芝麻MATE基因家族的全基因组鉴定与表达分析

植物为了维持其生命系统的正常运转,需要对各种代谢产物和毒素进行转运和排出.多药与毒性化合物排出转运蛋白(multidrug and toxic compound extrusion,MATE)在多种底物和毒素的运输中起到重要作用.本研究利用生物信息学手段对芝麻MATE基因家族进行了全基因组分析,鉴定得到67个MATE基因,分布于全部13条染色体上,亚细胞定位预测表明这些基因主要位于质膜上.串联复制和全基因组复制是芝麻MATE基因家族扩增的主要动力.比较基因组学分析发现在芝麻和拟南芥中具有许多共线性的MATE基因,且大部分串联复制SiMATE基因产生于芝麻和拟南芥分化之后.系统进化分析可将芝麻MATE成员分为4个亚家族,大部分相似功能的己知植物MATE成员被聚在同一分枝中,进化树中关系较近的芝麻MATE成员往往具有相似的基因结构和保守基序.基因表达分析表明一半以上的SiMATE基因具有组织表达特异性.这些结果为芝麻MATE基因功能的研究提供了重要参考.     

芝麻MATE基因家族的全基因组鉴定与表达分析

植物为了维持其生命系统的正常运转,需要对各种代谢产物和毒素进行转运和排出.多药与毒性化合物排出转运蛋白(multidrug and toxic compound extrusion,MATE)在多种底物和毒素的运输中起到重要作用.本研究利用生物信息学手段对芝麻MATE基因家族进行了全基因组分析,鉴定得到67个MATE基因,分布于全部13条染色体上,亚细胞定位预测表明这些基因主要位于质膜上.串联复制和全基因组复制是芝麻MATE基因家族扩增的主要动力.比较基因组学分析发现在芝麻和拟南芥中具有许多共线性的MATE基因,且大部分串联复制SiMATE基因产生于芝麻和拟南芥分化之后.系统进化分析可将芝麻MATE成员分为4个亚家族,大部分相似功能的己知植物MATE成员被聚在同一分枝中,进化树中关系较近的芝麻MATE成员往往具有相似的基因结构和保守基序.基因表达分析表明一半以上的SiMATE基因具有组织表达特异性.这些结果为芝麻MATE基因功能的研究提供了重要参考.     

普通烟草MATE基因家族分析及功能预测

摘要：植物多药和有毒化合物排出家族（multidrug and toxic compound extrusion,MATE）是一类可转运毒素、金属离子、次级代谢产物的次级转运蛋白家族。该家族主要在植物的解毒机制中发挥作用,部分成员也参与植物的形态建成过程。MATE家族在烟草基因组中的数量、特征及功能目前尚未开展系统分析。本研究利用生物信息学方法对普通烟草（Nicotiana tabacum）基因组中的MATE基因进行了预测分析,共预测到131个基因,分为4个亚家族。亚家族3在进化树中形成较为独立的分枝,其跨膜区数量、亚细胞定位、保守结构域方面与其他亚家族不同。转录组数据显示,相当一部分MATE家族基因在所有组织中低量表达。GO功能注释结果表明该家族成员主要作为一种转运体,在应激响应、生物调控等过程中发挥作用。本研究为烟草及其他植物中MATE家族的鉴定和功能研究提供了数据基础。     

植物多药和有毒化合物排出转运蛋白研究进展

植物在生长及适应环境的过程中会吸收很多有益或有害的物质,自身也会产生大量代谢物,植物对这些物质的转运是植物生长发育及适应环境的重要环节,有多种转运蛋白家族参与其中。多药和有毒化合物排出转运蛋白(MATEs)是生物体中重要的转运蛋白家族之一,而植物中MATE基因的丰富程度要远远高于其他生物。根据植物MATEs的蛋白结构,这些基因被分为4个主要的亚家族,即MATE I,MATEⅡ,MATEⅢ和MATE IV。同一亚家族或同一MATE基因簇的基因还具有相同或相似的功能。植物MATEs定位于细胞的各种生物膜上,如细胞质膜、液泡膜、高尔基膜及囊泡膜等。此外,一些MATEs的表达还具有组织特异性,它们转运的底物也具有多样性和特异性,使得MATEs呈现出多种生物学功能。它们在外源性物质的排出、次生代谢产物的转运和累积、铁转运、铝脱毒和植物激素信号传递及植物的抗病性等方面都起着重要作用。该文对MATEs的发现、基因分类、亚细胞定位及生理功能等方面进行了概述,对深入研究该基因家族提供了思路,对该基因家族的应用进行了展望。     

拟南芥液泡膜Na+/H+逆向转运蛋白的研究进展

拟南芥液泡膜Na /H 逆向转运蛋白是由AtNHX1基因编码的一个在盐胁迫中起重要作用的蛋白。本文综述了AtNHX1的基本结构、功能及作用机制,展望其作为有效植物耐盐基因的前景,并对拟南芥液泡膜Na /H 逆向转运蛋白基因家族其他成员的研究,也做了相应的概括。     

拟南芥MATE家族成员DTX18表达调控

拟南芥多药物和有毒化合物排出家族(MATE)属次级转运蛋白家族, 此类转运蛋白与解毒内源的次生代谢物和外源的有毒化合物有关.通过 PCR 的方法从拟南芥基因组中扩增到该家族成员DTX18的启动子序列,构建重组质粒后,通过农杆菌介导的方法获得转基因植物.GUS 组织化学染色发现此基因的表达受到伤害和茉莉酸甲酯(MJ)诱导.同时结合半定量 PCR 的方法检测该基因在伤害及 MJ 处理下转录本丰度的变化,进一步证实了此结果.另外,此基因在突变体coi1,ein2中的表达量明显降低,这一点揭示了此基因表达的调控机制,即与植物激素JA/ET的信号传导密切相关.     

拟南芥MATE家族基因DTX12的表达模式分析

拟南芥多药物和有毒化合物排出家族属次级转运蛋白家族,此类转运蛋白与解毒内源的次生代谢物和外源的有毒化合物有关。通过PCR的方法从拟南芥基因组中扩增到该家族成员DTX12的启动子序列,构建双元载体pBI101.2-ProDTX12-GUS,通过农杆菌介导的方法转化拟南芥,然后对转基因植株用GUS底物进行组织化学显色分析。同时,通过半定量RT-PCR的方法,进一步验证了DTX12在不同组织中的表达情况。结果表明该基因在成熟的花器官的花药中和幼苗的根尖特异表达,另外,在子叶的尖端也有少量的表达。由于DTX12编码的是一个具有转运有毒化合物功能的蛋白,推测其功能可能是转运与细胞分裂或生长有关的次生代谢物。     

拟南芥AAP基因家族的生物信息学分析

氨基酸通透酶(amino acid permease,AAP)是一种跨膜转运蛋白,广泛参与氨基酸的吸收、转运。本研究采用生物信息学方法对拟南芥AAP基因家族8个成员(编号AtAAP1~At AAP8)进行染色体定位、蛋白质理化性质、亚细胞定位、三级结构、跨膜区、基因结构及调控元件等进行分析,为探索AAP基因在拟南芥氨基酸吸收转运中的作用及进一步研究AtAAP基因家族的功能提供理论依据。     

大叶藻基因组铵根转运蛋白AMT的生物信息学特征

本研究利用生物信息学方法,对大叶藻基因组中8个铵根转运蛋白(ZmAMTs)基因特征、氨基酸组成成分、理化性质以及二级结构进行预测和分析,同时还分析了大叶藻与拟南芥、水稻、烟草及百脉根的AMT基因家族之间的联系。大叶藻基因组中8个AMT基因分为AMT1 (5个成员)和AMT2 (3个成员)两个子家族,所编码的蛋白质含有9～11个跨膜区,且均为疏水性蛋白质,二级结构均由α螺旋、直链延伸和无规卷曲三种形式构成。除此之外,大叶藻AMT家族蛋白具有相似的三维结构,多数成员定位于细胞质、质膜和叶绿体膜上。本研究对大叶藻铵根转运蛋白进行了详细的生物信息学分析,可为今后深入研究该家族基因的结构特征和功能提供参考。     

葡萄中蔗糖转运蛋白家族的序列分析及功能推测

以葡萄中的蔗糖转运蛋白为主要研究对象,结合了功能研究较为深入的拟南芥和水稻蔗糖转运蛋白家族序列,分析讨论了这些基因在启动子区域顺式作用元件的异同,以及这些差异可能对mRNA的转录带来的影响;同时,根据蔗糖转运蛋白氨基酸序列对其家族进行了分类,分析了不同亚类蔗糖转运蛋白基因结构的特点;最后还对蔗糖转运蛋白家族中氨基酸的保守性进行了分析。这些分析将为后续蔗糖转运蛋白功能基因组学的研究以及通过基因工程技术精确调节植物代谢提供一定的依据。     

The multidrug/oligosaccharidyl-lipid/polysaccharide (MOP) exporter superfamily.

The multidrug/oligosaccharidyl-lipid/polysaccharide (MOP) exporter superfamily (TC #2.A.66) consists of four previously recognized families: (a) the ubiquitous multi-drug and toxin extrusion (MATE) family; (b) the prokaryotic polysaccharide transporter (PST) family; (c) the eukaryotic oligosaccharidyl-lipid flippase (OLF) family and (d) the bacterial mouse virulence factor family (MVF). Of these four families, only members of the MATE family have been shown to function mechanistically as secondary carriers, and no member of the MVF family has been shown to function as a transporter. Establishment of a common origin for the MATE, PST, OLF and MVF families suggests a common mechanism of action as secondary carriers catalyzing substrate/cation antiport. Most protein members of these four families exhibit 12 putative transmembrane alpha-helical segments (TMSs), and several have been shown to have arisen by an internal gene duplication event; topological variation is observed for some members of the superfamily. The PST family is more closely related to the MATE, OLF and MVF families than any of these latter three families are related to each other. This fact leads to the suggestion that primordial proteins most closely related to the PST family were the evolutionary precursors of all members of the MOP superfamily. Here, phylogenetic trees and average hydropathy, similarity and amphipathicity plots for members of the four families are derived and provide detailed evolutionary and structural information about these proteins. We show that each family exhibits unique characteristics. For example, the MATE and PST families are characterized by numerous paralogues within a single organism (58 paralogues of the MATE family are present in Arabidopsis thaliana), while the OLF family consists exclusively of orthologues, and the MVF family consists primarily of orthologues. Only in the PST family has extensive lateral transfer of the encoding genes occurred, and in this family as well as the MVF family, topological variation is a characteristic feature. The results serve to define a large superfamily of transporters that we predict function to export substrates using a monovalent cation antiport mechanism.     

From organelle to organ: ZRIZI MATE-Type transporter is an organelle transporter that enhances organ initiation

Plant architecture is a predictable but flexible trait. The timing and position of organ initiation from the shoot apical meristem (SAM) contribute to the final plant form. While much progress has been made recently in understanding how the site of leaf initiation is determined, the mechanism underlying the temporal interval between leaf primordia is still largely unknown. The Arabidopsis ZRIZI (ZRZ) gene belongs to a large gene family encoding multidrug and toxic compound extrusion (MATE) transporters. Unique among plant MATE transporters identified so far, ZRZ is localized to the membrane of a small organelle, possibly the mitochondria. Plants overexpressing ZRZ in initiating leaves are short, produce leaves much faster than wild-type plants and show enhanced growth of axillary buds. These results suggest that ZRZ is involved in communicating a leaf-borne signal that determines the rate of organ initiation.     

How a microbial drug transporter became essential for crop cultivation on acid soils: aluminium tolerance conferred by the multidrug and toxic compound extrusion (MATE) family

Background

Aluminium (Al) toxicity is a major agricultural constraint for crop cultivation on acid soils, which comprise a large portion of the world''s arable land. One of the most widely accepted mechanisms of Al tolerance in plants is based on Al-activated organic acid release into the rhizosphere, with organic acids forming stable, non-toxic complexes with Al. This mechanism has recently been validated by the isolation of bona-fide Al-tolerance genes in crop species, which encode membrane transporters that mediate Al-activated organic acid release leading to Al exclusion from root apices. In crop species such as sorghum and barley, members in the multidrug and toxic compound extrusion (MATE) family underlie Al tolerance by a mechanism based on Al-activated citrate release.

Scope and Conclusions

The study of Al tolerance in plants as conferred by MATE family members is in its infancy. Therefore, much is yet to be discovered about the functional diversity and evolutionary dynamics that led MATE proteins to acquire transport properties conducive to Al tolerance in plants. In this paper we review the major characteristics of transporters in the MATE family and will relate this knowledge to Al tolerance in plants. The MATE family is clearly extremely flexible with respect to substrate specificity, which raises the possibility that Al tolerance as encoded by MATE proteins may not be restricted to Al-activated citrate release in plant species. There are also indications that regulatory loci may be of pivotal importance to fully explore the potential for Al-tolerance improvement based on MATE genes.     

外排泵介导鲍曼不动杆菌耐药性的研究进展

目的鲍曼不动杆菌的多重耐药性问题日趋严重,该菌外膜上外排泵过表达是导致其耐药性的重要机制。详尽地研究多药外排泵的机制以及寻找阻断其功能的外排泵抑制剂,将为多耐药鲍曼不动杆菌的治疗开辟新的路径。本文就近年来鲍曼不动杆菌外排泵的研究现状进行综述,着重描述多药外排泵RND家族的耐药谱特征及其表达调控机制,同时,还阐述了MFS和MATE家族外排泵的研究进展。     

Genome-wide identification and expression analysis of MATE gene family in citrus fruit (Citrus clementina)

Multidrug and toxic compound extrusion (MATE) proteins are a class of secondary active multidrug transporters. In plants, this family has significantly expanded and is involved in numerous plant physiological processes. Although MATE proteins have been identified in an increasing number of species, the understanding about this family in citrus remains unclear. In this study, a total of 69 MATE transporters were identified in the citrus genome (Citrus clementina) and classified into four groups by phylogenetic analysis. Tandem and segmental duplication events were the main causes of the citrus MATE family expansion. RNA-seq and qRT-PCR analyses were performed during citrus fruit development. The results indicated that CitMATE genes showed specific expression profiles in citrus peels and flesh at different developmental stages. Combined with the variations of flavonoids and citrate levels in citrus fruit, we suggested that CitMATE43 and CitMATE66 may be involved in the transport process of flavonoids and citrate in citrus fruit, respectively. In addition, two flavonoids positive regulators, CitERF32 and CitERF33, both directly bind to and activated the CitMATE43 promoter. Our results provide comprehensive information on citrus MATE genes and valuable understanding for the flavonoids and citrate metabolism in citrus fruit.