Research Article: Plasmodium falciparum Nucleosomes Exhibit Reduced Stability and Lost Sequence Dependent Nucleosome Positioning

Date Published: December 29, 2016

Publisher: Public Library of Science

Author(s): Elisabeth Silberhorn, Uwe Schwartz, Patrick Löffler, Samuel Schmitz, Anne Symelka, Tania de Koning-Ward, Rainer Merkl, Gernot Längst, Kirk W. Deitsch.

http://doi.org/10.1371/journal.ppat.1006080

Abstract

The packaging and organization of genomic DNA into chromatin represents an additional regulatory layer of gene expression, with specific nucleosome positions that restrict the accessibility of regulatory DNA elements. The mechanisms that position nucleosomes in vivo are thought to depend on the biophysical properties of the histones, sequence patterns, like phased di-nucleotide repeats and the architecture of the histone octamer that folds DNA in 1.65 tight turns. Comparative studies of human and P. falciparum histones reveal that the latter have a strongly reduced ability to recognize internal sequence dependent nucleosome positioning signals. In contrast, the nucleosomes are positioned by AT-repeat sequences flanking nucleosomes in vivo and in vitro. Further, the strong sequence variations in the plasmodium histones, compared to other mammalian histones, do not present adaptations to its AT-rich genome. Human and parasite histones bind with higher affinity to GC-rich DNA and with lower affinity to AT-rich DNA. However, the plasmodium nucleosomes are overall less stable, with increased temperature induced mobility, decreased salt stability of the histones H2A and H2B and considerable reduced binding affinity to GC-rich DNA, as compared with the human nucleosomes. In addition, we show that plasmodium histone octamers form the shortest known nucleosome repeat length (155bp) in vitro and in vivo. Our data suggest that the biochemical properties of the parasite histones are distinct from the typical characteristics of other eukaryotic histones and these properties reflect the increased accessibility of the P. falciparum genome.

Partial Text

The human malaria parasite, Plasmodium falciparum, yearly responsible for an estimated 600,000 deaths (WHO Report 2014), has the AT-richest genome sequenced to date. The AT-content averages 80.6% genome wide, but reaches up to 90% in introns and intergenic regions [1]. P. falciparum shows a complex life cycle in two hosts, exhibiting dramatic changes in the gene expression program. At least 60% of the genome is transcriptionally active during erythrocytic development with gene expression being activated in form of a cascade and tightly regulated during developmental stage transition [2,3].

The sequences of plasmodial histones are highly divergent from those of other eukaryotes. We questioned whether this difference represents an adaptation to the extraordinarily high AT-content of P. falciparum and whether these amino acid replacements do alter the physicochemical properties of the nucleosome. The results presented in this study are un-expected, showing that the observed mutations do not result in better binding of AT-rich DNA. In contrast, we even observe a reduced stability of the nucleosomes on GC-rich DNA, accompanied by a reduction in the thermal stability of the octamer on DNA. In agreement with the reduced thermal stability, we also observe reduced salt stability of H2A and H2B, the histones with the majority of sequence alterations.

 

Source:

http://doi.org/10.1371/journal.ppat.1006080

 

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