Assembly and phylogenomic analysis of cotton mitochondrial genomes provide insights into the history of cotton evolution

Cotton is a major crop that provides the most important renewable textile fibers in the world.Studies of the taxonomy and evolution of cotton species have received wide attentions,not only due to cotton’s economic value but also due to the fact that Gossypium is an ideal model system to study the origin,evolution,and cultivation of polyploid species.Previous studies suggested the involvement of mitochondrial genome editing sites and copy number as well as mitochondrial functions in cotton fiber elongation.Whereas,with only a few mitogenomes assembled in the cotton genus Gossypium,our knowledge about their roles in cotton evolution and speciation is still scarce.To close this gap,here we assembled 20 mitogenomes from 15 cotton species spanning all the cotton clades(A–G,K,and AD genomes)and 5 cotton relatives using short and long sequencing reads.Systematic analyses uncovered a high level of mitochondrial gene sequence conservation,abundant sequence repeats and many insertions of foreign sequences,as well as extensive structural variations in cotton mitogenomes.The sequence repeats and foreign sequences caused significant mitogenome size inflation in Gossypium and its close relative Kokia in general,while there is no significant difference between the lint and fuzz cotton mitogenomes in terms of gene content,RNA editing,and gene expression level.Interestingly,we further revealed the specific presence and expression of two novel mitochondrial open reading frames(ORFs)in lint-fiber cotton species.Finally,these structural features and novel ORFs help us gain valuable insights into the history of cotton evolution and polyploidization and the origin of species producing long lint fibers from a mitogenomic perspective.

Mitigating growth-stress tradeoffs via elevated TOR signaling in rice

Rice production accounts for approximately half of the freshwater resources utilized in agriculture,result-ing in greenhouse gas emissions such as methane(CH4)from flooded paddy fields.To address this chal-lenge,environmentally friendly and cost-effective water-saving techniques have become widely adopted in rice cultivation.However,the implementation of water-saving treatments(WsTs)in paddy-field rice has been associated with a substantial yield loss of up to 50%as well as a reduction in nitrogen use efficiency(NUE).In this study,we discovered that the target of rapamycin(TOR)signaling pathway is compromised in rice under WsT.Polysome profiling-coupled transcriptome sequencing(polysome-seq)analysis unveiled a substantial reduction in global translation in response to WST associated with the downregulation of TOR activity.Molecular,biochemical,and genetic analyses revealed new insights into the impact of the positive TOR-S6K-RPS6 and negative TOR-MAF1 modules on translation repression under WST.Intriguingly,ammonium exhibited a greater ability to alleviate growth constraints under WsT by enhancing TOR signaling,which simultaneously promoted uptake and utilization of ammonium and nitrogen allocation.We further demonstrated that TOR modulates the ammonium transporter AMT1;1 as well as the amino acid permease APP1 and dipeptide transporter NPF7.3 at the translational level through the 5'untranslated region.Collectively,these findings reveal that enhancing TOR signaling could mitigate rice yield penalty due to WST by regulating the processes involved in protein synthesis and NUE.Our study will contribute to the breeding of new rice varieties with increased water and fertilizer utilization efficiency.

Impact of acute heat stress on mitochondrial function, ultrastructure and cardiolipin distribution in Arabidopsis

Besides providing energy to sustain life,mitochondria also play crucial roles in stress response and programmed cell death.The mitochondrial hallmark lipid,cardiolipin(CL),is essential to the maintenance of mitochondrial structure and function.However,how mitochondria and CL are involved in stress response is not as well defined in plants as in animal and yeast cells.We previously revealed a role for CL in mitochondrial fission and in heat stress response in Arabidopsis.To further determine the involvement of mitochondria and CL in plant heat response,here we treated Arabidopsis seedlings with varied lengths of acute heat stress.These treatments resulted in decreases in mitochondrial membrane potential,disruption of mitochondrial ultrastructure,accumulation of mitochondrial reactive-oxygen species(ROS),and redistribution of CL to the outer mitochondrial membrane and to a novel type of vesicle.The level of the observed changes correlated with the severeness of the heat stress,indicating the strong relevance of these processes to stress response.Our findings provide the basis for studying mechanisms underpinning the role of mitochondria and CL in plant stress response.

Protein ubiquitination in plant peroxisomes

Protein ubiquitination regulates diverse cellular processes in eukaryotic organisms,from growth and development to stress response.Proteins subjected to ubiquitination can be found in virtually all subcellular locations and organelles,including peroxisomes,singlemembrane and highly dynamic organelles ubiquitous in eukaryotes.Peroxisomes contain metabolic functions essential to plants and animals such as lipid catabolism,detoxification of reactive oxygen species(ROS),biosynthesis of vital hormones and cofactors,and photorespiration.Plant peroxisomes possess a complex proteome with functions varying among different tissue types and developmental stages,and during plant response to distinct environmental cues.However,how these diverse functions are regulated at the post-translational level is poorly understood,especially in plants.In this review,we summarized current knowledge of the involvement of protein ubiquitination in peroxisome protein import,remodeling,pexophagy,and metabolism,focusing on plants,and referencing discoveries from other eukaryotic systems when relevant.Based on previous ubiquitinomics studies,we compiled a list of 56 ubiquitinated Arabidopsis peroxisomal proteins whose functions are associated with all the major plant peroxisomal metabolic pathways.This discovery suggests a broad impact of protein ubiquitination on plant peroxisome functions,therefore substantiating the need to investigate this significant regulatory mechanism in peroxisomes at more depths.

Proteome analysis of peroxisomes from dark-treated senescent Arabidopsis leaves

Peroxisomes compartmentalize a dynamic suite of biochemical reactions and play a central role in plant metabolism, such as the degradation of hydrogen peroxide, metabolism of fatty acids, photorespiration, and the biosyn- thesis of plant hormones. Plant peroxisomes have been traditionally classified into three major subtypes, and in-depth mass spectrometry （MS）-based proteomics has been per- formed to explore the proteome of the two major subtypes present in green leaves and etiolated seedlings. Here, we carried out a comprehensive proteome analysis of perox- isomes from Arabidopsis leaves given a 48-h dark treatment. Our goal was to determine the proteome of the third major subtype of plant peroxisomes from senescent leaves, and further catalog the plant peroxisomal proteome. We identified a total of 111 peroxisomal proteins and verified the peroxisomal localization for six new proteins with potential roles in fatty acid metabolism and stress response by in vivo targeting analysis. Metabolic pathways compartmentalized in the three major subtypes of peroxisomes were also compared, which revealed a higher number of proteins involved in the detoxification of reactive oxygen species in peroxisomes from senescent leaves. Our study takes an important step towards mapping the full function of plant peroxisomes.

Peroxisomes in plant reproduction and seed-related development

Peroxisomes are small multi-functional organelles essential for plant development and growth.Plant peroxisomes play various physiological roles,including phytohormone biosynthesis,lipid catabolism,reactive oxygen species metabolism and many others.Mutant an alysis dem on strated key roles for peroxisomes in plant reproduction,seed development and germination and post-germinative seedling establishment;however,the underlying mechanisms remain to be fully elucidated.This review summarizes fin dings that reveal the importance and complexity of the role of peroxisomes in the pertinent processes.Theβ-oxidation pathway plays a central role,whereas other peroxisomal pathways are also involved.Understanding the biochemical and molecular mechanisms of these peroxisomal functions will be instrumental to the improvement of crop plants.

Arabidopsis Forkhead-Associated Domain Protein 3 negatively regulates peroxisome division

Peroxisomes are ubiquitous and dynamic eukaryotic organelles capable of altering their abun- dance in response to environmental and developmental cues, yet the regulatory mechanism of plant peroxisome division/proliferation is unclear. To identify transcriptional regulators of the peroxisome division factor gene PEX 11b, we performed a nuclear pull-clown experiment and identified Arabidopsis Forkhead- Associated Domain Protein 3 （FHA3） as a novel protein that binds to the promoter of PEX 11b. Our data supported the conclusion that, in contrast to the previously identified HY5 HOMOLOG （HYH） protein that promotes the transcription of PEX 11b, FHA3 is a negative regulator of PEX 11b expression and peroxisome division.

De Novo Biosynthesis of Vindoline and Catharanthine in Saccharomyces cerevisiae

Vinblastine has been used clinically as one of the most potent therapeutics for the treatment of several types of cancer.However,the traditional plant extraction method suffers from unreliable supply,low abundance,and extremely high cost.Here,we use synthetic biology approach to engineer Saccharomyces cerevisiae for de novo biosynthesis of vindoline and catharanthine,which can be coupled chemically or biologically to vinblastine.On the basis of a platform strain with sufficient supply of precursors and cofactors for biosynthesis,we reconstituted,debottlenecked,and optimized the biosynthetic pathways for the production of vindoline and catharanthine.The vindoline biosynthetic pathway represents one of the most complicated pathways ever reconstituted in microbial cell factories.Using shake flask fermentation,our engineered yeast strains were able to produce catharanthine and vindoline at a titer of 527.1 and 305.1μg·liter^(−1),respectively,without accumulating detectable amount of pathway intermediates.This study establishes a representative example for the production of valuable plant natural products in yeast.