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Table 3 The 35 tomato plant DEGs associated with molecular signaling. DEGs were sorted by log2-fold change (log2FC). These DEGs were identified in the transcriptome analysis comparing psyllid-infested and uninfested tomato plants 3 weeks after infestation (P < 0.01). NCBI Blast searches were used to identify Gene IDs and protein products in tomatoes as well as their homologs in other species. Specifically, the expression changes in 28 genes (85%, in bold) would have resulted in improvements to molecular signaling pathways. These DEGs were related to protein phosphorylation and mobilization to the vacuole

From: Lasting consequences of psyllid (Bactericera cockerelli L.) infestation on tomato defense, gene expression, and growth

Tomato gene ID

Gene ID

Homolog

Log2FC

Protein name

Uniprot description

Effect of psyllid infestation

Citation

Solyc08g083360.2

PNSB3

AT3G16250

-1.23

photosynthetic NDH subunit of subcomplex B 3, chloroplastic

NDH shuttles electrons from NAD(P)H:plastoquinone to quinones in the photosynthetic chain; Couples the redox reaction to proton translocation

Decreased photosynthetic electron transport

Qian, Haifeng, et al. "PGR5 and NDH pathways in photosynthetic cyclic electron transfer respond differently to sublethal treatment with photosystem-interfering herbicides." Journal of agricultural and food chemistry 62.18 (2014): 4083-4089.

Solyc01g087690.1

SIGD

AT5G13730

-1.06

RNA polymerase sigma factor sigD, chloroplastic

Promotes the attachment of plastid-encoded RNA polymerase; Regulates transcription of the ndhF gene

Decreased response to light stimulus; Decreased transcription; Decreased regulation of RNA biosynthesis

Lerbs-Mache, Silva. "Function of plastid sigma factors in higher plants: regulation of gene expression or just preservation of constitutive transcription?." Plant molecular biology 76.3-5 (2011): 235-249.

Solyc02g085950.2

RBCS3B

AT5G38410

-1.03

Ribulose bisphosphate carboxylase small chain

RuBisCO catalyzes two reactions: the carboxylation of D-ribulose 1,5-bisphosphate as well as the oxidative fragmentation of the pentose substrate; Both reactions occur simultaneously and in competition at the same active site

Decarbon fixation; Decreased chloroplast ribulose bisphosphate carboxylase complex assembly; Decreased photorespiration and photosynthesis; Decreaesed response to blue and red light

Menges, Margit, et al. "Cell cycle-regulated gene expression inArabidopsis." Journal of Biological Chemistry 277.44 (2002): 41987-42002.

Solyc12g036170.1

PNSB4

AT1G18730

-1.03

photosynthetic NDH subunit of subcomplex B 4, chloroplastic

NDH shuttles electrons from NAD(P)H:plastoquinone to quinones in the photosynthetic chain; Couples the redox reaction to proton translocation

Decreased photosynthetic electron transport

Qian, Haifeng, et al. "PGR5 and NDH pathways in photosynthetic cyclic electron transfer respond differently to sublethal treatment with photosystem-interfering herbicides." Journal of agricultural and food chemistry 62.18 (2014): 4083-4089.

Solyc11g006020.1

ndhO

AT1G74880

-0.93

NAD(P)H-quinone oxidoreductase subunit O, chloroplastic

NDH shuttles electrons from NAD(P)H:plastoquinone to quinones in the photosynthetic chain; Couples the redox reaction to proton translocation

Decreased NADH dehydrogenase complex assembly; Decreased photosynthesis

Ishikawa, Noriko, Tsuyoshi Endo, and Fumihiko Sato. "Electron transport activities of Arabidopsis thaliana mutants with impaired chloroplastic NAD (P) H dehydrogenase." Journal of plant research 121.5 (2008): 521-526.

Solyc02g066920.2

CRR7

AT5G39210

-0.84

protein CHLORORESPIRATORY REDUCTION 7, chloroplastic

Required for both formation and activity of the chloroplast NAD(P)H dehydrogenase complex of the photosynthetic electron transport chain; Required for the accumulation of NDH subcomplex A; Involved in post-translational steps during the biogenesis of subcomplex A

Decreased NAD(P)H dehydrogenase complex assembly

Kamruzzaman Munshi, M., Yoshichika Kobayashi, and Toshiharu Shikanai. "Identification of a novel protein, CRR7, required for the stabilization of the chloroplast NAD (P) H dehydrogenase complex in Arabidopsis." The Plant Journal 44.6 (2005): 1036-1044.

Solyc04g082930.1

LHCB7

AT1G76570

-0.82

chlorophyll a-b binding protein 7, chloroplastic

Captures and delivers excitation energy; Functions in non-photochemical quenching to dissipate energy; Contributes to primary photochemistry

Decreased photosynthesis and light harvesting in photosystem I; Impaired protein-chromophore linkage; Decreased response to blue and far-red light

Peterson, Richard B., and Neil P. Schultes. "Light-harvesting complex B7 shifts the irradiance response of photosynthetic light-harvesting regulation in leaves of Arabidopsis thaliana." Journal of plant physiology 171.3-4 (2014): 311-318.

Solyc10g077040.1

CRD1

AT3G56940

-0.80

magnesium-protoporphyrin monomethyl ester cyclase

Catalyzes the formation of the isocyclic ring in chlorophyll biosynthesis; Mediates the cyclase reaction

Decreased chlorophyll biosynthesis; Decreased chloroplast organization; Decreased photosynthesis; Decreased regulation of tetrapyrrole metabolic process

Tottey, Stephen, et al. "Arabidopsis CHL27, located in both envelope and thylakoid membranes, is required for the synthesis of protochlorophyllide." Proceedings of the National Academy of Sciences 100.26 (2003): 16119-16124.

Solyc06g048410.2

FSD1

AT4G25100

-0.79

iron superoxide dismutase [Fe] 1, chloroplastic

Breaks down superoxide anion radicals

Decreased response to cadmium stress; Decreased response to copper ion; Decreased response to light intensity; Decreased response to oxidative stress and ozone

Kuo, W. Y., et al. "CHAPERONIN 20 mediates iron superoxide dismutase (Fe SOD) activity independent of its co-chaperonin role in Arabidopsis chloroplasts." New Phytologist 197.1 (2013): 99-110.

Solyc02g080540.1

ATPC1

AT4G04640

-0.74

ATP synthase gamma chain, chloroplastic

Produces ATP from ADP in the presence of a proton gradient across the membrane

Decreased ATP biosynthesis; Decreased ATP synthesis coupled proton transport; Decreased photosynthetic electron transport in photosystem II

Dal Bosco, Cristina, et al. "Inactivation of the chloroplast ATP synthase γ subunit results in high non-photochemical fluorescence quenching and altered nuclear gene expression in Arabidopsis thaliana." Journal of Biological Chemistry 279.2 (2004): 1060-1069.

Solyc03g097320.2

SIGA

AT1G64860

-0.72

RNA polymerase sigma factor sigA

Essential protein; Controls the transcription of the psaA gene and thus modulates photosystem stoichiometry; Maintains a harmonious electron flow and photosynthetic efficiency

Decreased response to light stimulus; Decreased cellular response to redox state; Decreased DNA-templated transcription; Impaired photosystem stoichiometry adjustment; Decreased regulation of RNA biosynthesis

Hakimi, Mohamed-Ali, et al. "Evolutionary conservation of C-terminal domains of primary sigma70-type transcription factors between plants and bacteria." Journal of Biological Chemistry 275.13 (2000): 9215-9221.

Solyc07g032640.1

PSBO1

AT5G66570

-0.66

oxygen-evolving enhancer protein 1-1, chloroplastic

Stabilizes the manganese cluster which is the primary site of water splitting

Decreased defense response to bacteria; Decreased photoinhibition; Decreased photosynthesis; Decreased photosystem II assembly and stabilization; Decreased regulation of protein dephosphorylation

Murakami, Reiko, et al. "Characterization of an Arabidopsis thaliana mutant with impaired psbO, one of two genes encoding extrinsic 33-kDa proteins in photosystem II." FEBS letters 523.1-3 (2002): 138-142.

Solyc03g120430.2

GLYK

AT1G80380

-0.66

D-glycerate 3-kinase, chloroplastic

Indispensable ancillary metabolic pathway to the photosynthetic C3 cycle that enables land plants to grow in an oxygen-containing atmosphere

Impaired oxidative photosynthetic carbon pathway; Decreased photorespiration

Boldt, Ralf, et al. "D-GLYCERATE 3-KINASE, the last unknown enzyme in the photorespiratory cycle in Arabidopsis, belongs to a novel kinase family." The Plant Cell 17.8 (2005): 2413-2420.

Solyc08g080050.2

PGRL1A

AT4G22890

-0.64

PGR5 protein 1A, chloroplastic

Ferredoxin-plastoquinone reductase involved in cyclic electron flow around photosystem I

Decreased photosynthesis; Decreased photosynthetic electron transport in photosystem I

DalCorso, Giovanni, et al. "A complex containing PGRL1 and PGR5 is involved in the switch between linear and cyclic electron flow in Arabidopsis." Cell 132.2 (2008): 273-285.

Solyc10g007690.2

LHCA3

AT1G61520

-0.62

Photosystem I chlorophyll a/b-binding protein 3-1, chloroplastic

The light-harvesting complex functions as a light receptor; Captures and delivers excitation energy to photosystems with which it is closely associated

Decreased photosynthesis; Impaired protein-chromophore linkage; Decreased response to cold and light stress

Ganeteg, Ulrika, et al. "The properties of the chlorophyll a/b-binding proteins Lhca2 and Lhca3 studied in vivo using antisense inhibition." Plant physiology 127.1 (2001): 150-158.

Solyc01g005520.2

MET1

AT1G55480

-0.62

protein MET1, chloroplastic

Involved in photosystem II supercomplex formation and repair

Decreased photosynthesis

Ishikawa, Atsushi, et al. "Molecular characterization of the ZKT gene encoding a protein with PDZ, K-Box, and TPR motifs in Arabidopsis." Bioscience, biotechnology, and biochemistry 69.5 (2005): 972-978.

Solyc04g064670.2

PPD4

AT1G77090

-0.62

psbP domain-containing protein 4, chloroplastic

Involved in photosynthesis

Decreased photosynthesis

Dal Bosco, Cristina, et al. "Inactivation of the chloroplast ATP synthase γ subunit results in high non-photochemical fluorescence quenching and altered nuclear gene expression in Arabidopsis thaliana." Journal of Biological Chemistry 279.2 (2004): 1060-1069.

Solyc05g026550.2

ndhL

AT1G70760

-0.60

NAD(P)H-quinone oxidoreductase subunit L, chloroplastic

NDH shuttles electrons from NAD(P)H:plastoquinone to quinones in the photosynthetic chain; Couples the redox reaction to proton translocation

Decreased NADH dehydrogenase complex (plastoquinone) assembly; Decreased photosynthetic electron transport in photosystem I

Thieme, Christoph J., et al. "Endogenous Arabidopsis messenger RNAs transported to distant tissues." Nature Plants 1.4 (2015): 15025.

Solyc11g008620.1

PGLP1B

AT5G36790

-0.56

phosphoglycolate phosphatase 1B, chloroplastic

Photorespiratory enzyme that dephosphorylates the 2-phosphoglycolate produced by the RuBisCO oxygenation reaction

Decreased dephosphorylation; Decreased photorespiration

Reiland, Sonja, et al. "Large-scale Arabidopsis phosphoproteome profiling reveals novel chloroplast kinase substrates and phosphorylation networks." Plant physiology 150.2 (2009): 889-903.

Solyc04g057980.2

ndhH

ATCG01110

-0.56

NAD(P)H-quinone oxidoreductase subunit H, chloroplastic

NDH shuttles electrons from NAD(P)H:plastoquinone to quinones in the photosynthetic chain; Couples the redox reaction to proton translocation

Decreased photosynthesis; Decreased reaction to light

Lerbs-Mache, Silva. "Function of plastid sigma factors in higher plants: regulation of gene expression or just preservation of constitutive transcription?." Plant molecular biology 76.3-5 (2011): 235-249.

Solyc02g091560.2

SHM1

AT4G37930

-0.53

serine hydroxymethyltransferase 1, mitochondrial

Catalyzes interconversion of serine and glycine in the photorespiratory pathway; Involved in controlling cell damage caused by abiotic stress; Regulates the hypersensitive defense response

Decreased response to tetrahydrofolate; Decreased L-serine metabolism; Decreased one-carbon metabolism; Decreased photorespiration; Decreased hypersensitive response; Decreased response to cadmium, cold, heat, and light stress

Moreno, Juan Ignacio, et al. "Arabidopsis SHMT1, a serine hydroxymethyltransferase that functions in the photorespiratory pathway influences resistance to biotic and abiotic stress." The Plant Journal 41.3 (2005): 451-463.

Solyc05g052600.2

N/a

AT3G55800

-0.50

sedoheptulose-1,7-bisphosphatase, chloroplastic

Involved in fructose 1,6-biphosphate metabolism

Decreased defense response to bacteria; Decreased gluconeogenesis; Impaired reductive pentose-phosphate cycle; Decreased photosynthesis

Kiddle, Guy, et al. "Effects of leaf ascorbate content on defense and photosynthesis gene expression in Arabidopsis thaliana." Antioxidants and Redox Signaling 5.1 (2003): 23-32.

Solyc01g107660.2

SEP1

AT4G34190

-0.47

stress enhanced protein 1 protein

Involved in non-photochemical quenching; Plays a role in the thylakoid membrane in response to light stress

Decreased response to high light intensity; Decreased photosynthesis; Decreased response to wounding

Maejima, Kensaku, et al. "Degradation of class E MADS-domain transcription factors in Arabidopsis by a phytoplasmal effector, phyllogen." Plant signaling & behavior 10.8 (2015): e1042635.

Solyc10g080080.1

NTRC

AT2G41680

-0.46

NADPH-dependent thioredoxin reductase 3

Electron donor for plastidial 2-Cys peroxiredoxin; Required for chlorophyll biosynthesis and biogenesis of the photosynthetic apparatus; Regulates starch biosynthesis by redox activation of the ADP-glucose pyrophosphorylase

Impaired cell redox homeostasis; Decreased hydrogen peroxide catabolic process; Decreased regulation of chlorophyll biosynthesis; Decreased regulation of starch biosynthesis; Decreased removal of superoxide radicals

Moon, Jeong Chan, et al. "The C-type Arabidopsis thioredoxin reductase ANTR-C acts as an electron donor to 2-Cys peroxiredoxins in chloroplasts." Biochemical and biophysical research communications 348.2 (2006): 478-484.

Solyc02g072140.1

GIL1

AT5G58960

-0.44

protein GRAVITROPIC IN THE LIGHT 1

Required for red and far-red light-induced and phytochrome-mediated deregulation of negative gravitropism leading to randomization of hypocotyl growth orientation

Impaired gravitropism; Decreased response to red or far red light

Allen, Trudie, et al. "Phytochrome-mediated agravitropism in Arabidopsis hypocotyls requires GIL1 and confers a fitness advantage." The Plant Journal 46.4 (2006): 641-648.

Solyc11g008990.1

VIPP1

AT1G65260

-0.36

membrane-associated protein VIPP1, chloroplastic

Required for plastid vesicle formation and thylakoid membrane biogenesis

Decreased thylakoid membrane organization; Decreased vesicle organization

Kroll, Daniela, et al. "VIPP1, a nuclear gene of Arabidopsis thaliana essential for thylakoid membrane formation." Proceedings of the National Academy of Sciences 98.7 (2001): 4238-4242.

Solyc05g014310.2

HHL1

AT1G67700

-0.34

protein HHL1, chloroplastic

Involved in photoprotection; Forms a complex with LQY1 that is involved in the repair and reassembly cycle of the PSII-LHCII supercomplex under high-light conditions

Increased response to light stress

Jin, Honglei, et al. "HYPERSENSITIVE TO HIGH LIGHT1 interacts with LOW QUANTUM YIELD OF PHOTOSYSTEM II1 and functions in protection of photosystem II from photodamage in Arabidopsis." The Plant Cell 26.3 (2014): 1213-1229.

Solyc05g050680.1

CKB4

AT2G44680

0.28

casein kinase II subunit beta-4

Regulates the basal catalytic activity of the alpha subunit; Involved in the proteasome-dependent degradation of PIF1 and promotion of photomorphogenesis; Participates in the regulation of the initiation of translation

Improved circadian rhythm; Improved photoperiodism, Increased flowering

Dennis, Michael D., and Karen S. Browning. "Differential phosphorylation of plant translation initiation factors by Arabidopsis thaliana CK2 holoenzymes." Journal of Biological Chemistry 284.31 (2009): 20602-20614.

Solyc02g091410.2

DEGP7

AT3G03380

0.29

protease Do 7

Serine protease

Increased photoinhibition

Sun, Xuwu, et al. "The stromal chloroplast Deg7 protease participates in the repair of photosystem II after photoinhibition in Arabidopsis." Plant physiology 152.3 (2010): 1263-1273.

Solyc05g055470.2

NAC078

AT5G04410

0.29

NAC domain-containing protein 78

Transcriptional activated by transmembrane proteolysis; Induces flavonoid biosynthesis and required for the accumulation of anthocyanins in response to high light stress

Increased transcription; Increased regulation of flavonoid biosynthesis; Increased response to high light intensity

Morishita, Teruyuki, et al. "Arabidopsis NAC transcription factor, ANAC078, regulates flavonoid biosynthesis under high-light." Plant and Cell Physiology 50.12 (2009): 2210-2222.

Solyc08g076100.2

BZIP16

AT2G35530

0.33

bZIP transcription factor 16

Transcriptional activator; G-box and G-box-like motifs are cis-acting elements defined in promoters of certain plant genes

Increased transcription; Increased intercellular signaling; Increased photosynthesis; Increased plant growth

Shen, Huaishun, et al. "AtbZIP16 and AtbZIP68, two new members of GBFs, can interact with other G group bZIPs in Arabidopsis thaliana." BMB reports 41.2 (2008): 132-138.

Solyc11g017300.1

CSN5A

AT1G22920

0.33

COP9 signalosome complex subunit 5a

Involved in photomorphogenesis and response to jasmonate; Essential regulator of the ubiquitin conjugation pathway; Involved in repression of photomorphogenesis in darkness; Required for degradation of PSIAA6

Decreased photomorphogenesis; Increased cellular turnover; Increased protein deneddylation; Increased red light phototransduction; Increased defense response; Increased response to auxin; Increased floral organ development

Kwok, Shing F., et al. "Arabidopsis homologs of a c-Jun coactivator are present both in monomeric form and in the COP9 complex, and their abundance is differentially affected by the pleiotropic cop/det/fus mutations." The Plant Cell 10.11 (1998): 1779-1790.

Solyc08g007270.2

HAT4

AT4G16780

0.34

homeobox-leucine zipper protein HAT4

Negative regulator of cell elongation and specific cell proliferation processes ; Mediator of the red light response under light stress; Negatively regulates its own expression

Increased lateral root formation; Increased red light phototransduction; Increased response to auxin; Increased response to cytokinin; Increased secondary thickening; Increased shade avoidance

Schena, Mark, Alan M. Lloyd, and Ronald W. Davis. "The HAT4 gene of Arabidopsis encodes a developmental regulator." Genes & development 7.3 (1993): 367-379.

Solyc04g082810.2

AHL27

AT1G20900

0.35

AT-hook motif nuclear-localized protein 27

Negatively regulates innate immunity to pathogens through the down-regulation of PAMP-triggered FRK1 expression; Regulates flowering and hypocotyl elongation; Chromatin remodeling factor that negatively regulates leaf senescence

Increased chromatin organization; Increased flower development; Impaired innate immune response; Increased leaf senescence; Increased photomorphogenesis; Increased vegetative to reproductive phase transition of meristem

Lim, Pyung Ok, et al. "Overexpression of a chromatin architecture-controlling AT-hook protein extends leaf longevity and increases the post-harvest storage life of plants." The Plant Journal 52.6 (2007): 1140-1153.

Solyc12g026400.1

DEGP9

AT5G40200

0.41

protease Do 9

Serine protease that degrades the two-component response regulator ARR4; Acts upstream of ARR4 and regulates the activity of ARR4 in cytokinin and light-signaling pathways; Mediates the cross-talk between light and cytokinin signaling

Increased photosynthesis

Chi, Wei, et al. "DEG9, a serine protease, modulates cytokinin and light signaling by regulating the level of ARABIDOPSIS RESPONSE REGULATOR 4." Proceedings of the National Academy of Sciences 113.25 (2016): E3568-E3576.