Accession numbers of <i>Paramyxovirinae</i> C proteins.

<p>(*) Proposed genus.</p

Organization of the P/V/C gene of <i>Paramyxovirinae</i> and phylogeny of the C proteins.

<p>A. Organization of the P/V/C gene transcription unit of <i>Paramyxovirinae</i>. PNT: N-terminal moiety of P; PCT: C-terminal moiety of P. The V protein is composed of PNT fused, by co-transcriptional editing (arrow) of the P mRNA, to a zinc finger domain encoded in a different frame. For clarity, only the C-terminal zinc finger of V is shown. B. Clustering of <i>Paramyxovirinae</i> C proteins by sequence similarity. The cladograms represent the measles, Nipah and Sendai groups.</p

Evolution and Structural Organization of the C Proteins of <i>Paramyxovirinae</i>

<div><p>The phosphoprotein (P) gene of most <i>Paramyxovirinae</i> encodes several proteins in overlapping frames: P and V, which share a common N-terminus (PNT), and C, which overlaps PNT. Overlapping genes are of particular interest because they encode proteins originated <i>de novo</i>, some of which have unknown structural folds, challenging the notion that nature utilizes only a limited, well-mapped area of fold space. The C proteins cluster in three groups, comprising measles, Nipah, and Sendai virus. We predicted that all C proteins have a similar organization: a variable, disordered N-terminus and a conserved, α-helical C-terminus. We confirmed this predicted organization by biophysically characterizing recombinant C proteins from Tupaia paramyxovirus (measles group) and human parainfluenza virus 1 (Sendai group). We also found that the C of the measles and Nipah groups have statistically significant sequence similarity, indicating a common origin. Although the C of the Sendai group lack sequence similarity with them, we speculate that they also have a common origin, given their similar genomic location and structural organization. Since C is dispensable for viral replication, unlike PNT, we hypothesize that C may have originated <i>de novo</i> by overprinting PNT in the ancestor of <i>Paramyxovirinae</i>. Intriguingly, in measles virus and Nipah virus, PNT encodes STAT1-binding sites that overlap different regions of the C-terminus of C, indicating they have probably originated independently. This arrangement, in which the same genetic region encodes simultaneously a crucial functional motif (a STAT1-binding site) and a highly constrained region (the C-terminus of C), seems paradoxical, since it should severely reduce the ability of the virus to adapt. The fact that it originated twice suggests that it must be balanced by an evolutionary advantage, perhaps from reducing the size of the genetic region vulnerable to mutations.</p></div

Circular Dichroism (CD) spectra of the C proteins of hPIV1 and Tupaia PMV.

<p>Circular Dichroism (CD) spectra of the C proteins of hPIV1 and Tupaia PMV.</p

Alignment of the C proteins of the measles and Nipah groups.

<p>Conventions are the same as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090003#pone-0090003-g002" target="_blank">Figure 2</a>. Several positions appear conserved but have not been indicated, because their alignment is not reliable (see text).</p

Alignment of the C proteins of the measles group.

<p>Numbering corresponds to <i>measles virus</i>. The N-terminus of C is highly variable and shown for information only. Only the C-terminal moiety of C (helices α2 to α4) is reliably aligned; positions that appear conserved but are outside this region are thus not indicated. Residues that have been experimentally substituted (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090003#pone-0090003-t002" target="_blank">Table 2</a>) are in bold. N-terminal sequences of fragments of Tupaia PMV C obtained after limited proteolysis are underlined. Overlapping motifs of the PNT frame overlapping C are indicated above the alignment.</p

Selected experimental substitutions in C and their effect.

<p>These studies used either recombinant viruses, minigenome systems, or eukaryotic expression systems. Substituted residues that are conserved in a group are in bold. For a more comprehensive list of studies on <i>Paramyxovirinae</i> C, please see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090003#pone.0090003.s002" target="_blank">Table S1</a>.</p