Genome-wide identification and analyses of tomato (Solanum lycopersicum L.) high-affinity nitrate transporter 2 (NRT2) family genes and their responses to drought and salinity

High-affinity nitrate transporter 2 (NRT2) proteins have vital roles in nitrate (NO3-) uptake and translocation in plants. The gene families coding NRT2 proteins have been identified and functionally characterized in many plant species. However, no systematic identification of NRT2 family members have been reported in tomato (Solanum lycopersicum). There is also little known about their expression profiles under environmental stresses. Accordingly, the present study aimed to identify NRT2 gene family in the tomato genome; then, investigate them in detail through bioinformatics, physiological and expression analyses. As a result, four novel NRT2 genes were identified in the tomato genome, all of which contain the same domain belonging to the Major Facilitator Superfamily (PF07690). The co-expression network of SlNRT genes revealed that they were co-expressed with several other genes in many different molecular pathways including transport, photosynthesis, fatty acid metabolism and amino acid catabolism. Programming many crucial physiological and metabolic pathways, various numbers of phosphorylation sites were predicted in the NRT2 proteins.

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Genome-wide identification and characterization of SPX-domain-containing protein gene family in Solanum lycopersicum

PeerJ ◽

10.7717/peerj.12689 ◽

2021 ◽

Vol 9 ◽

pp. e12689

Author(s):

Chunwei Li ◽

Qiuye You ◽

Panfeng Zhao

Keyword(s):

Gene Family ◽

Solanum Lycopersicum ◽

Protein Gene ◽

Expression Profiles ◽

Expression Patterns ◽

Major Facilitator Superfamily ◽

Phosphate Ions ◽

Genome Wide ◽

New Gene ◽

Major Facilitator

The SYG1, PHO81, and XPR1 (SPX) domain is named after the suppressor of yeast gpa1 (Syg1), yeast phosphatase (Pho81) and the human Xenotropic and Polytrophic Retrovirus receptor1 (XPR1). SPX-domain-containing proteins play pivotal roles in maintaining phosphate ions (Pi) homeostasis in plant. This study was to genome-wide identification and analysis of Solanum lycopersicum SPX-domain-containing protein gene family. The Solanum lycopersicum genome contains 19 SPX-domain-containing protein genes. These SPX-domain-containing protein genes were located in seven of the 12 chromosomes. According to the different conserved domains, the proteins encoded by those genes could be divided into four SPX-domain-containing protein families, which included SPX Family, SPX-ERD1/XPR1/SYG1(SPX-EXS) Family, SPX-Major Facilitator Superfamily (SPX-MFS) Family and SPX-Really Interesting New Gene (SPX-RING) Family. Phylogenetic analysis of SPX-domain-containing protein genes in Arabidopsis thaliana, Solanum tuberosum, Capsicum annuum and Solanum lycopersicum classified these genes into eight clades. Expression profiles derived from transcriptome (RNA-seq) data analysis showed 19 SPX-domain-containing protein genes displayed various expression patterns. SPX-domain-containing protein may play different roles in phosphate nutrition of Solanum lycopersicum different tissues and development stages. And, this study can provide the selection of candidate genes for functional research and genome editing in Solanum lycopersicum phosphate ions (Pi) nutrition.

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Genome-wide identification of tomato (Solanum lycopersicum L.) lipoxygenases coupled with expression profiles during plant development and in response to methyl-jasmonate and wounding

Journal of Plant Physiology ◽

10.1016/j.jplph.2018.10.001 ◽

2018 ◽

Vol 231 ◽

pp. 318-328 ◽

Cited By ~ 8

Author(s):

Rakesh K. Upadhyay ◽

Autar K. Mattoo

Keyword(s):

Methyl Jasmonate ◽

Solanum Lycopersicum ◽

Plant Development ◽

Expression Profiles ◽

Solanum Lycopersicum L ◽

Genome Wide

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Concomitant phytonutrient and transcriptome analysis of mature fruit and leaf tissues of tomato (Solanum lycopersicum L. cv. Oregon Spring) grown using organic and conventional fertilizer

10.1101/755769 ◽

2019 ◽

Cited By ~ 2

Author(s):

Richard M Sharpe ◽

Luke Gustafson ◽

Seanna Hewitt ◽

Benjamin Kilian ◽

James Crabb ◽

...

Keyword(s):

Secondary Metabolites ◽

Solanum Lycopersicum ◽

Organic Fertilizer ◽

Agricultural Practices ◽

Organic Soil ◽

Fertilizer Treatment ◽

Tomato Genome ◽

Mature Fruit ◽

Solanum Lycopersicum L ◽

Leaf Tissues

ABSTRACTEnhanced levels of antioxidants, phenolic compounds, carotenoids and vitamin C have been reported for several crops grown under organic fertilizer, albeit with yield penalties. As organic agricultural practices continue to grow and find favor it is critical to gain an understanding of the molecular underpinnings of the factors that limit the yields in organically farmed crops. Concomitant phytochemical and transcriptomic analysis was performed on mature fruit and leaf tissues derived from Solanum lycopersicum L. ‘Oregon Spring’ grown under organic and conventional fertilizer conditions to evaluate the following hypotheses. 1. Organic soil fertilizer management results in greater allocation of photosynthetically derived resources to the synthesis of secondary metabolites than to plant growth, and 2. Genes involved in changes in the accumulation of phytonutrients under organic fertilizer regime will exhibit differential expression, and that the growth under different fertilizer treatments will elicit a differential response from the tomato genome. Both these hypotheses were supported, suggesting an adjustment of the metabolic and genomic activity of the plant in response to different fertilizers. Organic fertilizer treatment showed an activation of photoinhibitory processes through differential activation of nitrogen transport and assimilation genes resulting in higher accumulation of phytonutrients. This information can be used to identify alleles for breeding crops that allow for efficient utilization of organic inputs.Significance statementOrganic fertilizer changes the expression of the tomato genome, induces photosynthetic stress which elicits higher production of secondary metabolites.

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Phylogenomic and Microsynteny Analysis Provides Evidence of Genome Arrangements of High-Affinity Nitrate Transporter Gene Families of Plants

International Journal of Molecular Sciences ◽

10.3390/ijms222313036 ◽

2021 ◽

Vol 22 (23) ◽

pp. 13036

Author(s):

Normig M. Zoghbi-Rodríguez ◽

Samuel David Gamboa-Tuz ◽

Alejandro Pereira-Santana ◽

Luis C. Rodríguez-Zapata ◽

Lorenzo Felipe Sánchez-Teyer ◽

...

Keyword(s):

Functional Characterization ◽

Nitrate Assimilation ◽

Gene Families ◽

Land Plants ◽

Nitrate Transport ◽

Phylogenomic Analysis ◽

Evolutionary Constraint ◽

N Availability ◽

Nitrate Transporter ◽

High Affinity

Nitrate transporter 2 (NRT2) and NRT3 or nitrate-assimilation-related 2 (NAR2) proteins families form a two-component, high-affinity nitrate transport system, which is essential for the acquisition of nitrate from soils with low N availability. An extensive phylogenomic analysis across land plants for these families has not been performed. In this study, we performed a microsynteny and orthology analysis on the NRT2 and NRT3 genes families across 132 plants (Sensu lato) to decipher their evolutionary history. We identified significant differences in the number of sequences per taxonomic group and different genomic contexts within the NRT2 family that might have contributed to N acquisition by the plants. We hypothesized that the greater losses of NRT2 sequences correlate with specialized ecological adaptations, such as aquatic, epiphytic, and carnivory lifestyles. We also detected expansion on the NRT2 family in specific lineages that could be a source of key innovations for colonizing contrasting niches in N availability. Microsyntenic analysis on NRT3 family showed a deep conservation on land plants, suggesting a high evolutionary constraint to preserve their function. Our study provides novel information that could be used as guide for functional characterization of these gene families across plant lineages.

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Novel and Unexpected Functions of SGLTs

Physiology ◽

10.1152/physiol.00021.2017 ◽

2017 ◽

Vol 32 (6) ◽

pp. 435-443 ◽

Cited By ~ 13

Author(s):

Ernest M. Wright ◽

Chiara Ghezzi ◽

Donald D. F. Loo

Keyword(s):

Pregnancy Loss ◽

Recurrent Pregnancy Loss ◽

Glucose Sensor ◽

Human Gene ◽

Gene Families ◽

Major Facilitator Superfamily ◽

Sodium Glucose Cotransporter ◽

Major Facilitator ◽

Familial Renal Glucosuria ◽

Opening And Closing

It has been 30 years since the intestinal sodium glucose cotransporter SGLT1 was cloned, and, in the intervening years, there have been many advances that have influenced physiology and medicine. Among the first was that SGLT1 is the founding member of the human gene family SLC5, containing 11 diverse transporters and a glucose sensor. Equally surprising was that SGLTs are members of a structural family of cotransporters and exchangers in different gene families. This led to the conclusion that these proteins operate by a mechanism where transport involves the opening and closing of external and internal gates. The mechanism is shared by a wide variety of transporters in different structural families, e.g., the human facilitated glucose transporters (SLC2) in the huge major facilitator superfamily (MFS). Not surprising is the finding that mutations in Sglt genes cause the rare diseases glucose-galactose-malabsorption (GGM) and familial renal glucosuria (FRG). However, it was not envisaged that SGLT inhibitors would be used to treat diabetes mellitus, and these drugs may be able to treat cancer. Finally, in 2017, we have just learned that SGLT1 may be required to resist infection and to avoid recurrent pregnancy loss.

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Pathogenesis related protein-1 (PR-1) genes in tomato (Solanum lycopersicum L.): Bioinformatics analyses and expression profiles in response to drought stress

Genomics ◽

10.1016/j.ygeno.2020.07.004 ◽

2020 ◽

Vol 112 (6) ◽

pp. 4089-4099

Author(s):

M. Aydın Akbudak ◽

Sukran Yildiz ◽

Ertugrul Filiz

Keyword(s):

Drought Stress ◽

Solanum Lycopersicum ◽

Expression Profiles ◽

Related Protein ◽

Bioinformatics Analyses ◽

Solanum Lycopersicum L ◽

Pathogenesis Related Protein ◽

Pathogenesis Related

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Aspergillus niger mstA encodes a high-affinity sugar/H+ symporter which is regulated in response to extracellular pH

Biochemical Journal ◽

10.1042/bj20030624 ◽

2004 ◽

Vol 379 (2) ◽

pp. 375-383 ◽

Cited By ~ 58

Author(s):

Patricia A. vanKUYK ◽

Jasper A. DIDERICH ◽

Andrew P. MacCABE ◽

Oscar HERERRO ◽

George J. G. RUIJTER ◽

...

Keyword(s):

Aspergillus Niger ◽

Ph Regulation ◽

Functional Characterization ◽

Carbon Sources ◽

Sugar Transport ◽

Major Facilitator Superfamily ◽

Northern Analysis ◽

High Affinity ◽

Hexose Uptake ◽

Major Facilitator

A sugar-transporter-encoding gene, mstA, which is a member of the major facilitator superfamily, has been cloned from a genomic DNA library of the filamentous fungus Aspergillus niger. To enable the functional characterization of MSTA, a full-length cDNA was expressed in a Saccharomyces cerevisiae strain deficient in hexose uptake. Uptake experiments using 14C-labelled monosaccharides demonstrated that although able to transport d-fructose (Km, 4.5±1.0 mM), d-xylose (Km, 0.3±0.1 mM) and d-mannose (Km, 60±20 µM), MSTA has a preference for d-glucose (Km, 25±10 µM). pH changes associated with sugar transport indicate that MSTA catalyses monosaccharide/H+ symport. Expression of mstA in response to carbon starvation and upon transfer to poor carbon sources is consistent with a role for MSTA as a high-affinity transporter for d-glucose, d-mannose and d-xylose. Northern analysis has shown that mstA is subject to CreA-mediated carbon catabolite repression and pH regulation mediated by PacC. A. niger strains in which the mstA gene had been disrupted are phenotypically identical with isogenic reference strains when grown on 0.1–60 mM d-glucose, d-mannose, d-fructose or d-xylose. This indicates that A. niger possesses other transporters capable of compensating for the absence of MSTA.

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The Major Facilitator Superfamily-Type Transporter YmfE and the Multidrug-Efflux Activator Mta Mediate Bacillibactin Secretion in Bacillus subtilis

Journal of Bacteriology ◽

10.1128/jb.00464-08 ◽

2008 ◽

Vol 190 (15) ◽

pp. 5143-5152 ◽

Cited By ~ 24

Author(s):

Marcus Miethke ◽

Sarah Schmidt ◽

Mohamed A. Marahiel

Keyword(s):

Bacillus Subtilis ◽

Iron Acquisition ◽

Transcriptional Regulator ◽

Major Facilitator Superfamily ◽

Second Step ◽

Mutant Library ◽

Multidrug Efflux ◽

High Affinity ◽

Regulatory Aspect ◽

Major Facilitator

ABSTRACT High-affinity iron acquisition in Bacillus subtilis is mediated via the bacillibactin catechole siderophore pathway. Three of the four essential pathway steps, bacillibactin synthesis, Fe-bacillibactin uptake, and Fe-bacillibactin hydrolysis have been characterized previously. The functional and regulatory components for bacillibactin secretion, the second step of the siderophore pathway, remained unknown. In this study, the screening of a B. subtilis exporter mutant library led to the identification of the YmfE major facilitator superfamily (MFS)-type transporter as a target for bacillibactin export. Analysis of iron-limited ymfE mutant cultures displayed an eightfold reduced bacillibactin secretion and, on the other hand, a 25-fold increased secretion of the bacillibactin precursor 2,3-dihydroxybenzoate. Investigation of the regulatory aspect revealed that bacillibactin secretion is, in contrast to all other components of the pathway, independent of the ferric uptake repressor Fur. Indeed, the MerR-type transcriptional regulator Mta was found to activate both bacillibactin secretion and ymfE gene expression, exposing Mta as an additional regulatory member of the bacillibactin pathway.

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Transmembrane segments 1, 5, 7 and 8 are required for high-affinity glucose transport by Saccharomyces cerevisiae Hxt2 transporter

Biochemical Journal ◽

10.1042/bj20030044 ◽

2003 ◽

Vol 372 (1) ◽

pp. 247-252 ◽

Cited By ~ 18

Author(s):

Toshiko KASAHARA ◽

Michihiro KASAHARA

Keyword(s):

Saccharomyces Cerevisiae ◽

Glucose Transport ◽

Glucose Transporter ◽

Amino Acid Identity ◽

Major Facilitator Superfamily ◽

Transport Activity ◽

Transmembrane Segments ◽

High Affinity ◽

Yeast Transformants ◽

Major Facilitator

Hxt2 is a high-affinity facilitative glucose transporter of Saccharomyces cerevisiae and belongs to the major facilitator superfamily. Hxt1 shares ≈ 70% amino acid identity with Hxt2 in its transmembrane segments (TMs) and inter-TM loops, but transports d-glucose with an affinity about one-tenth of that of Hxt2. To determine which TMs of Hxt2 are important for high-affinity glucose transport, we constructed chimaeras of Hxt2 and Hxt1 by randomly replacing each of the 12 TMs of Hxt2 with the corresponding segment of Hxt1, for a total of 4096 different transporters. Among > 20000 yeast transformants screened, 39 different clones were selected by plate assays of high-affinity glucose-transport activity and sequenced. With only two exceptions, the selected chimaeras contained Hxt2 TMs 1, 5, 7 and 8. We then constructed chimaeras corresponding to all 16 possible combinations of Hxt2 TMs 1, 5, 7 and 8. Only one chimaera, namely that containing all four Hxt2 TMs, exhibited transport activity comparable with that of Hxt2. The Km and Vmax values for d-glucose transport, and the substrate specificity of this chimaera were almost identical with those of Hxt2. These results indicate that TMs 1, 5, 7 and 8 are necessary for exhibiting high-affinity glucose-transport activity of Hxt2.

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