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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.

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.

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Sequence logos for C-rich motif-sets identified by MEME in the upstream regions of the set of 15 mitochondrial genes. Motif-sets are given in Additional file 2:37 and logo captions are explained in the legend to Figure 1.
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Figure 2: Sequence logos for C-rich motif-sets identified by MEME in the upstream regions of the set of 15 mitochondrial genes. Motif-sets are given in Additional file 2:37 and logo captions are explained in the legend to Figure 1.

Mentions: An examination of the 27 strong motif groups showed that there were only 4 unique motifs, and that none, some or all 4 of them appeared as over-represented motifs in the upstream regions of the 13 sets of genes. The 4 motifs have been referred to, in the present study, as the G-rich motif, the C-rich motif, the CACA motif and the TGTG motif; examples of these motifs are shown in Figures 1, 2, 3 and 4, respectively. The G-rich motif has a core sequence consisting of 3 to 4 Gs (GGG, GGGG), the C-rich motif has a core sequence consisting of 3 to 4 Cs (CCC, CCCC), the CACA motif has the CACA core sequence and the TGTG motif has a core sequence of more than one TG pair (TGTG, TGTATG). The motif groups (or, simply, motifs) occurring in the upstream regions of each of the 13 sets of genes are given in Table 1.


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)

Sequence logos for C-rich motif-sets identified by MEME in the upstream regions of the set of 15 mitochondrial genes. Motif-sets are given in Additional file 2:37 and logo captions are explained in the legend to Figure 1.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 2: Sequence logos for C-rich motif-sets identified by MEME in the upstream regions of the set of 15 mitochondrial genes. Motif-sets are given in Additional file 2:37 and logo captions are explained in the legend to Figure 1.
Mentions: An examination of the 27 strong motif groups showed that there were only 4 unique motifs, and that none, some or all 4 of them appeared as over-represented motifs in the upstream regions of the 13 sets of genes. The 4 motifs have been referred to, in the present study, as the G-rich motif, the C-rich motif, the CACA motif and the TGTG motif; examples of these motifs are shown in Figures 1, 2, 3 and 4, respectively. The G-rich motif has a core sequence consisting of 3 to 4 Gs (GGG, GGGG), the C-rich motif has a core sequence consisting of 3 to 4 Cs (CCC, CCCC), the CACA motif has the CACA core sequence and the TGTG motif has a core sequence of more than one TG pair (TGTG, TGTATG). The motif groups (or, simply, motifs) occurring in the upstream regions of each of the 13 sets of genes are given in Table 1.

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