle genes between temperate bacteriophages present in taxa that are beyond the typical range of the latter. This enhances phages diversification and has multiple impacts on bacterial evolution.

scholarly journals Genome Sequencing Analysis of Scleromitrula shiraiana, a Causal Agent of Mulberry Sclerotial Disease With Narrow Host Range

2021 ◽  
Vol 11 ◽  
Author(s):  
Zhiyuan Lv ◽  
Ziwen He ◽  
Lijuan Hao ◽  
Xin Kang ◽  
Bi Ma ◽  
...  
Keyword(s):  
Host Range ◽  
Molecular Mechanisms ◽  
Genomic Analysis ◽  
Effector Proteins ◽  
Ecological Niches ◽  
Comparative Genomic ◽  
Sequencing Analysis ◽  
Cell Wall Degrading Enzymes ◽  
Narrow Host Range ◽  
Genes Encoding

Scleromitrula shiraiana is a necrotrophic fungus with a narrow host range, and is one of the main causal pathogens of mulberry sclerotial disease. However, its molecular mechanisms and pathogenesis are unclear. Here, we report a 39.0 Mb high-quality genome sequence for S. shiraiana strain SX-001. The S. shiraiana genome contains 11,327 protein-coding genes. The number of genes and genome size of S. shiraiana are similar to most other Ascomycetes. The cross-similarities and differences of S. shiraiana with the closely related Sclerotinia sclerotiorum and Botrytis cinerea indicated that S. shiraiana differentiated earlier from their common ancestor. A comparative genomic analysis showed that S. shiraiana has fewer genes encoding cell wall-degrading enzymes (CWDEs) and effector proteins than that of S. sclerotiorum and B. cinerea, as well as many other Ascomycetes. This is probably a key factor in the weaker aggressiveness of S. shiraiana to other plants. S. shiraiana has many species-specific genes encoding secondary metabolism core enzymes. The diversity of secondary metabolites may be related to the adaptation of these pathogens to specific ecological niches. However, melanin and oxalic acid are conserved metabolites among many Sclerotiniaceae fungi, and may be essential for survival and infection. Our results provide insights into the narrow host range of S. shiraiana and its adaptation to mulberries.

scholarly journals Comparative genomic analysis of three intestinal species reveals reductions in secreted pathogenesis determinants in bovine-specific and non-pathogenic Cryptosporidium species

2020 ◽  
Vol 6 (6) ◽  
Author(s):  
Zhixiao Xu ◽  
Na Li ◽  
Yaqiong Guo ◽  
Yaoyu Feng ◽  
Lihua Xiao
Keyword(s):  
Host Range ◽  
Gene Families ◽  
Copy Number Variations ◽  
Gene Organization ◽  
Nucleotide Metabolism ◽  
Comparative Genomic ◽  
Secretory Proteins ◽  
Broad Host Range ◽  
Biological Studies ◽  
Genes Encoding

The three common intestinal Cryptosporidium species in cattle differ significantly in host range, pathogenicity and public health significance. While Cryptosporidium parvum is pathogenic in pre-weaned calves and has a broad host range, C. bovis and C. ryanae are largely non-pathogenic and bovine-specific species in post-weaned calves. Thus far, only the genome of C. parvum has been sequenced. To improve our understanding of the genetic determinants of biological differences among Cryptosporidium spcies, we sequenced the genomes of C. bovis and C. ryanae and conducted a comparative genomics analysis. The genome of C. bovis has a gene content and organization more similar to C. ryanae than to other Cryptosporidium species sequenced to date; the level of similarity in amino acid and nucleotide sequences between the two species is 75.2 and 69.4 %, respectively. A total of 3723 and 3711 putative protein-encoding genes were identified in the genomes of C. bovis and C. ryanae, respectively, which are fewer than the 3981 in C. parvum. Metabolism is similar among the three species, although energy production pathways are further reduced in C. bovis and C. ryanae. Compared with C. parvum, C. bovis and C. ryanae have lost 14 genes encoding mucin-type glycoproteins and three for insulinase-like proteases. Other gene gains and losses in the two bovine-specific and non-pathogenic species also involve the secretory pathogenesis determinants (SPDs); they have lost all genes encoding MEDLE, FLGN and SKSR proteins, and two of the three genes for NFDQ proteins, but have more genes encoding secreted WYLE proteins, secreted leucine-rich proteins and GPI-anchored adhesin PGA18. The only major difference between C. bovis and C. ryanae is in nucleotide metabolism. In addition, half of the highly divergent genes between C. bovis and C. ryanae encode secreted or membrane-bound proteins. Therefore, C. bovis and C. ryanae have gene organization and metabolic pathways similar to C. parvum, but have lost some invasion-associated mucin glycoproteins, insulinase-like proteases, MEDLE secretory proteins and other SPDs. The multiple gene families under positive selection, such as helicase-associated domains, AMP-binding domains, protein kinases, mucins, insulinases and TRAPs could contribute to differences in host specificity and pathogenicity between C. parvum and C. bovis. Biological studies should be conducted to assess the contribution of these copy number variations to the narrow host range and reduced pathogenicity of C. bovis and C. ryanae.

scholarly journals A Novel Broad Host Range Phage Infecting Alteromonas

Viruses ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 987
Author(s):  
Xuejin Feng ◽  
Wei Yan ◽  
Anan Wang ◽  
Ruijie Ma ◽  
Xiaowei Chen ◽  
...  
Keyword(s):  
Host Range ◽  
Burst Size ◽  
Nucleotide Metabolism ◽  
Lytic Cycle ◽  
Nucleoside Triphosphate ◽  
Broad Host Range ◽  
Ecological Features ◽  
Wide Host Range ◽  
Genes Encoding ◽  
Ecological Importance

Bacteriophages substantially contribute to bacterial mortality in the ocean and play critical roles in global biogeochemical processes. Alteromonas is a ubiquitous bacterial genus in global tropical and temperate waters, which can cross-protect marine cyanobacteria and thus has important ecological benefits. However, little is known about the biological and ecological features of Alteromonas phages (alterophages). Here, we describe a novel alterophage vB_AmeP-R8W (R8W), which belongs to the Autographiviridae family and infects the deep-clade Alteromonas mediterranea. R8W has an equidistant and icosahedral head (65 ± 1 nm in diameter) and a short tail (12 ± 2 nm in length). The genome size of R8W is 48,825 bp, with a G + C content of 40.55%. R8W possesses three putative auxiliary metabolic genes encoding proteins involved in nucleotide metabolism and DNA binding: thymidylate synthase, nucleoside triphosphate pyrophosphohydrolase, and PhoB. R8W has a rapid lytic cycle with a burst size of 88 plaque-forming units/cell. Notably, R8W has a wide host range, such that it can infect 35 Alteromonas strains; it exhibits a strong specificity for strains isolated from deep waters. R8W has two specific receptor binding proteins and a compatible holin–endolysin system, which contribute to its wide host range. The isolation of R8W will contribute to the understanding of alterophage evolution, as well as the phage–host interactions and ecological importance of alterophages.

scholarly journals Withanolide D Enhances Radiosensitivity of Human Cancer Cells by Inhibiting DNA Damage Non-homologous End Joining Repair Pathway

2020 ◽  
Vol 9 ◽  
Author(s):  
Jerome Lacombe ◽  
Titouan Cretignier ◽  
Laetitia Meli ◽  
E. M. Kithsiri Wijeratne ◽  
Jean-Luc Veuthey ◽  
...  
Keyword(s):  
Dna Damage ◽  
Cancer Cells ◽  
Human Cancer ◽  
Repair Pathway ◽  
End Joining ◽  
Human Cancer Cells ◽  
Non Homologous End Joining
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