Lysine Methylation Modulates the Interaction of Archaeal Chromatin Protein Cren7 With DNA.

Niannian Ding,Cheng Zhong,Yuanyuan Chen,Zhenfeng Zhang,Li Huang,Yindi Chu

doi:10.3389/fmicb.2022.837737

Abstract

Cren7 and Sis7d, two chromatin proteins from Sulfolobus islandicus, undergo extensive methylations at multiple lysine residues to various extents. Whether this highly conserved protein serves an epigenetic role in the regulation of the structure and function of the chromosome remains unclear. In the present study, we show that methylation significantly affects Cren7, but not Sis7d, in the ability to bind DNA and to constrain negative DNA supercoils. Strikingly, methylated Cren7 was significantly less efficient in forming oligomers or mediating intermolecular DNA bridging. Single-site substitution mutation with glutamine reveals that methylation of the four lysine residues (K24, K31, K42, and K48) of Cren7 at the protein-DNA interface, which are variably conserved among Cren7 homologues from different branches of the Crenarchaeota, influenced Cren7-DNA interactions in different manners. We suggest that dynamic methylation of Cren7 may represent a potential epigenetic mechanism involved in the chromosomal regulation in crenarchaea.

Highlights

In all cellular organisms, the genomic DNA is packaged into a highly compressed and ordered structure found in nucleus of Eukaryotes or nucleoid of Bacteria and Archaea by a set of chromatin proteins (Dame et al, 2020; Chen et al, 2021; Laursen et al, 2021)
To learn if growth temperature affected the methylation of Cren7 and Sis7d in vivo, we purified the two proteins from S. islandicus strain E234 grown at 65, 75, and 85◦C in SCVyU medium to the midexponential phase and subjected them to mass spectrometry (MS)
To determine if the observed changes in the level of methylation of the two proteins involved an increase in the number of sites of methylation, we purified native Cren7 and Sis7d from wildtype S. islandicus grown at 75 and 85◦C and digested them with trypsin

Summary

Introduction

The genomic DNA is packaged into a highly compressed and ordered structure found in nucleus of Eukaryotes or nucleoid of Bacteria and Archaea by a set of chromatin proteins (Dame et al, 2020; Chen et al, 2021; Laursen et al, 2021). A large number of studies have firmly established the importance of post-translational modifications (PTMs) of chromatin proteins to chromosome remodeling and epigenetic regulation. It is well known that PTMs, including acetylation, methylation, phosphorylation, ubiquitination, and biotinylation, on the N-terminal tail of histones from eukaryotes are involved in a number of cellular processes such as gene expression regulation and DNA damage response (Kouzarides, 2007; Zhao and Garcia, 2015). Among the PTMs of histones, dynamic methylation is considered to serve a key role in epigenetic regulation as it has been reported in the regulation of gene transcription (Shilatifard, 2008) and in the formation of heterochromatin (Martin and Zhang, 2005). Lysine methylation has been reported for proteins involved in DNA transcription, Function Roles of Cren Methylation

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Results

Conclusion