Abstract
BackgroundHistone modifications and histone variants are of importance in many biological processes. To understand the biological functions of the global dynamics of histone modifications and histone variants in higher plants, we elucidated the variants and post-translational modifications of histones in soybean, a legume plant with a much bigger genome than that of Arabidopsis thaliana.ResultsIn soybean leaves, mono-, di- and tri-methylation at Lysine 4, Lysine 27 and Lysine 36, and acetylation at Lysine 14, 18 and 23 were detected in HISTONE H3. Lysine 27 was prone to being mono-methylated, while tri-methylation was predominant at Lysine 36. We also observed that Lysine 27 methylation and Lysine 36 methylation usually excluded each other in HISTONE H3. Although methylation at HISTONE H3 Lysine 79 was not reported in A. thaliana, mono- and di-methylated HISTONE H3 Lysine 79 were detected in soybean. Besides, acetylation at Lysine 8 and 12 of HISTONE H4 in soybean were identified. Using a combination of mass spectrometry and nano-liquid chromatography, two variants of HISTONE H3 were detected and their modifications were determined. They were different at positions of A31F41S87S90 (HISTONE variant H3.1) and T31Y41H87L90 (HISTONE variant H3.2), respectively. The methylation patterns in these two HISTONE H3 variants also exhibited differences. Lysine 4 and Lysine 36 methylation were only detected in HISTONE H3.2, suggesting that HISTONE variant H3.2 might be associated with actively transcribing genes. In addition, two variants of histone H4 (H4.1 and H4.2) were also detected, which were missing in other organisms. In the histone variant H4.1 and H4.2, the amino acid 60 was isoleucine and valine, respectively.ConclusionThis work revealed several distinct variants of soybean histone and their modifications that were different from A. thaliana, thus providing important biological information toward further understanding of the histone modifications and their functional significance in higher plants.
Highlights
Histone modifications and histone variants are of importance in many biological processes
Mass spectrometry (MS) analysis covered most of the amino acid sequence of histone H3, which consists of 135 amino acid residues
Our results showed some differences that exist between soybean and the model dicot A. thaliana: monoand di- methylation of Lysine 79 were detected in soybean but such Posttranslational modifications (PTMs) were not found in A. thaliana [17]
Summary
Histone modifications and histone variants are of importance in many biological processes. The N terminus of histone H3 and H4, and N and C terminus of H2A and H2B are prone to being covalently modified by many enzymes, such as HMT (histone methyltransferase) and HAT (histone acetyltransferase). These modifications include methylation, acetylation, phosphorylation, ubiquitination, glycosylation, ADP ribosylation, carbonylation, sumoylation and biotinylation. Most of these modifications are dynamic and can be reversed by other enzymes, such as histone demethylase and HDAC (histone deacetylase). Mass spectrometry (MS) allows us to deduce the amino acid sequence of a peptide, and to identify the exact sites and type of modifications in the peptide via the modified peptide mass shifts
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