Conservation of Domain Structure in a Fast-Evolving Heterochromatic SUUR Protein in Drosophilids

Abstract

Different genomic regions replicate at a distinct time during S-phase. The SuUR mutation alters replication timing and the polytenization level of intercalary and pericentric heterochromatin in Drosophila melanogaster salivary gland polytene chromosomes. We analyzed SuUR in different insects, identified conserved regions in the protein, substituted conserved amino acid residues, and studied effects of the mutations on SUUR function. SuUR orthologs were identified in all sequenced drosophilids, and a highly divergent ortholog was found in the mosquito genome. We demonstrated that SUUR evolves at very high rate comparable with that of Transformer. Remarkably, upstream ORF within 59 UTR of the gene is more conserved than SUUR in drosophilids, but it is absent in the mosquito. The domain structure and charge of SUUR are maintained in drosophilids despite the high divergence of the proteins. The N-terminal part of SUUR with similarity to the SNF2/SWI2 proteins displays the highest level of conservation. Mutation of two conserved amino acid residues in this region impairs binding of SUUR to polytene chromosomes and reduces the ability of the protein to cause DNA underreplication. The least conserved middle part of SUUR interacting with HP1 retains positively and negatively charged clusters and nuclear localization signals. The C terminus contains interlacing conserved and variable motifs. Our results suggest that SUUR domains evolve with different rates and patterns but maintain their features.

Regulatory functions and chromatin loading dynamics of linker histone H1 during endoreplication in Drosophila

“…Thus, the physical interaction between H1 and the central fragment of SUUR is direct. Importantly, an overlapping fragment of SUUR (361-599) has been shown previously to be required for the localization of SUUR to chromatin, including IH, in vivo (Kolesnikova et al 2005;Yurlova et al 2009). Therefore, the central region of SUUR, which encompasses a positively charged domain and the nuclear localization signal (NLS), is sufficient to mediate a strong physical interaction with H1 and may be involved in tethering SUUR to H1-containing chromatin in vivo.…”

“…We now demonstrate that the central region of SUUR is also sufficient for binding directly to H1 in vitro. Considering that the central region of SUUR is essential for the faithful localization of the protein to chromatin in vivo, including underreplicated IH (Kolesnikova et al 2005;Yurlova et al 2009), it seems likely that H1 directly mediates the tethering of SUUR to chromatin in underreplicated regions.…”

The effects of SUUR protein suggest its role in repressive chromatin renewal during replication inDrosophila

“…11,13 It is worth mentioning that SuUR is a fast-evolving gene that was found only in Diptera. 16 Despite the low evolutionary conservation, recent studies revealed several important features of Figure 1. Replication and under-replication in polytene chromosome.…”

“…16 However, it is unlikely that chromatindependent regulation of replication fork progression is a phenomenon restricted to Diptera. In mammals and other eukaryotes, SUUR function may well be performed by a different protein.…”

Induced decondensation of heterochromatin inDrosophila melanogasterpolytene chromosomes under condition of ectopic expression of theSupressor of underreplicationgene

“…15 Targeted mutation of two aminoacid residues in this domain renders the protein incapable of forming the swellings. 24 SWI2/SNF2 family ATP-binding domains normally play catalytic roles in a plethora of chromatin remodeling complexes. Such complexes can have specific genomic targets and mediate local structural changes in chromatin.…”