The Unique Genome of the Virus and Alternative Strategies for its Realization

Abstract

Dedicated to the 130th anniversary of Dmitry Ivanovsky's discovery of the virus kingdom as a new form of biological life. The genome of some RNA-containing viruses comprises ambipolar genes that are arranged in stacks (one above the other) encoding proteins in opposite directions. Ambipolar genes provide a new approach for developing viral diversity when virions possessing an identical genome may differ in its expression scheme (strategy) and have distinct types of progeny virions varying in the genomic RNA polarity and the composition of proteins expressed by positive- or negative-sense genes, the so-called ambipolar virions. So far, this pathway of viral genome expression remains hypothetical and hidden from us, like the dark side of the Moon, and deserves a detailed study.

Keywords: ambisense genes; genome strategy; virus classification; virus diversity.

Fig. 1

Localization of ambipolar genes in the RNA genome of the influenza A virus and coronavirus and the formation of ambipolar virions. (A) Scheme of gene coding in the influenza virus genome segment NS in the A/Aichi/2/68 (H3N2) model. The influenza virus has a negative-sense genome that encodes three proteins: negative-sense NS1 and NEP and the positive-sense stacking protein NSP8. The canonical pathway strategy for segment 8 (NS) is shown. This pathway is realized through synthesis of the NS1 and NEP proteins, formation of classical enveloped virions containing the PB1, PB2, PA, HA, NP, NA, M1, and M2 proteins, and a possible alternative pathway with the formation of the non-canonical (ambipolar) NSP8 protein and similar ambipolar proteins of positive-sense genes, found in the PB1, PB2, PA, NP, M, and NS segments (NSP1–NSP8 proteins, respectively, according to the numbering of RNA segments in the viral genome). Non-canonical ambipolar virions decorated with NSP1–NSP8 proteins have not yet been found and remain hypothetical in nature (dotted arrow). (B) Scheme of gene coding in the RNA genome of coronavirus in the SARS-CoV2 model. Coronavirus has a positive-sense genome encoding five major structural (S1/S2, N, E, M) and 16 (nsp 1–16) accessory non-structural polypeptides. The classical pathway of positive-sense strategy leads to the formation of classical enveloped virions containing the S1/S2, N, E, and M proteins (solid arrow). The negative genome direction (3’ → 5’) encodes extended open reading frames in complimentary positive polarity (5’ → 3’) RNA molecules possessing all essential elements, such as the initiator AUG, Kozak element, IRES, and stop codons. These translational frames (genes) are designated as negative gene proteins (NGPs), and the most extended NGPs, NGP1–GP5, have a molecular weight in the range of 7–0 kDa [17]. The dash arrow shows an alternative pathway of genome strategy with the formation of non-canonical (ambipolar) virions. The double arrow shows proteins and the direction of their coding in the genome. Ambipolar NGP1–GP5 polypeptides are synthetized through the formation of a subgenomic (–-mRNA and its translation (pathway I), and also through translation of a full-length complementary genomic (–-cRNA (pathway II)

Fig. 2

Alternative strategies of the influenza virus negative- sense genome and the formation of ambipolar virions. The diagram illustrates the alternative strategies of the viral genome using the influenza virus (A) and coronavirus (B) genome models and is applicable to other viruses (pneumo-, paramyxo-, rhabdo-, filoviruses, etc.) possessing a negative-sense RNA genome (–R). Genome strategy is outlined as a viral genome replication pathway leading to the formation of canonical viral particles of a given structure and composition, both in terms of viral genome polarity and protein composition of the viral envelope. Three alternative strategies possible for one unique viral genome are shown. Currently, pathway 1 is considered as canonical, while four other strategies remain hypothetical. Probably, in a given biochemical context of infected cells, strategies II–V may be implemented, when full-length genomic RNA chains ((+)R and (±)R) are packaged by proteins of distinct compositions (denoted by different symbols ( , , , ), including proteins of ambipolar genes. In this case, different virion types may have different envelope structures with/without cellular lipids, the so-called enveloped and non-enveloped virions. Genetic realization of viral genome replication is performed by RNA-dependent polymerase that can be included in the virion and provide the beginning of viral replication in the target cell. (+) R, (–)R, and (±)R are three possible variants of a progeny virion genomic RNA with a single-stranded positive/negative sense and double-stranded structure, respectively. Possible pathways to alter the genome expression strategy in one species of virus are shown by dotted arrows and labels (II–V); the classical pathway of the negative-sense strategy for the influenza virus is shown by the main arrow (I), respectively. A targeted search for the virions of the indicated non-canonical structural classes II–V is required to pinpoint strategies II–V

Fig. 3

Schematic diagram of the bipolar (ambisense) strategy of the arenavirus genome (Arenaviridae family; Mammarenavirus genus). The arenavirus genome (lymphocytic choriomeningitis virus (LCMV); ac.n. AY847350; AY847351) is used. The family combines pathogens of severe human hemorrhagic fevers (Lassa, Lujo, Machupo, Junin, Chapare, Guanarito, Sabia, etc.). The arenavirus genome contains four genes that encode: (A) polymerase protein (L, 110 kDa) and non-structural multifunctional protein (Z, 11 kDa); (B) nucleocapsid protein (N, 55 kDa) and surface glycoprotein (GPC; 90 kDa) [31]. Coding of the L and N genes has negative polarity, and that of the GPC and Z genes has opposite (positive) polarity. All four genes are uncoupled in the arenavirus genome and do not overlap, and expression of each of the genes in infected cells requires the synthesis of individual 5’-capped mRNAs