The 12th Protein (N40): Identification of a Novel PB1-Related Protein Translated from Influenza A Virus Segment 2 mRNA

[mixin]

Influenza A virus segment 2 is known to encode two polypeptides in overlapping open reading frames: PB1, the polymerase, and PB1-F2, a proapoptotic virulence factor. We show that a third major polypeptide is synthesized from PB1 mRNA via differential AUG codon usage. PB1 codon 40 directs translation of an N-terminally truncated version of the polypeptide (N40) that lacks transcriptase function but nevertheless interacts with PB2 and the polymerase complex in the cellular environment.

Importantly, the expression of N40, PB1-F2, and PB1 are interdependent, and certain mutations previously used to ablate PB1-F2 production affected N40 accumulation. Removal of the PB1-F2 AUG upregulated N40 synthesis, while truncating PB1-F2 after codon 8 (with a concomitant M40I change in PB1) abolished N40 expression. A virus lacking both N40 and PB1-F2 replicated normally. However, viruses that did not express N40 but retained an intact PB1-F2 gene overexpressed PB1 early in infection and replicated slowly in tissue culture.

Thus, the influenza A virus proteome includes a 12th primary translation product that (similarly to PB1-F2) is nonessential for virus viability but whose loss, in particular genetic backgrounds, is detrimental to virus replication.

http://jvi.asm.org/cgi/content/abstract/83/16/8021

[gsgs]

Re: The 12th Protein (N40): Identification of a Novel PB1-Related Protein Translated from Influenza A Virus Segment 2 mRNA

AUG is ATG, amino acid M, the start of a protein

PB1-F2 starts at nucleotide 95 , amino acid #32
in the frame one nucleotide more than PB1

N40 starts at amino acid 40 ?


------------------------

>A/******/index/2009-02-01
PB1,758,
MDVNPTLLFLKIPAQNAISTTFPYTGDPPYSHGTGTGYTMDTVNRTHQYSEKGKWTTNTETGAP...
1        .         .         .         .40

PB1-F2,91,
MEQEQDTPWTQ}TEHTNTQKRESGRQTQRLVHPSSTRLMDHYLRIMNQVGMHKQTVF}RLWLSLKNPTQEYLRIHALKQWKLFNKQG}IN}



>A/Brevig Mission/1/1918(H1N1)
PB1,758,
MDVNPTLLFLKVPAQNAISTTFPYTGDPPYSHGTGTGYTMDTVNRTHQYSEKGRWT...
         .         .         .         .40

PB1-F2,91,MGQEQDTPWILSTGHISTQKREDGQQTPRLEHHNSTRLMDHCQKTMNQVVMPKQIVYWKQWLSLRSPTPVSLKTRVLKRWRLFSKHEWTS}





>A/******/index/2009-02-01
segment 2,reading frame +2
GCQSDSTFPKNSSAKCHKHHIPLYWRSSIQPWNRNRIHHGHSKQNTPILRKGKVDDKHRDWCTPAQPD}WTTT}G}}TKWVCTNRLCSRGYGFP}RIPPRNI}EFMP}NNGSCSTNKGR}TNSRSPDL}LDIKQKSTGSNCIGQHHRSL}IEWPNS}}VRKANRFLKGCNGINEQRGNRDNNPLSKKKESKRQHDQEDGHAKNNREEKTKTE}ERLSNKSTDIKYDDQRCRERQVKKKGYRNTWDAD}RFRILC}NFS}EHLRKA}TVWAPSRGQ}KEGQTGKCCEKDDD}FTRHRDFFHNHWGQH}VE}KSKSSNVPGDDYIYHQKSTRVVQKHPEHGTHNVLKQNGKTRERVHVRE}KNEDSNTNTSRNASKH}PEVLQ}INKEEN}ENKASSNRWHSITESWDDDGHVQHAKYGLGSLDTESWTKEIHQDNILVGWAPIIRRFCSHSECTKP}GNTSRSGQILQDLQVSGNQHEQKEVLYK}DRDI}IHKLFLSLWICG}F}HGATQLWSVWSK}IS}HEYWSNSDKEQHDKQ}PWTCNGPDGSSIVHQRLQIHI}VP}GRHTNSDEKII}VKEAVGSNPIKGRAISIRWRTKLIQYTESSHS}SLLKMGANG}}LSGKTL}SPESLCQS}RD}FCKQCCGNASPWSSQKHGI}CRCNYTFLDSQEESFYSQHKPKGNS}G}TDVPEVLQSIREIFP}QFI}ETGWNF}HGGGHGV}GPD}CQGRLRVWTDQERRVL}DHEDLFHH}RTQTAKI-
         .         .         .         .

>A/Brevig Mission/1/1918(H1N1)
segment 2, reading frame +2
GCQSDFTFLESASAKCYKHNVPLYWRPSLQPWDRNRIHHGYCQQDTSVLRKGKMDNKHRDWSTTTQPD}WT...

[Mamabird]

Re: The 12th Protein (N40): Identification of a Novel PB1-Related Protein Translated from Influenza A Virus Segment 2 mRNA

AUG is ATG, amino acid M, the start of a protein

PB1-F2 starts at nucleotide 95 , amino acid #32
in the frame one nucleotide more than PB1

N40 starts at amino acid 40 ?

The M (methionine) is usually at position 40 of PB1 as well, so the N40 must just be the name of the 12th protein.

[mixin]

Re: The 12th Protein (N40): Identification of a Novel PB1-Related Protein Translated from Influenza A Virus Segment 2 mRNA

Is this loss something you can see in a sequence or is it something that only shows up under a microscope?

[Mamabird]

Re: The 12th Protein (N40): Identification of a Novel PB1-Related Protein Translated from Influenza A Virus Segment 2 mRNA

Is this loss something you can see in a sequence or is it something that only shows up under a microscope?

I have ocassionally seen PB1 position 40 with an "L" instead of the normal "M", but I do not know its significance.

As to whether the F2 protein codes in PB1 you can look at the sequence at the nucleoid level, one reading frame up, and look for a stop condon between positions 94 and 355. If no "taa" found, then one would presume that the protein could otherwise be fully formed. If a stop condon was found, then the protein might only be partially formed (truncated), or not at all.

[gsgs]

Re: The 12th Protein (N40): Identification of a Novel PB1-Related Protein Translated from Influenza A Virus Segment 2 mRNA

sequences with M40I in PB1, only these few:

>A/chukkar/Shantou/89/05(H6N1)
>A/chukkar/Shantou/1530/05(H6N1)
>A/Gs/Shantou/18442/05(H5N1)
>A/Ck/Laos/P0171/07(H5N1)
>A/Dk/Nong-Khai/THA/KU-56/07(H5N1)
>A/Ck/Hunan/774/02(H9N2)
>A/Ck/Shantou/2994/04(H9N2)
>A/Ck/Shantou/7920/04(H9N2)
>A/pheasant/Shantou/111/05(H9N2)
>A/Ck/Shantou/55/05(H9N2)
>A/partridge/Shantou/7936/04(H9N2)
>A/silky Ck/Shantou/3581/05(H9N2)
>A/silky Ck/Shantou/1826/04(H9N2)
>A/Ck/Shantou/1926/04(H9N2)
>A/Ck/Shantou/2692/04(H9N2)
>A/turkey/Shantou/1915/04(H6N2)
>A/partridge/Shantou/1913/04(H6N2)
>A/Ck/Shantou/19465/05(H9N2)
>A/Dk/Germany/1215/1973(H2N3)
>A/Ck/Italy/322/01(H7N1)
>A/turkey/Italy/1351/01(H7N1)
>A/silky Ck/Korea/S3/03(H9N2)
>A/Ck/HK/739/94(H9N2)
>A/N.pintail/Alaska/44204-075/06(H3N8)
>A/Ck/Chis/15224/97(H5N2)
>A/NY/123/04(H3N2)
>A/Canterbury/96/00(H3N2)
>A/Canterbury/92/00(H3N2)
>A/Canterbury/97/00(H3N2)
>A/Canterbury/61/02(H3N2)
>A/Ontario/1252/07(H3N2)
>A/Sw/Alberta/56626/03(H1N1)
>A/Sw/Iowa/2/1987(H1N1)
>A/Sw/Tennessee/23/1976(H1N1)
>A/Sw/Tennessee/48/1977(H1N1)
>A/Sw/Ontario/57561/03(H1N1)
>A/Sw/Saitama/96(H1N2)

[gsgs]

Re: The 12th Protein (N40): Identification of a Novel PB1-Related Protein Translated from Influenza A Virus Segment 2 mRNA

Gibbs says it's in the same reading frame as PB1 (+0)
while PB1-F2 is +1