Global analysis of the MATE gene family of metabolite transporters in tomato

Santos, Adolfo Luís dos; Chaves-Silva, Samuel; Yang, Lina; Maia, Lucas Gontijo Silva; Chalfun-Júnior, Antônio; Sinharoy, Senjuti; Zhao, Jian; Benedito, Vagner A.

doi:10.1186/s12870-017-1115-2

Cited by 73 publications

(63 citation statements)

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“…The soybean genome contains a high number (103) of BAHD genes as compared to 69 in Cynara cardunculus [49], 64 in A. thaliana [17], but less the 119 BAHD genes in the Oryza sativa genome [16]. This large gene family might be the result of the two rounds of whole-genome duplication (WGD) events that occurred 58-60 (the Papilionoideae allotetraploidization event) and 13 Mya (recent soybean allotetraploidization) in soybean [66]. The presence of paralogous genes in a plant genome is more often related to their functional category than the genetic proximity between species [67].…”

Section: Chromosomal Localization and Duplication Of Soybean Bahd Genesmentioning

confidence: 99%

Global dissection of the BAHD acyltransferase gene family in soybean: Expression profiling, metabolic functions, and evolution

Ahmad¹,

Zeng²,

Dong³

et al. 2020

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Background: Members of the BAHD acyltransferase (ACT) family play important roles in plant defence against biotic and abiotic stresses. Previous genome-wide studies explored different acyltransferase gene families, but not a single study was found so far on the overall genome-wide or positive selection analyses of the BAHD family genes in Glycine max . A better understanding of the functions that specific members of this family play in stress defence can lead to better breeding strategies for stress tolerance. Results: A total of 103 genes of the BAHD family (GmACT genes) were mined from the soybean genome, which could be grouped into four phylogenetic clades (I- IV). Clade III was further divided into two sub-clades (IIIA and IIIB). In each clade, the constituent part of the gene structures and motifs were relatively conserved. These 103 genes were distributed unequally on all 20 chromosomes, and 16 paralogous pairs were found within the family. Positive selection analysis revealed important amino acids under strong positive selection, which suggests that the evolution of this gene family modulated soybean domestication. Most of the expression of ACT genes in soybean was repressed with Al 3+ and fungal elicitor exposure, except for GmACT84 , which expression increased in these conditions 2- and 3-fold, respectively. The promoter region of GmACT84 contains the maximum number of stress-responsive elements among all GmACT genes and is especially enriched in MYB-related elements. Some GmACT genes showed expression specific under specific conditions, while others showed constitutive expression in all soybean tissues or conditions analysed. Conclusions: This study provided a genome-wide analysis of the BAHD gene family and assessed their expression profiles. We found evidence of a strong positive selection of GmACT genes. Our findings will help efforts of functional characterisation of ACT genes in soybean in order to discover their involvement in growth, development, and defence mechanisms.

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Section: Chromosomal Localization and Duplication Of Soybean Bahd Genesmentioning

confidence: 99%

Global dissection of the BAHD acyltransferase gene family in soybean: Expression profiling, metabolic functions, and evolution

Ahmad¹,

Zeng²,

Dong³

et al. 2020

Preprint

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“…The MATE gene family comprises one of the largest family of genes that encode transporters in plants, and the members are involved in many physiological processes during plant growth and development. At present, the structure and function of the members of the MATE transporter family have been analyzed in many plant species, such as Arabidopsis [24,25], soybean [26], tomato [27], and sesame [28]; however, this information has not been reported in rice.…”

Section: Discussionmentioning

confidence: 99%

Genome-wide Analysis of the Rice Mate Gene Family: Identification, Genomic Organization and Expression Profiles in Response to Abiotic Stresses

Zheng

et al. 2020

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Background: Multidrug and toxic compound extrusion (MATE) proteins are involved in many physiological functions of plant growth and development. Although an increasing number of MATE proteins have been identified, the understanding of MATE proteins is still very limited in rice.Results: In this study, 46 MATE proteins were identified from the rice (Oryza sativa) genome by homology searches and domain prediction. In addition, physical and chemical properties of the encoded proteins, subcellular localization, chromosome localization, stress-related cis-elements in abiotic stresses were determined, and a phylogenetic analysis and conserved motif analysis were performed. The rice MATE family can be divided into four subfamilies. It is speculated that members of the rice MATE family have many potential functions, such as the transport and accumulation of flavonoids and alkaloids, the extrusion of plant or exogenous compounds, the regulation of disease resistance and the response to abiotic stress, based on the proteins and cis-acting elements with known functions in the same subfamily. Analysis of gene expression showed that most of the genes were constitutively expressed. Furthermore, eight MATE genes were chosen for qRT-PCR-based analysis and showed differential expression patterns in response to salt and drought stress. Conclusions: Phylogenetic analysis, element prediction, expression data and homology with other species provided strong evidence for functional homology of MATE gene in rice. The analysis results of this study provide comprehensive information on the MATE gene family in rice and will aid in understanding the functional divergence of MATE genes.

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“…Eckardt, 2001;Kuroda and Tsuchiya, 2009; Moriyama et al, 2008). (Santos et al, 2017;, while there are only two genes encoding MATE transporters (hMATE1 and hMATE2) in humans .…”

Section: Resultsmentioning

confidence: 99%

“…Plant genomes usually contain a high number of MATE genes, in contrast to those of prokaryotes and animals, which harbor just a few. For instance, there are 56 MATE genes in the A. thaliana genome , 117 in Glycine max , 46 in Oryza sativa , 67 in Solanum lycopersicum (Santos et al, 2017), and 70 in M. truncatula . Meanwhile, there are only two in humans (HsMATE1 and HsMATE2) (Omote et al, 2006).…”

Section: Referencesmentioning

confidence: 99%

“…The expression analysis used the following programs in the Galaxy platform (https://usegalaxy.org): reads went through FastQC (FastQC v0.10.1 )for the quality control, and then trimmed with Trimmomatic (v. 0.36.5), and the alignment and transcript quantification were carried out with Salmon (Galaxy version 0.9.1) using the Medicago truncatula genome version 4.0 as reference. Expression correlations between MtSLAC1 and each gene annotated in the genome were calculated using Spearman's rank correlation coefficient in Microsoft Excel for Mac as previously described (Santos et al, 2017) (Santos et al, 2017). Supplementary Figure S4.…”

Section: Gene Expression Association Analysesmentioning

confidence: 99%

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Characterization of nodule-specific, SLAC and MATE membrane transporters in Medicago truncatula

Yang¹

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Characterization of nodule-specific, SLAC and MATE membrane transporters in Medicago truncatula Lina Yang Legumes play a crucial role in sustainable agriculture because of their intrinsic ability to reduce atmospheric N2 into NH3 via symbiotic nitrogen fixation (SNF). SNF is carried out in the symbiosome, a quasi-organelle containing endosymbiotic rhizobial bacteria in the cytoplasm of infected cells of the nodule. Therefore, the bacteria are surrounded by a symbiosome membrane (SM), which is derived from the plant plasma membrane during infection. SNF requires constant nutritional exchanges between symbionts, including reduced carbon (dicarboxylates) from the plant for reduced nitrogen (NH4 +) from the bacteroids. This exchange of nutrients and signals is fundamental to SNF and occurs through various transporters in several membranes, and critically through the SM. However, despite the fact that many nodule-specific or high-expressed putative transport genes have been identified in nodules at the genetic level, little is still known about their biochemical and physiological roles for SNF. Thus, we functionally characterized two transporter genes exclusively or highly expressed in the nodules of Medicago truncatula, a well-established legume model species: MtSLAH1 (Medtr4g049640, TCDB 2.A.16.5) of the Tellurite-resistance/Dicarboxylate transporter family, and MtMATE30 (Medtr7g082810, TCDB 2.A.66.1) of the Multidrug and toxic compound Extrusion family. There are seven SLAC (Slow Anion Channel associated) and 70 MATE (Multidrug and Toxic compound Extrusion) family members in the M. truncatula genome. MtSLAH1 is the SLAC transporter with highest expression value in nodules among seven members. Its expression is reduced 5-fold in 2 days after application of nitrate, a known SNF repressor. MtSLAH1 is highly expressed in infected cells and requires bacteroid differentiation for induction. MtSLAH1 channel permeability to dicarboxylates was tested by patch-clamp of Xenopus oocytes, but no current was detected. MtSLAH1 either requires a cofactor for activation or facilitates the efflux a different anion (e.g., nitrate, chloride). On the other hand, MtMATE30 is the MATE gene with highest expression in nodules. It is induced 100-fold by low nitrogen while strongly repressed by nitrate, suggesting a role in symbiotic nitrogen fixation. It starts to express in immature nodules (6 days post-inoculation, dpi), reaches its peak in young, mature nodules (10 dpi) and maintains consistent expression in older nodules. It is expressed in all nodule zones, except the meristem. MtMATE30 canonically belongs to a phylogenetic clade that includes transporters with affinity to alkaloids. Trigonelline is a widely distributed alkaloid and commonly found in legumes. Previous research showed that rhizobia are able to catabolize trigonelline by the trc gene located in the rhizobial pSym megaplasmid. We confirmed the presence of trigonelline in nodules of M. truncatula and showed MtMATE30 affinity to trigonelline in a heterologous bacteria syste...

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Global analysis of the MATE gene family of metabolite transporters in tomato

Cited by 73 publications

References 100 publications

Global dissection of the BAHD acyltransferase gene family in soybean: Expression profiling, metabolic functions, and evolution

Global dissection of the BAHD acyltransferase gene family in soybean: Expression profiling, metabolic functions, and evolution

Genome-wide Analysis of the Rice Mate Gene Family: Identification, Genomic Organization and Expression Profiles in Response to Abiotic Stresses

Characterization of nodule-specific, SLAC and MATE membrane transporters in Medicago truncatula

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