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Conference Poster Year : 2021

A family for lambda: a possible genome-based taxonomy for lambdoid viruses?

Abstract

Discovered by Esther Lederberg in 1951, the temperate bacterial virus (or bacteriophage) lambda infecting the laboratory Escherichia coli strain K-12 has notably owed its fame to being at the center of the molecular genetic universe during three decades1. Over the years, many phages related to lambda, and susceptible to recombine with it, were isolated and named « lambdoids » (or « lambda-like »). Due to the sequencing development, the ill-defined term of lambdoid was expanded to mean a phage with the same functional gene order as lambda and carrying patches of nucleotide sequence similarity with it or another lambdoid phage [1]. Whole genomic comparison indeed revealed that lambdoid phage genomes were highly mosaic with each other and thus appeared to regularly share and exchange a wide pool of genes. Since the 2000s and especially in recent years, the Bacterial and Archaeal Viruses Subcommittee of the International Committee on Taxonomy of Viruses has moved largely to a molecular taxonomy based upon overall DNA and protein similarity [2]. The question raised whether lambdoid genomes, despite their recombinational flexibility, could be placed into a classification scheme. For this, we started with a set of 70 complete lambdoid genomes, and submitted them to analysis with two recent tools: VIRIDIC (Virus Intergenomic Distance Calculator), computing pairwise ANI-like intergenomic distances/similarities amongst phage genomes [3] and ViPTree, which is a viral proteomic tree server based on genome-wide sequence similarities computed by tBLASTx [4]. The first one was used for species and genus delineations using respective thresholds of 95% and 70% nucleotide identity while the second helped us to distinguish a potential family demarcation. Only 43 of the 70 genomes, (representing 30 species and 12 genera), could be included in a modern, genome-based “lambdoid” family subdivided into three distinct subfamilies, while the remaining genomes did not share enough ancestry to be included into a family. The structural genes coding for virion components were delineating clearly these subfamilies, while four tail tip encoding-genes (I, J, K, L on lambda) formed the core genome of the lambdoid family level. This classification scheme seemed robust, as a challenge with 36 new E.coli prophages (size >42kb) did not perturb the ViPTree-based subfamily branchings. We propose that despite its mosaicism, the lambdoid family can be recognized as such, with a core genome restricted to its tail tip (>73% aa identity). [1] S. R. Casjens, R. W. Hendrix. Virology. 479-480, 310-330 (2015). [2] D. Turner, A. M. Kropinski, E. M. Adriaenssens. Viruses. 13, 506 (2021). [3] C. Moraru, A. Varsani, A. M. Kropinski. Viruses. 12, 1268 (2020). [4] Y. Nishimura, T. Yoshida, M. Kuronishi, H. Uehara, H. Ogata, S. Goto. Bioinformatics. 33, 2379-2380 (2017).
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Dates and versions

hal-04334546 , version 1 (11-12-2023)

Identifiers

  • HAL Id : hal-04334546 , version 1

Cite

Lossouarn Julien, Lehman Susan M., Adriaenssens Evelien M., Kropinski Andrew M., Rocha Eduardo, et al.. A family for lambda: a possible genome-based taxonomy for lambdoid viruses?. Phages in Roscoff, Oct 2021, Roscoff (29680), France. ⟨hal-04334546⟩
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