Interestingly, the analysis of upregulated genes also identified GO categories related to cytokinesis. Two upregulated genes were involved in callose synthesis during cell plate formation: ENDOXYLOGLUCAN TRANSFERASE (DECOY) and CALLOSE SYNTHASE1, both of which are implicated in cell wall/cell plate formation (Table 3  
Table 3.

Upregulated Genes in hub1-1 Compared with Ler


Fold Change

P Value

Gene Code

Gene Description

GO Category
37.692.34E-03At3g04070No apical meristem (NAM) family proteinRegulation of transcription
24.631.66E-08At5g18270No apical meristem (NAM) family proteinRegulation of transcription
17.955.09E-09At1g05480SNF2 domain-containing proteinRegulation of transcription
15.264.58E-09At1g32870No apical meristem (NAM) family proteinRegulation of transcription
5.632.98E-08At3g10500No apical meristem (NAM) family proteinRegulation of transcription
5.034.96E-08At3g13210Crooked neck protein, putative cell cycle protein
4.822.98E-06At2g18060No apical meristem (NAM) family proteinRegulation of transcription
4.804.23E-05At5g64060No apical meristem (NAM) family proteinRegulation of transcription
4.599.95E-07At5g14000No apical meristem (NAM) family proteinRegulation of transcription
4.452.66E-02At5g53980Homeobox-leucine zipper family proteinRegulation of transcription
3.496.37E-07At1g62360Homeobox protein SHOOT MERISTEMLESS (STM)Regulation of transcription
3.433.97E-02At1g02220No apical meristem (NAM) family proteinRegulation of transcription
3.181.31E-02At3g53230Cell division cycle protein 48 (CDC48), putativeNucleotide binding
3.166.31E-05At5g13180No apical meristem (NAM) family proteinRegulation of transcription
3.148.62E-05At5g66130Cell cycle checkpoint protein-related (ATRAD17)
2.833.82E-03At5g27950Kinesin motor protein-relatedMicrotubule-based movement
2.721.13E-02At3g03060AAA-type ATPase family protein (CDC48-like)
2.629.77E-04At1g70510Homeobox protein knotted-1 like 2 (KNAT2) (K1)Specification of carpel identity
2.621.12E-02At2g16700Actin-depolymerizing factor 5 (ADF5)Biological process unknown
2.533.51E-02At5g04470SIAMESE proteinBiological process unknown
2.501.52E-03At1g23380Homeobox transcription factor (KNAT6)Regulation of transcription
2.424.94E-02At3g58160Myosin heavy chain, putativeActin filament-based movement
2.393.62E-02At1g23370Homeobox transcription factor (KNAT6)Regulation of transcription
2.307.34E-03At2g22430Homeobox-leucine zipper protein 6 (HB-6)Regulation of transcription
2.272.95E-02At4g01550No apical meristem (NAM) family proteinRegulation of transcription
2.271.23E-02At1g05570Callose synthase 1 (CALS1)/1,3-β-glucan synthase 1β-1,3 Glucan biosynthesis
2.061.62E-02At1g52880No apical meristem (NAM) family proteinRegulation of transcription
1.941.10E-04At5g03455GTPV2 (putative CDC25 homolog)Protein amino acid phosphorylation
1.931.37E-02At5g54310ARF GAP-like zinc finger-containing protein ZIGA3 (ZIGA3)Regulation of GTPase activity
1.921.72E-02At3g55005Tonneau 1b (TON1b)Microtubule cytoskeleton organization and biogenesis
1.85.10E-03At1g59610Dynamin-like protein, putative (ADL3)
1.712.30E-02At4g29230No apical meristem (NAM) family proteinRegulation of transcription
1.694.42E-02At5g02470DP-2 transcription factor, putative (DPA)Regulation of progression through cell cycle
1.671.31E-02At2g14120Dynamin-like protein 2b (ADL2b/DRP2b)
1.663.94E-02At3g46010Actin-depolymerizing factor 1 (ADF1)Actin filament organization
1.643.64E-02At1g14620DECOY, endoxyloglucan transferase family (EXGT)Biological process unknown
1.66.97E-03At1g08620Transcription factor jumonji (jmj) family proteinRegulation of transcription
1.6
7.02E-03
At5g43900
Myosin heavy chain (MYA2)
Actin filament-based movement

Fold Change

P Value

Gene Code

Gene Description

GO Category
37.692.34E-03At3g04070No apical meristem (NAM) family proteinRegulation of transcription
24.631.66E-08At5g18270No apical meristem (NAM) family proteinRegulation of transcription
17.955.09E-09At1g05480SNF2 domain-containing proteinRegulation of transcription
15.264.58E-09At1g32870No apical meristem (NAM) family proteinRegulation of transcription
5.632.98E-08At3g10500No apical meristem (NAM) family proteinRegulation of transcription
5.034.96E-08At3g13210Crooked neck protein, putative cell cycle protein
4.822.98E-06At2g18060No apical meristem (NAM) family proteinRegulation of transcription
4.804.23E-05At5g64060No apical meristem (NAM) family proteinRegulation of transcription
4.599.95E-07At5g14000No apical meristem (NAM) family proteinRegulation of transcription
4.452.66E-02At5g53980Homeobox-leucine zipper family proteinRegulation of transcription
3.496.37E-07At1g62360Homeobox protein SHOOT MERISTEMLESS (STM)Regulation of transcription
3.433.97E-02At1g02220No apical meristem (NAM) family proteinRegulation of transcription
3.181.31E-02At3g53230Cell division cycle protein 48 (CDC48), putativeNucleotide binding
3.166.31E-05At5g13180No apical meristem (NAM) family proteinRegulation of transcription
3.148.62E-05At5g66130Cell cycle checkpoint protein-related (ATRAD17)
2.833.82E-03At5g27950Kinesin motor protein-relatedMicrotubule-based movement
2.721.13E-02At3g03060AAA-type ATPase family protein (CDC48-like)
2.629.77E-04At1g70510Homeobox protein knotted-1 like 2 (KNAT2) (K1)Specification of carpel identity
2.621.12E-02At2g16700Actin-depolymerizing factor 5 (ADF5)Biological process unknown
2.533.51E-02At5g04470SIAMESE proteinBiological process unknown
2.501.52E-03At1g23380Homeobox transcription factor (KNAT6)Regulation of transcription
2.424.94E-02At3g58160Myosin heavy chain, putativeActin filament-based movement
2.393.62E-02At1g23370Homeobox transcription factor (KNAT6)Regulation of transcription
2.307.34E-03At2g22430Homeobox-leucine zipper protein 6 (HB-6)Regulation of transcription
2.272.95E-02At4g01550No apical meristem (NAM) family proteinRegulation of transcription
2.271.23E-02At1g05570Callose synthase 1 (CALS1)/1,3-β-glucan synthase 1β-1,3 Glucan biosynthesis
2.061.62E-02At1g52880No apical meristem (NAM) family proteinRegulation of transcription
1.941.10E-04At5g03455GTPV2 (putative CDC25 homolog)Protein amino acid phosphorylation
1.931.37E-02At5g54310ARF GAP-like zinc finger-containing protein ZIGA3 (ZIGA3)Regulation of GTPase activity
1.921.72E-02At3g55005Tonneau 1b (TON1b)Microtubule cytoskeleton organization and biogenesis
1.85.10E-03At1g59610Dynamin-like protein, putative (ADL3)
1.712.30E-02At4g29230No apical meristem (NAM) family proteinRegulation of transcription
1.694.42E-02At5g02470DP-2 transcription factor, putative (DPA)Regulation of progression through cell cycle
1.671.31E-02At2g14120Dynamin-like protein 2b (ADL2b/DRP2b)
1.663.94E-02At3g46010Actin-depolymerizing factor 1 (ADF1)Actin filament organization
1.643.64E-02At1g14620DECOY, endoxyloglucan transferase family (EXGT)Biological process unknown
1.66.97E-03At1g08620Transcription factor jumonji (jmj) family proteinRegulation of transcription
1.6
7.02E-03
At5g43900
Myosin heavy chain (MYA2)
Actin filament-based movement

Data were obtained from the ATH1 microarray experiment with RNA from shoot apex of young plants grown under in vitro conditions. The P values were calculated according to a Bayesian test of linear model and corrected by the Holm's method.

Table 3.

Upregulated Genes in hub1-1 Compared with Ler


Fold Change

P Value

Gene Code

Gene Description

GO Category
37.692.34E-03At3g04070No apical meristem (NAM) family proteinRegulation of transcription
24.631.66E-08At5g18270No apical meristem (NAM) family proteinRegulation of transcription
17.955.09E-09At1g05480SNF2 domain-containing proteinRegulation of transcription
15.264.58E-09At1g32870No apical meristem (NAM) family proteinRegulation of transcription
5.632.98E-08At3g10500No apical meristem (NAM) family proteinRegulation of transcription
5.034.96E-08At3g13210Crooked neck protein, putative cell cycle protein
4.822.98E-06At2g18060No apical meristem (NAM) family proteinRegulation of transcription
4.804.23E-05At5g64060No apical meristem (NAM) family proteinRegulation of transcription
4.599.95E-07At5g14000No apical meristem (NAM) family proteinRegulation of transcription
4.452.66E-02At5g53980Homeobox-leucine zipper family proteinRegulation of transcription
3.496.37E-07At1g62360Homeobox protein SHOOT MERISTEMLESS (STM)Regulation of transcription
3.433.97E-02At1g02220No apical meristem (NAM) family proteinRegulation of transcription
3.181.31E-02At3g53230Cell division cycle protein 48 (CDC48), putativeNucleotide binding
3.166.31E-05At5g13180No apical meristem (NAM) family proteinRegulation of transcription
3.148.62E-05At5g66130Cell cycle checkpoint protein-related (ATRAD17)
2.833.82E-03At5g27950Kinesin motor protein-relatedMicrotubule-based movement
2.721.13E-02At3g03060AAA-type ATPase family protein (CDC48-like)
2.629.77E-04At1g70510Homeobox protein knotted-1 like 2 (KNAT2) (K1)Specification of carpel identity
2.621.12E-02At2g16700Actin-depolymerizing factor 5 (ADF5)Biological process unknown
2.533.51E-02At5g04470SIAMESE proteinBiological process unknown
2.501.52E-03At1g23380Homeobox transcription factor (KNAT6)Regulation of transcription
2.424.94E-02At3g58160Myosin heavy chain, putativeActin filament-based movement
2.393.62E-02At1g23370Homeobox transcription factor (KNAT6)Regulation of transcription
2.307.34E-03At2g22430Homeobox-leucine zipper protein 6 (HB-6)Regulation of transcription
2.272.95E-02At4g01550No apical meristem (NAM) family proteinRegulation of transcription
2.271.23E-02At1g05570Callose synthase 1 (CALS1)/1,3-β-glucan synthase 1β-1,3 Glucan biosynthesis
2.061.62E-02At1g52880No apical meristem (NAM) family proteinRegulation of transcription
1.941.10E-04At5g03455GTPV2 (putative CDC25 homolog)Protein amino acid phosphorylation
1.931.37E-02At5g54310ARF GAP-like zinc finger-containing protein ZIGA3 (ZIGA3)Regulation of GTPase activity
1.921.72E-02At3g55005Tonneau 1b (TON1b)Microtubule cytoskeleton organization and biogenesis
1.85.10E-03At1g59610Dynamin-like protein, putative (ADL3)
1.712.30E-02At4g29230No apical meristem (NAM) family proteinRegulation of transcription
1.694.42E-02At5g02470DP-2 transcription factor, putative (DPA)Regulation of progression through cell cycle
1.671.31E-02At2g14120Dynamin-like protein 2b (ADL2b/DRP2b)
1.663.94E-02At3g46010Actin-depolymerizing factor 1 (ADF1)Actin filament organization
1.643.64E-02At1g14620DECOY, endoxyloglucan transferase family (EXGT)Biological process unknown
1.66.97E-03At1g08620Transcription factor jumonji (jmj) family proteinRegulation of transcription
1.6
7.02E-03
At5g43900
Myosin heavy chain (MYA2)
Actin filament-based movement

Fold Change

P Value

Gene Code

Gene Description

GO Category
37.692.34E-03At3g04070No apical meristem (NAM) family proteinRegulation of transcription
24.631.66E-08At5g18270No apical meristem (NAM) family proteinRegulation of transcription
17.955.09E-09At1g05480SNF2 domain-containing proteinRegulation of transcription
15.264.58E-09At1g32870No apical meristem (NAM) family proteinRegulation of transcription
5.632.98E-08At3g10500No apical meristem (NAM) family proteinRegulation of transcription
5.034.96E-08At3g13210Crooked neck protein, putative cell cycle protein
4.822.98E-06At2g18060No apical meristem (NAM) family proteinRegulation of transcription
4.804.23E-05At5g64060No apical meristem (NAM) family proteinRegulation of transcription
4.599.95E-07At5g14000No apical meristem (NAM) family proteinRegulation of transcription
4.452.66E-02At5g53980Homeobox-leucine zipper family proteinRegulation of transcription
3.496.37E-07At1g62360Homeobox protein SHOOT MERISTEMLESS (STM)Regulation of transcription
3.433.97E-02At1g02220No apical meristem (NAM) family proteinRegulation of transcription
3.181.31E-02At3g53230Cell division cycle protein 48 (CDC48), putativeNucleotide binding
3.166.31E-05At5g13180No apical meristem (NAM) family proteinRegulation of transcription
3.148.62E-05At5g66130Cell cycle checkpoint protein-related (ATRAD17)
2.833.82E-03At5g27950Kinesin motor protein-relatedMicrotubule-based movement
2.721.13E-02At3g03060AAA-type ATPase family protein (CDC48-like)
2.629.77E-04At1g70510Homeobox protein knotted-1 like 2 (KNAT2) (K1)Specification of carpel identity
2.621.12E-02At2g16700Actin-depolymerizing factor 5 (ADF5)Biological process unknown
2.533.51E-02At5g04470SIAMESE proteinBiological process unknown
2.501.52E-03At1g23380Homeobox transcription factor (KNAT6)Regulation of transcription
2.424.94E-02At3g58160Myosin heavy chain, putativeActin filament-based movement
2.393.62E-02At1g23370Homeobox transcription factor (KNAT6)Regulation of transcription
2.307.34E-03At2g22430Homeobox-leucine zipper protein 6 (HB-6)Regulation of transcription
2.272.95E-02At4g01550No apical meristem (NAM) family proteinRegulation of transcription
2.271.23E-02At1g05570Callose synthase 1 (CALS1)/1,3-β-glucan synthase 1β-1,3 Glucan biosynthesis
2.061.62E-02At1g52880No apical meristem (NAM) family proteinRegulation of transcription
1.941.10E-04At5g03455GTPV2 (putative CDC25 homolog)Protein amino acid phosphorylation
1.931.37E-02At5g54310ARF GAP-like zinc finger-containing protein ZIGA3 (ZIGA3)Regulation of GTPase activity
1.921.72E-02At3g55005Tonneau 1b (TON1b)Microtubule cytoskeleton organization and biogenesis
1.85.10E-03At1g59610Dynamin-like protein, putative (ADL3)
1.712.30E-02At4g29230No apical meristem (NAM) family proteinRegulation of transcription
1.694.42E-02At5g02470DP-2 transcription factor, putative (DPA)Regulation of progression through cell cycle
1.671.31E-02At2g14120Dynamin-like protein 2b (ADL2b/DRP2b)
1.663.94E-02At3g46010Actin-depolymerizing factor 1 (ADF1)Actin filament organization
1.643.64E-02At1g14620DECOY, endoxyloglucan transferase family (EXGT)Biological process unknown
1.66.97E-03At1g08620Transcription factor jumonji (jmj) family proteinRegulation of transcription
1.6
7.02E-03
At5g43900
Myosin heavy chain (MYA2)
Actin filament-based movement

Data were obtained from the ATH1 microarray experiment with RNA from shoot apex of young plants grown under in vitro conditions. The P values were calculated according to a Bayesian test of linear model and corrected by the Holm's method.

). Furthermore, the SIAMESE (SIM) gene, with a function in endoreduplication during trichome formation on leaves, and the E2F dimerization partner (DPa) transcription factor gene were upregulated (Table 3). Finally, some overexpressed genes in hub1-1 were related to meristem development, such as the homeodomain genes KNOTTED1-LIKE2 (KNAT2), KNAT6, SHOOT MERISTEMLESS, and 12 NO APICAL MERISTEM genes (Table 3). A total of 13 homeotic genes had an altered expression in hub1-1, among which were two SNF2 proteins (At3g63950 and At1g05480) and a BRAHMA-like protein (At3g06010) of the Polycomb group of proteins in fruitfly (Drosophila melanogaster). Other categories downregulated in hub1-1 comprised genes involved in carboxylic acid metabolism, fatty acid metabolism, lipid biosynthesis, vitamin biosynthesis, cofactor biosynthesis, chlorophyll biosynthesis, transfer RNA metabolism, photosynthesis, and protein targeted to chloroplast (Figure 5  
GO Analysis of 934 Downregulated Genes in Shoot Apices of hub1-1 in the ATH1 Microarray Experiment.
Figure 5.

GO Analysis of 934 Downregulated Genes in Shoot Apices of hub1-1 in the ATH1 Microarray Experiment.

The yellow to orange color of the circles correspond to the level of significance of the overrepresented GO category from 0.05 and below according to a multiple t test with false discovery rate–corrected P value. The size of the circle is proportional to the number of genes in the category.

). Biological processes, such as response to stress, proton transport, cell redox homeostasis, hexose metabolism, cellular respiration, and cofactor catabolism, were significantly overexpressed in hub1-1. Thus, besides effects on meristem development and cell cycle control, the hub1-1 mutant was generally defective in plant metabolism at the transcriptional level, possibly reflecting secondary effects on the observed growth defects.
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