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SUPPLEMENTAL TABLES Table S1 Table S1. Genes differentially regulated in yda11 1 day after PcBMM inoculation. AGI ID Fold change1 Gene description AT3G10930 16,607 unknown protein AT1G73260 7,619 ATKTI1, KTI1, kunitz trypsin inhibitor 1 AT5G47230 6,857 ATERF-5, ATERF5, ERF5, ethylene responsive element binding factor 5 AT3G04640 6,748 glycine-rich protein AT1G76650 6,690 CML38, calmodulin-like 38 AT3G19580 6,101 AZF2, ZF2, zinc-finger protein 2 AT3G55980 5,941 ATSZF1, SZF1, salt-inducible zinc finger 1 AT2G41640 5,550 Glycosyltransferase family 61 protein AT1G35210 5,488 unknown protein AT1G68765 5,240 IDA, INFLORESCENCE DEFICIENT IN ABSCISSION AT2G35730 5,004 Heavy metal transport/detoxification superfamily protein AT2G31945 4,675 unknown protein AT3G14470 4,568 NB-ARC domain-containing disease resistance protein AT2G28400 4,536 Protein of unknown function, DUF584 AT5G07010 4,505 ATST2A, ST2A, sulfotransferase 2A AT5G09800 4,327 ARM repeat superfamily protein AT4G34150 4,318 Calcium-dependent lipid-binding (CaLB domain) family protein AT3G04070 4,280 anac047, NAC047, NAC domain containing protein 47 AT5G49680 4,090 KIP, Golgi-body localisation protein domain ;RNA pol II promoter Fmp27 protein domain AT1G51915 4,038 cryptdin protein-related AT2G39380 3,818 ATEXO70H2, EXO70H2, exocyst subunit exo70 family protein H2 AT4G31950 3,810 CYP82C3, cytochrome P450, family 82, subfamily C, polypeptide 3 AT4G24110 3,748 unknown protein AT4G00700 3,684 C2 calcium/lipid-binding plant phosphoribosyltransferase family protein AT2G37980 3,680 O-fucosyltransferase family protein AT5G59550 3,608 zinc finger (C3HC4-type RING finger) family protein AT2G15042 3,476 Leucine-rich repeat (LRR) family protein AT1G22900 3,416 Disease resistance-responsive (dirigent-like protein) family protein AT2G41010 3,336 ATCAMBP25, CAMBP25, calmodulin (CAM)-binding protein of 25 kDa AT3G52450 3,329 PUB22, plant U-box 22 AT5G16080 3,314 AtCXE17, CXE17, carboxyesterase 17 AT1G20310 3,274 unknown protein AT1G47890 3,226 AtRLP7, RLP7, receptor like protein 7 AT1G19610 3,223 LCR78, PDF1.4, Arabidopsis defensin-like protein AT5G59700 3,195 Protein kinase superfamily protein AT1G65610 3,182 ATGH9A2, KOR2, Six-hairpin glycosidases superfamily protein AT4G18170 3,144 ATWRKY28, WRKY28, WRKY DNA-binding protein 28 AT5G01600 3,129 ATFER1, FER1, ferretin 1 AT5G25450 3,115 Cytochrome bd ubiquinol oxidase, 14kDa subunit AT1G02220 3,095 ANAC003, NAC003, NAC domain containing protein 3 AT2G39650 3,068 Protein of unknown function (DUF506) AT1G17170 3,063 ATGSTU24, GST, GSTU24, glutathione S-transferase TAU 24 AT1G68690 3,039 AtPERK9, PERK9, Protein kinase superfamily protein AT5G01560 2,984 LECRKA4.3, lectin receptor kinase a4.3 AT2G25000 2,976 ATWRKY60, WRKY60, WRKY DNA-binding protein 60 AT1G32690 2,967 unknown protein AT5G14760 2,925 AO, L-aspartate oxidase AT5G17330 2,922 GAD, GAD1, glutamate decarboxylase AT2G04430 2,920 atnudt5, NUDT5, nudix hydrolase homolog 5 AT5G62180 2,895 AtCXE20, CXE20, carboxyesterase 20 AT4G37010 2,890 CEN2, centrin 2 AT1G14730 2,869 Cytochrome b561/ferric reductase transmembrane protein family AT5G46780 2,856 VQ motif-containing protein AT3G21780 2,847 UGT71B6, UDP-glucosyl transferase 71B6 AT5G25910 2,823 AtRLP52, RLP52, receptor like protein 52 AT3G13380 2,811 BRL3, BRI1-like 3 AT3G53150 2,804 UGT73D1, UDP-glucosyl transferase 73D1 AT2G48010 2,788 RKF3, receptor-like kinase in in flowers 3 AT4G02410 2,784 Concanavalin A-like lectin protein kinase family protein AT3G46930 2,765 Protein kinase superfamily protein AT5G64660 2,741 ATCMPG2, CMPG2, CYS, MET, PRO, and GLY protein 2 AT3G25250 2,729 AGC2, AGC2 KINASE 1, AGC2-1, ATOXI1, OXI1, OXIDATIVE SIGNAL-INDUCIBLE AT1G61610 2,722 S-locus lectin protein kinase family protein AT1G02430 2,713 ARFD1B, ATARFD1B, ADP-ribosylation factor D1B ARFD1A, ATARFD1A, ADP-ribosylation factor D1A AT2G36780 2,709 UDP-Glycosyltransferase superfamily protein UDP-Glycosyltransferase superfamily protein AT5G45110 2,674 ATNPR3, NPR3, NPR1-like protein 3 AT2G16720 2,657 ATMYB7, ATY49, MYB7, myb domain protein 7 AT4G30230 2,657 unknown protein AT2G16500 2,657 ADC1, ARGDC, ARGDC1, SPE1, arginine decarboxylase 1 AT5G16230 2,648 Plant stearoyl-acyl-carrier-protein desaturase family protein AT1G51860 2,640 Leucine-rich repeat protein kinase family protein AT4G30640 2,610 Leucine-rich repeat protein kinase family protein AT1G15890 2,598 Disease resistance protein (CC-NBS-LRR class) family 2 Table S1 AGI ID Fold change1 Gene description AT3G15760 2,577 unknown protein AT4G13410 2,570 ATCSLA15, CSLA15, Nucleotide-diphospho-sugar transferases superfamily protein AT5G25820 2,546 Exostosin family protein AT5G22540 2,532 Plant protein of unknown function (DUF247) AT5G59450 2,519 GRAS family transcription factor AT4G32870 2,518 Polyketide cyclase/dehydrase and lipid transport superfamily protein AT1G29280 2,508 ATWRKY65, WRKY65, WRKY DNA-binding protein 65 AT1G58420 2,487 Uncharacterised conserved protein UCP031279 AT4G35380 2,482 SEC7-like guanine nucleotide exchange family protein AT3G22620 2,481 Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin superfamily protein AT1G14780 2,461 MAC/Perforin domain-containing protein AT1G32640 2,453 ATMYC2, JAI1, JIN1, MYC2, RD22BP1, ZBF1, Basic helix-loop-helix (bHLH) DNA-binding family protein AT5G66890 2,446 Leucine-rich repeat (LRR) family protein AT5G11650 2,445 alpha/beta-Hydrolases superfamily protein AT3G18560 2,438 unknown protein AT3G54950 2,437 PLA IIIA, PLP7, pPLAIIIbeta, patatin-like protein 6 AT3G50760 2,430 GATL2, galacturonosyltransferase-like 2 AT1G58340 2,419 BCD1, ZF14, ZRZ, MATE efflux family protein AT3G18690 2,409 MKS1, MAP kinase substrate 1 AT3G26230 2,390 CYP71B24, cytochrome P450, family 71, subfamily B, polypeptide 24 AT1G07160 2,386 Protein phosphatase 2C family protein AT2G29110 2,367 ATGLR2.8, GLR2.8, GLR2.8, glutamate receptor 2.8 AT3G45640 2,351 ATMAPK3, ATMPK3, MPK3, mitogen-activated protein kinase 3 AT3G62260 2,347 Protein phosphatase 2C family protein AT5G58730 2,343 pfkB-like carbohydrate kinase family protein AT4G17670 2,339 Protein of unknown function (DUF581) AT3G26470 2,317 Powdery mildew resistance protein, RPW8 domain AT3G29575 2,282 AFP3, ABI five binding protein 3 AT5G41860 2,278 unknown protein AT4G33920 2,269 Protein phosphatase 2C family protein AT2G42350 2,252 RING/U-box superfamily protein AT2G03760 2,240 AtSOT1, AtSOT12, ATST1, RAR047, SOT12, ST, ST1, sulphotransferase 12 AT3G49210 2,232 O-acyltransferase (WSD1-like) family protein AT4G04960 2,225 Concanavalin A-like lectin protein kinase family protein AT2G41730 2,206 unknown protein AT5G47960 2,191 ATRABA4C, RABA4C, SMG1, RAB GTPase homolog A4C AT2G39350 2,187 ABCG1, ABC-2 type transporter family protein AT1G67470 2,179 Protein kinase superfamily protein AT3G45330 2,174 Concanavalin A-like lectin protein kinase family protein AT2G34960 2,172 CAT5, cationic amino acid transporter 5 AT5G15850 2,167 ATCOL1, COL1, CONSTANS-like 1 AT2G45290 2,166 Transketolase AT3G11580 2,140 AP2/B3-like transcriptional factor family protein AT4G35600 2,138 CST, CX32, Kin4, Protein kinase superfamily protein AT5G55120 2,132 VITAMIN C DEFECTIVE 5, VTC5 AT1G50360 2,128 ATVIIIA, VIIIA, P-loop containing nucleoside triphosphate hydrolases superfamily protein AT2G22860 2,124 ATPSK2, PSK2, phytosulfokine 2 precursor AT5G25770 2,123 alpha/beta-Hydrolases superfamily protein AT5G14930 2,122 SAG101, senescence-associated gene 101 AT5G61250 2,122 AtGUS1, GUS1, glucuronidase 1 AT1G17600 2,117 Disease resistance protein (TIR-NBS-LRR class) family AT4G26090 2,099 RPS2, NB-ARC domain-containing disease resistance protein AT3G57480 2,088 zinc finger (C2H2 type, AN1-like) family protein AT3G52190 2,079 AtPHF1, PHF1, phosphate transporter traffic facilitator1 AT1G33420 2,072 RING/FYVE/PHD zinc finger superfamily protein AT1G29050 2,067 TBL38, TRICHOME BIREFRINGENCE-LIKE 38 AT2G47180 2,065 AtGolS1, GolS1, galactinol synthase 1 AT2G28755 2,049 UDP-D-glucuronate carboxy-lyase-related AT1G18590 2,048 ATSOT17, ATST5C, SOT17, sulfotransferase 17 AT1G24180 2,033 IAR4, Thiamin diphosphate-binding fold (THDP-binding) superfamily protein AT1G66620 2,018 Protein with RING/U-box and TRAF-like domains AT2G43320 2,010 S-adenosyl-L-methionine-dependent methyltransferases superfamily protein AT3G05630 2,010 PDLZ2, PLDP2, PLDZETA2, phospholipase D P2 AT5G60460 2,004 Preprotein translocase Sec, Sec61-beta subunit protein AT5G62570 2,003 Calmodulin binding protein-like AT1G62840 1,996 Protein of unknown function (DUF1442) AT3G54620 1,994 ATBZIP25, BZIP25, BZO2H4, basic leucine zipper 25 AT2G23620 1,988 ATMES1, MES1, methyl esterase 1 AT1G53030 1,981 Cytochrome C oxidase copper chaperone (COX17) AT3G10640 1,977 VPS60.1, SNF7 family protein AT5G54780 1,963 Ypt/Rab-GAP domain of gyp1p superfamily protein AT2G04160 1,953 AIR3, Subtilisin-like serine endopeptidase family protein AT5G37740 1,946 Calcium-dependent lipid-binding (CaLB domain) family protein AT4G00240 1,939 PLDBETA2, phospholipase D beta 2 AT1G54100 1,926 ALDH7B4, aldehyde dehydrogenase 7B4 AT4G23100 1,925 ATECS1, CAD2, GSH1, GSHA, PAD2, RML1, glutamate-cysteine ligase AT3G04670 1,925 ATWRKY39, WRKY39, WRKY DNA-binding protein 39 3 Table S1 AGI ID Fold change1 Gene description AT3G11040 1,910 AtENGase85B, ENGase85B, Glycosyl hydrolase family 85 AT1G76470 1,896 NAD(P)-binding Rossmann-fold superfamily protein AT5G02290 1,886 NAK, Protein kinase superfamily protein AT5G29000 1,882 PHL1, Homeodomain-like superfamily protein AT5G04860 1,881 unknown protein AT1G62422 1,879 unknown
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  • Dependent Enzymes. a Hypothesis Philipp Christen*, Patrik Kasper, Heinz Gehring, Michael Sterk Bioehemisches Institut, Universitgit Ziirich, Winterthurerstr

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    FEBS Letters 389 (1996) 12-14 FEBS 16909 Minireview Stereochemical constraint in the evolution of pyridoxal-5'-phosphate- dependent enzymes. A hypothesis Philipp Christen*, Patrik Kasper, Heinz Gehring, Michael Sterk Bioehemisches Institut, Universitgit Ziirich, Winterthurerstr. 190, CH-8057 Ziirieh, Switzerland Received 11 January 1996 cular evolution of B6 enzymes. Alanine aminotransferase, as- Abstract In the transamination reactions undergone by pyri- doxal-5'-phosphate-dependent enzymes that act on L-amino partate aminotransferase, 2,2-dialkylglycine decarboxylase, acids, the C4' atom of the cofactor is without exception glutamate decarboxylase, and serine hydroxymethyltransfer- protonated from the si side. This invariant absolute stereo- ase indeed belong to the large c~ family of homologous B6 chemistry of enzymes not all of which are evolutionarily related enzymes [1-3]. However, the pyridoxal-5'-phosphate-depen- to each other and the inverse stereochemistry in the case of D- dent 13 subunit of tryptophan synthase which shows the alanine aminotransferase might reflect a stereochemical con- same stereochemistry is a member of the [3 family of B6 en- straint in the evolution of these enzymes rather than an zymes which is not homologous with the e~ family [1,4]. accidental historical trait passed on from a common ancestor (About the seventh enzyme, pyridoxamine pyruvate amino- enzyme. Conceivably, the coenzyme and substrate binding sites transferase, no information on primary or tertiary structure of primordial pyridoxal-5'-phosphate-dependent
  • (12) Patent Application Publication (10) Pub. No.: US 2016/0115499 A1 CUI Et Al

    (12) Patent Application Publication (10) Pub. No.: US 2016/0115499 A1 CUI Et Al

    US 2016O115499A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2016/0115499 A1 CUI et al. (43) Pub. Date: Apr. 28, 2016 (54) MATERALS AND METHODS FOR Publication Classification CONTROLLING BUNDLE SHEATH CELL FATE AND FUNCTION IN PLANTS (51) Int. Cl. CI2N 5/82 (2006.01) (71) Applicant: FLORIDA STATE UNIVERSITY (52) U.S. Cl. RESEARCH FOUNDATION, INC., CPC ........ CI2N 15/8269 (2013.01); C12N 15/8225 Tallahassee, FL (US) (2013.01) (57) ABSTRACT (72) Inventors: HONGCHANG CUI, TALLAHASSEE, The Subject invention concerns materials and methods for FL (US); DANYUKONG, increasing and/or improving photosynthetic efficiency in BLACKSBURG, VA (US); YUELING plants, and in particular, C3 plants. In particular, the Subject HAO, TALLAHASSEE, FL (US) invention provides for means to increase the number of bundle sheath (BS) cells in plants, to improve the efficiency of (21) Appl. No.: 14/898,046 photosynthesis in BS cells, and to increase channels between BS and mesophyll (M) cells. In one embodiment, a method of (22) PCT Fled: Jun. 11, 2014 the invention concerns altering the expression level or pattern of one or more of SHR, SCR, and/or SCL23 in a plant. The (86) PCT NO.: PCT/US2014/041975 Subject invention also pertains to genetically modified plants, S371 (c)(1), and in particular, C3 plants, that exhibit increased expression (2) Date: Dec. 11, 2015 of one or more of SHR, SCR, and/or SCL23. Transformed and transgenic plants are contemplated within the scope of the invention. The Subject invention also concerns methods for increasing expression of photosynthetically important Related U.S.
  • The 58-Kilodalton Calmodulin-Binding Glutamate Decarboxylase Is a Ubiquitous Protein in Petunia Organs and Its Expression Is Developmentally Regulated'

    The 58-Kilodalton Calmodulin-Binding Glutamate Decarboxylase Is a Ubiquitous Protein in Petunia Organs and Its Expression Is Developmentally Regulated'

    Plant Physiol. (1994) 106: 1381-1387 The 58-Kilodalton Calmodulin-Binding Glutamate Decarboxylase Is a Ubiquitous Protein in Petunia Organs and Its Expression Is Developmentally Regulated' Yali Chen, Gideon Baum, and Hillel Fro"* Department of Plant Genetics, Weizmann Institute of Science, 761O0 Rehovot, Israel et al., 1984); heat shock (Mayer et al., 1990); and water stress A cDNA coding for a 58-kD calcium-dependent calmodulin (Rhodes et al., 1986), which is consistent with this role. (CaM)-binding glutamate decarboxylase (GAD) previously isolated Moreover, GAD activity is enhanced at relatively acidic pH in our laboratory from petunia (Petunia hybrida) (G. Baum, Y. (Snedden et al., 1992; Crawford et al., 1994). It was also Chen, T. Arazi, H. Takatsuji, H. Fromm [1993] J Biol Chem 268: suggested that transamination of a-ketoglutarate by GABA 19610-19617) was used to conduct molecular studies of GAD (producing succinic semialdehyde and glutamate) could reg- expression. GAD expression was studied during petunia organ ulate carbon flow through the tricarboxylic acid cycle by development using the GAD cDNA as a probe to detect the GAD mRNA and by the anti-recombinant GAD serum to monitor the bypassing the direct conversion of a-ketoglutarate to succi- levels of GAD. GAD activity was studied in extracts of organs in nate, a step that may be inhibited under certain physiological the course of development. lhe 58-kD CaM-binding GAD is ex- situations (Dixon and Fowden, 1961). In addition, GABA can pressed in all petunia organs tested (flowers and all floral parts, be transaminated even more effectively with pyruvate to leaves, stems, roots, and seeds).