Supplement to
"Identification and comparative analysis of components from the signal recognition particle in the lower eukaryotes".

M. Alm Rosenblad, C. Zwieb, T. Samuelsson (ref. Rosenblad,MA , Zwieb,C , Samuelsson,T )
BMC Genomics 2004 5:5
Acknowledgements  T.cruzi : The source is the TIGR-SBRI-KI T. cruzi sequencing consortium (TSK-TSC). Chlamydomonas : These sequence data were produced by the US Department of Energy Joint Genome Institute, http://www.jgi.doe.gov/ and are provided for use in this publication/correspondence only. Giardia : Giardia lamblia Genome Project, Marine Biological Laboratory at Woods Hole, funded by the NIAID/NIH under cooperative agreement AI 043273. Eimeria, Theileria, Leishmania : These sequence data were produced by the resp. Sequencing Group at the Sanger Institute and can be obtained from ftp://ftp.sanger.ac.uk/pub/. Candida albicans : Sequence data was obtained from the Stanford Genome Technology Center website at http://www-sequence.stanford.edu/group/candida. Sequencing of Candida albicans was accomplished with the support of the NIDR and the Burroughs Wellcome Fund.
Table 1 update

RNA

SRP RNA sequences:

Predicted SRP RNAs (postscript, pdf) Comments:
Chlamydomonas reinhardtii : The two found sequences, one of which is equal to X71484, may be folded according to the consensus structure, but the 5' end differs (GCGCC, GCC). Above is a folding where the first and last nucleotides (TTT) have been removed.
Plasmodium falciparum : The found SRPRNA overlaps with the last exon of a putative RNAhelicase protein in the annotation. The last exon of this predicted protein is, however, not supported by homology to other proteins (not even in P.yoelii) and is therefore probably not correct.
Plasmodium alignments: The found Plasmodium SRPRNAs may be divided into three groups. Primary sequence alignments with additional sequences were made with clustalw. P.chabaudi is cut in the 5' end because contig ended there.

Protein

Additional SRP21 secondary structure predictions

Update of Table 1 with new candidates (these are not confirmed):

Organism                SRPRNA     SRP9/21   SRP14             SRP19     SRP54        SRP68     SRP72
--------                ------     -------   ----------------  --------  -----        -----     -----
Giardia lamblia         p [e]      ?         ?                 EAA38699  +            +         +

Entamoeba histolytica   + [f]      ?         ?                 +         81.m00151[d] +         +

C. reinhardtii          +          +         +                 818 [a]   +            +         +

Neurospora crassa       +          +         +[XP_331181.1]    +         +            +         +
Aspergillus nidulans    +          EAA65246  EAA60923 [b]      EAA65148  +            +         +
Candida                 +          +         + [c]             +         +            +         +

'+' = found according to paper; '?' = not yet found; 
Accession given for new candidates found by blast searches (not confirmed in any other way!).
[a] scaffold_818 (from chlre1.fasta) join(30398..30415,30504..30579,30659..30729,301538..301634,302501..302691).
    BLAST hits and Genscan prediction.
[b] Start of sequence does not match well to other SRP14 and structure prediction.
[c] Found in scrap file (by Blackwell, van Nues, Brown) not included in genome assembly.
[d] E.histolytica TIGR DB, temporary identifier. Pos 4026-5488 on assembly Scaffold 00081.
[e] S-domain identified
[f] SRP RNA identified in 5 Entamoeba species (unpublished)


Updated: 2004-Oct-20, MAR