A Genome-Wide Survey of MATE Transporters in Brassicaceae and Unveiling Their Expression Profiles under Abiotic Stress in Rapeseed

Qiao, Cailin; Yang, Jing; Wan, Yuanyuan; Xiang, Sirou; Guan, Mingwei; Du, Hongwu; Tang, Zhongjie; Lu, Kun; Li, Jiana; Qu, Cunmin

doi:10.3390/plants9091072

Cited by 12 publications

(6 citation statements)

References 90 publications

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“…For example, our CarMATEs count ( n = 48) is relatively low compared to that reported by Zhang et al (2020) , who identified 56 CarMATEs using the reference genome of the CDC Frontier available in the NCBI database (BioProject: PRJNA190909 ). At the same time, compared with previous studies, we identified comparable numbers of MATEs in the dicot model Arabidopsis ( Arabidopsis thaliana ; n = 57) and the monocot model rice ( Oryza sativa ; n = 55; Huang et al, 2019 ; Qiao et al, 2020 ), which further validates our identification strategy based on the MATE-domain based hmm profile search.…”

Section: Discussionsupporting

confidence: 81%

A Systematic Phylogenomic Classification of the Multidrug and Toxic Compound Extrusion Transporter Gene Family in Plants

et al. 2022

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Multidrug and toxic compound extrusion (MATE) transporters comprise a multigene family that mediates multiple functions in plants through the efflux of diverse substrates including organic molecules, specialized metabolites, hormones, and xenobiotics. MATE classification based on genome-wide studies remains ambiguous, likely due to a lack of large-scale phylogenomic studies and/or reference sequence datasets. To resolve this, we established a phylogeny of the plant MATE gene family using a comprehensive kingdom-wide phylogenomic analysis of 74 diverse plant species. We identified more than 4,000 MATEs, which were classified into 14 subgroups based on a systematic bioinformatics pipeline using USEARCH, blast+ and synteny network tools. Our classification was performed using a four-step process, whereby MATEs sharing ≥ 60% protein sequence identity with a ≤ 1E-05 threshold at different sequence lengths (either full-length, ≥ 60% length, or ≥ 150 amino acids) or retaining in the similar synteny blocks were assigned to the same subgroup. In this way, we assigned subgroups to 95.8% of the identified MATEs, which we substantiated using synteny network clustering analysis. The subgroups were clustered under four major phylogenetic groups and named according to their clockwise appearance within each group. We then generated a reference sequence dataset, the usefulness of which was demonstrated in the classification of MATEs in additional species not included in the original analysis. Approximately 74% of the plant MATEs exhibited synteny relationships with angiosperm-wide or lineage-, order/family-, and species-specific conservation. Most subgroups evolved independently, and their distinct evolutionary trends were likely associated with the development of functional novelties or the maintenance of conserved functions. Together with the systematic classification and synteny network profiling analyses, we identified all the major evolutionary events experienced by the MATE gene family in plants. We believe that our findings and the reference dataset provide a valuable resource to guide future functional studies aiming to explore the key roles of MATEs in different aspects of plant physiology. Our classification framework can also be readily extendable to other (super) families.

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Section: Discussionsupporting

confidence: 81%

A Systematic Phylogenomic Classification of the Multidrug and Toxic Compound Extrusion Transporter Gene Family in Plants

et al. 2022

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“…In plants, they participate in diverse functions that regulate plant development and adaptation to stresses, by transporting and sequestering harmful substances and secondary metabolites. Although MATE genes have been identified in several plant genomes [50][51][52][53][54][55][56][57][58][59], little is known about the function of MATE transporters in Solanaceous species, which are of high economic and agronomic importance. Here, we performed a comprehensive genome-wide identification of MATE genes in pepper and potato, two members of the Solanaceae, identifying 42 CaMATE and 60 StMATE genes.…”

Section: Discussionmentioning

confidence: 99%

“…From the Leguminosae family in the eudicots, 70 were identified in M. truncatula [53], 117 in soybean [54], and 67 in pigeon pea (Cajanus cajan) [55]. In other eudicots, 71 were identified in poplar (Populus trichocarpa) [56], 73 in flax (Linum usitassimum) [57], 67 in Citrus sinensis [58], 56 in Arabidopsis [50], and 79-130 in four Brassicaceae species [59].…”

Section: Introductionmentioning

confidence: 99%

Identification and Expression of the Multidrug and Toxic Compound Extrusion (MATE) Gene Family in Capsicum annuum and Solanum tuberosum

Chen

Wang

Liu

et al. 2020

Plants

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Multidrug and Toxic Compound Extrusion (MATE) proteins are essential transporters that extrude metabolites and participate in plant development and the detoxification of toxins. Little is known about the MATE gene family in the Solanaceae, which includes species that produce a broad range of specialized metabolites. Here, we identified and analyzed the complement of MATE genes in pepper (Capsicum annuum) and potato (Solanum tuberosum). We classified all MATE genes into five groups based on their phylogenetic relationships and their gene and protein structures. Moreover, we discovered that tandem duplication contributed significantly to the expansion of the pepper MATE family, while both tandem and segmental duplications contributed to the expansion of the potato MATE family, indicating that MATEs took distinct evolutionary paths in these two Solanaceous species. Analysis of ω values showed that all potato and pepper MATE genes experienced purifying selection during evolution. In addition, collinearity analysis showed that MATE genes were highly conserved between pepper and potato. Analysis of cis-elements in MATE promoters and MATE expression patterns revealed that MATE proteins likely function in many stages of plant development, especially during fruit ripening, and when exposed to multiple stresses, consistent with the existence of functional differentiation between duplicated MATE genes. Together, our results lay the foundation for further characterization of pepper and potato MATE gene family members.

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“…Along with the ABC transporters, involvement of other transporters including multidrug and toxic compound extrusion (MATE) family proteins [ 189 , 190 ], zinc-iron permease ( ZIP) , iron-regulated transporters ( IRT1 ) [ 190 ], natural resistance-associated macrophage proteins (NRAMP), copper transporters (Ctr/COPT), and heavy metal ATPase (HMA) transporters [ 191 ] has also been highlighted in tolerance to HM toxicity. These metal transporters are involved in mediating metal intake and translocation in plants [ 192 ].…”

Section: Sequestration and Compartmentalization: Plants’ Way To Alleviate The Hm Toxicitymentioning

confidence: 99%

A Comprehensive Review on the Heavy Metal Toxicity and Sequestration in Plants

et al. 2021

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Heavy metal (HM) toxicity has become a global concern in recent years and is imposing a severe threat to the environment and human health. In the case of plants, a higher concentration of HMs, above a threshold, adversely affects cellular metabolism because of the generation of reactive oxygen species (ROS) which target the key biological molecules. Moreover, some of the HMs such as mercury and arsenic, among others, can directly alter the protein/enzyme activities by targeting their –SH group to further impede the cellular metabolism. Particularly, inhibition of photosynthesis has been reported under HM toxicity because HMs trigger the degradation of chlorophyll molecules by enhancing the chlorophyllase activity and by replacing the central Mg ion in the porphyrin ring which affects overall plant growth and yield. Consequently, plants utilize various strategies to mitigate the negative impact of HM toxicity by limiting the uptake of these HMs and their sequestration into the vacuoles with the help of various molecules including proteins such as phytochelatins, metallothionein, compatible solutes, and secondary metabolites. In this comprehensive review, we provided insights towards a wider aspect of HM toxicity, ranging from their negative impact on plant growth to the mechanisms employed by the plants to alleviate the HM toxicity and presented the molecular mechanism of HMs toxicity and sequestration in plants.

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A Genome-Wide Survey of MATE Transporters in Brassicaceae and Unveiling Their Expression Profiles under Abiotic Stress in Rapeseed

Cited by 12 publications

References 90 publications

A Systematic Phylogenomic Classification of the Multidrug and Toxic Compound Extrusion Transporter Gene Family in Plants

A Systematic Phylogenomic Classification of the Multidrug and Toxic Compound Extrusion Transporter Gene Family in Plants

Identification and Expression of the Multidrug and Toxic Compound Extrusion (MATE) Gene Family in Capsicum annuum and Solanum tuberosum

A Comprehensive Review on the Heavy Metal Toxicity and Sequestration in Plants

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