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Identification of putative regulatory motifs in the upstream regions of co-expressed functional groups of genes in Plasmodium falciparum.

Iengar P, Joshi NV - BMC Genomics (2009)

Bottom Line: While over half the genes are estimated to be regulated at the transcriptional level, few regulatory motifs and transcription regulators have been found.The same motifs were sometimes identified for multiple functional groups; differences in location and abundance of the motifs appear to ensure different modes of action.The identification of positionally conserved over-represented upstream motifs throws light on putative regulatory elements for transcription in Pf.

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Affiliation: Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India. pi@mbu.iisc.ernet.in

ABSTRACT

Background: Regulation of gene expression in Plasmodium falciparum (Pf) remains poorly understood. While over half the genes are estimated to be regulated at the transcriptional level, few regulatory motifs and transcription regulators have been found.

Results: The study seeks to identify putative regulatory motifs in the upstream regions of 13 functional groups of genes expressed in the intraerythrocytic developmental cycle of Pf. Three motif-discovery programs were used for the purpose, and motifs were searched for only on the gene coding strand. Four motifs -- the 'G-rich', the 'C-rich', the 'TGTG' and the 'CACA' motifs -- were identified, and zero to all four of these occur in the 13 sets of upstream regions. The 'CACA motif' was absent in functional groups expressed during the ring to early trophozoite transition. For functional groups expressed in each transition, the motifs tended to be similar. Upstream motifs in some functional groups showed 'positional conservation' by occurring at similar positions relative to the translational start site (TLS); this increases their significance as regulatory motifs. In the ribonucleotide synthesis, mitochondrial, proteasome and organellar translation machinery genes, G-rich, C-rich, CACA and TGTG motifs, respectively, occur with striking positional conservation. In the organellar translation machinery group, G-rich motifs occur close to the TLS. The same motifs were sometimes identified for multiple functional groups; differences in location and abundance of the motifs appear to ensure different modes of action.

Conclusion: The identification of positionally conserved over-represented upstream motifs throws light on putative regulatory elements for transcription in Pf.

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Feature map marking the locations of CACA containing motif occurrences in the CACA motif group identified by MEME in the upstream regions of the proteasome set of genes (motif group shown in Additional file 2:29).
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Figure 8: Feature map marking the locations of CACA containing motif occurrences in the CACA motif group identified by MEME in the upstream regions of the proteasome set of genes (motif group shown in Additional file 2:29).

Mentions: The motif occurrences in the 27 strong motif groups, identified in the upstream regions of the 13 sets of genes, were sorted [see Additional files 5 and 6] and then visualized using feature maps (Additional file 7 and Figures 5, 6, 7, 8, 9, 10 and 11; cf., Methods). An interesting feature observed in some of the feature maps was that, in subsets of gene upstream regions, there was a preferential positioning of motifs relative to the TLS (examples discussed below); i.e., motifs show a preference to occur at a particular upstream position relative to the start of translation. In the literature, this has been referred to as 'positional bias', and TFBMs are known to display such a bias or preference [25]. In [21], 'positional enrichment' of motifs relative to the start codon has been noted for some clusters of Pf genes (sexual development, cytosolic ribosome and antigenic variation clusters), and the enrichment has been regarded as an indication that the motif is functionally important.


Identification of putative regulatory motifs in the upstream regions of co-expressed functional groups of genes in Plasmodium falciparum.

Iengar P, Joshi NV - BMC Genomics (2009)

Feature map marking the locations of CACA containing motif occurrences in the CACA motif group identified by MEME in the upstream regions of the proteasome set of genes (motif group shown in Additional file 2:29).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2662883&req=5

Figure 8: Feature map marking the locations of CACA containing motif occurrences in the CACA motif group identified by MEME in the upstream regions of the proteasome set of genes (motif group shown in Additional file 2:29).
Mentions: The motif occurrences in the 27 strong motif groups, identified in the upstream regions of the 13 sets of genes, were sorted [see Additional files 5 and 6] and then visualized using feature maps (Additional file 7 and Figures 5, 6, 7, 8, 9, 10 and 11; cf., Methods). An interesting feature observed in some of the feature maps was that, in subsets of gene upstream regions, there was a preferential positioning of motifs relative to the TLS (examples discussed below); i.e., motifs show a preference to occur at a particular upstream position relative to the start of translation. In the literature, this has been referred to as 'positional bias', and TFBMs are known to display such a bias or preference [25]. In [21], 'positional enrichment' of motifs relative to the start codon has been noted for some clusters of Pf genes (sexual development, cytosolic ribosome and antigenic variation clusters), and the enrichment has been regarded as an indication that the motif is functionally important.

Bottom Line: While over half the genes are estimated to be regulated at the transcriptional level, few regulatory motifs and transcription regulators have been found.The same motifs were sometimes identified for multiple functional groups; differences in location and abundance of the motifs appear to ensure different modes of action.The identification of positionally conserved over-represented upstream motifs throws light on putative regulatory elements for transcription in Pf.

View Article: PubMed Central - HTML - PubMed

Affiliation: Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India. pi@mbu.iisc.ernet.in

ABSTRACT

Background: Regulation of gene expression in Plasmodium falciparum (Pf) remains poorly understood. While over half the genes are estimated to be regulated at the transcriptional level, few regulatory motifs and transcription regulators have been found.

Results: The study seeks to identify putative regulatory motifs in the upstream regions of 13 functional groups of genes expressed in the intraerythrocytic developmental cycle of Pf. Three motif-discovery programs were used for the purpose, and motifs were searched for only on the gene coding strand. Four motifs -- the 'G-rich', the 'C-rich', the 'TGTG' and the 'CACA' motifs -- were identified, and zero to all four of these occur in the 13 sets of upstream regions. The 'CACA motif' was absent in functional groups expressed during the ring to early trophozoite transition. For functional groups expressed in each transition, the motifs tended to be similar. Upstream motifs in some functional groups showed 'positional conservation' by occurring at similar positions relative to the translational start site (TLS); this increases their significance as regulatory motifs. In the ribonucleotide synthesis, mitochondrial, proteasome and organellar translation machinery genes, G-rich, C-rich, CACA and TGTG motifs, respectively, occur with striking positional conservation. In the organellar translation machinery group, G-rich motifs occur close to the TLS. The same motifs were sometimes identified for multiple functional groups; differences in location and abundance of the motifs appear to ensure different modes of action.

Conclusion: The identification of positionally conserved over-represented upstream motifs throws light on putative regulatory elements for transcription in Pf.

Show MeSH
Related in: MedlinePlus