Elsevier

Virus Research

Volume 185, 24 June 2014, Pages 53-63
Virus Research

Review
Molecular mechanisms enhancing the proteome of influenza A viruses: An overview of recently discovered proteins

https://doi.org/10.1016/j.virusres.2014.03.015Get rights and content

Highlights

Abstract

Influenza A virus is one of the major human pathogens. Despite numerous efforts to produce absolutely effective anti-influenza drugs or vaccines, no such agent has been developed yet. One of the main reasons for this complication is the high mutation rate and the specific structure of influenza A viruses genome. For more than 25 years since the first mapping of the viral genome, it was believed that its 8 genome segments encode 10 proteins. However, the proteome of influenza A viruses has turned out to be much more complex than previously thought. In 2001, the first accessory protein, PB1-F2, translated from the alternative open reading frame, was discovered. Subsequently, six more proteins, PB1-N40, PA-X, PA-N155, PA-N182, M42, and NS3, have been found. It is important to pay close attention to these novel proteins in order to evaluate their role in the pathogenesis of influenza, especially in the case of outbreaks of human infections with new avian viruses, such as H5N1 or H7N9. In this review we summarize the data on the molecular mechanisms used by influenza A viruses to expand their proteome and on the possible functions of the recently discovered viral proteins.

Introduction

Influenza is an acute respiratory infection annually affecting millions of people worldwide (WHO, 2013). The etiological agents of the disease are influenza A, B, and C viruses of the family Orthomyxoviridae (Kawaoka, 2006). The most diverse and epidemiologically significant are influenza A viruses. They are also associated with the most severe manifestations of the disease in humans (Deeva et al., 2006, Kawaoka, 2006, Shindo and Briand, 2012). The genome of influenza A viruses consists of eight negative-sense RNA segments (Palese and Schulman, 1976, Ritchey et al., 1976). Positive-sense mRNAs, used for the translation of viral proteins, are transcribed on the templates of the genomic RNAs in the nucleus of the infected cells (Kawaoka, 2006). Due to the small size of its genome (about 13 Kb), influenza A viruses have evolved different molecular mechanisms providing the expression of multiple proteins from a single gene segment. These mechanisms include the alternative splicing of viral mRNAs as well as the non-canonical translation, such as leaky ribosomal scanning, non-AUG initiation, re-initiation, and even ribosomal frameshifting (Firth and Brierley, 2012, Yewdell and Ince, 2012).

The genome of influenza A virus was mapped during the 1970s (Palese and Schulman, 1976, Ritchey et al., 1976). Since that time, it was believed that eight viral genome segments encode ten proteins: the polymerase basic proteins 1 (PB1) and 2 (PB2), the polymerase acidic protein (PA), nucleoprotein (NP), hemagglutinin (HA), neuraminidase (NA), matrix proteins 1 (M1) and 2 (M2), and non-structural proteins 1 (NS1) and 2 (NS2) (Kawaoka, 2006) (Fig. 1). However, in 2001 an eleventh influenza A virus protein, PB1-F2, was discovered which was translated from the alternative open reading frame (ORF) (Chen et al., 2001). Since then, six additional viral proteins, PB1-N40 (Wise et al., 2009), PA-X (Jagger et al., 2012), PA-N155 (Muramoto et al., 2013), PA-N182 (Muramoto et al., 2013), M42 (Wise et al., 2012), and NS3 (Selman et al., 2012), have been found and/or re-discovered. Additionally, a hypothetical NEG8 ORF has already been predicted (Clifford et al., 2009, Zhirnov et al., 2007).

Here we briefly review the molecular mechanisms used by influenza A virus to expand its proteome and summarize the available data on the possible functions of the recently discovered viral proteins. We also have evaluated the presence of these ORFs in human influenza A/H7N9 viruses (Table 1).

Section snippets

PB1-N40 is the N-terminally truncated form of PB1

Segment 2 of the influenza A virus genome was known to encode at least two proteins, both of each are translated from a single mRNA. The major product, PB1, is the catalytic subunit of the viral RNA-dependent RNA polymerase and is required for both replication and transcription (Braam et al., 1983, Fodor, 2013). In 2001, the non-spliced alternative ORF at the +1 position relative to PB1, which probably has evolved secondarily to the PB1 ORF, was discovered in the segment 2 mRNA (Chen et al.,

PA-X, PA-N155, and PA-N182 are the isoforms of the PA subunit of the viral RNA-dependent RNA polymerase

Segment 3 of the influenza A virus genome encodes the PA subunit of the viral RNA-dependent RNA polymerase (Braam et al., 1983, Fodor, 2013). The N-terminal domain of PA provides an RNA endonuclease activity required for the cleavage of the short-capped fragments from the cellular pre-mRNAs which are used as primers for viral transcription (Dias et al., 2009, Hara et al., 2006). The C-terminal domain of PA is responsible for interaction with the PB1 subunit of the viral polymerase (Coloma et

M42 is the M2 isoform with an alternative ectodomain

Segment 7 of the influenza A virus genome encodes two well-recognized matrix (M1) and ion channel (M2) proteins (Allen et al., 1980, Lamb et al., 1981). M1 underlies the viral envelope and plays multiple roles in virion assembly and infection (Ali et al., 2000, Rossman and Lamb, 2011). M2 is a short, multifunctional integral membrane protein that forms a proton channel that is activated by acidic pH; M2 is important for genome unpacking during virus entry (Pinto et al., 1992, Schnell and Chou,

Segment 8 encodes an internally deleted NS1 isoform and contains the conservative open reading frame in the genomic strand

Segment 8 of the influenza A virus genome encodes at least 2 proteins, NS1 and NS2, which are derived from the alternatively spliced mRNAs (Baez et al., 1980). NS1 is a multifunctional protein that is involved in numerous virus-host interactions, including escape from the antiviral mechanisms of host cells as well as regulation of host and viral gene expression (Egorov et al., 1998, García-Sastre et al., 1998, Hale et al., 2008, Romanova et al., 2009). NS2, also known as the nuclear export

Accessory proteins in the proteome of human A/H7N9 viruses

Human infections with avian influenza A viruses are usually sporadic, but these viruses have pandemic potential since they can acquire the ability to transmit efficiently from person to person (Belser et al., 2010). The last outbreak of human infections with a new avian-origin reassortant influenza A/H7N9 virus took place in China in 2013 (Gao et al., 2013). Since the recently discovered influenza A virus proteins can participate in virus-host interactions and hence can potentially influence

Conclusions

Influenza viruses, like most RNA viruses, have a very compact genome which undergoes constant and intense selective pressure. Ten major influenza A virus proteins, most of them structural, were determined in the 1980s. However, it is now clear that the protein coding capacity of the influenza A virus genome has not been fully determined. Viral protein synthesis is dependent upon the translational machinery of the host cells. Furthermore, while cellular mRNAs are usually monocistronic, RNA

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