M. B. Dion, F. Oechslin, and S. Moineau, Phage diversity, genomics and phylogeny, 2020.

M. Krupovic, V. Cvirkaite-krupovic, J. Iranzo, D. Prangishvili, and E. V. Koonin, Viruses of 521 archaea: Structural, functional, environmental and evolutionary genomics, Virus Res, vol.522, pp.181-193, 2018.

D. Prangishvili, D. H. Bamford, P. Forterre, J. Iranzo, E. V. Koonin et al., , 2017.

K. Kamada, F. Hanaoka, and S. K. Burley, Crystal structure of the MazE/MazF complex: 605 Molecular bases of antidote-toxin recognition, Mol Cell, vol.11, pp.875-884, 2003.

M. Coles, S. Djuranovic, J. Soding, T. Frickey, K. Koretke et al., AbrB-like transcription factors assume a swapped hairpin fold that is evolutionarily 608 related to double-psi ? barrels, Structure, vol.607, pp.919-928, 2005.

I. Asen, S. Djuranovic, A. N. Lupas, and K. Zeth, Crystal structure of SpoVT, the final 610 modulator of gene expression during spore development in Bacillus subtilis, J Mol Biol, vol.611, pp.962-975, 2009.

L. Xiong, S. Liu, S. Chen, Y. Xiao, B. Zhu et al., , p.613

L. Wang and S. Chen, A new type of DNA phosphorothioation-based antiviral system in 614 archaea, Nat Commun, vol.10, p.1688, 2019.

T. A. Demina, M. K. Pietila, J. Svirskaite, J. J. Ravantti, N. S. Atanasova et al., HCIV-1 and other tailless icosahedral internal membrane-containing viruses of the, vol.616

A. Ramirez-peralta, K. A. Stewart, S. K. Thomas, B. Setlow, Z. Chen et al., , 2012.

, Effects of the SpoVT regulatory protein on the germination and germination protein levels of 620 spores of Bacillus subtilis, J Bacteriol, vol.194, pp.3417-3442

I. Bagyan, J. Hobot, and S. Cutting, A compartmentalized regulator of developmental gene 622 expression in Bacillus subtilis, J Bacteriol, vol.178, pp.4500-4507, 1996.

O. Chumsakul, H. Takahashi, T. Oshima, T. Hishimoto, S. Kanaya et al., , p.624

, Genome-wide binding profiles of the Bacillus subtilis transition state regulator AbrB 625 and its homolog Abh reveals their interactive role in transcriptional regulation, Nucleic Acids 626 Res, vol.39, pp.414-442

E. Aizenman, H. Engelberg-kulka, and G. Glaser, An Escherichia coli chromosomal 628 "addiction module" regulated by guanosine 3',5'-bispyrophosphate: a model for programmed 629 bacterial cell death, Proc Natl Acad Sci U S A, vol.93, pp.6059-63, 1996.

N. Nikolic, Autoregulation of bacterial gene expression: lessons from the MazEF 631 toxin-antitoxin system, Curr Genet, vol.65, pp.133-138, 2019.

S. Fusco, M. Aulitto, I. Iacobucci, G. Crocamo, P. Pucci et al., , 2020.

, tyrosine integrases encoded by the temperate pleolipovirus SNJ2, Nucleic Acids Res, vol.649, pp.2521-2536

R. L. Charlebois, W. L. Lam, S. W. Cline, and W. F. Doolittle, , p.651, 1987.

, Halobacterium volcanii and its use in demonstrating transformation of an archaebacterium

, Proc Natl Acad Sci U S A, vol.84, pp.8530-8534

S. W. Cline, W. L. Lam, R. L. Charlebois, L. C. Schalkwyk, and W. F. Doolittle, Transformation 654 methods for halophilic archaebacteria, Can J Microbiol, vol.35, pp.148-52, 1989.

J. P. Huff, B. J. Grant, C. A. Penning, and K. F. Sullivan, Optimization of routine transformation of 656, 1990.

, Escherichia coli with plasmid DNA. Biotechniques, vol.9, pp.576-583

S. Cai, L. Cai, D. Zhao, G. Liu, J. Han et al., A novel DNA-binding protein, p.658, 2015.

. Phar, plays a central role in the regulation of polyhydroxyalkanoate accumulation and granule 659 formation in the haloarchaeon Haloferax mediterranei, Appl Environ Microbiol, vol.81, p.54

Y. Mei, J. Chen, D. Sun, D. Chen, Y. Yang et al., Induction and preliminary 661 characterization of a novel halophage SNJ1 from lysogenic Natrinema sp. F5, Can J Microbiol, vol.662, pp.1106-1116, 2007.

S. Breuert, T. Allers, G. Spohn, and J. Soppa, Regulated polyploidy in halophilic archaea, 2006.

, PLoS One, vol.1, p.56

K. J. Livak and T. D. Schmittgen, Analysis of relative gene expression data using real-time 666 quantitative PCR and the 2 -??CT method, Methods, vol.25, pp.402-410, 2001.

Y. Wang, B. Chen, M. Cao, L. Sima, D. Prangishvili et al., Rolling-circle 668 replication initiation protein of haloarchaeal sphaerolipovirus SNJ1 is homologous to bacterial 669 transposases of the IS91 family insertion sequences, J Gen Virol, 2018.

B. B. Oberto, SyntTax: a web server linking synteny to prokaryotic taxonomy, BMC 671 Bioinf, vol.14, p.4, 2013.
URL : https://hal.archives-ouvertes.fr/hal-00779628

L. Zimmermann, A. Stephens, S. Z. Nam, D. Rau, J. Kubler et al., Lupas 673 AN, Alva V, A completely reimplemented MPI Bioinformatics Toolkit, p.674, 2018.

, HHpred server at its core, J Mol Biol, vol.430, pp.2237-2243

D. T. Jones, Protein secondary structure prediction based on position-specific scoring 676 matrices, J Mol Biol, vol.292, pp.195-202, 1999.

, location of the genomic deletion. (z) represented the genome size of mutant SNJ1 724 viruses and the smaller genomes were noted in bold

, Late exponential 729 phase culture of CJ7 was infected with SNJ1 orf4 mut and SNJ1 ?orf4 viruses (generated 730 from CJ7/pYC-S-4M and CJ7/pYC-S D1-575 culture respectively), and only clear 731 plaques were observed. b. Expression of ORF4 in trans restored turbid plaque 732 formation of clear-plaque SNJ1 mutant viruses and inhibited plaque formation 733 dramatically. Ten-fold serial dilutions of SNJ1 viruses or its clear plaque mutants were 734 spotted onto the lawns of CJ7-F/pFJ6-MCS, or CJ7-F/pFJ6-1-656 (with orf4), Fig 3. Identification of orf4 as a critical factor for SNJ1 lysis-lysogeny switch. a. 728 orf4 disrupted viruses formed only clear plaques on lawns of CJ7

, Cells 746 were collected by centrifugation and washed twice in same volume of 18% MGM to 747 remove MMC. Cell pellets were resuspended in 18% MGM + Mev medium and 748 cultured for 24 h. Samples were taken for qPCR analysis using primer pairs 749 vector-F/vector-R, orf14-F/orf14-R and radA-F/radA-R to determine the relative 750 plasmid copy number to chromosome. Three independent experiments were 751 performed, and error bars indicated standard deviations. b. Plasmid stability of 752 pYC-SHS and pYC-SHS

, 4M+pFJ6-1-656 was 754 inoculated into 5 mL of Halo-2 medium every day. Samples were taken and measured 755 by qPCR using primer pairs vector-F/vector-R, orf14-F/orf14-R and radA-F/radA-R 756 for five days. Three independent experiments were performed

, and SpoVT (residues 1-55, PDB code 2W1T)(35) are aligned with ORF4 768 by Clustal Omega. The secondary-structure of ORF4 was predicted by PSIPRED in

, The same color is used for other proteins. c. The 771 N-terminal 33 amino acids of SNJ1 were necessary and sufficient for immunity to 772 against SNJ1. Ten-fold serial dilutions of SNJ1 were spotted onto lawns of CJ7-F 773 harboring plasmid pFJ6-MCS or its derivatives carrying different portion of ORF4, 774 superscript denotes the amino acid residues of ORF4. Hpro stands for the promoter of 775 heat-shock protein 70 from Haloferax volcanii DS52, MPI Bioinformatics Toolkit. ORF4 contains 5 b-strands (light-grey arrows) and one 770 a-helix (dark-grey cylinder)

, ORF4 blocks SNJ1 infection by inhibiting viral gDNA replication. a. ORF4 779 did not affect SNJ1 adsorption to host cells CJ7. SNJ1 was incubated with 780 early-exponential phase cultures of CJ7, J7-1, CJ7-F/pFJ6-MCS (-orf4) and

. Cj7-f, /pFJ6-Hpro-orf4 (+ orf4) at different MOI (0.1, 1 and 10) for about 1 h at 45?