Limits...
In silico analysis of protein Lys-N(šœ€)-acetylation in plants.

Rao RS, Thelen JJ, Miernyk JA - Front Plant Sci (2014)

Bottom Line: Herein we present a bioinformatics-based overview of reversible protein Lys-acetylation, including some comparisons with reversible protein phosphorylation.The study of Lys-acetylation of plant proteins has lagged behind studies of mammalian and microbial cells; 1000s of acetylation sites have been identified in mammalian proteins compared with only hundreds of sites in plant proteins.While most previous emphasis was focused on post-translational modifications of histones, more recent studies have addressed metabolic regulation.

View Article: PubMed Central - PubMed

Affiliation: Division of Biochemistry, University of Missouri Columbia, MO, USA ; Interdisciplinary Plant Group, University of Missouri Columbia, MO, USA.

ABSTRACT
Among post-translational modifications, there are some conceptual similarities between Lys-N(šœ€)-acetylation and Ser/Thr/Tyr O-phosphorylation. Herein we present a bioinformatics-based overview of reversible protein Lys-acetylation, including some comparisons with reversible protein phosphorylation. The study of Lys-acetylation of plant proteins has lagged behind studies of mammalian and microbial cells; 1000s of acetylation sites have been identified in mammalian proteins compared with only hundreds of sites in plant proteins. While most previous emphasis was focused on post-translational modifications of histones, more recent studies have addressed metabolic regulation. Being directly coupled with cellular CoA/acetyl-CoA and NAD/NADH, reversible Lys-N(šœ€)-acetylation has the potential to control, or contribute to control, of primary metabolism, signaling, and growth and development.

No MeSH data available.


A plant Lys-Nšœ€-acetyl-protein interactome. (A) The BRD-proteins are presented as squares, KATs as arrow-heads, KDACs as diamonds, and PKA proteins as circles. Some of the PKA proteins [histone H4 (AT1G07660) and H3.2 (AT1G09200), GTP-binding EF-Tu (AT1G07930), and nuclear PGK1 (AT3G12780)] interact with BRD-proteins. However, either no interactions or only self-interactions are known for the majority of plant PKA-proteins (āˆ¼69%; B). The interactome information was collected from TAIR (), AtPID (), AtPIN (), CCSB (), and PAIR (), and visualized using Cytoscape. Edge color (red is negative and green is positive) and width are proportional to gene co-expression (correlation coefficient) of genes based on GSE3011 from NCBI-GEO (). Nodes with no known interactions have not been included. Node size is proportional to the number of interactions. Node colors indicate subcellular protein localization, based on information from the TAIR database. (C) The percentage of currently known plant PKA-proteins in different subcellular localization categories is shown. The A. thaliana homologs of known PKA-proteins from other plants species were obtained using BLAST.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4120686&req=5

Figure 3: A plant Lys-Nšœ€-acetyl-protein interactome. (A) The BRD-proteins are presented as squares, KATs as arrow-heads, KDACs as diamonds, and PKA proteins as circles. Some of the PKA proteins [histone H4 (AT1G07660) and H3.2 (AT1G09200), GTP-binding EF-Tu (AT1G07930), and nuclear PGK1 (AT3G12780)] interact with BRD-proteins. However, either no interactions or only self-interactions are known for the majority of plant PKA-proteins (āˆ¼69%; B). The interactome information was collected from TAIR (), AtPID (), AtPIN (), CCSB (), and PAIR (), and visualized using Cytoscape. Edge color (red is negative and green is positive) and width are proportional to gene co-expression (correlation coefficient) of genes based on GSE3011 from NCBI-GEO (). Nodes with no known interactions have not been included. Node size is proportional to the number of interactions. Node colors indicate subcellular protein localization, based on information from the TAIR database. (C) The percentage of currently known plant PKA-proteins in different subcellular localization categories is shown. The A. thaliana homologs of known PKA-proteins from other plants species were obtained using BLAST.

Mentions: In A. thaliana there are 29 BRD-proteins3, which can be separated into multiple groups (Figure 2A). The number of BRD-proteins varies considerably among plants, from as many as 57 in G. max to as few as nine in the red nanoalga Cyanidioschyzon merolae. There are only a few instances of plant proteins that include more than a single BRD (Figure 2C). The relationship between BRDs and Lys-acetylated client proteins (Figure 3) has been compared with the recognition and binding of O-phosphorylated client proteins with the SH2 domain or with 14-3-3 proteins (Yang, 2004a; de Boer et al., 2013). It is not yet clear if recognition and binding involve only acetylated-Lys residues or if these residues must be in a particular context/domain/environment.


In silico analysis of protein Lys-N(šœ€)-acetylation in plants.

Rao RS, Thelen JJ, Miernyk JA - Front Plant Sci (2014)

A plant Lys-Nšœ€-acetyl-protein interactome. (A) The BRD-proteins are presented as squares, KATs as arrow-heads, KDACs as diamonds, and PKA proteins as circles. Some of the PKA proteins [histone H4 (AT1G07660) and H3.2 (AT1G09200), GTP-binding EF-Tu (AT1G07930), and nuclear PGK1 (AT3G12780)] interact with BRD-proteins. However, either no interactions or only self-interactions are known for the majority of plant PKA-proteins (āˆ¼69%; B). The interactome information was collected from TAIR (), AtPID (), AtPIN (), CCSB (), and PAIR (), and visualized using Cytoscape. Edge color (red is negative and green is positive) and width are proportional to gene co-expression (correlation coefficient) of genes based on GSE3011 from NCBI-GEO (). Nodes with no known interactions have not been included. Node size is proportional to the number of interactions. Node colors indicate subcellular protein localization, based on information from the TAIR database. (C) The percentage of currently known plant PKA-proteins in different subcellular localization categories is shown. The A. thaliana homologs of known PKA-proteins from other plants species were obtained using BLAST.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4120686&req=5

Figure 3: A plant Lys-Nšœ€-acetyl-protein interactome. (A) The BRD-proteins are presented as squares, KATs as arrow-heads, KDACs as diamonds, and PKA proteins as circles. Some of the PKA proteins [histone H4 (AT1G07660) and H3.2 (AT1G09200), GTP-binding EF-Tu (AT1G07930), and nuclear PGK1 (AT3G12780)] interact with BRD-proteins. However, either no interactions or only self-interactions are known for the majority of plant PKA-proteins (āˆ¼69%; B). The interactome information was collected from TAIR (), AtPID (), AtPIN (), CCSB (), and PAIR (), and visualized using Cytoscape. Edge color (red is negative and green is positive) and width are proportional to gene co-expression (correlation coefficient) of genes based on GSE3011 from NCBI-GEO (). Nodes with no known interactions have not been included. Node size is proportional to the number of interactions. Node colors indicate subcellular protein localization, based on information from the TAIR database. (C) The percentage of currently known plant PKA-proteins in different subcellular localization categories is shown. The A. thaliana homologs of known PKA-proteins from other plants species were obtained using BLAST.
Mentions: In A. thaliana there are 29 BRD-proteins3, which can be separated into multiple groups (Figure 2A). The number of BRD-proteins varies considerably among plants, from as many as 57 in G. max to as few as nine in the red nanoalga Cyanidioschyzon merolae. There are only a few instances of plant proteins that include more than a single BRD (Figure 2C). The relationship between BRDs and Lys-acetylated client proteins (Figure 3) has been compared with the recognition and binding of O-phosphorylated client proteins with the SH2 domain or with 14-3-3 proteins (Yang, 2004a; de Boer et al., 2013). It is not yet clear if recognition and binding involve only acetylated-Lys residues or if these residues must be in a particular context/domain/environment.

Bottom Line: Herein we present a bioinformatics-based overview of reversible protein Lys-acetylation, including some comparisons with reversible protein phosphorylation.The study of Lys-acetylation of plant proteins has lagged behind studies of mammalian and microbial cells; 1000s of acetylation sites have been identified in mammalian proteins compared with only hundreds of sites in plant proteins.While most previous emphasis was focused on post-translational modifications of histones, more recent studies have addressed metabolic regulation.

View Article: PubMed Central - PubMed

Affiliation: Division of Biochemistry, University of Missouri Columbia, MO, USA ; Interdisciplinary Plant Group, University of Missouri Columbia, MO, USA.

ABSTRACT
Among post-translational modifications, there are some conceptual similarities between Lys-N(šœ€)-acetylation and Ser/Thr/Tyr O-phosphorylation. Herein we present a bioinformatics-based overview of reversible protein Lys-acetylation, including some comparisons with reversible protein phosphorylation. The study of Lys-acetylation of plant proteins has lagged behind studies of mammalian and microbial cells; 1000s of acetylation sites have been identified in mammalian proteins compared with only hundreds of sites in plant proteins. While most previous emphasis was focused on post-translational modifications of histones, more recent studies have addressed metabolic regulation. Being directly coupled with cellular CoA/acetyl-CoA and NAD/NADH, reversible Lys-N(šœ€)-acetylation has the potential to control, or contribute to control, of primary metabolism, signaling, and growth and development.

No MeSH data available.