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Diversity, specificity and molecular evolution of the lytic arsenal of Pseudomonas phages: in silico perspective.

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Title: Diversity, specificity and molecular evolution of the lytic arsenal of Pseudomonas phages: in silico perspective.
Authors: Valero‐Rello, Ana1 (AUTHOR) anavalerorello@gmail.com
Source: Environmental Microbiology. Nov2019, Vol. 21 Issue 11, p4136-4150. 15p.
Subjects: Molecular evolution, Bacteriophages, Bacterial proteins, Pseudomonas, Molecular association, Surface structure, Peptidase, Polyketide synthases
Abstract: Summary: Bacteriophages encode an arsenal of proteins to lyse bacteria by breaking their surface structures, constituting a promising alternative to antibiotics. However, the selection and bioengineering of endolysins and other phage lytic proteins need to be assisted by a previous knowledge of their molecular characteristics. In this study, all putative lytic proteins encoded in Pseudomonas phages were in silico examined to describe their diversity, host association and molecular evolution. A total of 491 proteins were identified among 223 phages, including endolysins, holins, pinholins, spanins, lipases and peptidases. Protein families and combination of functional domains were characteristic of phages belonging to the same genus, and these tended to infect a single host species. Clustering and phylogenetic analysis showed a protein grouping associated with bacterial host, and some functional domains being specific. Interestingly, most putative lytic proteins from phages infecting P. fluorescens and P. putida had negative net charges, opposed to most endolysins. Phage lifestyle also had an impact on protein variability, with transglycosylases, glucosaminidases, holins and spanins from lysogenic phages clustering into monophyletic nodes, suggesting the effect of a different selection pressure as a result of the co‐option of a new function in the lysogenized bacteria. [ABSTRACT FROM AUTHOR]
Copyright of Environmental Microbiology is the property of Wiley-Blackwell and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
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  Data: Diversity, specificity and molecular evolution of the lytic arsenal of Pseudomonas phages: in silico perspective.
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  Data: <searchLink fieldCode="AR" term="%22Valero‐Rello%2C+Ana%22">Valero‐Rello, Ana</searchLink><relatesTo>1</relatesTo> (AUTHOR)<i> anavalerorello@gmail.com</i>
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  Data: <searchLink fieldCode="JN" term="%22Environmental+Microbiology%22">Environmental Microbiology</searchLink>. Nov2019, Vol. 21 Issue 11, p4136-4150. 15p.
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  Data: <searchLink fieldCode="DE" term="%22Molecular+evolution%22">Molecular evolution</searchLink><br /><searchLink fieldCode="DE" term="%22Bacteriophages%22">Bacteriophages</searchLink><br /><searchLink fieldCode="DE" term="%22Bacterial+proteins%22">Bacterial proteins</searchLink><br /><searchLink fieldCode="DE" term="%22Pseudomonas%22">Pseudomonas</searchLink><br /><searchLink fieldCode="DE" term="%22Molecular+association%22">Molecular association</searchLink><br /><searchLink fieldCode="DE" term="%22Surface+structure%22">Surface structure</searchLink><br /><searchLink fieldCode="DE" term="%22Peptidase%22">Peptidase</searchLink><br /><searchLink fieldCode="DE" term="%22Polyketide+synthases%22">Polyketide synthases</searchLink>
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  Data: Summary: Bacteriophages encode an arsenal of proteins to lyse bacteria by breaking their surface structures, constituting a promising alternative to antibiotics. However, the selection and bioengineering of endolysins and other phage lytic proteins need to be assisted by a previous knowledge of their molecular characteristics. In this study, all putative lytic proteins encoded in Pseudomonas phages were in silico examined to describe their diversity, host association and molecular evolution. A total of 491 proteins were identified among 223 phages, including endolysins, holins, pinholins, spanins, lipases and peptidases. Protein families and combination of functional domains were characteristic of phages belonging to the same genus, and these tended to infect a single host species. Clustering and phylogenetic analysis showed a protein grouping associated with bacterial host, and some functional domains being specific. Interestingly, most putative lytic proteins from phages infecting P. fluorescens and P. putida had negative net charges, opposed to most endolysins. Phage lifestyle also had an impact on protein variability, with transglycosylases, glucosaminidases, holins and spanins from lysogenic phages clustering into monophyletic nodes, suggesting the effect of a different selection pressure as a result of the co‐option of a new function in the lysogenized bacteria. [ABSTRACT FROM AUTHOR]
– Name: AbstractSuppliedCopyright
  Label:
  Group: Ab
  Data: <i>Copyright of Environmental Microbiology is the property of Wiley-Blackwell and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract.</i> (Copyright applies to all Abstracts.)
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        Value: 10.1111/1462-2920.14767
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      – Code: eng
        Text: English
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        PageCount: 15
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      – SubjectFull: Molecular evolution
        Type: general
      – SubjectFull: Bacteriophages
        Type: general
      – SubjectFull: Bacterial proteins
        Type: general
      – SubjectFull: Pseudomonas
        Type: general
      – SubjectFull: Molecular association
        Type: general
      – SubjectFull: Surface structure
        Type: general
      – SubjectFull: Peptidase
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      – SubjectFull: Polyketide synthases
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      – TitleFull: Diversity, specificity and molecular evolution of the lytic arsenal of Pseudomonas phages: in silico perspective.
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              M: 11
              Text: Nov2019
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              Y: 2019
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