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Research article
Gitanjali Yadav
University of Cambridge
Corresponding Author
ORCiD: https://orcid.org/0000-0001-6591-9964
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Background The three helical Histone Fold Motif (HFM) of core histone proteins provides an evolutionarily favoured site for the protein-DNA interface. Despite significant variation in sequence, the HFM retains a distinctive structural fold that has diversified into several non-histone protein families in. In this work we explore the ancestry of non-histone HFM containing families in the plant kingdom.
Results A sequence search algorithm was developed using iterative profile Hidden Markov Models to identify remote homologs of core-histone proteins. The resulting hits were functionally annotated, classified into families, and subjected to comprehensive phylogenetic analyses via Maximum likelihood and Bayesian methods. We have identified over 4000 HFM containing proteins in the plant kingdom that are not histones, mostly existing as diverse transcription factor families, distributed widely within and across taxonomic groups.
Conclusion Patterns of homology suggest that core histone subunit H2A has evolved into newer families like NF-YC and DrAp1, whereas the H2B subunit of core histones shares a common ancestry with NF-YB and Dr1 class of TFs. Core histone subunits H3 and H4 were found to have evolved into DPE and TAF proteins, respectively. Taken together these results provide insights into diversification events during the evolution of the histone fold motif, including sub-functionalization and neo-functionalization of the HFM.
Keywords
Histone Fold Motif, Plant genome, HMM, core histones, evolution, Nuclear Factor-Y, TAF, DR1
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A new preprint design is coming!
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This is a preprint, a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.
Research article
Gitanjali Yadav
University of Cambridge
Corresponding Author
ORCiD: https://orcid.org/0000-0001-6591-9964
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
History
CURRENT STATUS: Posted
Version 1
Posted 08 Sep, 2019
No community comments so far
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
License:
This work is licensed under a CC BY 4.0 License. Read Full License
Background The three helical Histone Fold Motif (HFM) of core histone proteins provides an evolutionarily favoured site for the protein-DNA interface. Despite significant variation in sequence, the HFM retains a distinctive structural fold that has diversified into several non-histone protein families in. In this work we explore the ancestry of non-histone HFM containing families in the plant kingdom.
Results A sequence search algorithm was developed using iterative profile Hidden Markov Models to identify remote homologs of core-histone proteins. The resulting hits were functionally annotated, classified into families, and subjected to comprehensive phylogenetic analyses via Maximum likelihood and Bayesian methods. We have identified over 4000 HFM containing proteins in the plant kingdom that are not histones, mostly existing as diverse transcription factor families, distributed widely within and across taxonomic groups.
Conclusion Patterns of homology suggest that core histone subunit H2A has evolved into newer families like NF-YC and DrAp1, whereas the H2B subunit of core histones shares a common ancestry with NF-YB and Dr1 class of TFs. Core histone subunits H3 and H4 were found to have evolved into DPE and TAF proteins, respectively. Taken together these results provide insights into diversification events during the evolution of the histone fold motif, including sub-functionalization and neo-functionalization of the HFM.
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
This is a list of supplementary files associated with this preprint. Click to download.
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