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Identification and Characterization of Switchgrass Histone H3 and CENH3 Genes.

Miao J, Frazier T, Huang L, Zhang X, Zhao B - Front Plant Sci (2016)

Bottom Line: 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.The remaining two genes were found to be homologous to CENH3.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Horticulture, Virginia TechBlacksburg, VA, USA; Department of Grassland Science, Sichuan Agricultural UniversityYa'an, China.

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.

No MeSH data available.


Related in: MedlinePlus

Alignment and phylogenetic analysis of the protein sequences of switchgrass histone H3 and histone H3 from other organisms. (A) Multiple alignments between switchgrass histone H3s and other species. Four amino acid positions (32, 42, 88, 91) that are different between H3.1 and H3.3 are labeled. Red boxes indicate helices within histone fold domain; (B) A neighbor-joining tree of switchgrass and Arabidopsis histone H3s.
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Figure 1: Alignment and phylogenetic analysis of the protein sequences of switchgrass histone H3 and histone H3 from other organisms. (A) Multiple alignments between switchgrass histone H3s and other species. Four amino acid positions (32, 42, 88, 91) that are different between H3.1 and H3.3 are labeled. Red boxes indicate helices within histone fold domain; (B) A neighbor-joining tree of switchgrass and Arabidopsis histone H3s.

Mentions: 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_066403.2, and NP_002098.1), mouse (NP_659539.1, NP_038576.1, and NP_032236.1), Arabidopsis (At1g09200, At4g40030, and At1g01370), rice (Os01g0866200, Os03g0390600, and Os05g0489800) and maize (NP_001131276.1, AFW71933.1, and NP_001105520.1) histone H3 and CENH3 proteins (Figure 1A). All of the switchgrass histone H3 proteins, except for Pavir.J05674.2 and Pavir.J25829.1, which encode putative CENH3 proteins, display a high degree of homology and conservation to the histone proteins of these different species.


Identification and Characterization of Switchgrass Histone H3 and CENH3 Genes.

Miao J, Frazier T, Huang L, Zhang X, Zhao B - Front Plant Sci (2016)

Alignment and phylogenetic analysis of the protein sequences of switchgrass histone H3 and histone H3 from other organisms. (A) Multiple alignments between switchgrass histone H3s and other species. Four amino acid positions (32, 42, 88, 91) that are different between H3.1 and H3.3 are labeled. Red boxes indicate helices within histone fold domain; (B) A neighbor-joining tree of switchgrass and Arabidopsis histone H3s.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4940616&req=5

Figure 1: Alignment and phylogenetic analysis of the protein sequences of switchgrass histone H3 and histone H3 from other organisms. (A) Multiple alignments between switchgrass histone H3s and other species. Four amino acid positions (32, 42, 88, 91) that are different between H3.1 and H3.3 are labeled. Red boxes indicate helices within histone fold domain; (B) A neighbor-joining tree of switchgrass and Arabidopsis histone H3s.
Mentions: 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_066403.2, and NP_002098.1), mouse (NP_659539.1, NP_038576.1, and NP_032236.1), Arabidopsis (At1g09200, At4g40030, and At1g01370), rice (Os01g0866200, Os03g0390600, and Os05g0489800) and maize (NP_001131276.1, AFW71933.1, and NP_001105520.1) histone H3 and CENH3 proteins (Figure 1A). All of the switchgrass histone H3 proteins, except for Pavir.J05674.2 and Pavir.J25829.1, which encode putative CENH3 proteins, display a high degree of homology and conservation to the histone proteins of these different species.

Bottom Line: 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.The remaining two genes were found to be homologous to CENH3.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Horticulture, Virginia TechBlacksburg, VA, USA; Department of Grassland Science, Sichuan Agricultural UniversityYa'an, China.

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.

No MeSH data available.


Related in: MedlinePlus