Research

Viral functions at the molecular level

We are interested in understanding the molecular principles of the functions of viruses and how viruses interact with their host cells. In addition, we investigate how sequence or structural similarity reflects the common evolution of viruses which are infecting different cellular domains of life. Results will be also exploited to establish genome-based classification criteria that will serve as the basis for virus taxonomy.

We study the extent of viral genetic diversity and various aspects of virus biology including virus-host interactions, molecular mechanisms of virus entry and virion assembly with a special focus on archaeal viruses and specific model systems or groups of double-stranded DNA bacteriophages including Antactic sea ice and Finnish fresh water phages.

Archaeal viruses form a special group of viruses of which we know very much less than about bacterial and eukaryotic viruses. Many archaeal viruses present their own unique virus families. Most of the characterized archaeal viruses infect extremophilic hosts e.g. from high salinity or temperature. We have a large number of culturable archaeal viruses isolated from high-salt environmental samples (e.g. 2012, 2015, 2019) and we are investigating their functions and relationships.

Selected references:
Santos-Pérez I, Charro D, Gil-Carton D, Azkargorta M, Elortza F, Bamford DH, Oksanen HM, Abrescia NGA. 2019. Structural basis for assembly of vertical single β-barrel viruses. Nat Commun. 10:1184.

Mizuno CM, Prajapati B, Lucas-Staat S, Sime-Ngando T, Forterre P, Bamford DH, Prangishvili D, Krupovic M, Oksanen HM. 2019. Novel haloarchaeal viruses from Lake Retba infecting Haloferax and Halorubrum species. Environ Microbiol. 21:2129-2147.

Atanasova NS, Heiniö CH, Demina TA, Bamford DH, Oksanen HM. 2018. The unexplored diversity of pleolipoviruses: the surprising case of two viruses with identical major structural modules. Genes. 9:131.

New era of virus taxonomy

The International Committee on Taxonomy of Viruses (ICTV) oversees the official classification of viruses and nomenclature of taxa (Virus Taxonomy). The recent and rapid development in discovery of new viruses and the accumulation of metagenomic sequence data has led to a change in virus taxonomy. This has resulted in modernization of the rank structure of virus taxonomy, which has been recently reported in Nature Microbiology (2020). New levels of the virus taxonomy will also stimulate further research on virus origins and evolution.
It is our responsibility to coordinate the family Corticoviridae as the Chair of the Study Group in the Bacterial and Archaeal Viruses Subcommittee. We have also contributed into the description of the families of Spherolipoviridae, Tectiviridae, Pleolipoviridae, Finnlakeviridae, and Halspiviridae. We are also working on archaeal tailed double-stranded DNA viruses originating from highly saline environments to understand their relationships and position in the virus taxonomy.

Selected references:
Demina TA, Oksanen HM. 2020. Pleomorphic archaeal viruses: the family Pleolipoviridae is expanding by seven new species. Arch Virol. Epub ahead of print

Barylski J, Enault F, Dutilh BE, Schuller MB, Edwards RA, Gillis A, Klumpp J, Knezevic P, Krupovic M, Kuhn JH, Lavigne R, Oksanen HM, Sullivan MB, Jang HB, Simmonds P, Aiewsakun P, Wittmann J, Tolstoy I, Brister JR, Kropinski AM, Adriaenssens EM. 2020. Analysis of spounaviruses as a case study for the overdue reclassification of tailed phages. Syst Biol. 69:110-123.

Demina TA, Pietilä MK, Svirskaitė J, Ravantti JJ, Atanasova NS, Bamford DH, Oksanen HM. 2017. HCIV-1 and other tailless icosahedral internal membrane-containing viruses of the family Sphaerolipoviridae. Viruses. 9:32.

Resource:
Virus Taxonomy: The ICTV Report on Virus Classification and Taxon Nomenclature (the 10th ICTV report, Online)

Method development - Biomolecular complex separation

Large biocomplexes such as viruses, virus-like particles, exosomes, vesicles or large protein complexes cannot be purified by conventional protein purification methods. We are developing new strategies for purifying large complexes in connection with the Biocomplex core facility that we co-host. Main technologies are ultracentrifugation, asymmetrical flow field-flow fractionation and monolithic chromatography. We also coordinate the national Structural Biology Finland Research Infrastructure and the ESFRI Instruct-ERIC Centre Finland.

Selected references:
Eskelin K, Poranen MM, Oksanen HM. 2019. Asymmetrical flow field-flow fractionation on virus and virus-like particle applications. Microorganisms. 7:555.

Eskelin K, Lampi M, Meier F, Moldenhauer E, Bamford DH, Oksanen HM. 2016. Asymmetric flow field flow fractionation methods for virus purification. J Chromatogr A. 1469:108-119.

Oksanen HM, Domanska A, Bamford DH. 2012. Monolithic ion exchange chromatographic methods for virus purification. Virology. 434:271-277.