In depth characterization of an archaeal virus-host system reveals numerous virus exclusion mechanisms

Abstract

Deep Lake, Antarctica, is a hypersaline lake characterized by a very low microbial diversity, dominated by archaea, and a lack of grazing organisms, making viruses important players in regulating community structure. Here we present an in-depth characterization of an archaeal virus-host system isolated from Deep Lake. Upon purifying the environmental virus lysate through plaque assays, with the intention to generate a clean and stable virus-host system, we select for a virus variant with an exclusively lytic life cycle (HRTV-DL1). The host Halorubrum lacusprofundi exhibits a large arsenal of virus exclusion mechanisms, indicating a long ongoing arms race with viruses. However, we uncover that the majority of this arsenal was lost spontaneously in a strain grown under non-challenging laboratory conditions. By challenging both the parental strain and the sensitive strain with HRTV-DL1, we discovered a number of putative virus exclusion mechanisms that are only activated in the sensitive strain upon the lack of defense systems present in the parental strain. We identify one of two S-layer proteins as primary receptor for HRTV-DL1 and conclude that the presence of two different S-layer proteins in one strain provides a strong advantage in the arms race with viruses. We propose the involvement of origin recognition proteins (ORC1/CDC6) in virus exclusion. While Hrr. lacusprofundi and HRTV-DL1 represent a great archaeal model system to observe the arms race between viruses and hosts, our work also demonstrates that an isolated model virus-host systems does not reflect the entire spectrum of interactions as they occur in the environment.

Influence of N-Glycosylation on Virus–Host Interactions in Halorubrum lacusprofundi

“…In brief, EVs were isolated from the culture supernatant ( n = 3 for each strain) via centrifugation (45 min, 4500× g ) and precipitated from the culture supernatant with PEG 6000 . Precipitated vesicles were resuspended in DBCM2 salt solution [ 26 ], filtered through syringe-top filters (0.8, 0.45 and 2× 0.2 µm in sequence) and stained with 500 nM MitoTracker Green FM (Invitrogen) for 30 min. Subsequently, EVs were precipitated after overnight incubation with PEG 6000 (final concentration of 10%) via centrifugation at 20,000× g for 40 min.…”

“…SS7-4 was found to trigger fusion of the membrane enveloped Halorubrum Pleomorphic Virus-6 (HRPV-6) with the host cell via the virus spike protein, an interaction that is dependent on the specific host S-layer [ 24 ]. The S-layer protein has also been identified as a potential receptor for several archaeal head-tailed viruses [ 25 , 26 , 27 ] infecting haloarchaea. Archaeal head-tailed viruses do not contain membrane lipids and exit host cells by lysis.…”

“…Furthermore, we tested the impact of N-glycosylation on virus particle stability at different NaCl concentrations. Halorubrum Tailed Virus DL1 (HRTV-DL1) is an archaeal head-tailed virus that was shown to use the S-layer glycoprotein as its primary receptor [ 26 ]. Haloferax Pleomorphic Virus 1 (HFPV-1), a membrane-enveloped pleolipovirus [ 39 , 40 ], exhibits a glycosylated spike protein similar to HRPV-1 [ 12 , 13 ].…”

Improving the genetic system for Halorubrum lacusprofundi to allow in-frame deletions

“…Hrr. lacusprofundi ACAM34_UNSW is a variant with a reduced genome, derived from an original ACAM34 strain, and has been described in Mercier et al (2022). The standard medium for cultivation was DBCM2 (Dyall-Smith, 2009b), with slight modifications.…”

“…Several different viruses were shown to infect Hrr. lacusprofundi (Nuttall and Dyall-Smith, 1993;Dyall-Smith, 2009d;Krupovič et al, 2010;Atanasova et al, 2012;Porter et al, 2013;Li et al, 2014;Tschitschko et al, 2015;Alarcón-Schumacher et al, 2022;Mercier et al, 2022). Additionally, the formation of plasmid vesicles (PVs), proposed to be an evolutionary precursor of viruses, has only been reported for Hrr.…”