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Virus Taxonomy
The ICTV Report on Virus Classification and Taxon Nomenclature
Finnlakeviridae Chapter

Finnlakeviridae

Sari Mäntynen#, Elina Laanto#, Lotta-Riina Sundberg, Minna M. Poranen, and Hanna M. Oksanen
# Shared first authorship

The citation for this ICTV Report chapter is the summary published as Mäntynen et al., (2020):
ICTV Virus Taxonomy Profile: Finnlakeviridae Journal of General Virology, (In Press)

Corresponding author: Hanna M. Oksanen (hanna.oksanen@helsinki.fi)

Edited by: Evelien Adriaenssens and Stuart G. Siddell
Posted: July 2020

Summary
Finnlakeviridae is a family of icosahedral, internal membrane-containing bacterial viruses with circular, single-stranded DNA genomes (Table
1.Finnlakeviridae). The family includes a single genus, Finnlakevirus, with one species, Flavobacterium virus FLiP. Flavobacterium phage FLiP
was isolated with its gram-negative host bacterium from a boreal freshwater habitat in Central Finland in 2010. It is the first described single-
stranded DNA virus with an internal membrane. Flavobacterium phage FLiP shares minimal sequence similarity with other known viruses. The
virion organization (pseudo T = 21 dextro) and major capsid protein fold (double-ß-barrel) of Flavobacterium phage FLiP resemble those of
Pseudoalteromonas phage PM2 (family Corticoviridae) that has a double-stranded DNA genome. A similar major capsid protein fold is also found
in other double-stranded DNA viruses in the kingdom Bamfordvirae. Since only one genus is currently recognized within the family
Finnlakeviridae, the genus description corresponds to the family description.

Table 1.Finnlakeviridae. Characteristics of members of the family Finnlakeviridae.

Characteristic Description

Typical
Flavobacterium phage FLiP (MF361639), species Flavobacterium virus FLiP, genus Finnlakevirus
member

Icosahedral, internal membrane-containing virions, approximately 59 nm in diameter (from vertex to vertex). Spikes protrude
Virion
from the virion surface

Genome 9.2 kb of circular, single-stranded DNA

Replication Possibly rolling circle replication (not experimentally shown)

Translation Prokaryotic translation

Host range Gram-negative bacteria from the genus Flavobacterium

Taxonomy One genus with one species

Virion
Morphology

The virion of Flavobacterium phage FLiP consists of an icosahedral protein shell and an internal membrane, which are uniquely combined with a
circular single-stranded DNA genome (Figure 1.Finnlakeviridae). The diameter of the virion is about 59 nm (vertex-to-vertex). The inner surface of
the icosahedral protein capsid is covered by a lipid bilayer membrane (5 nm thick), enclosing the single-stranded DNA genome. The major capsid
proteins (MCPs) forming the outer protein shell follow a pseudo T = 21 dextro icosahedral capsid organization, previously described only for
marine double-stranded DNA Pseudoalteromonas phage PM2 (Huiskonen et al., 2004). The Flavobacterium phage FLiP MCPs consist of two β-
barrels with jellyroll topology and arrange into trimers to form pseudohexameric molecules. The five-fold vertices are occupied by pentameric
spike complexes (Laanto et al., 2017).

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Figure 1.Finnlakeviridae. (A) Cryo-electron microscopic reconstruction of the Flavobacterium phage FLiP virion ( Laanto et al., 2017). (B)
Flavobacterium phage FLiP virions negatively-stained with 2% phosphotungstic acid (pH 8.5) and visualized under transmission electron
microscopy. Scale bar represents 100 nm.

Physicochemical and physical properties

The virions of FLiP are sensitive to chloroform. Their buoyant density is 1.21 g/ mL in CsCl and 1.18 g/mL in sucrose ( Laanto et al., 2017). Viruses
are sensitive to temperature and infectivity drops one order of magnitude in a week at 22 °C.

Nucleic acid

Flavobacterium phage FLiP virions contain a single copy of a circular single-stranded DNA of 9,174 nucleotides and the GC content of the
genome is 34% (Laanto et al., 2017).

Proteins

The viral genome contains 16 predicted coding sequences (CDSs), five of which have been shown to encode structural proteins (P7-P9, P11, P14;
Figure 2.Finnlakeviridae). The MCP P8 (encoded by CDS8) is the most abundant protein in the virion. CDS14 shares a significant sequence
similarity with several lytic transglycosylases, suggesting that P14 is a lytic protein present in the virion (Laanto et al., 2017) and likely assisting in
the penetration of peptidoglycan layer during entry.

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Figure 2.Finnlakeviridae. Genome organization of Flavobacterium phage FLiP. Nucleotide numbering starts from a unique EcoRII restriction
site. Sixteen predicted coding sequences are marked with arrows indicating the direction of transcription. CDS encoding structural proteins are
indicated by light blue colour and labelled with the protein they encode.

Lipids

Lipids form an internal membrane that also contains virus-encoded proteins. The major lipid class of the virion membrane is ceramide (60 % of the
total lipid composition). The viral lipid composition differs from that of the host cytoplasmic membrane indicating selective uptake of the lipids
during virion assembly (Laanto et al., 2017).

Genome organization and replication

All of the 16 predicted CDSs are oriented in the same direction (Figure 2 .Finnlakeviridae). They show a limited sequence identity to other
sequences in the public databases. Five of the CDSs encode structural proteins (CDS7-9, 11, 14). CDS14 shares homology with lytic enzymes.
Flavobacterium phage FLiP does not encode any identifiable DNA or RNA polymerase. Sequence resemblance of CDS15 to rolling circle
replication initiator proteins, and especially to replication proteins of filamentous M13-like inoviruses, suggests a replication mechanism typical of
single-stranded DNA phages (Laanto et al., 2017, Yutin et al., 2018). The absence of a putative packaging ATPase implies that a viral-encoded
ATPase is not required for the encapsidation of the Flavobacterium phage FLiP genome (Yutin et al., 2018).

Biology
Flavobacterium phage FLiP is a virulent virus that induces host cell lysis at the end of the viral reproduction cycle. The isolation host of
Flavobacterium phage FLiP is a member of genus Flavobacterium (Laanto et al., 2017). Flavobacterium species are commonly found in boreal
freshwater habitats (Bernardet and Bowman 2006).

Derivation of names
Finnlakeviridae: from English Finn (Finnish) and from English lake in reference to the isolation locality

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Relationships with other taxa

Flavobacterium phage FLiP shows only limited sequence identity to other known viruses. However, Flavobacterium phage FLiP shares striking
structural similarities with Pseudoalteromonas phage PM2 (family Corticoviridae), both in terms of the unique capsid organization (pseudo T = 21
dextro) and the major capsid protein fold (double-ß-barrel) (Laanto et al., 2017, Abrescia et al., 2008). Similar major capsid protein folds can be
found in members of the kingdom Bamfordvirae (Koonin et al., 2020 ), such as Enterobacteria phage PRD1 (family Tectiviridae) (Benson et al.,
1999), archaeal virus Sulfolobus turreted icosahedral virus 1 (family Turriviridae) (Maaty et al., 2006), eukaryotic viruses Paramecium bulsaria
Chlorella virus 1 (family Phycodnaviridae) (Nandhagopal et al., 2002), Chilo iridescent virus (family Iridoviridae) (Yan et al., 2009) and human
adenovirus (family Adenoviridae) (Rux et al., 2003), as well as in Sputnik virophage (a satellite virus of Mimivirus, family Lavidaviridae) (Zhang et
al., 2012). Based on phylogenetic analysis of the MCP sequences, Flavobacterium phage FLiP forms its own group among the tailless prokaryotic
DNA viruses and proviruses with double-ß-barrel MCPs (Yutin et al., 2018).

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Genus: Finnlakevirus
Since only one genus (Finnlakevirus) is currently recognized in the family Finnlakeviridae, the family description above corresponds to the genus
description. For clarity, the additional information that can be found on the genus page is also presented below.

Species demarcation criteria

Not applicable.

Member species
★ Exemplar isolate of the species
Species Virus name Isolate Accession number RefSeq number Available sequence Virus Abbrev.
★ Flavobacterium virus FLiP Flavobacterium phage FLiP MF361639 NC_047837 Complete genome FLiP

Virus names, the choice of exemplar isolates, and virus abbreviations, are not official ICTV designations.

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Authors: Finnlakeviridae

Dr Sari Mäntynen#
Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences
University of Helsinki
P.O. Box 56 (Viikinkaari 9)
00014 University of Helsinki
Finland
Tel: +358 2941 59097
E-mail: sari.mantynen@helsinki.fi
&
Department of Microbiology and Molecular Genetics
University of California, Davis
One Shields Avenue
Davis, California 95616
USA

Dr Elina Laanto #
Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences
University of Helsinki
P.O. Box 56 (Viikinkaari 9)
00014 University of Helsinki
Finland
Tel: +358 2941 59097
E-mail: elina.laanto@helsinki.fi

Dr Lotta-Riina Sundberg
Department of Biological and Environmental Science and Nanoscience center
University of Jyvaskyla, P.O. Box 35,
40014 University of Jyväskylä
Finland
Tel: +358 4080 53931
E-mail: lotta-riina.sundberg@jyu.fi

Dr Minna Poranen
Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences
University of Helsinki
P.O. Box 56 (Viikinkaari 9)
00014 University of Helsinki
Finland
Tel: +358 2941 59106
E-mail: minna.poranen@helsinki.fi

Dr Hanna Oksanen*
Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences
University of Helsinki
P.O. Box 56 (Viikinkaari 9)
00014 University of Helsinki
Finland
Tel: +358 2941 59104
E-mail: hanna.oksanen@helsinki.fi

* to whom correspondence should be addressed

# shared first authorship

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Resources: Finnlakeviridae

Sequence alignments and tree files:

None currently associated with this report.

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References: Finnlakeviridae

Abrescia, N. G., J. M. Grimes, H. M. Kivelä, R. Assenberg, G. C. Sutton, S. J. Butcher, J. K. Bamford, D. H. Bamford and D. I. Stuart
(2008). Insights into virus evolution and membrane biogenesis from the structure of the marine lipid-containing bacteriophage PM2. Mol Cell 31:
749-761. [PubMed]

Benson, S. D., J. K. Bamford, D. H. Bamford and R. M. Burnett (1999). Viral evolution revealed by bacteriophage PRD1 and human
adenovirus coat protein structures. Cell 98: 825-833. [PubMed]

Bernardet, J. F. and J. P. Bowman (2006). The genus Flavobacterium. In The Prokaryotes: a Handbook on the Biology of Bacteria , pp. 481-531.
Edited by M. Dworkin. New York: Springer.

Huiskonen, J. T., H. M. Kivelä, D. H. Bamford and S. J. Butcher (2004). The PM2 virion has a novel organization with an internal membrane
and pentameric receptor binding spikes. Nat Struct Mol Biol 11: 850-856. [PubMed]

Koonin, E. V., Dolja, V. V., Krupovic, M., Varsani, A., Wolf, Y. I., Yutin, N., Zerbini, F. M. & Kuhn, J. H. (2020). Global organization and
proposed megataxonomy of the virus world. Microbiol Mol Biol Rev 84, doi: 10.1128/mmbr.00061-00019. [ PubMed]

Laanto, E., S. Mäntynen, L. De Colibus, J. Marjakangas, A. Gillum, D. I. Stuart, J. J. Ravantti, J. T. Huiskonen and L. R. Sundberg (2017).
Virus found in a boreal lake links ssDNA and dsDNA viruses. Proc Natl Acad Sci U S A 114: 8378-8383. [PubMed]

Maaty, W. S., A. C. Ortmann, M. Dlakic, K. Schulstad, J. K. Hilmer, L. Liepold, B. Weidenheft, R. Khayat, T. Douglas, M. J. Young and B.
Bothner (2006). Characterization of the archaeal thermophile Sulfolobus turreted icosahedral virus validates an evolutionary link among double-
stranded DNA viruses from all domains of life. J Virol 80: 7625-7635. [PubMed]

Nandhagopal, N., A. A. Simpson, J. R. Gurnon, X. Yan, T. S. Baker, M. V. Graves, J. L. Van Etten and M. G. Rossmann (2002). The structure
and evolution of the major capsid protein of a large, lipid-containing DNA virus. Proc Natl Acad Sci U S A 99: 14758-14763. [PubMed]

Rux, J. J., P. R. Kuser and R. M. Burnett (2003). Structural and phylogenetic analysis of adenovirus hexons by use of high-resolution x-ray
crystallographic, molecular modeling, and sequence-based methods. J Virol 77: 9553-9566. [PubMed]

Yan, X., Z. Yu, P. Zhang, A. J. Battisti, H. A. Holdaway, P. R. Chipman, C. Bajaj, M. Bergoin, M. G. Rossmann and T. S. Baker (2009). The
capsid proteins of a large, icosahedral dsDNA virus. J Mol Biol 385: 1287-1299. [PubMed]

Yutin, N., D. Bäckström, T. J. G. Ettema, M. Krupovic and E. V. Koonin (2018). Vast diversity of prokaryotic virus genomes encoding double
jelly-roll major capsid proteins uncovered by genomic and metagenomic sequence analysis. Virol J 15: doi: 10.1186/s12985-12018-10974-y.
[PubMed]

Zhang, X., S. Sun, Y. Xiang, J. Wong, T. Klose, D. Raoult and M. G. Rossmann (2012). Structure of Sputnik, a virophage, at 3.5-Å resolution.
Proc Natl Acad Sci U S A 109: 18431-18436. [PubMed]

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Citation: Finnlakeviridae

A summary of this ICTV Report chapter has been published as an ICTV Virus Taxonomy Profile article in the Journal of General Virology, and
should be cited when referencing this online chapter as follows:

Sari Mäntynen, Elina Laanto, Lotta-Riina Sundberg, Minna M. Poranen, Hanna M. Oksanen and ICTV Report Consortium. 2020, ICTV Virus
Taxonomy Profile: Finnlakeviridae, Journal of General Virology, (In Press)

Funding support
Support for the preparation of this ICTV Report chapter and associated Journal of General Virology taxonomy profile, was funded by a grant from
the Wellcome Trust (WT108418AIA).

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