Table 3.

Expression Levels of Selected S-Regulated Genes

Fold Change Expression (Log2)
Wild Type −S/Wild Type +Ssnrk2.1/Wild Type (+S)snrk2.1/Wild Type (−S)Transcript Abundance (RPKM)a
IDName/DescriptionSQSQSQWild Type −SWild Type +Ssnrk2.1 −Ssnrk2.1 +S
Sulfur acquisition and assimilation
    205496ARS1, arylsulfatase (ext)10.59.5−1.2−0.5−16.1−12.02717201
    55757ARS2, arylsulfatase (ext)8.212.21.0−2.9−11.1−15.184001
    205502SLT1, Na+/SO42− transporter type (p)6.97.9−6.3−7.3−15.0−20.423412000
    205501SLT2, Na+/SO42− transporter type (p)6.39.3−2.5−1.0−9.8−10.313391713
    150514SULTR2, H+/SO42− transporter type (p)5.37.7−4.5−3.9−6.4−7.5152420
    196910ATS1, ATP sulfurylase1.61.6−1.2−1.3−3.0−2.92137723275305
    133924ATS2, ATP sulfurylase (chl)2.83.60.00.0−4.4−3.6254361237
    128906SULP1, chl. SO42− transport system2.4−0.6−3.4147281418
    116547SULP2, chl. SO42− transport system1.5−0.7−2.256201212
    182359SBP1, chl. SO42− transport system1.5−1.1−2.779281213
    194724SABC (CysA), chl. SO42− transport system2.4−0.3−2.820433
    184419APK, APS kinase (chl.)0.41.30.5−0.7−1.7−1.639291241
    131444APR (MET16), APS sulforeductase (chl.)0.51.4−0.90.8−2.3−0.628519757105
    206154SIR1, ferredoxin-sulfite reductase (chl.)2.0−1.1−2.3124312614
    205485SIR2, ferredoxin-sulfite reductase2.2−0.7−2.259712613280
    189320OASTL4a, O-acetylserine(thiol)-lyase (chl.)2.95.6−0.3−0.3−5.0−6.697612831103
    205985SAT1a, serineacetyl transferase (chl.)5.14.2−0.70.1−4.3−4.3794234014
    24268CGS1 (METB), cystathionine g-synthase (chl.)–1.6−0.61.423716349
    127384THS1, Thr synthase (chl.)−1.4−0.7−0.3541384284
    196483METC, cystathionine b-lyase (chl.)−0.5−0.51.324345724
    154307METE, Met synthase−0.60.24660654395
    76715METH1, Met synthase (cobalamin)−0.9−0.2331342972
    195332METH2, Met synthase (cobalamin)−0.81.13021165123
    182408METM, S-adenosylmethionine synthetase−0.2−0.352622884201976
    129593SAH1, S-adenosylhomocysteine hydrolase−0.4−0.9152129883952
    183928DCA1, S-adenosylmethionine decarboxylase−0.31.554184149146
    206104AOT2, a.a/polyamine transporter (p)4.13.6−5.5−2.4−9.8−6.336200
    206105AOT4, a.a/polyamine transporter (p)3.94.0−8.0−8.8−13.0−13.13112100
    185190THI4a, thiazole biosynthetic enzyme−0.1−2.82031859291682
    196899THI4b, THI4 regulatory protein−0.1−2.81881715271557
    192720THICa, hydroxymethylpyrimidine phosphate synthase−0.4−3.3695174
    196900THICb, hydroxymethylpyrimidine phosphate synthase−0.4−3.4692172
    142289BIOB1, biotin synthase1.1−0.5210123
    97943BIOB2, biotin synthase−0.1−1.62386877
    181975GSH1, γ-glutamylcysteine synthetase (chl.)0.10.00.135333834
    189020GSH2, glutathione synthetase (chl.)−0.3−0.3−1.42025820
    170508GTP1, γ-glutamyl transpeptidase0.20.70.725234137
Redistribution and recycling of S
    143892CDO1, Cys dioxygenase4.74.5−1.4−4.0−7.3−8.4138512
    127464TAUD1, taurin dioxigenase7.15.6−3.5−5.3−11.7−12.514171001
    77600TAUD2, taurin dioxigenase5.26.6−0.40.9−5.1−6.4632171913
    59800SUOX1, sulfite oxidase, mit.2.0−0.2−1.8149364231
    183511RDP3, small rodhanase4.14.4−0.8−2.7−4.0−6.6369212412
    132010TST, mercaptopyruvate sulfurtransferase0.20.4−1.52219826
    167884CSD2 (NIFS2), Cys desulfurase1.6−0.2−2.043141012
    98369d-Cys desulfhydrase2.20.2−2.537879
Lipid metabolism
    144554Esterase/lipase/thioesterase3.1−0.5−1.6657215
    27658SQD1, UDP-sulfoquinovose synthase1.7−0.9−4.13361021957
    206163SQD2, sulfolipid synthase1.5−0.3−5.15319216
    196477LPB1, low phosphate bleaching4.14.2−1.6−0.7−5.5−5.81711983933
Photosynthesis
    Stress-related genes
        148916ELIP3, chlorophyll a/b binding protein2.90.00.2456506
        184724LHCSR1, light-harvesting stress-related protein (chl.)1.82.20.61.2−1.3−2.1631181255277
        184731LHCSR2, light-harvesting stress-related protein (chl.)2.24.61.45.90.52.026258366158
        184730LHCSR3, light-harvesting stress-related protein (chl.)2.45.51.27.00.13.0680133743312
    Major light-harvesting proteins of PSII
        185533LHCBM1 (chl.)2.90.00.0426426
        184067LHCBM2 (chl.)1.82.20.61.2−1.6−2.1596174202257
        195162LHCBM3 (chl.)2.14.61.45.90.42.024456315148
        191690LHCBM4 (chl.)2.35.51.17.0−0.13.0611128564275
        184775LHCBM5 (chl.)−0.60.2−1.15425801925849327
        184490LHCBM6 (chl.)−0.20.2−0.62705318817403774
        184071LHCBM7 (chl.)–1.70.5−0.267622626063112
        205752LHCBM8 (chl.)−0.30.3−2.27479511631160
        184479LHCBM9 (chl.)−1.40.6−2.65641485952292
Carbon metabolism
    196354SHMT2, Ser hydroxymethyltransferase 2–3.0−0.40.53125443196
    1015286-Phosphogluconolactonase-like protein2.0−0.2−1.340110016085
    163301GLD2-C, glucose-6-phosphate dehydrogenase2.3−0.3−2.177161813
    192597GND1a, 6-phosphogluconate dehydrogenase (decarboxylating) (chl.)1.9−0.2−1.63088310174
    158911GND1b, 6-phosphogluconate dehydrogenase (decarboxylating) (cyt.)1.9−0.2−1.63138610274
    163238RIBA, bifunctional GTP cyclohydrolase II/3,4-dihydroxy-2butanone-4-phosphate synthase1.7−0.7−2.483261516
    196834CAH9, carbonic anhydrase (cyt?)5.0−1.1−6.81952621828
    Folate metabolism
        206121MTDH/MTCH2, methylenetetrahydrofolate dehydrogenase/methylenetetrahydrofolate cyclohydrolase−1.6−0.2−1.51340535
        127560FTHFS, 10-formyltetrahydrofolate synthetase–2.50.3−1.81059371
        30522ADCL1, aminotransferase related to 4-amino-4-deoxychorismate lyase−1.7−0.20.223732665
        111330MTHFR, 5,10-methylenetetrahydrofolate reductase–3.1−0.10.111921286
        182461GGH1, γ-glutamyl hydrolase3.9−0.6−6.236202
Extracellular/cell wall proteins
    168785HAP1, vanadium haloperoxidase7.97.8−0.2-2.0−8.4−11.7739323
    143696HAP2, vanadium haloperoxidase8.47.1−0.1−0.6−11.6−11.51044303
    182794HAP3, vanadium haloperoxidase7.16.5−3.2−1.0−11.1−7.214561011
    130684ECP76, extracellular protein10.710.3−0.8−0.4−13.1−11.8899100
    137329ECP88, extracellular protein13.4−2.3−15.92295000
    119420ECP61, extracellular protein8.5−0.6−11.0268100
    194201ECP56, extracellular protein8.6−4.2−13.0317100
  • Fold change (log2 values) in transcript levels under specified conditions as determined by RNA-seq (S) and, when available, by qRT-PCR (Q). Values above 1.5 or below −1.5 are marked in bold type. Some genes for which expression is not affected by −S conditions are included for informative purposes. Putative subcellular localizations are denoted in parentheses after the transcript names as cyt, cytosolic; mit, mitochondria; chl, chloroplast; and ext, extracellular. ID, JGI protein accession number; p, putative; nd, not enough high-quality data for statistical tests.

  • a Transcript abundance obtained from RNA-seq data is indicated as RPKMs (see Methods).