''Spiraviridae'' is a family of ''
incertae sedis
or is a term used for a taxonomy (biology), taxonomic group where its broader relationships are unknown or undefined. Alternatively, such groups are frequently referred to as "enigmatic taxa". In the system of open nomenclature, uncertainty ...
''
virus
A virus is a submicroscopic infectious agent that replicates only inside the living Cell (biology), cells of an organism. Viruses infect all life forms, from animals and plants to microorganisms, including bacteria and archaea. Viruses are ...
es that replicate in
hyperthermophilic archaea
Archaea ( ) is a Domain (biology), domain of organisms. Traditionally, Archaea only included its Prokaryote, prokaryotic members, but this has since been found to be paraphyletic, as eukaryotes are known to have evolved from archaea. Even thou ...
of the genus ''
Aeropyrum'', specifically ''
Aeropyrum pernix''.
The family contains one genus, ''Alphaspiravirus'', which contains one species, Aeropyrum coil-shaped virus (ACV, ''Alphaspiravirus yamagawaense'').
The
virion
A virion (plural, ''viria'' or ''virions'') is an inert virus particle capable of invading a Cell (biology), cell. Upon entering the cell, the virion disassembles and the genetic material from the virus takes control of the cell infrastructure, t ...
s of ACV are
non-enveloped and in the shape of hollow cylinders that are formed by a coiling fiber that consists of two intertwining halves of the circular DNA strand inside a
capsid
A capsid is the protein shell of a virus, enclosing its genetic material. It consists of several oligomeric (repeating) structural subunits made of protein called protomers. The observable 3-dimensional morphological subunits, which may or m ...
. An appendage protrudes from each end of the cylindrical virion. The viral
genome
A genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding genes, other functional regions of the genome such as ...
is
ssDNA(+) and encodes for significantly more
gene
In biology, the word gene has two meanings. The Mendelian gene is a basic unit of heredity. The molecular gene is a sequence of nucleotides in DNA that is transcribed to produce a functional RNA. There are two types of molecular genes: protei ...
s than other known ssDNA viruses. ACV is also unique in that it appears to lack its own enzymes to aid replication, instead likely using the host cell's
replisomes. ACV has no known relation to any other archaea-infecting viruses, but it does share its coil-like morphology with some other archaeal viruses, suggesting that such viruses may be an ancient lineage that only infect archaea.
Name
The names ''Alphaspiravirus'' and ''Spiraviridae'' are both from latin ''spira'' for "coil".
Structure
Virions of ACV are non-enveloped and in the shape of hollow cylinders approximately 230±10 by 19±1 nanometers (nm) in size. The cylindrical shape is formed by the coiling of a nucleoprotein filament as a helical spring. This coil-like structure is itself formed by two intertwining halves of a circular, ssDNA molecule in another helical shape that is covered by capsid proteins. Each end of the cylindrical virion has an appendage about 20±2 nm in length protruding from the virion at a 45° angle relative to the axis of the virion.
Genome
ACV contains a single molecule of circular, positive-sense, single-stranded DNA ((+)ssDNA) that is 24,893 nucleotides in length. The GC-content
In molecular biology and genetics, GC-content (or guanine-cytosine content) is the percentage of nitrogenous bases in a DNA or RNA molecule that are either guanine (G) or cytosine (C). This measure indicates the proportion of G and C bases out of ...
of the genome is 46.7%. The genome is predicted to have 57 open reading frame
In molecular biology, reading frames are defined as spans of DNA sequence between the start and stop codons. Usually, this is considered within a studied region of a prokaryotic DNA sequence, where only one of the six possible reading frames ...
s (ORFs) larger than 40 codon
Genetic code is a set of rules used by living cells to translate information encoded within genetic material (DNA or RNA sequences of nucleotide triplets or codons) into proteins. Translation is accomplished by the ribosome, which links prote ...
s, such ORFs comprising 93.5% of the genome. All but one ORF has the same directionality as the DNA strand, indicating that the genome is positive-sense. The number of predicted genes is much greater than other known ssDNA viruses. These include genes that encode for a putative trypsin
Trypsin is an enzyme in the first section of the small intestine that starts the digestion of protein molecules by cutting long chains of amino acids into smaller pieces. It is a serine protease from the PA clan superfamily, found in the dig ...
-like serine protease
Serine proteases (or serine endopeptidases) are enzymes that cleave peptide bonds in proteins. Serine serves as the nucleophilic amino acid at the (enzyme's) active site.
They are found ubiquitously in both eukaryotes and prokaryotes. Serin ...
, a tyrosine
-Tyrosine or tyrosine (symbol Tyr or Y) or 4-hydroxyphenylalanine is one of the 20 standard amino acids that are used by cells to synthesize proteins. It is a conditionally essential amino acid with a polar side group. The word "tyrosine" is ...
recombinase
Recombinases are genetic recombination enzymes.
Site specific recombinases
DNA recombinases are widely used in multicellular organisms to manipulate the structure of genomes, and to control gene expression. These enzymes, derived from bacteria ( ...
, two thioredoxin
Thioredoxin (TRX or TXN) is a class of small redox proteins known to be present in all organisms. It plays a role in many important biological processes, including redox signaling. In humans, thioredoxins are encoded by ''TXN'' and ''TXN2'' genes ...
-like proteins, proteins involved in carbohydrate metabolism
Carbohydrate metabolism is the whole of the biochemistry, biochemical processes responsible for the metabolic anabolism, formation, catabolism, breakdown, and interconversion of carbohydrates in life, living organisms.
Carbohydrates are central t ...
, and DNA-binding proteins.
Replication
ACV does not encode any identifiable DNA or RNA polymerase
In biochemistry, a polymerase is an enzyme (Enzyme Commission number, EC 2.7.7.6/7/19/48/49) that synthesizes long chains of polymers or nucleic acids. DNA polymerase and RNA polymerase are used to assemble DNA and RNA molecules, respectively, by ...
s, nor does it encode any proteins homologous to known Rep proteins used by most known ssDNA viruses in replication. As such, ACV is likely to replicate in a manner that depends on the host replisome. After replication, virions leave the host cell without the host cell undergoing lysis
Lysis ( ; from Greek 'loosening') is the breaking down of the membrane of a cell, often by viral, enzymic, or osmotic (that is, "lytic" ) mechanisms that compromise its integrity. A fluid containing the contents of lysed cells is called a ...
, or cell death.
Evolution
ACV has no known relation to any other viruses. However, some other archaeal viruses also have coil-shaped virions like ACV, which may indicate such morphology is an ancient form that is not represented among viruses that infect eukaryotes and other prokaryotes.
History
ACV was first isolated from a sample of '' Aeropyrum pernix'' (''A. pernix'') taken from the coastal Yamagawa Hot Spring, where the temperature can reach 109 °C, in Japan in 2010. As ''A. pernix'' was the only organism present in the culture, it was recognized as the host of ACV. ACV could not be replicated in other strains of ''A. pernix'' or in '' Aeropyrum camini'', so the original ''A. pernix'' culture was used for study.
References
{{Taxonbar, from=Q18811971
Single-stranded DNA viruses
Virus families