Segmented genome

These genes are encoded on either RNA or DNA polymers, and are either single stranded or
double stranded. ... While most genomes are non-segmented (the genome is all on one
piece of RNA or DNA), some genomes are segmented, meaning there are several fragments
of genetic material that make a complete virus genome. eg.
 Viruses with Single-Stranded, Segmented, Negative-Sense RNA Genomes

There are three virus families containing a negative-sense RNA genome, which does not exist as a
continuous molecule, but is present in several segments. These are the
families Arenaviridae, Bunyaviridae and Orthomyxoviridae. Similarly to members of the
order Mononegavirales , they also require the presence of a special enzyme (RNA-dependent RNA
polymerase) to perform the synthesis and replication of messenger RNA (mRNA); it reaches the cell
along with other viral components during infection.

A segmented genome enables the virus to generate reassortants. In this process, the RNA molecules
of different virus strains are mixed or reshuffled in doubly infected cells during replication and
morphogenesis. In this way, progeny viruses can obtain new combinations of RNA segments and thus
gain novel properties. This mechanism, which is referred to as antigenic shift, is particularly common
and well studied in influenza A viruses, the causative agents of viral influenza or genuine flu.
Viruses with Single-Stranded, Segmented, Negative-Sense RNA Genomes

• Segmented virus genomes are those that are divided into two or more physically separate
molecules of nucleic acid, all of which are then packaged into a single virus particle

• Segmentation of the virus genome has a number of advantages and disadvantages. There is
an upper limit to the size of a nonsegmented virus genome which results from the physical
properties of nucleic acids, particularly the tendency of long molecules to break due to
shear forces (and, for each particular virus, the length of nucleic acid that can be packaged
into the capsid)
• Segmentation means that the virus avoids “having all its eggs in one basket” and also
reduces the probability of breakages due to shearing, thus increasing the total potential
coding capacity of the entire genome. The disadvantage of segmentation is that all the
individual genome segments must be packaged into each virus particle or the virus will be
defective as a result of loss of genetic information. Segmentation means that the virus avoids
“having all its eggs in one basket” and also reduces the probability of breakages due to
shearing, thus increasing the total potential coding capacity of the entire genome. The
disadvantage of segmentation is that all the individual genome segments must be packaged
into each virus particle or the virus will be defective as a result of loss of genetic information.
 Influenza virus

• The influenza A, B, and C viruses, representing three of the five genera of the
family Orthomyxoviridae, are characterized by segmented, negative-strand RNA genomes.

• The influenza A and B virus genomes each comprise eight negative-sense, single-stranded viral
RNA (vRNA) segments, while influenza C virus has a seven-segment genome.

• The eight segments of influenza A and B viruses (and the seven segments of influenza C virus) are
numbered in order of decreasing length. In influenza A and B viruses, segments 1, 3, 4, and 5
encode just one protein per segment: the PB2, PA, HA and NP proteins. All influenza viruses
encode the polymerase subunit PB1 on segment 2; in some strains of influenza A virus, this
segment also codes for the accessory protein PB1-F2, a small, 87-amino acid protein with pro-
apoptotic activity

• The genomic organization of influenza C viruses is generally similar to that of influenza A and B
viruses; however, the HEF protein of influenza C replaces the HA and NA proteins, and thus the
influenza C virus genome has one fewer segment than that of influenza A or B viruses.
THE BIOLOGY OF INFLUENZA VIRUSES
Nicole M. Bouvier and Peter Palese*
Schematic diagrams of influenza A virus and surface hemagglutinin protein. (A) The segmented negative-
sense RNA genome of influenza A virus encodes three envelope proteins (hemagglutinin, neuraminidase,
and ion channel M2 protein), and internal nucleoprotein (NP), polymerases (PA, PB1, and PB2), matrix
protein 1 (M1), and non-structural proteins (NS). The lipid bilayer is derived from host cell membrane. (B)
The cylindrical HA is a homo-trimeric protein consisting of a variable globular head and a conserved stem
domain.
 Multipartite viruses

• Multipartite viruses have genomes segmented in pieces enclosed in different

capsids that are independently transmitted.

• This is found for both DNA and RNA plant viruses.

• Although multipartite genomes are also segmented, each genome segment is

packaged into a separate virus particle. These discrete particles are structurally
similar and may contain the same component proteins, but they often differ in
size depending on the length of the genome segment package
 Non-segmented genome

A viral genome that consists of one continuous nucleic acid molecule.

 Picornaviridae

• The Picornaviridae represent a large family of small plus-strand RNA viruses that cause a
bewildering array of human and animal diseases ranging from severe (poliomyelitis,
encephalitis, meningitis, and hepatitis) to mild (common cold).

• The genome is a single sense-strand RNA (molecular weight, approximately 2 × 106 to

3 × 106) (Fig. 53-3). The RNA strand consists of approximately 7,500 nucleotides and is
covalently bonded to a noncapsid viral protein (VPg) at its 5′ end and to a
polyadenylated tail at its 3′ end. This genome RNA serves as an mRNA and initiates
the synthesis of virus macromolecules.

Medical Microbiology. 4th edition.

Chapter 53Picornaviruses
Marguerite Yin-Murphy and Jeffrey W. Almond.
 Capping and tailing (TMV )

▪ Most eukaryotic mRNAs have 5 and 3 untranslated regions (UTRs), a methylguanosine [m7G(5 )pppG] cap at
the 5 end, and a poly(A) tail at the 3 end.

▪ The cap and the poly(A) tail are required for efficient translation and mRNA stabilization.

▪ The 5’ end of tobacco mosaic virus (TMV) genomic RNA is capped with 7- methylguanosine.

▪ TMV belongs to a large group of alphaviruses, which has a 5 cap but lacks the poly(A) tail characteristic of
host mRNAs .

▪ In TMV, the 3 end of the vRNA ends in a series of pseudoknots and a terminal tRNA-like structure that
substitutes for the poly(A) tail of mRNAs .

▪ For mRNAs, and for many vRNAs, the cap structure plays central roles in RNA-associated functions, including
transport, translation and turnover and is also a major determinant of RNA decay, protecting the mRNA from
degradation by 5 –3 exonucleases. The cap also plays a central role in the recruitment of translation initiation
factors .

▪ All genomic and subgenomic TMV mRNAs contain the same 205-nucleotide 3 UTR region shown to promote
efficient translation and increase stability in a cap-dependent manner.
 Capping and tailing (TMV )
The genomic TMV RNA is a plus RNA (coding) and 6395 ntds long consists of cap at 5’ end with 67 nucleotide
leader sequence with AU rich sequences without any secondary structure, hence it is called ‘W’ sequence. The
5’End cap and structured leader sequence is a distinguishing feature of eukaryotic mRNAs, and TMV RNA has a
tRNA like secondary structure at the 3’ end which accepts histidine in the presence of synthase. TMV RNA can
be used as plant expression vector, Nobuhiko Takamatsu et al, https://www.ncbi.nlm.nih.gov.

TMV genome, 6395 ntds with

Transcription and translation
modes; It has three major
ORFs. Their was also found to be
a unique hairpin loop-encoding
sequence region for assembly
initiation – nicely rounding out pioneering work by PJ
Butler and colleagues and Genevieve Lebeurier and others – both
published in January 1977,
 Capping and tailing (TMV )

Schematic structure of
TMV and its mutants
with different lengths of
internal poly(A) tract
(24A, 42A and 62A)
introduced before the
upstream pseudo-
knotted domain (UPD).