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Table 3 Summary of selected differentially expressed genes in Suaeda fruticosa

From: Transcriptome assembly, profiling and differential gene expression analysis of the halophyte Suaeda fruticosa provides insights into salt tolerance

Differentially expressed Protein--‐coding genes 1 Putative function or role in salt tolerance Expression upon 300 mM salt treatment (upregulated or downregulated) Plants with orthologous genes References
General metabolism genes
Probable WRKY transcription factor 72 Sequence specific DNA binding transcription factor; Activators of ABA signaling Repressors of aleurone cells Upregulated Festuca rubra ssp litoralis [22,25,69]
Glycine soja
Glycine max
Oryza sativa
Porteresia coarctata
WRKY transcription factor 6--like Influence senescence and pathogen defense--‐associated PR1 promoter activity; mediates arsenate/phosphate transporter gene expression Downregulated Arabidopsis thaliana [22,23,25,26]
Festuca rubra ssp litoralis
Glycine soja
Glycine max
Porteresia coarctata
WRKY DNA binding protein isoform 2 Transcription factors involved in various regulations; crucial to salinity tolerance Downregulated Festuca rubra ssp litoralis [22-25,69]
Glycine soja
Glycine max
Porteresia coarctata
Gibberellin 2--beta--‐dioxygenase 2 family (GA2OX2) Gibberellin catabolic process; response to jasmonic acid and red light Downregulated Arabidopsis thaliana [28,70,71]
40S ribosomal protein S4 (RPS4) Disease resistance; SRP--‐dependent cotranslational protein Upregulated Arabidopsis thaliana [72,73]
Mesembryanthemum crystallinum
60S acidic ribosomal protein P2 Elongation step of protein synthesis Upregulated Zea mays [30,74]
60S ribosomal protein L18–2--‐like Plastidic and nuclear protein synthesis Upregulated Populus euphratica [31,34]
Suaeda maritima
Pre--mRNA processing protein 40C Coactivator involved in the regulated transcription of nearly all RNA polymerase II--‐dependent genes Downregulated Arabidopsis thaliana [30]
DNA--binding protein escarola--‐like Late flowering and leaf development Leaf senescence Upregulated Arabidopsis thaliana [30]
MADS--box transcription factor AGL24 Transcription activator that mediates floral transition in response to vernalizationl promotes inflorescence fate in apical meristem Downregulated Arabidopsis thaliana [23,30]
Porteresia coarctata
DNA binding protein with zinc finger isoform1 Binds DNA; structural regulation Downregulated Glycine max [30,69,75]
Malus zumi
Arabidopsis thaliana
F--box protein AT1g78280--‐like transferase Regulation of transcription; defense response by callose deposition Downregulated Arabidopsis thaliana [30,34,76]
Eutrema salsugineum
Suaeda maritima
Glutathione--S--‐transferase tau 1 Glutathione metabolism; and production; promoted a higher level of salt tolerance Upregulated Arabidopsis thaliana [2,31-33,35,36,69,77,78]
Glycine max
Glycine soja
Nicotiana tabacum
Populus euphratica
Reaumuria trigyna
Salicornia europaea
Suaeda maritima
Suaeda fruticosa
Suaeda salsa
Germin--like protein Salt--‐stress regulation marker Upregulated Arabidopsis thaliana [37,38]
Hordeum vulgare
Flowering promoting factor 1--like protein 3 Regulates flowering time Upregulated Arabidopsis thaliana [30]
Auxin--induced protein 5NG4--‐like Transport of molecules functioning downstream of the auxin response; Root formation Upregulated Arabidopsis thaliana [30]
Pathogenesis--related protein Defense response; Response to water deprivation; Upregulated Arabidopsis thaliana [30]
Chitinase Enhance biotic and abiotic stress tolerance; reduce chitin in the cell wall contributing to salt sensitivity Upregulated Glycine max [40,69]
Glycine soja
Nicotiana tabacum
Peroxisomal ascorbate peroxidase (APX) Response to oxidative stress; Regeneration of NAD+; induced by high temperature Upregulated Nicotiana tabacum [30,41]
Zea mays
Plant cadmium resistance 2--like Reduces cadmium accumulation Upregulated Atriplex halimus [42-44]
Chaperone protein DNAJ–16 like Protein folding; protein partitioning into organelles; signal transduction; directly interacts with HSP70; induced by heat shock and prevents apoptosis Downregulated Arabidopsis thaliana [34,45,46,79,80]
Atriplex nummularia
Suaeda maritima
Spartina maritima
Spartina alterniflora
Ethylene--responsive transcription factor rap2--‐7 like isoform Transcriptional activator; binds to GCC box pathogenesis related promoter; Involved in the regulation of gene expression by stress factors; negatively regulates transition to flowering time Downregulated Arabidopsis thaliana [30,34]
Suaeda maritima
Senescence--associated protein Induced by abscisic acid; regulated during natural and artificially induced leaf senescence Downregulated Arabidopsis thaliana [72,81]
Mesembryanthemum crystallinum
Stem specific protein TSJT1--like Stem--‐specific (active at lower levels in other organs) Downregulated Nicotiana tabacum [30]
Protein F3H11–7 Positive regulation of transcription; leaf morphogenesis Downregulated Arabidopsis thaliana [30]
Cell wall protein AWA1--like Cell wall organization and biosynthesis Downregulated Theobroma cacao [30]
Callose synthase 7 Callose synthesis at forming cell plate during cytokinesis; transitory component of the cell plate in dividing cells Downregulated Arabidopsis thaliana [30]
Calcineurin B--like protein (CBL) 4--‐1 SOS like--‐gene; Acts as a calcium sensor involved in regulatory pathway for the control of Na + and K+ homeostasis and salt tolerance; Activates in synergy with CIPK24/SOS2 to activate Na+/H+ antiporter SOS1 Downregulated Arabidopsis thaliana [47,82,83]
Eutrema salsugineum
Calmodulin binding isoform 1 Regulates transcriptional activity in response to calcium signals; activates the expression of the V--‐PPase proton pump in pollen Downregulated Arabidopsis thaliana [47,48,69,84]
Glycine max
Glycine soja
Leymus chinensis
Photosystem II protein z (PsbZ) Controls photosystem II cores with the light-­‐harvesting antenna Upregulated Arabidopsis thaliana [30,72,75]
Malus zumi
Mesembryanthemum crystallinum
Photosystem D2 protein chloroplastic (psbD) One of the two reaction center proteins of photosystem II; needed for assembly of a stable PSII complex Upregulated Arabidopsis thaliana [30]
Photosystem II CP43 chlorophyll apoprotein (psbC) Component of the core antenna complex of photosystem II; binds chlorophyll and helps catalyze the primary light--‐induced photochemical processes of photosystem II Upregulated Arabidopsis thaliana [30]
Hypothetical Chloroplast RF19 (ycf1) Unknown; may have a function which is probably not related to photosynthesis. Upregulated Arabidopsis thaliana [30]
Zeaxanthin epoxidase, Chloroplastic--like isofom X2 Precursor to abscisic acid; involved in response to salt and heavy metal tolerance; required for resistance to osmotic and drought stresses, ABA--‐dependent stomatal closure, seed development and dormancy, modulation of defense gene expression; disease resistance Upregulated Arabidopsis thaliana 30,80]
Spartina maritima
Spartina alterniflora
Sufe--like chloroplastic like Cysteine desulfurization in chloroplast and mitochondria; iron--‐sulfur cluster biosynthesis Upregulated Arabidopsis thaliana [30]
High Light--induced chloroplastic protein Possible role in chlorophyll and/or carotenoid binding Downregulated Arabidopsis thaliana [30]
CRS2--associated factor chloroplastic like Required for the splicing of group IIB introns in chloroplast; mRNA processing; intron specificity Downregulated Arabidopsis thaliana [30]
Zea mays
Thioredoxin--like protein z chloroplastic like Redox regulation in the apoplast; cell division; cell differentiation; pollen germination; stress responses Downregulated Reaumuria trigyna [32,80]
Spartina alterniflora
Spartina maritima
Triose phosphate chloroplastic like isoform X2 Exports photoassimilates from chloroplast; transports inorganic phosphate, 3--‐phosphoglycerate and triose phosphate Downregulated Arabidopsis thaliana [30]
Probable chlorophyll b reductase chloroplastic--like Chlorophyll B degradation Downregulated Arabidopsis thaliana [30]
Phosphate chloroplastic like Hypothetical protein Downregulated Arabidopsis thaliana [30]
Ion transporters
Aquaporin tonoplast intrinsic protein 1 Water channel; facilitates the transport of water across cell membrane; osmoregulation; hydrogen peroxide transmembrane transport Upregulated Arabidopsis thaliana [30,31,52,53,69,75,85]
Glycine max
Glycine soja
Malus zumi
Oryza sativa
Populus euphratica
Schrenkiella parvula
High affinity nitrate transporter 3.1 like High--‐affinity nitrate transport; repressor of lateral root initiation; nitrate assimilation; response to wounding Upregulated Arabidopsis thaliana [30]
Oryza sativa
Nitrate transporter 1.5 Transmembrane nitrate transporter; involved in xylem transport of nitrate from root to shoot; induced in response to nitrate Upregulated Arabidopsis thaliana [30]
Aluminum--activated malate transporter 10 Malate transporter critical for aluminum tolerance; response to aluminum ion Upregulated Arabidopsis thaliana [30]
Flavonol 4’--sulfotransferase, putative Auxin transport; catalyze the sulfate conjugation Upregulated Flaveria chlorifolia [30]
Bidirectional sugar transporter SWEET3 Mediates low affinity uptake and efflux of sugar across the plasma membrane Upregulated Arabidopsis thaliana [30]
Glucosyltransferase Catalyzes the glycosylation of flavonoids from UDP glucose Upregulated Arabidopsis thaliana [30,31]
Populus euphratica
Populus pruinosa
Seed storage/lipid transfer protein Bifunctional inhibitor/lipid transfer protein/seed storage 2S albumin superfamily Upregulated Arabidopsis thaliana [30,31,86]
Populus euphratica
Thellungiella halophila
ATPase subunit 1 (chloroplast) Maintainance of the pH of endomembrane compartments Upregulated Arabidopsis thaliana [30]
Leymus chinensis
Thellungiella halophila
Sodium HKT1--like Plant salt tolerance; response to salt and osmotic stress; involves in Na + recirculation; potassium ion transmembrane transporter Downregulated Arabidopsis thaliana [30,32,33,53,86]
Populus trichocarpa
Reaumuria trigyna
Salicornia europaea
Schrenkiella parvula
Thellungiella halophila
Thellungiella salsuginea
Sodium pyruvate chloroplastic cotransporter Pyruvate transport across chloroplast envelope Downregulated Arabidopsis thaliana [30]
Magnesium transporter NIPA2 Magnesium ion transmembrane transport; can transport other divalent cations Downregulated Arabidopsis thaliana [30]
Vacuolar Iron transporter family Regulation of iron distribution; cellular response to ethylene stimulus; cellular response to nitric oxide; iron ion homeostasis; ion transport Downregulated Arabidopsis thaliana [30]
Vacuolar proton ATPase A1--like Essential component of the vacuolar proton pump (V--‐ATPase); cell expansion; ATP hydrolysis Downregulated Arabidopsis thaliana [30,84]
Leymus chinensis
ATPase ASNA1 homolog Required for the post--‐translational delivery of tail anchored proteins to the endoplasmic reticulum; binds the transmembrane domain of tail--‐anchored proteins in the cytosol Downregulated Arabidopsis thaliana [30]
Glutamyl--tRNA amidotransferase subunit chloroplastic mitochondrial--‐like Allows the formation of correctly charged Gln--‐tRNA; ATP binding; glutaminyl--‐tRNAGln biosynthesis; mitochondrial translation Downregulated Arabidopsis thaliana [30]
Tonoplast dicarboxylate transporter--like protein Malate transmembrane transport; critical for pH homeostasis; indirectly involved in the uptake of malate and fumarate to the vacuole Downregulated Arabidopsis thaliana [30]
Probable Galacturonosyltransferase 12-like Involved in pectin assembly and/or distribution; cell wall organization Downregulated Arabidopsis thaliana [30]
Regulatory molecules
Cysteine rich receptor like protein kinase ATP binding; defense responses; disease resistance Upregulated Arabidopsis thaliana [30]
Phosphatase 2C family protein Stress responses; metal ion binding; protein dephosphorylation; Serine/threonine phosphatase activity Downregulated Arabidopsis thaliana [30,31,58,69,80,87]
Ceriops tagal
Glycine max
Glycine soja
Populus trichocarpa
Spartina maritima
Spartina alterniflora
Thellungiella salsuginea
Phosphatase 2C 76 isoform 1 Metal ion binding; Binds 2 magnesium or manganese ions Downregulated Arabidopsis thaliana [30]
CDPK related kinase 1 Signal transduction pathways that involve calcium as second messenger; ATP binding; Ca2 + binding; protein autophosphorylation Downregulated Arabidopsis thaliana [30,34,75,76]
Eutrema salsugineum
Malus zumi
Suaeda maritima
PERK1 receptor protein kinase Protein autophosphorylation; response to wounding; ATP binding Downregulated Arabidopsis thaliana [30]
Casein kinase I--2--‐like protein ATP binding; protein serine/threonine kinase activity Downregulated Arabidopsis thaliana [30]
Serine--threonine protein kinase (histidine transporter) HT1 Control stomatal movement; shows a reduced response to ABA or light Downregulated Arabidopsis thaliana [30,57]
Oryza sativa
Phosphotidylinositol 4--kinase gamma 4 Phosphatidylinositol phosphorylation; Response to salt stress; Protein autophosphorylation Downregulated Arabidopsis thaliana [30]
Serine threonine protein phosphatase pp1--like Binds 2 manganese ions per subunit; protein dephosphorylation; serine/threonine phosphatase activity Downregulated Arabidopsis thaliana [30]
Serine threonine--protein phosphatase PP2A catalytic subunit Metal ion binding; serine/threonine phosphatase activity Downregulated Arabidopsis thaliana [30]
Late embryogenesis abundant proteins
Dehydration--responsive RD22--‐like Induced by salt stress; stress response Upregulated Malus zumi [88]
Populus euphratica
Populus pruinosa
HSP20--like chaperones superfamily protein Associated with stress and other abiotic factors Downregulated Glycine max [89,90]
Oryza sativa
  1. 1Identified and annotated using BLAST nr database using BLAST2GO.