Host-parasite relations of bacteria and phages can be unveiled by Oligostickiness, a measure of relaxed sequence similarity

MOTIVATION The recent metagenome analysis has been producing a large number of host-unassigned viruses. Although assigning viruses to their hosts is basically important not only for virology but also for prevention of epidemic, it has been a laborious and difficult task to date. The only effective method for this purpose has been to find them in a same microscopic view. Now, we tried a computational approach based on genome sequences of bacteria and phages, introducing a physicochemical parameter, SOSS (set of oligostickiness similarity score) derived from oligostickiness, a measure of binding affinity of oligonucleotides to template DNA. RESULTS We could confirm host-parasite relationships of bacteria and their phages by SOSS analysis: all phages tested (25 species) had a remarkably higher SOSS value with its host than with unrelated bacteria. Interestingly, according to SOSS values, lysogenic phages such as lambda phage (host: Escherichia coli) or SPP1 (host: Bacillus subtilis) have distinctively higher similarity with its host than its non-lysogenic (excretive or virulent) ones such as fd and T4 (host: E.coli) or phages gamma and PZA (host: B.subtilis). This finding is very promising for assigning host-unknown viruses to its host. We also investigated the relationship in codon usage frequency or G+C content of genomes to interpret the phenomenon revealed by SOSS analysis, obtaining evidences which support the hypothesis that higher SOSS values resulted from the cohabitation in the same environment which may cause the common biased mutation. Thus, lysogenic phages which stay inside longer resemble the host.

[1]  M. Syvanen,et al.  Horizontal Gene Transfer , 2015, Evolution, Medicine, and Public Health.

[2]  Massimo Vergassola,et al.  Causes for the intriguing presence of tRNAs in phages. , 2007, Genome research.

[3]  E. Koonin Orthologs, Paralogs, and Evolutionary Genomics 1 , 2005 .

[4]  H. Matsuda,et al.  Biased biological functions of horizontally transferred genes in prokaryotic genomes , 2004, Nature Genetics.

[5]  J. W. Little,et al.  Robustness of a gene regulatory circuit , 1999, The EMBO journal.

[6]  M. Gefter,et al.  DNA Replication , 2019, Advances in Experimental Medicine and Biology.

[7]  S. Karlin,et al.  Comparative DNA analysis across diverse genomes. , 1998, Annual review of genetics.

[8]  E. Kejnovský,et al.  High intrachromosomal similarity of retrotransposon long terminal repeats: evidence for homogenization by gene conversion on plant sex chromosomes? , 2007, Gene.

[9]  Lon R. Cardon,et al.  A first-generation linkage disequilibrium map of human chromosome 22 , 2002, Nature.

[10]  R. Edwards,et al.  Viral metagenomics , 2005, Nature Reviews Microbiology.

[11]  J. Livny,et al.  Characterizing spontaneous induction of Stx encoding phages using a selectable reporter system , 2004, Molecular microbiology.

[12]  K. Sneppen,et al.  . s of t ] 1 9 O ct 2 00 0 Stability Puzzles in Phage λ , 2008 .

[13]  Koichi Nishigaki,et al.  Genome structures embossed by oligonucleotide-stickiness , 2002, Bioinform..

[14]  O. White,et al.  Environmental Genome Shotgun Sequencing of the Sargasso Sea , 2004, Science.

[15]  B. Rieland,et al.  Prevalence of Broad-Host-Range Lytic Bacteriophages of Sphaerotilus natans, Escherichia coli, andPseudomonas aeruginosa , 1998, Applied and Environmental Microbiology.

[16]  James M. Musser,et al.  Prophage Induction and Expression of Prophage-EncodedVirulence Factors in Group A Streptococcus Serotype M3 StrainMGAS315 , 2003, Infection and Immunity.

[17]  M. Hattori,et al.  The genome sequence of Clostridium botulinum type C neurotoxin-converting phage and the molecular mechanisms of unstable lysogeny. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[18]  S Karlin,et al.  Similarities and dissimilarities of phage genomes. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[19]  E. Koonin Orthologs, paralogs, and evolutionary genomics. , 2005, Annual review of genetics.

[20]  J. Lake,et al.  Horizontal gene transfer among genomes: the complexity hypothesis. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[21]  S Karlin,et al.  Heterogeneity of genomes: measures and values. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[22]  K. Nishigaki,et al.  Homogenization of Chromosomes Revealed by Oligonucleotide-Stickiness , 2004 .