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Table 2 Specific salt-responsive transcripts influenced by AtNHX1, organized by functional category

From: Impact of AtNHX1, a vacuolar Na+/H+ antiporter, upon gene expression during short- and long-term salt stress in Arabidopsis thaliana

   P(f)a Treatment influenced by AtNHX1b Transcripts intensity under the influenced treatmentc
Accession Funtional Classes and Gene Descriptions L LxT   nhx1 d wild-type NHX1::nhx1
  A. DNA binding elements       
At3g53730 histone H4   ** Control 2511.1 3461.3 4184.2
At5g67580 myb family transcription factor * * Control 287.4 123.8 149.1
At5g35330 methyl-CpG-binding domain-containing protein *** *** Control 772.7 526.9 508.3
At1g14685 BASIC PENTACYSTEINE 2, BPC2   ** Control 555.1 370.5 390.9
At2g36960 myb family transcription factor   * 12 h 298.0 368.5 476.0
At2g26150 heat shock transcription factor family protein   * 12 h 684.1 98.8 181.5
At3g24500 Transcriptional Coactivator Multiprotein Bridging Factor 1c.   * 12 h 1024.0 261.8 393.4
At1g69010 basic helix-loop-helix (bHLH) family protein ** ** 48 h 422.3 278.1 243.7
At3g56980 basic helix-loop-helix (bHLH) family protein   * 48 h 503.2 304.3 130.8
At4g25490 DRE-binding protein (DREB1B)/CRT/CRE-binding factor 1 (CBF1)   * 48 h 758.3 522.5 569.9
At1g69580 myb family transcription factor ** * 48 h 236.4 141.3 135.7
At3g54810 zinc finger (GATA type) family proteine   ** 1 wk 1168.0 571.7 340.6
At2g31730 putative ethylene-responsive protein   * 1 wk 293.2 147.8 47.1
At1g21910 DREB A-5 subfamily member, ERF/AP2 transcription factor family   * 1 wk 1871.5 771.5 598.6
At3g54810 zinc finger (GATA type) family proteine   ** 2 wk 473.7 967.6 803.4
At4g00850 GRF1-interacting factor 3 (GIF3), SSXT family protein   ** 2 wk 366.7 273.8 86.5
At2g04240 zinc finger (C3HC4-type RING finger) family protein   ** 2 wk 1018.2 539.9 360.6
At5g57660 zinc finger (B-box type) family protein *   All 1108.0 1585.0 1545.2
At4g27410 no apical meristem (NAM) family protein (RD26) *   All 402.0 971.3 870.1
At5g56860 zinc finger (GATA type) family protein ***   All 244.5 157.7 125.6
At1g18710 myb family transcription factor (MYB47) **   All 257.3 460.3 467.0
  B. Signaling Elements       
At4g34150 C2 domain-containing, similar to calcium-dependent protein kinase *** ** 48 h 2199.5 4215.4 4558.0
At4g08960 phosphotyrosyl phosphatase activator (PTPA) family protein ** * 1 wk 542.6 377.1 279.9
At5g54380 protein kinase family protein   ** 1 wk 1866.1 1250.7 826.4
At5g54840 GTP-binding family protein   ** 1 wk 134.1 60.7 57.2
At5g66210 calcium-dependent protein kinase family protein (CPK28)   ** 1 wk 367.5 221.8 213.5
At1g52570 phospholipase D alpha 2 (PLD2)/choline phosphatase 2   * 2 wk 229.2 99.4 74.5
At2g24160 pseudogene, leucine rich repeat protein family   * 2 wk 349.8 160.4 71.7
At2g38750 annexin 4 (ANN4) ***   All 511.2 875.1 804.2
At3g09960 calcineurin-like phosphoesterase family protein *   All 59.2 98.7 104.2
At4g21370 putative S-locus protein kinase, pseudogene *   All 63.0 102.8 110.1
At4g04540 protein kinase family protein///protein kinase family protein **   All 412.6 289.1 220.3
At5g56040 leucine-rich repeat protein kinase, putative **   All 930.9 748.2 617.4
At5g67380 casein kinase II alpha chain 1 ***   All 637.3 496.1 488.6
  C. Metabolism/Energy Components       
At4g11600 putative glutathione peroxidase (AtGPX6) ** * 12 h 3636.1 5433.9 4962.7
At1g68290 bifunctional nuclease, putative *** * 12 h 105.1 236.2 244.6
At3g16050 putative pyridoxine (Vitamin B6) biosynthesis protein   * 12 h 403.6 121.1 227.3
At4g32360 NADP adrenodoxin-like ferredoxin reductase   * 48 h 102.5 172.0 203.7
At2g26560 putative patatin (PLP2) *** ** 48 h 1647.2 3298.0 3515.3
At1g56430 putative nicotianamine synthase   * 48 h 995.2 433.8 601.6
At3g03520 phosphoesterase family protein ** * 48 h 208.4 125.2 122.2
At5g05960 protease inhibitor/seed storage/lipid transfer protein (LTP) family protein   * 48 h 754.4 423.3 436.3
At3g63440 FAD-binding domain-containing protein/cytokinin oxidase family protein   ** 48 h 224.6 132.2 48.8
At4g04955 amidohydrolase family protein   * 1 wk 204.2 296.5 465.4
At1g63710 cytochrome P450, putative   ** 1 wk 126.9 67.9 25.9
At2g17570 undecaprenyl pyrophosphate synthetase family protein   ** 2 wk 112.5 206.2 310.0
At5g19890 putative peroxidase * ** 2 wk 212.8 99.3 79.7
At1g28480 glutaredoxin family protein ***   All 349.1 696.8 1131.5
At2g46650 cytochrome b5, putative **   All 1075.4 1748.2 1638.4
At5g17220 glutathione S-transferase (AtGSTF12, TT19) *   All 270.8 402.7 422.1
At4g39940 adenylylsulfate kinase 2 (AKN2) **   All 1940.2 2675.4 2748.4
At4g04610 5'-adenylylsulfate reductase (APR1)/PAPS reductase homolog (PRH19) *   All 507.7 1362.0 1284.4
At3g22740 homocysteine S-methyltransferase 3 (HMT-3) ***   All 622.8 928.0 1155.4
At1g21440 mutase family protein **   All 2176.8 2737.5 2793.7
At1g06520 phospholipid/glycerol acyltransferase family protein **   All 69.9 120.1 126.8
At1g16410 cytochrome P450 family protein (CYP79F1) (bushy1) ***   All 280.2 480.4 492.0
At2g32150 haloacid dehalogenase-like hydrolase family protein ***   All 357.9 720.0 857.9
At5g47240 MutT/nudix family protein ***   All 961.5 1939.5 1471.4
At2g06050 12-oxophytodienoate reductase (OPR3)/delayed dehiscence1 (DDE1) **   All 804.0 1315.1 1454.0
  D. Structure/Growth Components       
At2g20000 cell division cycle family protein/CDC family protein   * Control 429.7 274.3 260.2
At2g40610 expansin, putative (EXP8) * * 12 hours 792.4 462.8 381.2
At1g27630 cyclin family protein   ** 48 h 519.1 744.7 913.9
At3g02350 glycosyl transferase family 8 protein * * 48 h 1160.2 947.2 609.2
At1g19170 glycoside hydrolase family 28/polygalacturonase (pectinase) family * * 48 h 365.0 220.3 177.9
At3g45970 expansin family protein (EXPL1/AtEXLA1)   * 1 wk 3701.0 1684.2 1026.0
At3g62720 galactosyl transferase GMA12/MNN10 family protein   ** 1 wk 2237.1 1459.9 790.3
At5g57560 cell wall-modifying enzyme, endo-xyloglucan transferase (TCH4)   ** 1 wk 13493.5 6314.8 6047.0
At4g30470 cinnamoyl-CoA reductase-related   * 1 wk 756.6 478.9 512.6
At1g57590 putative pectinacetylesterase * * 2 wk 143.8 381.3 336.7
At1g16340 putative 3-deoxy-D-manno-2-octulosonate-8-phosphate synthase   * 2 wk 352.0 231.3 48.7
At4g16590 glucosyltransferase-related *   All 194.5 578.7 602.4
At1g24070 glycosyl transferase family 2 protein (AtCSLA10) **   All 280.2 509.7 495.6
  E. Protein Processing       
At3g17970 chloroplast outer membrane translocon subunit, putative   * Control 252.5 115.4 162.0
At2g20560 DNAJ heat shock family protein   * 12 h 413.3 159.6 155.0
At1g08780 prefoldin, putative   * 48 h 476.4 303.2 182.0
At2g47440 DNAJ heat shock N-terminal domain-containing protein   ** 1 wk 3769.5 2247.3 1271.8
At1g08730 myosin heavy chain (PCR43) (XIC) *** *** 2 wk 25.4 147.4 204.6
At5g58810 subtilisin-like serine protease, similar to prepro-cucumisin *** ** 2 wk 24.0 148.8 201.3
At5g59730 exocyst subunit EXO70 family protein *   All 768.8 1096.8 1199.6
At3g25150 nuclear transport factor 2 (NTF2) family protein ***   All 693.3 527.6 439.1
At5g64760 26S proteasome regulatory subunit, putative (RPN5) **   All 419.3 340.3 316.2
At1g22740 Ras-related protein (RAB7)/AtRab75/small GTP-binding ***   All 1324.9 892.1 703.5
At2g22040 transducin family protein/WD-40 repeat family protein ***   All 362.1 283.2 231.5
At5g47820 kinesin-like protein (FRA1) **   All 389.3 303.8 259.8
At4g34980 subtilase family protein (SLP2) **   All 1133.4 899.5 930.4
At3g23670 phragmoplast-associated kinesin-related protein, putative **   All 138.2 101.9 75.6
  F. Membrane Transport       
At2g23980 cyclic nucleotide-regulated ion channel (CNGC6) * * Control 393.3 259.6 180.7
At2g47830 cation efflux family/metal tolerance (MTPc1)   ** 48 h 73.9 149.7 166.0
At1g31470 nodulin-related   * 1 wk 223.1 148.5 110.3
At2g25520 phosphate translocator-related **   All 999.7 790.3 773.9
  1. a *, ** and *** indicate significant F values for the plant line effect and line × treatment interaction at the 0.05, 0.01 and 0.001 levels, respectively. An additional 58 salt-responsive AtNHX1 influenced transcripts with unclear functional assignment are not presented and can be found in Additional File 1
  2. b the specific treatment influenced by AtNHX1 for cases of significant interaction, or 'All' for cases where only the plant line effect was significant.
  3. c transcript intensity of the three plant lines for the treatment of interest, with the average expression value of all treatments used when only plant line effect was significant.
  4. d transcript intensity of the nhx1 line is in bold font for cases where the expression level is higher compared to the other lines, normal font signifies reduced expression.
  5. e At3g54810 is represented twice because it showed a significant influence of AtNHX1 at both one week and two weeks of salt treatment, with alternate relative levels of expression of the nhx1 line