Genome-scale analysis of regulatory protein acetylation enzymes from photosynthetic eukaryotes

Uhrig, R. Glen; Schläpfer, Pascal; Mehta, Devang; Hirsch-Hoffmann, Matthias; Gruissem, Wilhelm

doi:10.1186/s12864-017-3894-0

Title: Genome-scale analysis of regulatory protein acetylation enzymes from photosynthetic eukaryotes

Journal Article · Wed Jul 05 00:00:00 EDT 2017 · BMC Genomics

DOI:https://doi.org/10.1186/s12864-017-3894-0· OSTI ID:1626808

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^[1]; Gruissem, Wilhelm ^[1]

Eidgenoessische Technische Hochschule, Zurich (Switzerland). Inst. of Molecular Plant Biology. Dept. of Biology
Eidgenoessische Technische Hochschule, Zurich (Switzerland). Inst. of Molecular Plant Biology. Dept. of Biology; Carnegie Inst. of Science, Stanford, CA (United States)

Background: Reversible protein acetylation occurring on Lys-Ne has emerged as a key regulatory post-translational modification in eukaryotes. It is mediated by two groups of enzymes: lysine acetyltransferases (KATs) and lysine deacetylases (KDACs) that catalyze the addition and removal of acetyl groups from target proteins. Estimates indicate that protein acetylation is second to protein phosphorylation in abundance, with thousands of acetylated sites now identified in different subcellular compartments. Considering the important regulatory role of protein phosphorylation, elucidating the diversity of KATs and KDACs across photosynthetic eukaryotes is essential in furthering our understanding of the impact of reversible protein acetylation on plant cell processes. Results: We report a genome-scale analysis of lysine acetyltransferase (KAT)- and lysine deacetylase (KDAC)-families from 53 photosynthetic eukaryotes. KAT and KDAC orthologs were identified in sequenced genomes ranging from glaucophytes and algae to land plants and then analyzed for evolutionary relationships. Based on consensus molecular phylogenetic and subcellular localization data we found new sub-classes of enzymes in established KAT- and KDAC-families. Specifically, we identified a non-photosynthetic origin of the HD-tuin family KDACs, a new monocot-specific Class I HDA-family sub-class, and a phylogenetically distinct Class II algal/heterokont sub-class which maintains an ankyrin domain not conserved in land plant Class II KDACs. Protein structure analysis showed that HDA- and SRT-KDACs exist as bare catalytic subunits with highly conserved median protein length, while all KATs maintained auxiliary domains, with CBP- and TAFII250-KATs displaying protein domain gain and loss over the course of photosynthetic eukaryote evolution in addition to variable protein length. Lastly, promoter element enrichment analyses across species revealed conserved cis-regulatory sequences that support KAT and KDAC involvement in the regulation of plant development, cold/drought stress response, as well as cellular processes such as the circadian clock. Conclusions: Our results reveal new evolutionary, structural, and biological insights into the KAT- and KDAC-families of photosynthetic eukaryotes, including evolutionary parallels to protein kinases and protein phosphatases. Further, we provide a comprehensive annotation framework through our extensive phylogenetic analysis, from which future research investigating aspects of protein acetylation in plants can use to position new findings in a broader context.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1626808

Journal Information:: BMC Genomics, Vol. 18, Issue 1; ISSN 1471-2164

Publisher:: SpringerCopyright Statement

Country of Publication:: United States

Language:: English

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59 BASIC BIOLOGICAL SCIENCES
Biotechnology & Applied Microbiology
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Lysine Deacetylase
Genomics

Genome-scale analysis of regulatory protein acetylation enzymes from photosynthetic eukaryotes Uhrig, R.; SchlĂ¤Pfer, Pascal; Mehta, Devang https://doi.org/10.6084/m9.figshare.c.3819151 The current record is supplemented by this collection	collection	January 2017
Genome-scale analysis of regulatory protein acetylation enzymes from photosynthetic eukaryotes Uhrig, R.; SchlĂ¤Pfer, Pascal; Mehta, Devang https://doi.org/10.6084/m9.figshare.c.3819151.v1 The current record is supplemented by this collection	collection	January 2017
Additional file 1: of Genome-scale analysis of regulatory protein acetylation enzymes from photosynthetic eukaryotes Uhrig, R.; SchlĂ¤Pfer, Pascal; Mehta, Devang https://doi.org/10.6084/m9.figshare.c.3819151_d1 The current record is supplemented by this dataset	dataset	January 2017
Additional file 1: of Genome-scale analysis of regulatory protein acetylation enzymes from photosynthetic eukaryotes Uhrig, R.; SchlĂ¤Pfer, Pascal; Mehta, Devang https://doi.org/10.6084/m9.figshare.c.3819151_d1.v1 The current record is supplemented by this dataset	dataset	January 2017
Additional file 2: of Genome-scale analysis of regulatory protein acetylation enzymes from photosynthetic eukaryotes Uhrig, R.; SchlĂ¤Pfer, Pascal; Mehta, Devang https://doi.org/10.6084/m9.figshare.c.3819151_d2 The current record is supplemented by this text	text	January 2017
Additional file 2: of Genome-scale analysis of regulatory protein acetylation enzymes from photosynthetic eukaryotes Uhrig, R.; SchlĂ¤Pfer, Pascal; Mehta, Devang https://doi.org/10.6084/m9.figshare.c.3819151_d2.v1 The current record is supplemented by this text	text	January 2017
Additional file 3: of Genome-scale analysis of regulatory protein acetylation enzymes from photosynthetic eukaryotes Uhrig, R.; SchlĂ¤Pfer, Pascal; Mehta, Devang https://doi.org/10.6084/m9.figshare.c.3819151_d3 The current record is supplemented by this dataset	dataset	January 2017
Additional file 3: of Genome-scale analysis of regulatory protein acetylation enzymes from photosynthetic eukaryotes Uhrig, R.; SchlĂ¤Pfer, Pascal; Mehta, Devang https://doi.org/10.6084/m9.figshare.c.3819151_d3.v1 The current record is supplemented by this dataset	dataset	January 2017
Additional file 4: of Genome-scale analysis of regulatory protein acetylation enzymes from photosynthetic eukaryotes Uhrig, R.; SchlĂ¤Pfer, Pascal; Mehta, Devang https://doi.org/10.6084/m9.figshare.c.3819151_d4 The current record is supplemented by this dataset	dataset	January 2017
Additional file 4: of Genome-scale analysis of regulatory protein acetylation enzymes from photosynthetic eukaryotes Uhrig, R.; SchlĂ¤Pfer, Pascal; Mehta, Devang https://doi.org/10.6084/m9.figshare.c.3819151_d4.v1 The current record is supplemented by this dataset	dataset	January 2017
Additional file 5: of Genome-scale analysis of regulatory protein acetylation enzymes from photosynthetic eukaryotes Uhrig, R.; SchlĂ¤Pfer, Pascal; Mehta, Devang https://doi.org/10.6084/m9.figshare.c.3819151_d5 The current record is supplemented by this dataset	dataset	January 2017
Additional file 5: of Genome-scale analysis of regulatory protein acetylation enzymes from photosynthetic eukaryotes Uhrig, R.; SchlĂ¤Pfer, Pascal; Mehta, Devang https://doi.org/10.6084/m9.figshare.c.3819151_d5.v1 The current record is supplemented by this dataset	dataset	January 2017