Yeast - Actin related proteins (ARPs)

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ALIGNMENT DATA for YEAST vol. 13 (11) pp1053-1058

 

Who's Who among the S. cerevisiae Actin-Related Proteins?

- classification and nomenclature proposal for a large family

 

Olivier POCH and Barbara WINSOR

 

UPR 9005 du CNRS, Institut de Biologie Moléculaire et Cellulaire
15 Rue Rene Descartes, 67084 Strasbourg-cedex, France
poch@titus.u-strasbg.fr or winsor@ibmc.u-strasbg.fr

 

After inspection of the complete Saccharomyces cerevisiae genome sequence and analysis of the actin-related proteins found therein, ten actin-related proteins (ARPs) which contain substantial blocks of conservation relative to a chosen sub-set of actins were found and ordered relative to the group of actins. We propose to name the more distantly related ARP members according to their amino acid identity and similarity, Arp4 - Arp10. The authors welcome comments or discussion.

 

Bootstrapped non-rooted phylogenetic tree of the amino acid sequences in the alignment.

 

The tree was generated by the computer program CLUSTALW (Thompson, et al., 1994). The numbers of sequences are those indicated in the alignment legend shown above

 

Alignment comparing the amino acid sequences of actin-related proteins and 29 actins from diverse phyla.

 

Legend for the alignment and the phylogenetic tree:

Numbers in GREEN represent the position relative to the multiple alignment numbering.

Numbers in RED represent the position relative to the secondary structure.

b = beta sheet; h = alpha helix; ----- Ia or 1 = subdomains of actin.

Known areas of interaction are indicated in horizontal lines interspersed between groups of sequences.

n = nucleotide; + = cation; ----- = DNaseI loop; a = actin; m = myosin; p = profilin.

Swissprot databank mnemonics of the sequences are:

i) actin sequences: 1/ Acts_Human, 2/ Act4_Drome, 3/ Act3_Limpo, 4/ Actb_Xenbo, 5/ Actm_Aplca, 6/ Act1_Podca, 7/ Act3_Bommo, 8/ Act_Yeast, 9/ Act_Thela, 10/ Act_Schpo, 11/ Act_Cryne, 12/ Act1_Maize, 13/ Act3_Pea, 14/ Act1_Dauca, 15/ Act2_Dauca, 16/ Act2_Pea, 17/ Act3_Soybn, 18/ Act1_Acaca, 19/ Actd_Phypo, 20/ Act4_Dicdi, 21/ Act3_Dicdi, 22/ Act_Enthi, 23/ Act_Phyme, 24/ Act1_Naefo, 25/ Act1_Plafa, 26/ Act2_Plafa, 27/ Act_Leima, 28/ Act_Eupcr, 29/ Act1_Oxyno, Arp53D D mel/Acty_Drome;

ii) for ARP1 sequences: S cer/ Act5_Yeast, H sapa/ Actz_Human, H sapb/ Acty_Human, D mel/ Actz_Drome, P car/ Actz_Pneca, N cra/ Actz_Neucr;

iii) ARP2 sequences: S cer/ Act2_Yeast, A cas/ Actw_Acaca, C ele/ Actw_Caeel, G gal/ Actw_Chick, D mel/ Actw_Drome;

iv) ARP3 sequences: S pom/ Act2_Schpo, S cer/ Act4_Yeast; D mel/ Actv_Drome; B tau/ Actv_Bovin, D dis/ Actv_Dicdi, A cas/ Actv_Acaca;

v) distantly related ARPs: ARP4/ Act3_Yeast, Arp23D3 S pom/ Yae9_Schpo, ARP5/ Ynf9_Yeast, ArpX D mel/ Actu_Drome, ArpX C ele/ Yp86_Caeel.

The new Saccharomyces cerevisiae ARP sequences are taken from the PIR databank: ARP6=Accession number S64917, ARP7=S54508, ARP8=S61695, ARP9=S53950, ARP10=S52672.