Tissue and regional expression patterns of dicistronic tRNA–mRNA transcripts in grapevine (Vitis vinifera) and their evolutionary co-appearance with vasculature in land plants

Transfer RNAs(tRNA)are crucial adaptor molecules between messenger RNA(mRNA)and amino acids.Recent evidence in plants suggests that dicistronic tRNA-like structures also act as mobile signals for mRNA transcripts to move between distant tissues.Co-transcription is not a common feature in the plant nuclear genome and,in the few cases where polycistronic transcripts have been found,they include non-coding RNA species,such as small nucleolar RNAs and microRNAs.It is not known,however,the extent to which dicistronic transcripts of tRNA and mRNAs are expressed in field-grown plants,or the factors contributing to their expression.We analysed tRNA–mRNA dicistronic transcripts in the major horticultural crop grapevine(Vitis vinifera)using a novel pipeline developed to identify dicistronic transcripts from high-throughput RNA-sequencing data.We identified dicistronic tRNA–mRNA in leaf and berry samples from 22 commercial vineyards.Of the 124 tRNA genes that were expressed in both tissues,18 tRNA were expressed forming part of 19 dicistronic tRNA–mRNAs.The presence and abundance of dicistronic molecules was tissue and geographic sub-region specific.In leaves,the expression patterns of dicistronic tRNA–mRNAs significantly correlated with tRNA expression,suggesting that their transcriptional regulation might be linked.We also found evidence of syntenic genomic arrangements of tRNAs and protein-coding genes between grapevine and Arabidopsis thaliana,and widespread prevalence of dicistronic tRNA–mRNA transcripts among vascular land plants but no evidence of these transcripts in non-vascular lineages.This suggests that the appearance of plant vasculature and tRNA–mRNA occurred concurrently during the evolution of land plants.

Coordinated regulation of the mitochondrial retrograde response by circadian clock regulators and ANAC017

Mitochondrial retrograde signaling(MRS)supports photosynthetic function under a variety of conditions.Induction of mitochondrial dysfunction with myxothiazol(a specific inhibitor of the mitochondrial bc1 complex)or antimycin A(an inhibitor of the mitochondrial bc1 complex and cyclic electron transport in the chloroplast under light conditions)in the light and dark revealed diurnal control of MRS.This was evidenced by(1)significantly enhanced binding of ANAC017 to promoters in the light compared with the dark in Arabidopsis plants treated with myxothiazol(but not antimycin A),(2)overlap in the experimentally determined binding sites for ANAC017 and circadian clock regulators in the promoters of ANAC013 and AOX1a,(3)a diurnal expression pattern for ANAC017 and transcription factors it regulates,(4)altered expression of ANAC017-regulated genes in circadian clock mutants with and without myxothiazol treatment,and(5)a decrease in the magnitude of LHY and CCA1 expression in an ANAC017-overexpressing line and protein–protein interaction between ANAC017 and PIF4.This study also shows a large difference in transcriptome responses to antimycin A and myxothiazol in the dark:these responses are ANAC017 independent,observed in shoots and roots,similar to biotic challenge and salicylic acid responses,and involve ERF and ZAT transcription factors.This suggests that antimycin A treatment stimulates a second MRS pathway that is mediated or converges with salicylic acid signaling and provides a merging point with chloroplast retrograde signaling.

Anterograde and Retrograde Regulation of Nuclear Genes Encoding Mitochondrial Proteins during Growth, Development, and Stress

在植物的 Mitochondrial 生物的续生说和功能要求编码 mitochondrial 蛋白质(NGEMP ) 的超过 1000 原子基因的表示。这些基因的表达式被织物特定、发展、内部、外部的刺激 thatresult 在涉及的一个动态细胞器调整新陈代谢并且许多发信号的进程。尽管线粒体的新陈代谢的 andbiosynthetic 机械很好相对被理解，调整这些过程和 varioussignaling 小径的因素仅仅在分子的水平正在识别包含。anterograde 的分子的部件(对 mitochondrial 原子) 并且后退(mitochondrial 到原子) 与叶绿体调整 NGEMPsinteract 的表示的发信号的小径 -- ，生长 -- ，并且在在许多层次的房间的发信号压力的小径，与在这些信号的传播和执行的普通 componentsinvolved。这作为在 thecell，不是仅仅在 mitochondrial 功能本身的直接发信号，而且在察觉到或集成许多 otherinternal 和外部信号发信号的重要中心放线粒体。这与精力新陈代谢和压力回答集成并且优化生长，哪个在光合、非光合的 cells.Key 词的 isrequired：

Mitochondrial Composition,Function and Stress Response in Plants

The primary function of mitochondria is respiration,where catabolism of substrates is coupled to ATP synthesis via oxidative phosphorylation.In plants,mitochondrial composition is relatively complex and flexible and has specific pathways to support photosynthetic processes in illuminated leaves.This review begins with outlining current models of mitochondrial composition in plant cells,with an emphasis upon the assembly of the complexes of the classical electron transport chain (ETC).Next,we focus upon the comparative analysis of mitochondrial function from different tissue types.A prominent theme in the plant mitochondrial literature involves linking mitochondrial composition to environmental stressresponses,and this review then gives a detailed outline of how oxidative stress impacts upon the plant mitochondrial proteome with particular attention to the role of transition metals.This is followed by an analysis of the signaling capacity of mitochondrial reactive oxygen species,which studies the transcriptional changes of stress responsive genes as a framework to define specific signals emanating from the mitochondrion.Finally,specific mitochondrial roles during exposure to harsh environments are outlined,with attention paid to mitochondrial delivery of energy and intermediates,mitochondrial support for photosynthesis,and mitochondrial processes operating within root cells that mediate tolerance to anoxia and unfavorable soil chemistries.

Expression of Mitochondrial Gene Fragments within the Tapetum Induce Male Sterility by Limiting the Biogenesis of the Respiratory Machinery in Transgenic Tobacco

Plant mitochondrial genomes (mtDNAs) are large and undergo frequent recombination events. A common phenotype that emerges as a consequence of altered mtDNA structure is cytoplasmic-male sterility (CMS). The molecular basis for CMS remains unclear, but it seems logical that altered respiration activities would result in reduced pollen production. Analysis of tobacco (Nicotiana tabacum) mtDNAs indicated that CMS-associated loci often contain fragments of known organellar genes. These may assemble with organellar complexes and thereby interfere with normal respiratory functions. Here, we analyzed whether the expression of truncated fragments of mitochondrial genes (i.e. atp4, cox1 and rps3) may induce male sterility by limiting the biogenesis of the respiratory machinery. cDNA fragments corresponding to atp4f, cox1f and rps3f were cloned in-frame to a mitochondrial localization signal and a C-termini HA-tag under a tapetum-specific promoter and introduced to tobacco plants by Agrobacterium-mediated transformation. The constructs were then analyzed for their effect on mitochondrial activity and pollen fertility. Atp4f , Cox1f and Rps3f plants demonstrated male sterility phenotypes, which were tightly correlated with the expression of the recombinant fragments in the floral meristem. Fractionation of native organellar extracts showed that the recombinant ATP4f-HA, COX1f-HA and RPS3f-HA proteins are found in large membrane-associated particles. Analysis of the respiratory activities and protein profiles indicated that organellar complex I was altered in Atp4f, Cox1f and Rps3f plants.

Is resource allocation and grain yield of rice altered by inoculation with arbuscular mycorrhizal fungi?

Aims our study quantified the combined effects of fertilization and inoculation with arbuscular mycorrhizal fungi(AMF)on grain yield and allocation of biomass and nutrients in field-grown rice(Oryza sativa l.).Methods a two-factor experiment was conducted at a field site in northeast of China(in shuangcheng,Heilongjiang Province,songhua river basin):six nitrogen-phosphorus-potassium fertilizer levels were provided(0,20,40,60,80 and 100%of the local norm of ferti-lizer supply),with or without inoculation with Glomus mosseae.at maturity,we quantified the percentage of root length colonization by AMF,grain yield,shoot:root ratios,shoot N and P contents and nutrients allocated to panicles,leaves and stems.Important Findingsas expected,inoculation resulted in greatly increased AMF colo-nization,which in turn led to higher shoot:root ratios and greater shoot N contents.shoot:root ratios of inoculated rice increased with increasing fertilization while there was a significant interaction between fertilization and inoculation on shoot:root ratio.additionally,a F inoculation increased panicle:shoot ratios,panicle N:shoot N ratios and panicle P:shoot P ratios,especially in plants grown at low fertilizer levels.Importantly,inoculated rice exhibited higher grain yield,with the maximum improvement(near 62%)at the lower fertilizer end.our results showed that(i)AMFinoculated plants conform to the functional equilibrium theory,albeit to a reduced extent compared to non-inoculated plants and(ii)AMF inoculation resulted in greater allocation of shoot biomass to panicles and increased grain yield by stimulating N and P redis-tribution to panicles.

Integrative Multi-omics Analyses of Barley Rootzones under Salinity Stress Reveal Two Distinctive Salt Tolerance Mechanisms

The mechanisms underlying rootzone-localized responses to salinity during early stages of barley development remain elusive.In this study,we performed the analyses of multi-root-omes(transcriptomes,metabolomes,and lipidomes)of a domesticated barley cultivar(Clipper)and a landrace(Sahara)that maintain and restrict seedling root growth under salt stress,respectively.Novel generalized linear models were designed to determine differentially expressed genes(DEGs)and abundant metabolites(DAMs)specific to salt treatments,genotypes,or rootzones(meristematic Z1,elongation Z2,and maturation Z3).Based on pathway over-representation of the DEGs and DAMs,phenylpropanoid biosynthesis is the most statistically enriched biological pathway among all salinity responses observed.Together with histological evidence,an intense salt-induced lignin impregnation was found only at stelic cell wall of Clipper Z2,compared with a unique elevation of suberin deposition across Sahara Z2.This suggests two differential salt-induced modulations of apoplastic flow between the genotypes.Based on the global correlation network of the DEGs and DAMs,callose deposition that potentially adjusted symplastic flow in roots was almost independent of salinity in rootzones of Clipper,and was markedly decreased in Sahara.Taken together,we propose two distinctive salt tolerance mechanisms in Clipper(growth-sustaining)and Sahara(salt-shielding),providing important clues for improving crop plasticity to cope with deteriorating global soil salinization.

Histone Acetylation, VERNALIZATION INSENSITIVE 3, FLOWERING LOCUS C, and the Vernalization Response

由低温度的 VIN3 的量的正式就职在 Arabidopsis 为 FLC 的 PRC2 压抑和 flowering (开花结实促进法) 的提升被要求。Histone acetylation，通常与基因抄写联系的染色质修正，响应低温度在二个空间地并且时间地不同的阶段在 VIN3 染色质上增加了。在短期的冷暴露期间，在抄写开始地点的 histone H3 acetylation 很快增加了，暗示它为 VIN3 正式就职被要求。在 histone H3 和 H4 acetylation 的随后的变化发生了在延长冷暴露期间跟随继续的 VIN3 抄写。包括 histone acetyltransferase GCN5，它导致冷环境适应小径基因的表示，像英雄传奇的 transcriptional 适配器建筑群的成员不调整在冷暴露期间感应的 VIN3，显示冷环境适应小径并且 VIN3 冷正式就职被不同 transcriptional 机制调整。在另外的 11 histone acetyltransferase 基因的变化没影响 VIN3 正式就职。然而，在 VIN3 地点的菸碱，一个 histone deacetylase 禁止者，导致的 VIN3 和改变的 histone acetylation。VIN3 正式就职与菸碱处理的长度成正比，它与 FLC 的早花的显型和压抑被联系。然而， FLC 的压抑不同于开花结实促进法，独立于 VIN3 活动。菸碱处理没在 PRC2 建筑群的自治小径或成员在任何基因的表示引起一个变化， FLC 的很好描绘的抑压者。我们的数据建议 FLC 经由包含 histone deacetylases 的 SIR2 类的一条新奇小径被镇压。

Defining the Mitochondrial Stress Response in Arabidopsis thaliana

获得的全球概述线粒体对应力作出回应，我们试图定义工厂 mitochondrial 压力反应(MSR ) 。由联合通常认为地与压力相关的条件的 16 个 microarray 实验编码 mitochondrial 蛋白质的一套 1196 Arabidopsis thaliana 基因， 45 原子编码基因被定义为广泛地压力应答。用绿色荧光灯蛋白质(GFP ) 熔化试金，很多这些指向蛋白质的 mitochondrial 被测试，在是的总数 26 蛋白质证实 mitochondrially 指向了。几这些蛋白质被观察双指向了到线粒体和质体，包括小热吃惊蛋白质 sHSP23.5 和 sHSP23.6。除了线粒体的明确的压力部件，例如其他的 oxidases，菸碱腺嘌 dinucleotide (NAD (P) H ) 脱氢酶，和热震惊蛋白质，许多另外的蛋白质，许多与未知功能，被识别。mitochondrial 搬运人蛋白质家庭在压力应答的基因是过去代表的，建议那个压力越过 mitochondrial 为代谢物运输导致改变的需要内部膜。尽管这些蛋白质编码许多的基因包含普通行动 cis 规章的元素，很多个不同规章的过程或信号多半触发了 MSR，是明显的。因此，这些基因提供新模型系统学习 mitochondrial 后退规定，除了广泛地使用的其他的 oxidase 模型。另外，当在对应力应答的蛋白质的变化没在一个抄本与变化相关很好，铺平，它建议 post-transcriptional 机制也在定义 MSR 起一个重要作用。

An MCIA-like complex is required for mitochondrial complex Ⅰ assembly and seed development in maize

During adaptive radiation,mitochondria have co-evolved with their hosts,leading to gain or loss of subunits and assembly factors of respiratory complexes.Plant mitochondrial complex Ⅰ harbors40 nuclearand 9 mitochondrial-encoded subunits,and is formed by stepwise assembly during which different intermediates are integrated via various assembly factors.In mammals,the mitochondrial complex Ⅰ intermediate assembly(MCIA)complex is required for building the membrane arm module.However,plants have lost almost all of the MCIA complex components,giving rise to the hypothesis that plants follow an ancestral pathway to assemble the membrane arm subunits.Here,we characterize a maize crumpled seed mutant,crk1,and reveal by map-based cloning that CRK1 encodes an ortholog of human complex Ⅰ assembly factor 1,zNDUFAF1,the only evolutionarily conserved MCIA subunit in plants.zNDUFAF1 is localized in the mitochondria and accumulates in two intermediate complexes that contain complex Ⅰ membrane arm subunits.Disruption of zNDUFAF1 results in severe defects in complex Ⅰ assembly and activity,a cellular bioenergetic shift to aerobic glycolysis,and mitochondrial vacuolation.Moreover,we found that zNDUFAF1,the putative mitochondrial import inner membrane translocase ZmTIM17-1,and the isovaleryl-coenzyme A dehydrogenase ZmIVD1 interact each other,and could be co-precipitated from the mitochondria and co-migrate in the same assembly intermediates.Knockout of either ZmTIM17-1 or ZmIVD1 could lead to the significantly reduced complex Ⅰ stability and activity as well as defective seeds.These results suggest that zNDUFAF1,ZmTIM17-1 and ZmIVD1 probably form an MCIA-like complex that is essential for the biogenesis of mitochondrial complex Ⅰ and seed development in maize.Our findings also imply that plants and mammals recruit MCIA subunits independently for mitochondrial complex Ⅰ assembly,highlighting the importance of parallel evolution in mitochondria adaptation to their hosts.

Phenotypic plasticity in rice:responses to fertilization and inoculation with arbuscular mycorrhizal fungi

Aims Changes in the phenotype of crops(phenotypic plasticity)are known to play an important role in determining responses to nutrient availability,with the direction and magnitude of plasticity of individual traits being crucial for grain yields.Our study analysed the direction,magnitude and hierarchy of plastic responses of yieldrelated traits(i.e.biomass allocation and yield components)of rice(Oryza sativa L.)to nutrient availability.We estimated the effect of inoculation with arbuscular mycorrhizal fungi(AMF)on these characteristics of phenotypic plasticity.Methods A field experiment was carried out in northeast China,providing rice with six NPK fertilizer levels with or without inoculation with Glomus mosseae.At maturity,we quantified biomass allocation traits(shoot:root ratio and panicle:shoot ratio)and yield component traits(panicle number per hill,spikelet number per panicle,percentage of filled spikelets and seed weight).We also assessed the direction of change in each trait and the magnitude of trait plasticity.Important Findings In non-inoculated plants,we found that biomass allocation and seed-number traits(i.e.panicle number per hill,spikelet number per panicle and percentage of filled spikelets)responded to fertilization in the same direction,increasing with rising fertilization.Panicle formation was the most plastic trait,while seed mass was the least plastic trait.AMF inoculation nullified the relationship between most biomass allocation and seed-number traits(except for that between panicle:shoot ratio and the percentage of filled spikelets)but increased the magnitude of plasticity in biomass allocation traits without altering the hierarchy of traits’plasticity.These results underscore the importance of plasticity of yield-related traits per se,and the impact of AMF on plasticity,for maintaining rice yields under low fertilization regimes.

Crystal structure of Arabidopsis thaliana HPPK/DHPS,a bifunctional enzyme and target of the herbicide asulam

Herbicides are vital formodern agriculture,but their utility is threatened by genetic or metabolic resistance in weeds,as well as regulatory barriers.Of the known herbicide modes of action,7,8-dihydropterin synthase(DHPS),which is involved in folate biosynthesis,is targeted by just one commercial herbicide,asulam.A mimic of the substrate para-aminobenzoic acid,asulam is chemically similar to sulfonamide antibiotics,and although it is still in widespread use,asulam has faced regulatory scrutiny.With an entire mode of action represented by just one commercial agrochemical,we sought to improve the understanding of its plant target.Here we solve a 2.3A°resolution crystal structure for Arabidopsis thaliana DHPS that is conjoined to 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase(HPPK),and we reveal a strong structural conservation with bacterial counterparts at the sulfonamide-bindingpocket of DHPS.We demonstrate that asulamand the antibiotic sulfamethoxazole have herbicidal as well as antibacterial activity,andwe explore the structural basis of their potency by modeling these compounds in mitochondrial HPPK/DHPS.Our findings suggest limited opportunity for the rational design of plant selectivity fromasulamand indicate that pharmacokinetic or delivery differences between plants andmicrobesmight be the bestways to safeguard thismode of action.