Fungal CSL transcription factors

Abstract

Background: The CSL (CBF1/RBP-Jkappa/Suppressor of Hairless/LAG-1) transcription factor family members are well-known components of the transmembrane receptor Notch signaling pathway, which plays a critical role in metazoan development. They function as context-dependent activators or repressors of transcription of their responsive genes, the promoters of which harbor the GTG(G/A)GAA consensus elements. Recently, several studies described Notch-independent activities of the CSL proteins.

Results: We have identified putative CSL genes in several fungal species, showing that this family is not confined to metazoans. We have analyzed their sequence conservation and identified the presence of well-defined domains typical of genuine CSL proteins. Furthermore, we have shown that the candidate fungal protein sequences contain highly conserved regions known to be required for sequence-specific DNA binding in their metazoan counterparts. The phylogenetic analysis of the newly identified fungal CSL proteins revealed the existence of two distinct classes, both of which are present in all the species studied.

Conclusion: Our findings support the evolutionary origin of the CSL transcription factor family in the last common ancestor of fungi and metazoans. We hypothesize that the ancestral CSL function involved DNA binding and Notch-independent regulation of transcription and that this function may still be shared, to a certain degree, by the present CSL family members from both fungi and metazoans.

Figure 1

Fungal CSL proteins domain organization. Black lines represent the respective CSL protein sequences (see Table 1 for details). The structure of C. elegans LAG-1 is shown at the top for comparison [17]. Recognized Pfam domains are indicated: RHR-N in green, BTD in red and RHR-C in yellow (light yellow for low significance). The proteins are drawn to scale.

Figure 2

Evolutionary conservation of the DNA-binding regions. The alignment of fungal and selected metazoan CSL protein sequences (see Table 1 and Additional file 3 for details) shows high degree of conservation in regions responsible for DNA binding. Absolutely conserved residues are inverse-printed, positions with high residue similarity are boxed. Domain boundaries are indicated by color: green for RHR-N, red for BTD and blue for the βC4 linker connecting all three CSL domains. Red and cyan triangles below the alignment denote residues required for sequence specific and backbone DNA binding, respectively. The position numbering and secondary structures indicated above the sequences correspond to C. elegans LAG-1 [17]. The picture shows only a selected region of the whole alignment and, in order to save space, some parts of the long inserts are not shown (indicated by '//'). The picture was created using ESPript [50].

Figure 3

Evolutionary conservation of the DNA-binding regions – continued. The continuation of the alignment shown in Fig. 2.

Figure 4

Phylogenetic analysis of the CSL protein family. An unrooted neighbor-joining phylogenetic tree of the region corresponding to RHR-N and BTD domains (see Methods). For protein descriptions see Table 1 and Additional file 3. For class F2 only the unambiguous core, not including the S. pombe SPCC1223.13 and S. japonicus SjCSL2, is indicated by shading. Symbols at nodes indicate percentual bootstrap values, no symbol means less than 50% node stability. The scale bar indicates the number of amino acid substitutions per site.