Whole Genome Sequencing Identifies an Allele Responsible for Clear Vs. Turbid Plaque Morphology in a Mycobacteriophage

Overview

Journal BMC Microbiol

Publisher Biomed Central

Specialty Microbiology

Date 2020 Jun 10

PMID 32513117

Citations 3

Authors

Bhavani S Gudlavalleti

Trong Phung

Charles L Barton

Allysson Becker

Brittany L Graul

Jarod T Griffin

Connor J Hays

Bailey Horn

David R Liang

Lauren M Rutledge

Alexandria M Szalanczy

Bobby L Gaffney

Rodney A King

Claire A Rinehart

Amanda K Staples

Alexander A Stewart

Marie L Nydam

Kelly E OQuin

Affiliations

Soon will be listed here.

Abstract

Background: Whole genome sequencing promises to revolutionize our ability to link genotypic and phenotypic variation in a wide range of model and non-model species.

Results: Here we describe the isolation and characterization of a novel mycobacteriophage named BGlluviae that grows on Mycobacterium smegmatis mc155. BGlluviae normally produces turbid plaques but a spontaneous clear plaque was also recovered. The genomic DNA from pure populations of the BGlluviae phage and the clear plaque mutant were sequenced. A single substitution, at amino acid 54 (I to T), in the immunity repressor protein resulted in a clear plaque phenotype.

Conclusions: This substitution is predicted to be located at the subunit interaction interface of the repressor protein, and thus prevents the establishment of lysogeny.

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References

Chaisson M, Pevzner P . Short read fragment assembly of bacterial genomes. Genome Res. 2007; 18(2):324-30. PMC: 2203630. DOI: 10.1101/gr.7088808. View

Lu S, Wang J, Chitsaz F, Derbyshire M, Geer R, Gonzales N . CDD/SPARCLE: the conserved domain database in 2020. Nucleic Acids Res. 2019; 48(D1):D265-D268. PMC: 6943070. DOI: 10.1093/nar/gkz991. View

Ptashne M . ISOLATION OF THE lambda PHAGE REPRESSOR. Proc Natl Acad Sci U S A. 1967; 57(2):306-13. PMC: 335506. DOI: 10.1073/pnas.57.2.306. View

Meyer B, Kleid D, Ptashne M . Lambda repressor turns off transcription of its own gene. Proc Natl Acad Sci U S A. 1975; 72(12):4785-89. PMC: 388816. DOI: 10.1073/pnas.72.12.4785. View

Laslett D, Canback B . ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Res. 2004; 32(1):11-6. PMC: 373265. DOI: 10.1093/nar/gkh152. View

Brudno M, Do C, Cooper G, Kim M, Davydov E, Green E . LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA. Genome Res. 2003; 13(4):721-31. PMC: 430158. DOI: 10.1101/gr.926603. View

Russell D, Hatfull G . PhagesDB: the actinobacteriophage database. Bioinformatics. 2017; 33(5):784-786. PMC: 5860397. DOI: 10.1093/bioinformatics/btw711. View

Cole C, Barber J, Barton G . The Jpred 3 secondary structure prediction server. Nucleic Acids Res. 2008; 36(Web Server issue):W197-201. PMC: 2447793. DOI: 10.1093/nar/gkn238. View

Hatfull G, Jacobs-Sera D, Lawrence J, Pope W, Russell D, Ko C . Comparative genomic analysis of 60 Mycobacteriophage genomes: genome clustering, gene acquisition, and gene size. J Mol Biol. 2010; 397(1):119-43. PMC: 2830324. DOI: 10.1016/j.jmb.2010.01.011. View

10.

Pettersen E, Goddard T, Huang C, Couch G, Greenblatt D, Meng E . UCSF Chimera--a visualization system for exploratory research and analysis. J Comput Chem. 2004; 25(13):1605-12. DOI: 10.1002/jcc.20084. View

11.

Jordan S, Pabo C . Structure of the lambda complex at 2.5 A resolution: details of the repressor-operator interactions. Science. 1988; 242(4880):893-9. DOI: 10.1126/science.3187530. View

12.

Jones D . Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol. 1999; 292(2):195-202. DOI: 10.1006/jmbi.1999.3091. View

13.

Delcher A, Harmon D, Kasif S, White O, Salzberg S . Improved microbial gene identification with GLIMMER. Nucleic Acids Res. 1999; 27(23):4636-41. PMC: 148753. DOI: 10.1093/nar/27.23.4636. View

14.

Kaiser A . Mutations in a temperate bacteriophage affecting its ability to lysogenize Escherichia coli. Virology. 1957; 3(1):42-61. DOI: 10.1016/0042-6822(57)90022-3. View

15.

Bolger A, Lohse M, Usadel B . Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014; 30(15):2114-20. PMC: 4103590. DOI: 10.1093/bioinformatics/btu170. View

16.

Lowe T, Eddy S . tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 1997; 25(5):955-64. PMC: 146525. DOI: 10.1093/nar/25.5.955. View

17.

Berman H, Westbrook J, Feng Z, Gilliland G, Bhat T, Weissig H . The Protein Data Bank. Nucleic Acids Res. 1999; 28(1):235-42. PMC: 102472. DOI: 10.1093/nar/28.1.235. View

18.

Yang J, Yan R, Roy A, Xu D, Poisson J, Zhang Y . The I-TASSER Suite: protein structure and function prediction. Nat Methods. 2014; 12(1):7-8. PMC: 4428668. DOI: 10.1038/nmeth.3213. View

19.

Zhang Y . I-TASSER server for protein 3D structure prediction. BMC Bioinformatics. 2008; 9:40. PMC: 2245901. DOI: 10.1186/1471-2105-9-40. View

20.

Buchan D, Minneci F, Nugent T, Bryson K, Jones D . Scalable web services for the PSIPRED Protein Analysis Workbench. Nucleic Acids Res. 2013; 41(Web Server issue):W349-57. PMC: 3692098. DOI: 10.1093/nar/gkt381. View