Skip to main content

Table 4 The 33 tomato plant DEGs associated with photosynthesis. 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 only 7 genes (20%, in bold) would have resulted in improvements to photosynthesis. Simultaneously, 28 DEGs, especially those related to response to light stimulus and photorespiration, underwent expression changes that would have resulted in impairments to photosynthesis

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

Solyc06g073260.2

CSP41B

AT1G09340

-0.81

chloroplast stem-loop binding protein of 41 kDa b, chloroplastic

Associates with pre-ribosomal particles in chloroplasts and participates in chloroplast ribosomal RNA metabolism; Required for chloroplast integrity and embryo development; Regulates the circadian system; Regulates heteroglycans and monosaccharide mobilization

Impaired chloroplast organization; Impaired circadian rhythm; Decreased defense response to bacteria and wounding; Decreased galactose catabolism; Decreased monosaccharide metabolism; Decreased transcription and translation; Decreased response to cold and drought; Decreased rRNA processing

Raab, Sabine, et al. "ABA-responsive RNA-binding proteins are involved in chloroplast and stromule function in Arabidopsis seedlings." Planta 224.4 (2006): 900-914.

Solyc11g042940.1

XK1

AT2G21370

-0.53

D-ribulose kinase precursor

Can phosphorylate D-ribulose with low efficiency

Decreased phosphorylation

Xie, Yuan, et al. "Crystal Structures of Putative Sugar Kinases from Synechococcus Elongatus PCC 7942 and Arabidopsis Thaliana." PloS one 11.5 (2016): e0156067.

Solyc02g069010.2

IMPL1

AT1G31190

-0.39

phosphatase IMPL1, chloroplastic

Phosphatase acting preferentially on D-myoinositol 1-phosphate

Decreased inositol biosynthesis; Decreased signal transduction

Torabinejad, Javad, et al. "VTC4 is a bifunctional enzyme that affects myoinositol and ascorbate biosynthesis in plants." Plant physiology 150.2 (2009): 951-961.

Solyc04g080860.1

LON2

AT5G47040

-0.37

lon protease 2

Mediates the selective degradation of misfolded and unassembled polypeptides in the peroxisomal matrix; Necessary for type 2 peroxisome targeting signal-containing protein processing

Decreased lateral root development; Decreased protein transport; Decreased protein processing; Decreased protein quality control for misfolded or incompletely synthesized proteins; Decreased protein targeting to peroxisome

Lingard, Matthew J., and Bonnie Bartel. "Arabidopsis LON2 is necessary for peroxisomal function and sustained matrix protein import." Plant physiology 151.3 (2009): 1354-1365.

Solyc05g006990.2

NPF4.6

AT1G69850

-0.29

protein NRT1/ PTR FAMILY 4.6

Low-affinity proton-dependent nitrate transporter; Involved in constitutive nitrate uptake; Involved in (+)-abscisic acid (ABA) transport; Mediates cellular ABA uptake

Decreased abscisic acid transport; Decreased nitrate assimilation; Decreased regulation of stomatal movement; Decreased response to nematode

Huang, Nien-Chen, et al. "Cloning and functional characterization of an Arabidopsis nitrate transporter gene that encodes a constitutive component of low-affinity uptake." The Plant Cell 11.8 (1999): 1381-1392.

Solyc01g109520.2

RABG3F

AT3G18820

0.25

ras-related protein RABG3f

Essential for trafficking from prevacuolar compartments; Essential for plant growth; Participates in the recruitment of the core retromer components to the endosomal membrane

Increased intracellular protein transport; Increased late endosome to vacuole transport; Increased Rab protein signal transduction; Increased vacuole organization

Zelazny, Enric, et al. "Mechanisms governing the endosomal membrane recruitment of the core retromer in Arabidopsis." Journal of Biological Chemistry 288.13 (2013): 8815-8825.

Solyc09g074680.2

CUL1

AT4G02570

0.25

cullin-1

Involved in ubiquitination and subsequent proteasomal degradation; Regulator of mitotic processes during gametogenesis and embryogenesis; Involved in floral organ development; Involved in auxin signaling; Regulates responses to jasmonates; Involved in phytochrome A light signaling; Involved in leaf senescence

Increased auxin-activated signaling pathway; Increased cellular cycling; Increased embryo development; Increased jasmonic acid-mediated signaling; Increased phloem or xylem histogenesis; Increased protein ubiquitination; Disrupted circadian rhythm; Increased response to jasmonic acid; Increased protein catabolism

Feng, Suhua, et al. "Arabidopsis CAND1, an unmodified CUL1-interacting protein, is involved in multiple developmental pathways controlled by ubiquitin/proteasome-mediated protein degradation." The Plant Cell 16.7 (2004): 1870-1882.

Solyc03g034200.2

RCF3

AT5G53060

0.26

RNA-binding KH domain-containing protein RCF3

Negative regulator of osmotic stress-induced gene expression; Regulates thermotolerance responses under heat stress; Forms a complex with CPL1 that modulates co-transcriptional processes; Represses stress-inducible gene expression; Involved in primary miRNA processing and pre-miRNA biogenesis; Involved in JA-mediated fungal defense

Increased heat acclimation; Increased jasmonic acid-mediated signaling; Increased mRNA processing; Increased miRNA processing; Increased regulation of defense response to fungus; Increased regulation of gene expression; Increased response to osmotic stress; Increased RNA splicing

Xiong, Liming, et al. "HOS5–a negative regulator of osmotic stress-induced gene expression in Arabidopsis thaliana." The Plant Journal 19.5 (1999): 569-578.

Solyc12g095990.1

TIF4A-2

AT1G54270

0.26

eukaryotic initiation factor 4A-2

Subunit of the eIF4F complex involved in cap recognition; Required for mRNA binding to ribosome; Unwinds RNA secondary structures in the 5'-UTR of mRNAs; Necessary for efficient binding of the small ribosomal subunit

Increased cytoplasmic translational initiation; Increased response to cadmium ion

Vergnolle, Chantal, et al. "The cold-induced early activation of phospholipase C and D pathways determines the response of two distinct clusters of genes in Arabidopsis cell suspensions." Plant physiology 139.3 (2005): 1217-1233.

Solyc12g089150.1

SYP61

AT1G28490

0.26

syntaxin-61

Vesicle trafficking protein that functions in the secretory pathway; Involved in osmotic stress tolerance and in abscisic acid regulation of stomatal responses

Increased abscisic acid-activated signaling; Increased Golgi vesicle transport; Increased intracellular protein transport; Increased vesicle docking and fusion

Shahriari, Mojgan, et al. "The AAA-type ATPase AtSKD1 contributes to vacuolar maintenance of Arabidopsis thaliana." The Plant Journal 64.1 (2010): 71-85.

Solyc05g055600.2

VPS33

AT3G54860

0.27

vacuolar protein-sorting-associated protein 33 homolog

Involved in regulating membrane fusion at the tonoplast and the prevacuolar compartment

Increased vesicle docking involved in exocytosis

Rojo, Enrique, et al. "The AtC–VPS protein complex is localized to the tonoplast and the prevacuolar compartment in Arabidopsis." Molecular biology of the cell 14.2 (2003): 361-369.

Solyc08g065890.2

EPSIN1

AT5G11710

0.28

clathrin interactor EPSIN 1

Plays a role in transport via clathrin-coated vesicles from the trans-Golgi network to endosomes; Stimulates clathrin assembly; Plays a role in the vacuolar trafficking of soluble cargo proteins at the trans-Golgi network

Increased protein targeting to vacuole

Song, Jinhee, et al. "Arabidopsis EPSIN1 plays an important role in vacuolar trafficking of soluble cargo proteins in plant cells via interactions with clathrin, AP-1, VTI11, and VSR1." The Plant Cell 18.9 (2006): 2258-2274.

Solyc01g096290.2

RPL40A

AT2G36170

0.28

ubiquitin-60S ribosomal protein L40

Involved in protein degradation via the proteasome; Linear polymer chains formed via attachment by the initiator Met-lead during cellular signaling

Increased modification-dependent protein catabolism; Increased protein ubiquitination; Increased translation; Increased defense response to bacteria

Ditt, Renata F., et al. "The Arabidopsis thaliana transcriptome in response to Agrobacteria tumefaciens." Molecular plant-microbe interactions 19.6 (2006): 665-681.

Solyc08g007360.2

MAG5

AT5G47480

0.28

protein transport protein SEC16A homolog

Required for efficient protein export from the endoplasmic reticulum to the Golgi; Functions as a scaffold and regulator of COPII coat assembly at ER exit sites

Increased COPII vesicle coating; Increased endoplasmic reticulum organization; Increased protein transport

Takagi, Junpei, et al. "MAIGO5 functions in protein export from Golgi-associated endoplasmic reticulum exit sites in Arabidopsis." The Plant Cell 25.11 (2013): 4658-4675.

Solyc04g082560.2

ITSN2

N/a

0.29

intersectin-2

Adapter protein that provides indirect link between the endocytic membrane traffic and the actin assembly machinery; Regulates formation of clathrin-coated vesicles; Involved in endocytosis of integrin beta-1

Increased endocytosis; Increased dendrite extension; Increased regulation of Rho protein signal transduction; Increased viral process

Mettlen, Marcel, et al. "Endocytic accessory proteins are functionally distinguished by their differential effects on the maturation of clathrin-coated pits." Molecular biology of the cell 20.14 (2009): 3251-3260.

Solyc03g034180.2

GRF2

AT1G78300

0.31

14-3-3-like protein GF14 omega

Associated with a DNA binding complex that binds to the G box

Increased brassinosteroid-mediated signaling

DeLille, Justin M.,et al. "The Arabidopsis 14-3-3 family of signaling regulators." Plant Physiology 126.1 (2001): 35-38.

Solyc05g053830.2

N/a

AT4G14160

0.31

protein transport protein SEC23

Promotes the formation of transport vesicles from the endoplasmic reticulum

Increased COPII-coated vesicle cargo loading; Increased intracellular protein transport

De Craene, Johan-Owen, et al. "Study of the plant COPII vesicle coat subunits by functional complementation of yeast Saccharomyces cerevisiae mutants." PLoS One 9.2 (2014): e90072.

Solyc01g104970.2

BAK1

AT4G33430

0.31

brassinosteroid insensitive 1-associated receptor kinase 1

Involved in brassinosteroid signaling response to beacteria/fungi/oomycetes; Mediates programmed cell death

Increased brassinosteroid mediated signaling pathway; Increased programmed cell death; Increased defense response to bacteria/fungus/oomycetes

Li, Jia, et al. "BAK1, an Arabidopsis LRR receptor-like protein kinase, interacts with BRI1 and modulates brassinosteroid signaling." Cell 110.2 (2002): 213-222.

Solyc11g013260.1

PHB3

AT5G40770

0.32

prohibitin-3, mitochondrial

Holdase/unfoldase involved in the stabilization of newly synthesized mitochondrial proteins; Necessary for mitochondrial and cell metabolism and biogenesis; Required to regulate ethylene-mediated signaling; Involved in growth maintenance; Functions in nitric oxide-mediated responses

Increased cellular turnover; Increased defense response to bacteria; Increased lateral root development; Increased mitochondrion organization; Increased response to auxin, ethylene, and nitric oxide; Increased to salt stress; Increased salicylic acid biosynthesis

Christians, Matthew J., et al. "Mutational loss of the prohibitin AtPHB3 results in an extreme constitutive ethylene response phenotype coupled with partial loss of ethylene-inducible gene expression in Arabidopsis seedlings." Journal of experimental botany 58.8 (2007): 2237-2248.

Solyc09g061340.1

PCMP-E76

AT2G13600

0.33

pentatricopeptide repeat-containing protein At2g13600

Involved in mitochondrial mRNA modification during sugar metabolism

Increased mitochondrial mRNA modification; Increased RNA modification; Increased sugar-mediated signaling pathway; Increased sugar metabolism

Zhu, Qiang, et al. "SLO2, a mitochondrial pentatricopeptide repeat protein affecting several RNA editing sites, is required for energy metabolism." The Plant Journal 71.5 (2012): 836-849.

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 which are regulated by such diverse stimuli as light-induction or hormone control

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.

Solyc11g010950.1

ELP4

AT3G11220

0.33

elongator complex protein 4

Component of the RNA polymerase II elongator complex; Promotes organs development by modulating cell division rate; Regulates mechanisms producing carbon or importing sucrose; Involved in the repression of the abscisic acid signaling during seed germination; Required for auxin distribution or signaling; Prevents anthocyanins accumulation

Increased response to sucrose; Decreased anthocyanin metabolism; Increased cellular turnover; Increased auxin-mediated signaling; Increased regulation of carbon utilization; Increased regulation of leaf development; Increased response to oxidative stress; Increased tRNA wobble uridine modification

Nelissen, Hilde, et al. "The elongata mutants identify a functional Elongator complex in plants with a role in cell proliferation during organ growth." Proceedings of the National Academy of Sciences 102.21 (2005): 7754-7759.

Solyc11g033270.1

M3KE1

AT3G13530

0.34

MAP3K epsilon protein kinase

Serine/threonine-protein kinase involved in the spatial and temporal organization of cortical activity; Required for the normal functioning of the plasma membrane in developing pollen; Involved in the regulation of cell expansion, cell elongation, and embryo development

Increased cell division; Increased regulation of embryonic development; Increased regulation of cell growth; Increased signal transduction by protein phosphorylation

Seguí-Simarro, José M., et al. "Mitogen-activated protein kinases are developmentally regulated during stress-induced microspore embryogenesis in Brassica napus L." Histochemistry and cell biology 123.4-5 (2005): 541-551.

Solyc01g096350.2

CRK3

AT2G46700

0.34

CDPK-related kinase 3

Plays a role in signal transduction pathways that involve calcium as a second messenger; Serine/threonine kinase that phosphorylates histone H3 an GLN1-1

Increased response to abscisic acid stimulus; Increased intracellular signal transduction; Increased leaf senescence; Increased peptidyl-serine phosphorylation

Du, Wei, et al. "Biochemical and expression analysis of an Arabidopsis calcium-dependent protein kinase-related kinase." Plant science 168.5 (2005): 1181-1192.

Solyc05g052510.2

CHC1

AT3G11130

0.34

clathrin heavy chain 1

Clathrin is the major protein of the polyhedral coat of coated pits and vesicles; Mediates endocytosis and is required for a correct polar distribution of PIN auxin transporters

Increased clathrin-dependent endocytosis; Increased intracellular protein transport; Increased receptor-mediated endocytosis; Increased stomatal movement

Kitakura, Saeko, et al. "Clathrin mediates endocytosis and polar distribution of PIN auxin transporters in Arabidopsis." The Plant Cell 23.5 (2011): 1920-1931.

Solyc02g030210.2

N/a

AT2G41710

0.36

AP2 ethylene-responsive transcription factor At2g41710

Acts as a transcriptional activator; Binds to the GCC-box pathogenesis-related promoter element; Involved in the regulation of gene expression by stress factors and by components of stress signal transduction pathways

Increased ethylene-activated signaling pathway; Increased growth/development of reproductive tissues

Seki, Motoaki, et al. "Functional annotation of a full-length Arabidopsis cDNA collection." Science 296.5565 (2002): 141-145.

Solyc02g069310.2

NPR3

AT5G45110

0.36

regulatory protein NPR3

Substrate-specific adapter of an E3 ubiquitin-protein ligase complex; Mediates protein ubiquitination and subsequent proteasomal degradation; Regulates basal defense responses against pathogens

Increased defense response to bacteria and fungus; Increased protein ubiquitination; Increased jasmonic acid-mediated signaling; Increased systemic acquired resistance

Zhang, Yuelin, et al. "Negative regulation of defense responses in Arabidopsis by two NPR1 paralogs." The Plant Journal 48.5 (2006): 647-656.

Solyc05g021100.2

SWAP70

AT2G30880

0.36

switch-associated protein 70

Involved in intracellular signal transduction; Mediates defense response to bacteria

Increased defense response to bacteria; Increased intracellular signal transduction

Van Leeuwen, Wessel, et al. "Learning the lipid language of plant signalling." Trends in plant science 9.8 (2004): 378-384.

Solyc01g089900.2

ALG12

AT1G02145

0.39

dol-P-Man:Man(7)GlcNAc(2)-PP-Dol alpha-1,6-mannosyltransferase

Required for N-linked oligosaccharide assembly; Adds the eighth mannose residue in an alpha-1,6 linkage onto the dolichol-PP-oligosaccharide precursor dolichol-PP-Man7GlcNAc2

Increased dolichol-linked oligosaccharide biosynthesis; Increased N-linked glycosylation; Increased ERAD signaling

Hong, Zhi, et al. "Mutations of an α1, 6 mannosyltransferase inhibit endoplasmic reticulum–associated degradation of defective brassinosteroid receptors in Arabidopsis." The Plant Cell 21.12 (2009): 3792-3802.

Solyc10g074570.1

CPK4

AT4G09570

0.39

calcium-dependent protein kinase 4

Plays a role in signal transduction pathways that involve calcium as a second messenger; Regulator of the calcium-mediated abscisic acid signaling pathway

Increased intracellular signal transduction; Increased peptidyl-serine phosphorylation; Increased abscisic acid-activated signaling; Increased protein autophosphorylation

Rodriguez Milla, Miguel A., et al. "A novel yeast two-hybrid approach to identify CDPK substrates: Characterization of the interaction between AtCPK11 and AtDi19, a nuclear zinc finger protein1." FEBS letters 580.3 (2006): 904-911.

Solyc12g099010.1

GFS12

AT5G18525

0.40

protein GFS12

Acts predominantly to suppress BCHC1, which itself is a negative factor in protein storage vacuole trafficking regulation and plant effector triggered immunity

Increased defense response to bacteria; Increased protein targeting to vacuoles

Teh, Ooi-kock, et al. "BEACH-domain proteins act together in a cascade to mediate vacuolar protein trafficking and disease resistance in Arabidopsis." Molecular plant 8.3 (2015): 389-398.

Solyc08g005270.2

RCD1

AT1G32230

0.41

inactive poly [ADP-ribose] polymerase RCD1

Regulates hormonal responses during developmental; Required for embryogenesis, vegetative and reproductive development, and abiotic stress responses

Increased defense response to bacteria; Increased embryo development; Increased ethylene-activated signaling pathway; Increased jasmonic acid-mediated signaling; Increased lateral root morphogenesis; Increased nitric oxide biosynthesis; Increased programmed cell death; Increased response to drought, osmotic, ozone, and oxide stress

Ahlfors, Reetta, et al. "Arabidopsis RADICAL-INDUCED CELL DEATH1 belongs to the WWE protein–protein interaction domain protein family and modulates abscisic acid, ethylene, and methyl jasmonate responses." The Plant Cell 16.7 (2004): 1925-1937.

Solyc03g025940.1

N/a

AT3G48880

0.42

F-box/LRR-repeat protein

Involved in endogenous messenger response to Gram-negative bacteria

Increased RNA signaling; Increased defense response to Gram-negative bacteria

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

Solyc06g083510.2

PBL25

AT3G24790

0.44

serine/threonine-protein kinase PBL25

Involved in protein phosphorylation signaling during germination and plant defense

Increased defense response; Increased protein phosphorylation; Increased reproduction

Wang, Yi, et al. "Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in Arabidopsis." Plant physiology 148.3 (2008): 1201-1211.

Solyc01g100720.2

IMPA4

AT1G09270

0.45

importin subunit alpha-4

Mediates nuclear protein import across the nuclear envelope; Cellular receptor for the nuclear import of the virD2 protein of Agrobacteria

Increased defense response to symbiont of tumor, nodule or growth; Increased NLS-bearing protein transport into nucleus; Increased symbiont intracellular transport

Bhattacharjee, Saikat, et al. "IMPa-4, an Arabidopsis importin α isoform, is preferentially involved in Agrobacteria-mediated plant transformation." The Plant Cell 20.10 (2008): 2661-2680.

Solyc10g085000.1

BSK5

AT5G59010

0.55

serine/threonine-protein kinase BSK5

Positive regulator of brassinosteroid signaling; Involved in abiotic stress tolerance; Required for abscisic acid-mediated response to drought and salt stress

Increased brassinosteroid-mediated signaling; Increased response to abscisic acid; Increased response to cold; Increased response to salt stress

Tang, Wenqiang, et al. "BSKs mediate signal transduction from the receptor kinase BRI1 in Arabidopsis." Science 321.5888 (2008): 557-560.

Solyc09g008460.2

RABC2A

AT5G03530

0.60

ras-related protein RABC2a

Involved in intracellular vesicle trafficking and protein transport

Increased intracellular protein transport; Increased Rab protein signal transduction

Hashimoto, Kohsuke, et al. "An isoform of Arabidopsis myosin XI interacts with small GTPases in its C-terminal tail region." Journal of experimental botany 59.13 (2008): 3523-3531.

Solyc05g012210.2

AFP3

AT3G29575

0.76

ninja-family protein AFP3

Acts as a negative regulator of abscisic acid response and stress responses

Decreased transcription; Increased signal transduction

de Torres-Zabala, Marta, et al. "Pseudomonas syringae pv. tomato hijacks the Arabidopsis abscisic acid signalling pathway to cause disease." The EMBO journal 26.5 (2007): 1434-1443.