Abstract
Switchgrass is one of the most promising energy crops and only recently has been employed for biofuel production. The draft genome of switchgrass was recently released; however, relatively few switchgrass genes have been functionally characterized. CENH3, the major histone protein found in centromeres, along with canonical H3 and other histones, plays an important role in maintaining genome stability and integrity. Despite their importance, the histone H3 genes of switchgrass have remained largely uninvestigated. In this study, we identified 17 putative switchgrass histone H3 genes in silico. Of these genes, 15 showed strong homology to histone H3 genes including six H3.1 genes, three H3.3 genes, four H3.3-like genes and two H3.1-like genes. The remaining two genes were found to be homologous to CENH3. RNA-seq data derived from lowland cultivar Alamo and upland cultivar Dacotah allowed us to identify SNPs in the histone H3 genes and compare their differential gene expression. Interestingly, we also found that overexpression of switchgrass histone H3 and CENH3 genes in N. benthamiana could trigger cell death of the transformed plant cells. Localization and deletion analyses of the histone H3 and CENH3 genes revealed that nuclear localization of the N-terminal tail is essential and sufficient for triggering the cell death phenotype. Our results deliver insight into the mechanisms underlying the histone-triggered cell death phenotype and provide a foundation for further studying the variations of the histone H3 and CENH3 genes in switchgrass.
Highlights
Plant nucleosomes are composed of a protein octamer that contains two molecules of each of the core histone proteins: H2A, H2B, H3, and H4
The seventeen switchgrass histone H3 genes encode nine different proteins (Table 1). These nine proteins were aligned with human (NCBI Reference Sequence: NP_003520.1, NP_0 66403.2, and NP_002098.1), mouse (NP_659539.1, NP_03857 6.1, and NP_032236.1), Arabidopsis (At1g09200, At4g40030, and At1g01370), rice (Os01g0866200, Os03g0390600, and Os05g048 9800) and maize (NP_001131276.1, AFW71933.1, and NP_00110 5520.1) histone H3 and CENH3 proteins (Figure 1A)
We identified 17 potential switchgrass histone H3 genes in the draft switchgrass genome (v1.1)
Summary
Plant nucleosomes are composed of a protein octamer that contains two molecules of each of the core histone proteins: H2A, H2B, H3, and H4. The canonical histone H3 protein is one of the most important protein components of this complex. The histone H3 protein has a main globular domain (including αN-helix, α1-helix, Loop, α2-helix, Loop, and α3-helix motifs), a long Nterminal tail and is post-translationally modified significantly more than the other histone proteins (Ingouff and Berger, 2010). The histone H3 family consists of four main members. Three of these members, including H3.1, H3.2, and H3.3, share more than 95% identity. The fourth member consists of the histone H3 variant CENH3, which is highly divergent in sequence structure in comparison to canonical histone H3. CENH3 is present at centromeres and is essential for centromere and kinetochore formation in all organisms (Allshire and Karpen, 2008)
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