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In silico analysis of protein Lys-N(๐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(๐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(๐œ€)-acetylation has the potential to control, or contribute to control, of primary metabolism, signaling, and growth and development.

No MeSH data available.


Plant bromodomain proteins. (A) Phylogenetic analysis of the A. thaliana BRD-proteins. Distinct clusters (more than 50% bootstrap value) are colored differently in the tree. Sequences were aligned with MUSCLE and the tree was constructed using maximum likelihood method with 1000 bootstraps in MEGA5.The scale bar indicates the number of substitutions per site. (B) A representative BRD structure (AT3G54610.1) has four helices (Z, A, B, and C, each โˆผ110 residues in length). The ZA plus BC loops form the acetyl-Lys binding pocket. Unlike many mammalian and yeast proteins which include two or more BRD, most plant proteins have a single BRD. (C) An exception is the product of the Chlamydomonas reinhardtii (gi/ 159485810) locus which includes three BRD (plus a PHD domain). The C. reinhardtii protein structure was predicted using I-TASSER ().
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Figure 2: Plant bromodomain proteins. (A) Phylogenetic analysis of the A. thaliana BRD-proteins. Distinct clusters (more than 50% bootstrap value) are colored differently in the tree. Sequences were aligned with MUSCLE and the tree was constructed using maximum likelihood method with 1000 bootstraps in MEGA5.The scale bar indicates the number of substitutions per site. (B) A representative BRD structure (AT3G54610.1) has four helices (Z, A, B, and C, each โˆผ110 residues in length). The ZA plus BC loops form the acetyl-Lys binding pocket. Unlike many mammalian and yeast proteins which include two or more BRD, most plant proteins have a single BRD. (C) An exception is the product of the Chlamydomonas reinhardtii (gi/ 159485810) locus which includes three BRD (plus a PHD domain). The C. reinhardtii protein structure was predicted using I-TASSER ().

Mentions: Like a molecular barcode, the information present in acetylated-Lys must be recognized and decoded by some sort of โ€œreader.โ€ Originally discovered as a component of histone-binding proteins, bromodomains (BRD) are conserved structural motifs (Figure 2B) that recognize and bind PKA (Dhalluin et al., 1999; Zeng and Zhou, 2002; Sanchez and Zhou, 2009). The term โ€œBRDโ€ comes from brahma, a regulatory protein in Drosophila melanogaster. The human genome encodes at least 46 BRD-proteins (each of which has between one and six BRDs) which have been sorted into eight classes (Filippakopoulos et al., 2012). The yeast genome encodes at least nine BRD-proteins (Sanchez and Zhou, 2009; Table 1).


In silico analysis of protein Lys-N(๐œ€)-acetylation in plants.

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

Plant bromodomain proteins. (A) Phylogenetic analysis of the A. thaliana BRD-proteins. Distinct clusters (more than 50% bootstrap value) are colored differently in the tree. Sequences were aligned with MUSCLE and the tree was constructed using maximum likelihood method with 1000 bootstraps in MEGA5.The scale bar indicates the number of substitutions per site. (B) A representative BRD structure (AT3G54610.1) has four helices (Z, A, B, and C, each โˆผ110 residues in length). The ZA plus BC loops form the acetyl-Lys binding pocket. Unlike many mammalian and yeast proteins which include two or more BRD, most plant proteins have a single BRD. (C) An exception is the product of the Chlamydomonas reinhardtii (gi/ 159485810) locus which includes three BRD (plus a PHD domain). The C. reinhardtii protein structure was predicted using I-TASSER ().
© Copyright Policy - open-access
Related In: Results  -  Collection

License
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Figure 2: Plant bromodomain proteins. (A) Phylogenetic analysis of the A. thaliana BRD-proteins. Distinct clusters (more than 50% bootstrap value) are colored differently in the tree. Sequences were aligned with MUSCLE and the tree was constructed using maximum likelihood method with 1000 bootstraps in MEGA5.The scale bar indicates the number of substitutions per site. (B) A representative BRD structure (AT3G54610.1) has four helices (Z, A, B, and C, each โˆผ110 residues in length). The ZA plus BC loops form the acetyl-Lys binding pocket. Unlike many mammalian and yeast proteins which include two or more BRD, most plant proteins have a single BRD. (C) An exception is the product of the Chlamydomonas reinhardtii (gi/ 159485810) locus which includes three BRD (plus a PHD domain). The C. reinhardtii protein structure was predicted using I-TASSER ().
Mentions: Like a molecular barcode, the information present in acetylated-Lys must be recognized and decoded by some sort of โ€œreader.โ€ Originally discovered as a component of histone-binding proteins, bromodomains (BRD) are conserved structural motifs (Figure 2B) that recognize and bind PKA (Dhalluin et al., 1999; Zeng and Zhou, 2002; Sanchez and Zhou, 2009). The term โ€œBRDโ€ comes from brahma, a regulatory protein in Drosophila melanogaster. The human genome encodes at least 46 BRD-proteins (each of which has between one and six BRDs) which have been sorted into eight classes (Filippakopoulos et al., 2012). The yeast genome encodes at least nine BRD-proteins (Sanchez and Zhou, 2009; Table 1).

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(๐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(๐œ€)-acetylation has the potential to control, or contribute to control, of primary metabolism, signaling, and growth and development.

No MeSH data available.