Sequence analysis of the 22K, SH and G genes of turkey rhinotracheitis virus and their intergenic regions reveals a gene order different from that of other pneumoviruses

Abstract

The nucleotide and deduced amino acid sequences of three genes of turkey rhinotracheitis virus (TRTV) together with the nucleotide sequences of the relevant intergenic regions were determined. The deduced amino acid sequence of one of the genes shows significant identity (42 %) to that of the 22K protein of human respiratory syncytial virus (RSV). The TRTV 22K gene, like that of RSV, has a second open reading frame, although the amino acid sequence deduced from this reading frame does not show any similarity to the equivalent predicted RSV protein. The other two genes and their deduced amino acid sequences do not show any sequence similarity to the genes of other pneumoviruses. However, the hydrophobicity profiles of the predicted proteins do show similarities to those of the small hydrophobic (SH) and attachment protein (G) genes of RSV. The TRTV G gene is 1193 nucleotides in length and encodes a protein of 391 amino acids (M~ 42 984), which is rather larger than the RSV G protein (predicted M~ 36000). The TRTV SH gene is 589 nucleotides in length, encoding a protein of 174 amino acids (M~ 18 797), which is considerably larger than the size of the RSV SH protein (Mr 7500). The sequences of the intergenic regions derived from clones of polycistronic mRNAs and polymerase chain reaction products obtained with primers from different genes reveal the order on the virus genome to be 3' F-22K-SH-G 5'. This differs from the gene order of paramyxoviruses and morbilliviruses, which lack a 22K gene (and in some cases a SH gene), and the pneumoviruses RSV and pneumonia virus of mice, which have the F and 22K genes located after the G gene.

Subgroup C avian metapneumovirus (MPV) and the recently isolated human MPV exhibit a common organization but have extensive sequence divergence in their putative SH and G genes

“…Another striking conserved feature in the SH gene was the location of a stop codon several codons upstream of the typical transcription termination sequence (24 untranslated codons including two additional in-frame stop codons in Colorado versus 17 untranslated codons with two additional in-frame stop codons in hMPV; van den Hoogen et al, 2002). Such an organization is not found in the APV subgroup A SH gene, where no typical APV gene end signal (AGTTA) is apparent, although a poly(A) tract occurs 15 codons downstream of the stop codon (Ling et al, 1992). One possibility might be that truncated SH proteins have been produced in APV subgroup C and hMPV by the introduction of premature stop codons in longer ancestor sequences.…”

Sequence polymorphism of the predicted human metapneumovirus G glycoprotein

“…The G gene transcription initiation codon (ATG) was located four bases downstream of the gene start sequence (GGGACAAGT), which was conserved among all isolates and was identical to those described for the G gene of APV (Ling et al, 1992;Bäyon-Auboyer et al, 2000;Alvarez et al, 2003). A single potential ORF of variable length (654-711 nt) was identified.…”

Detection and differentiation of avian pneumoviruses (metapneumoviruses)

“…The first APV gene to be cloned and sequenced was that of the fusion (F) protein gene of a subtype A virus (Yu et al, 1991), since when all the other genes of a subtype A virus have been sequenced (Ling et al, 1992;Yu et al, 1992a,b;Ling et al, 1995;Li et al, 1996;Randhawa et al, 1996bRandhawa et al, , 1997. Fewer genes of subtype B virus have been sequenced: G protein (Juhasz & Easton, 1994), M protein (Randhawa et al, 1996a) and N protein (Li et al, 1996).…”