Skip to main content

Table 2 List of representative Arabidopsis orthologs of PS DEGs (nodes) forming subnetworks as shown in Fig. 6

From: Genome-wide transcriptional changes triggered by water deficit on a drought-tolerant common bean cultivar

DEG Cluster P. vulgaris ID Arabidopsis ortholog gene Gene symbol Function
Up-regulated Cell wall dynamics Phvul.009G242700 AT5G44030 CESA4 Cellulose synthase A4; required for beta-1,4-glucan microfibril crystallization, a major mechanism of the cell wall formation
Phvul.009G090100 AT4G18780 IRX1 IRREGULAR XYLEM 1; required for beta-1,4-glucan microfibril crystallization, a major mechanism of the cell wall formation
Phvul.003G154600 AT5G17420 IRX3 IRREGULAR XYLEM 3; required for beta-1,4-glucan microfibril crystallization, a major mechanism of the cell wall formation
Phvul.008G029000 AT5G15630 IRX6 IRREGULAR XYLEM 6, a COBRA-like extracellular glycosyl-phosphatidyl inositol-anchored protein family involved in secondary cell wall biosynthesis
Phvul.006G065800 AT2G38080 IRX12 Laccase-4; required for secondary xylem cell wall lignification
Phvul.009G148800 AT3G18660 PGSIP1 Plant glycogenin-like starch initiation protein 1; glycosyltransferase required for the addition of both glucuronic acid and 4-O-methylglucuronic acid branches to xylan in stem cell walls
Phvul.001G021800 AT4G33330 PGSIP3 Plant glycogenin-like starch initiation protein 3; glycosyltransferase required for the addition of both glucuronic acid and 4-O-methylglucuronic acid branches to xylan in stem cell walls
Phvul.005G091200 AT5G54690 GAUT12 Galacturonosyltransferase 12; involved in pectin assembly and/or distribution, and in the synthesis of secondary wall glucuronoxylan
Phvul.007G026900 AT1G68560 XYL1 Alpha-xylosidase 1; glycoside hydrolase releasing xylosyl residues from xyloglucan oligosaccharides at the non-reducing end
Phvul.006G133700 AT5G49720 GH9A1 Endoglucanase 25; required for cellulose microfibrils formation. Involved in cell wall assembly during cell elongation and cell plate maturation in cytokinesis
Phvul.009G016100 AT1G75680 GH9B7 Endoglucanase 10, glycosyl hydrolase 9B7. Endohydrolysis of (1- > 4)-beta-D-glucosidic linkages in cellulose, lichenin and cereal beta-D-glucans
Phvul.007G218400 AT4G02290 GH9B13 Endoglucanase 17, glycosyl hydrolase 9B13. Endohydrolysis of (1- > 4)-beta-D-glucosidic linkages in cellulose, lichenin and cereal beta-D-glucans
Phvul.010G123100 AT3G14310 PME3 Pectinesterase 3; acts in the modification of cell walls via demethylesterification of cell wall pectin
Phvul.008G288800 AT4G12730 FLA2 Fasciclin-like arabinogalactan 2; may be a cell surface adhesion protein
Phvul.005G011900 AT3G10720 AT3G10720 Pectinesterase 25; acts in the modification of cell walls via demethylesterification of cell wall pectin
Phvul.009G252200 AT3G16850 AT3G16850 Pectin lyase-like superfamily protein
Phvul.006G028800 AT4G23820 AT4G23820 Pectin lyase-like superfamily protein
Cell cycle, signaling and cytoskeleton organization Phvul.001G211000 AT1G02730 CSLD5 Cellulose synthase like D5; 1,4-beta-D-xylan synthase involved in stem and root growth
Phvul.009G017300 AT1G75780 TUB1 Tubulin beta; tubulin is the major constituent of microtubules
Phvul.009G114100 AT1G50010 TUA2 Tubulin alpha-2 chain; tubulin is the major constituent of microtubules
Phvul.007G047300 AT1G04820 TUA4 Tubulin alpha-4 chain. Encodes an alpha tubulin isoform, an structural constituent of cytoskeleton
Phvul.008G203300 AT2G26760 CYCB1;4 Cyclin B1;4, a G2/mitotic-specific cyclin-B involved in centrosome formation and ciliogenesis
Phvul.001G000500 AT1G20930 CDKB2;2 Cyclin-dependent kinase B2–2, regulation of G2/M transition of mitotic cell cycle
Phvul.003G293500 AT3G19050 POK2 Phragmoplast orienting kinesin 2; involved in the spatial control of cytokinesis by a proper phragmoplast guidance
Phvul.007G159100 AT2G37420 AT2G37420 ATP binding microtubule motor family protein; responsible for microtubule translocation
Phvul.006G052700 AT3G20150 AT3G20150 Kinesin motor family protein, ATP-dependent microtubule motor activity
Phvul.002G093500 AT1G70950 TPX2 Targeting protein for Xklp2; microtubule-associated protein (MAP) that regulates the orientation of interphase cortical microtubules
Phvul.001G028200 AT1G10200 WLIM1 LIM domain-containing protein WLIM1; binds to actin filaments and promotes cross-linking into thick bundles
Phvul.009G082500 AT2G26330 TE1 ERECTA; receptor kinase that, together with ERL1 and ERL2, regulates aerial architecture, including inflorescence and stomatal patterning
Phvul.007G063200 AT5G62230 ERL1 ERECTA-like 1; receptor kinase that regulates inflorescence architecture and organ shape as well as stomatal patterning, including density and clustering, together with ER and ERL2
Phvul.002G196200 AT5G46330 MPL12.8 FLAGELLIN-SENSITIVE 2; constitutes the pattern-recognition receptor (PPR) that determines the specific perception of flagellin (flg22)
Phvul.008G017400 AT3G28040 AT3G28040 Leucine-rich receptor-like protein kinase family protein, probably inactive
Phvul.005G099100 AT5G45970 RAC2 RAC-like 2; inactive GDP-bound Rho GTPases reside in the cytosol, are found in a complex with Rho GDP-dissociation inhibitors
Phvul.006G115500 AT1G01200 RABA3 Rab family protein; intracellular vesicle trafficking and protein transport
Down-regulated Protein folding Phvul.004G107700 AT5G52640 HSP90.1 Heat shock protein 81–1; functions as a holding molecular chaperone which stabilizes unfolding protein intermediates
Phvul.004G162100 AT3G24500 MBF1C Multiprotein bridging factor 1C; involved in the tolerance to heat and osmotic stress
Phvul.004G044100 AT1G74310 HSP101 Heat shock protein 101; molecular chaperone that plays an important role in thermotolerance
Phvul.009G078300 AT2G26150 HSFA2 Heat shock transcription factor A2; transcriptional activator involved in heat stress responses
Phvul.011G065000 AT3G12580 HSP70 Heat shock protein 70; a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes
Phvul.003G154800 AT1G16030 Hsp70b Heat shock protein 70B; in cooperation with other chaperones, stabilize preexistent proteins against aggregation and mediate the folding of newly translated polypeptides
Phvul.008G013000 AT5G02500 HSC70–1 Heat shock 70 kDa protein 1/8; a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes
Phvul.008G095600 AT3G08970 ATERDJ3A DnaJ domain-containing protein; regulates protein folding in the endoplasmic reticulum (ER) lumen
Phvul.010G024500 AT3G25230 ROF1 Rotamase FKBP 1; co-chaperone that positively modulates thermotolerance by interacting with HSP90 and increasing the HSFA2-mediated accumulation of chaperones of the small-HSPs family
Phvul.009G046500 AT4G27670 HSP21 Heat shock protein 21; protein processing in endoplasmic reticulum
Phvul.011G016100 AT4G25200 HSP23.6 Small heat shock protein 23.6; protein processing in endoplasmic reticulum
Phvul.010G024500 AT3G25230 ROF1 Rotamase FKBP 1; co-chaperone that positively modulates thermotolerance by interacting with HSP90 and increasing the HSFA2-mediated accumulation of chaperones of the small-HSPs family
Phvul.010G155300 AT1G52560 AT1G52560 HSP20-like chaperone; protein processing in endoplasmic reticulum
Phvul.002G095400 AT1G23100 AT1G23100 GroES-like protein; chaperone cofactor-dependent protein refolding
Chloroplast-associated processes Phvul.009G259600 AT2G46830 CCA1 Protein CCA1; transcription factor involved in the circadian clock and in the phytochrome regulation
Phvul.008G022800 AT3G02380 COL2 CONSTANS-like 2; putative transcription factor involved in chloroplast organization
Phvul.001G061400 AT5G24120 SIGE Sigma factor E; essential for blue light-mediated transcription of psbD, which encodes the photosystem II reaction center protein D2
Phvul.010G018200 AT3G17609 HYH HY5-homolog; transcription factor that promotes photomorphogenesis in light
Phvul.007G226300 AT5G03555 NCS1 Nucleobase cation symporter 1; nucleobase-proton symporter that facilitates uracil import into plastids
Phvul.008G254400 AT3G21150 BBX32 B-box 32 protein; repressor of light-mediated regulation of seedling development
Phvul.006G040800 AT4G27030 FADA Fatty acid desaturase A; fatty acid desaturase involved in the production of chloroplast-specific phosphatidylglycerol molecular species
Phvul.005G113200 AT3G21890 BBX31 B-box domain protein 31; involved in the CO-mediated long-day flowering-promotion pathway