Expression strategies of ambisense viruses

Abstract

Among the negative RNA viruses, ambisense RNA viruses or ‘ambisense viruses’ occupy a distinct niche. Ambisense viruses contain at least one ambisense RNA segment, i.e. an RNA that is in part of positive and in part of negative polarity. Because of this unique gene organization, one might expect ambisense RNA viruses to borrow expression strategies from both positive and negative RNA viruses. However, they have little in common with positive RNA viruses, but possess many features of negative RNA viruses. Transcription and/or replication of their RNAs appear generally to be coupled to translation. Such coupling might be important to ensure temporal control of gene expression, allowing the two genes of an ambisense RNA segment to be differently regulated. Ambisense viruses can infect one host asymptomatically and in certain cases, they can lethally infect two hosts of a different kingdom. A possible model to explain the differential behavior of a given virus in different hosts could be that perturbation of the translation machinery would lead to differences in the severity of symptoms.

Introduction

Single-stranded (ss) RNA viruses possess either positive or negative sense RNA genomes. Those with negative RNA genomes are themselves divided into segmented and non-segmented viruses. Among the segmented negative RNA viruses, not all viruses contain a strictly negative genome; several viruses possess (an) ambisense RNA segment(s) and therefore could constitute a distinct sub-category of multipartite ssRNA viruses: the ambisense RNA viruses (or ambisense viruses).

The genome of positive RNA viruses is of the same sense as mRNAs and thus, can serve directly as template for translation. Therefore, viral proteins are expressed upon entrance of the viral genomic (g) RNA into the cell.

In contrast, the genome of negative RNA viruses cannot be translated; a transcription step giving rise to positive, i.e. sense mRNAs is mandatory before expression of viral proteins is possible. To achieve this obligatory transcription step, negative RNA viruses encapsidate their RNA-dependent RNA polymerase (RdRp).

Ambisense RNA(s) of ambisense viruses are partly of positive and partly of negative polarity. The 5′ part of an ambisense RNA is of positive polarity containing an open reading frame (ORF) that can theoretically be directly translated. The 3′ part of this same RNA is of negative polarity. It contains an ORF, but in the complementary strand (Fig. 1). Indeed, this second part of the ambisense RNA must be transcribed prior to translation. To express this second gene, ambisense viruses also encapsidate their RdRp. This approach to stocking genetic information is designated the ambisense coding strategy (Ihara et al., 1984). The two coding regions of an ambisense RNA do not overlap, but are separated by a non-coding intergenic region (IR). Although ambisense viruses are considered ssRNA viruses, both strands of an ambisense RNA segment are usually found in the virion in unequal amounts (Fig. 1; reviewed in Ramirez and Haenni, 1994, Schmaljohn, 1996, Southern, 1996). To circumvent the designation positive or negative RNA, that would be inadequate, the term viral (v) is used to refer to the more abundant RNA strand present in the virus and viral complementary (vc) for the complementary strand (reviewed in Ramirez and Haenni, 1994, Schmaljohn, 1996, Southern, 1996).

Based on these observations, ambisense viruses could theoretically be expected to possess some characteristics of positive RNA viruses concerning their expression strategies and of negative RNA viruses in their transcription behavior. These unique features make ambisense viruses a remarkable ‘group’ of viruses. Furthermore, most ambisense viruses are not strictly ambisense, but contain negative as well as ambisense RNA segments and, to express their ambisense RNA segments, they must resort to similar strategies as ‘strict’ ambisense viruses.

Ambisense viruses comprise four genera (Arenavirus, Phlebovirus, Tospovirus and Tenuivirus), distributed between Arenaviridae and Bunyaviridae families and a small nonclassified genus of plant viruses, the tenuiviruses (Table 1). It has been proposed that tenuiviruses be included in the Bunyaviridae family (reviewed in Ramirez and Haenni, 1994). Arenaviruses and phleboviruses are animal or human-infecting viruses, whereas tospoviruses and tenuiviruses are plant-infecting viruses.

Ambisense viruses are found in very different eukaryotic systems. On the one hand, they infect humans and cause hemorrhagic fevers, such as Lassa and Rift Valley fevers (reviewed in Gonzalez-Scarano and Nathanson, 1996, Peters et al., 1996). On the other hand, they lead to economically important losses in animals (reviewed in Gonzalez-Scarano and Nathanson, 1996, Peters et al., 1996) and plants (reviewed in Gingery, 1988, Goldbach and Peters, 1994).

Ambisense viruses replicate in one or two hosts. The primary host is an insect (phleboviruses, tospoviruses and tenuiviruses) or a rodent (arenaviruses), which is a designated vector or reservoir of these viruses. Viral multiplication in these hosts is generally persistent and is asymptomatic, except in rare cases (reviewed in Ramirez and Haenni, 1994, Gonzalez-Scarano and Nathanson, 1996, Peters et al., 1996) or when induced in laboratory conditions. However, these viruses can be transmitted to a second host, either another animal or a plant host. It is often via infection with this second host that the most severe aspects of viral multiplication are observed, sometimes resulting in death of the infected organism. Some arenaviruses, such as TCRV arenavirus (see Table 1 for abbreviations), solely infect rodents and transmission to other animals or to humans has never been observed, whereas the LCMV arenavirus is a common human pathogen that has been extensively studied for immunological purposes (reviewed in Peters et al., 1996).

This review highlights the similarities found in all ambisense viruses whether or not they are ‘strict’ ambisense viruses and their close relationship with negative RNA viruses. No review describing ambisense viruses in this broad sense has appeared since the review by Bishop (1986). The review focuses on the transcription, replication and to a certain extent, on the translation strategies of ambisense viruses. Complementary information related to specific families and/or genera can be found elsewhere (reviewed in Salvato, 1993, Ramirez and Haenni, 1994, Elliott, 1996a, Peters et al., 1996, Schmaljohn, 1996, Southern, 1996, Lee and de la Torre, 2002, Meyer et al., 2002).

Viruses of the Arenaviridae and Bunyaviridae families are enveloped (reviewed in Southern, 1996, Schmaljohn, 1996). Tenuiviruses are considered non-enveloped viruses. However, sequence data indicate that they possess glycoproteins homologous to those of the envelope proteins of phleboviruses (de Miranda et al., 1996, Estabrook et al., 1996, Toriyama et al., 1998).

The Arenaviridae family is composed of one genus, the Arenavirus whose genome contains two ambisense RNA segments designated L (large) and S (small; Table 1; reviewed in Southern, 1996).

The Bunyaviridae family contains five genera, the Bunyavirus, Hantavirus, Nairovirus, Phlebovirus and Tospovirus (Table 1; reviewed in Schmaljohn, 1996). The genome of viruses of this family is composed of three RNA segments referred to as L, M (medium) and S. These segments are of negative polarity in bunyaviruses, hantaviruses and nairoviruses (Table 1). The S and/or M genome segments of the phleboviruses and tospoviruses are ambisense, whereas the L and/or M segments are negative (Table 1).

Tenuiviruses resort to similar coding strategies as ambisense viruses of the Bunyaviridae, but their genome is composed of four to six RNA segments of ambisense and/or negative polarities designated 1–6 in order of their decreasing size (Table 1; reviewed in Ramirez and Haenni, 1994, Toriyama et al., 1998).

Although ambisense viruses are found in distinct families and infect either plants or animals, they nevertheless share many characteristics. Some of these features are the following: (i) they possess a multipartite single-stranded RNA genome; (ii) at least one RNA segment is ambisense; (iii) the RNAs are encapsidated by the nucleocapsid protein to form ribonucleoproteins (RNPs); (iv) a viral RdRp is associated with the RNPs; (v) the largest RNA segment encodes the RdRp; (vi) the RNPs are enveloped by glycoproteins (except for the tenuiviruses for which no envelope has been detected); (vii) the 5′ and 3′ ends of each genome segment are conserved and can base-pair to form a panhandle structure; (viii) gRNAs of both polarities are found in the RNPs, the v-gRNAs being more abundant than the vc-gRNAs; (ix) they produce subgenomic RNAs (mRNAs) that contain non-viral nucleotides (nt) and a cap structure at their 5′ end, indicative of a cap-snatching mechanism for synthesis of the viral mRNAs; (x) the 3′ end of their mRNAs is not polyadenylated; and (xi) transcription and replication presumably occur in the cytoplasm.

Most of the ambisense virus features are also shared by multipartite negative RNA viruses, such as viruses within the Bunyavirus, Hantavirus and Nairovirus genera of the Bunyaviridae family (features i, iii–vii and ix–xi; reviewed in Schmaljohn, 1996) and viruses of the Orthomyxoviridae family (features i, iii–vii and ix; reviewed in Lamb and Krug, 1996).

In discussing strategies and when no clear data exist for ambisense viruses of the Bunyaviridae, we refer to the data obtained for the negative RNA viruses of this family, since many features of viruses of this family are believed to be shared by its various genera (reviewed in Elliott, 1996a, Schmaljohn, 1996).