Open Access Highly Accessed Research article

Putative SF2 helicases of the early-branching eukaryote Giardia lamblia are involved in antigenic variation and parasite differentiation into cysts

Pablo R Gargantini*, Marianela C Serradell, Alessandro Torri and Hugo D Lujan

Author Affiliations

Laboratory of Biochemistry and Molecular Biology, School of Medicine, Catholic University of Córdoba, Córdoba, X5004ASK, Argentina

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BMC Microbiology 2012, 12:284  doi:10.1186/1471-2180-12-284

Published: 28 November 2012

Additional files

Additional file 1: Table S1:

Putative SF2 Helicases from Giardia lamblia. The table indicates the Family, the gene number from the Assemblage A isolate WB (the number that is given should be preceded by the prefix GL50803_), the current Supercontig or positions where it is located, the number of nucleotides in base pairs (bp) and molecular mass of the putative protein in kDa, for each putative helicase. (DOCX 18 kb)

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Additional file 2: Table S2:

Average lengths (amino acid) of SF2 helicase families from Giardia lamblia. The table indicates the average length (in number of amino acids) of each SF2 helicase family. The incompletes sequences were not considered in the computation.

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Additional file 3: Figure S1:

Phylogenetic tree of the 46 putative SF2 helicase genes in Giardia lamblia. Phylogenetic tree derived from the alignment of the “Helicase Core Domain” amino acid sequences. Each helicase is named after its gene number, as in the GiardiaDB. The family groups are indicated as follows: DEAD-box (orange), DEAH-box (green), Ski2 (violet), RecQ (pink), Swi2/Snf2 (light orange) and Rad3 (light blue).

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Additional file 4: Table S3:

Giardia lamblia SF2 helicases homologues in human and yeast. The table indicates each putative Giardia helicase with its Accession Number and ORF, the protein length in aminoacid, its putative helicase homologue form human with the identity and similarity percentage, and its putative helicase homologue from yeast with their known functions.

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Additional file 5: Figure S2:

Alignment of conserved DEAD-box helicase motifs. The sequences were aligned using the “Multiple Align Show” software at “The Sequence Manipulation Suite” (http://www.bioinformatics.org/sms/index.html webcite). The residues conserved at 70% or more are highlighted in dark; other similar residues within each column are highlighted in grey.

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Additional file 6: Figure S3:

Alignment of conserved DEAH-box helicase motifs. The sequences were aligned using the “Multiple Align Show” as before. The residues conserved at 70% or more are highlighted in dark; other similar residues within each column are highlighted in grey.

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Additional file 7: Figure S4:

Alignment of conserved Ski2 helicase motifs. The sequences were aligned using the “Multiple Align Show” as before. The residues conserved at 70% or more are highlighted in dark; other similar residues within each column are highlighted in grey.

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Additional file 8: Figure S5:

Schematic diagram of the Swi2-Snf2 helicase family in G. lamblia. The SANT domain is represented in blue, the BROMO domain in brown, and the CHROMO domain in green. The SNF2N domains are represented in light grey, inside each one of them are the helicase motifs, when appropriate. The representation is to scale. Inset: sequence LOGO view of the consensus amino acids. The height of each amino acid represents the degree of conservation. Colors indicate properties of the amino acids, as follows: green (polar), blue (basic), red (acidic) and black (hydrophobic).

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Additional file 9: Figure S6:

Schematic diagram of the RecQ helicase family in G. lamblia. The representation is to scale. Inset: sequence LOGO view of the consensus amino acids. The height of each amino acid represents the degree of conservation. Colors mark properties of the amino acids as: green (polar); blue (basic); red (acidic) and black (hydrophobic).

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Additional file 10: Figure S7:

Schematic diagram of the Rad3 helicase family in G. lamblia. The representation is to scale. Inset: sequence LOGO view of the consensus amino acids. The height of each amino acid represents the degree of conservation. Colors indicate properties of the amino acids, as follows: green (polar), blue (basic), red (acidic) and black (hydrophobic).

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Additional file 11: Figure S8:

Western blot of trophozoites grown under proliferating conditions and after induction to encyst. Total protein extracts from trophozoites grown under normal proliferating conditions (Normal) or after 16hs induction in encystation medium (Encyst) were separated using a 10% SDS-polyacrylamide gel and transferred to a PVDF membrane. The membrane was incubated with a monoclonal antibody against CWP2. The iqual loading of the samples is shown in the figure at the right with a Ponceau S staining. The numbers indicate the molecular weight of protein standards in kDa.

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Additional file 12: Figure S9:

SAGE (Serial Analysis of Gene Expression) data. The graph represents the sense tag percentage from Giardia trophozoites (white bar) and four different encystation times (4, 12, 21 and 42 hours; grayscale bars). Under each ORF it is indicated if these ORFs were up-regulated (green up arrow), down-regulated (red down arrow) or remained unmodified (equal sign). A line graph is also provided for a better identification of the expression pattern. The colored boxes represent our RT-qPCR results (with the same color code), divided into families. The asterisk under each box stands for a correlation between the SAGE and the RT-qPCR data.

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Additional file 13: Figure S10:

Western blot during antigenic variation induction. Trophozoites were incubated for the indicated times with a 1:10.000 dilution of mAb 5C1directed against VSP-1267, mAb 7D2 against Cyst Wall Protein 2 or without antibody (Control). Total protein was electrophoresed, transferred to a PVDF membrane and incubated with a mAb against the VSP-1267. The molecular weights of standards are indicated in kDa.

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Additional file 14: Table S4:

Accession numbers. The table indicates a complete list of proteins cited in the manuscript, the organism it is derived and the NCBI Reference Sequence Number.

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