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Table 3 Subcellular localization of Class II and Class IV histone deacetylases in Arabidopsis were predicted using different databases and programs.

From: Phylogenetic analysis, subcellular localization, and expression patterns of RPD3/HDA1 family histone deacetylases in plants

HDA

TAIR

SLP-LA

(Reliability index)

WoLF PSORTB

NetNESC

(predicted NES)

PSORT II

(NLS score)D

AtHDA2

---

mitochondria (1)

cytosol (7)

nucleus (4)

chloroplast (1)

mitochondria (1)

182-I

252-L

254-V

---

---

-0.47

AtHDA5

nucleus & cytosol

nucleus or cytosol (2)

nucleus (6.5)

cytosol & nucleus (6.5)

cytosol (5.5)

---

10–26 aa

bipartite NLS

0.02

AtHDA8

---

nucleus or cytosol (2)

cytosol (10)

cytoskeleton(2)

nucleus (1)

168-L

---

---

-0.47

AtHDA14

chloroplast

chloroplast (1)

chloroplast (13)

---

406–412 aa

par7 NLS

-0.13

AtHDA15

---

nucleus or cytosol (3)

cytosol (8)

nucleus (2)

chloroplast (1)

plastids (1)

peroxisomes (1)

489-I

14–17 par4

521–537 bipartite

522–538 bipartite

0.70

AtHDA18

---

nucleus or cytosol (1)

cytosol (6)

nucleus (3)

chloroplast (2)

plastids (2)

541-L

43–59 bipartite

121–137 bipartite

0.51

  1. A Reliability index ranges from 1 to 10. As the RI increases, the prediction result becomes more reliable.
  2. B The predictions of WoLF PSORT is based on the protein's amino acid sequence identifying target signals from proteins in the dataset which truly localize in the area. The numbers in parenthesis indicate the prior probability that such protein localizes to a given site is equal to the proportion of proteins in WoLF PSORT's dataset which is 456 (nucleus), 432 (cytosol), 750 (chloroplast), 210 (mitochondria), 11 (cytosol & nucleus), 41 (cytoskeleton), 165 (plastids), and 52 (peroxisomes).
  3. C NetNES results indicate predicted nuclear export signal (NES) with the corresponding amino acid number and residue. A NetNES score of 0.5 was set as a threshold for positive NES prediction although residues surrounding the predicted NES usually exhibit signal intensities below the set threshold value.
  4. D Numbers reflect amino acid residues exhibiting nuclear localization signals (NLS). Types of NLS detected from Class II were either bipartite or the classical type, pat4 or pat7, derived from SV40 large T antigen. Pattern for bipartite NLS follows 2 basic K/R residues, 10 residue spacer, and another basic region composed of at least 3 K/R residues out of 5 amino acids. Pattern 4 (pat4) is composed of 4 basic residues (K or R) or 3 basic residues and either H or P. Pattern 7 (pat7) starts with P then followed within 3 residues by a basic segment with 3 K/R residues out of 4. NLS score delineates the tendency of the protein to be either nuclear or cytoplasmic which is calculated based on its amino acid composition according to the neural network developed by Reinhardt & Hubbard (1998). Positive numbers indicate higher probability for nuclear localization whereas negative numbers lean towards more cytoplasmic localization.
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BMC Plant Biology

ISSN: 1471-2229

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