Sequential light programs shape kale (Brassica napus) sproutappearance and alter metabolic and nutrient content

Different light wavelengths have specific effects on plant growth and development.Narrow-bandwidth light-emitting diode(LED)lighting may be used to directionally manipulate size,color and metabolites in high-value fruits and vegetables.In this report,Red Russian kale(Brassica napus)seedlings were grown under specific light conditions and analyzed for photomorphogenic responses,pigment accumulation and nutraceutical content.The results showed that this genotype responds predictably to darkness,blue and red light,with suppression of hypocotyl elongation,development of pigments and changes in specific metabolites.However,these seedlings were relatively hypersensitive to far-red light,leading to uncharacteristically short hypocotyls and high pigment accumulation,even after growth under very low fluence rates(,1 mmol m^(-2) s^(-1)).General antioxidant levels and aliphatic glucosinolates are elevated by far-red light treatments.Sequential treatments of darkness,blue light,red light and far-red light were applied throughout sprout development to alter final product quality.These results indicate that sequential treatment with narrow-bandwidth light may be used to affect key economically important traits in high-value crops.

Genome-wide identification and characterization of ACBP gene family in Populus reveal salinity alkali-responsive profiles

Acyl-CoA-binding proteins(ACBPs)are important for the transport of acyl groups for macro molecular biosynthesis involved in plant growth,development,and diverse stress(e.g.,cold,drought,salinity,and heavy metals)responses.Here,we report the phylogeny and characteristics of the ACBP family in the woody plant Populus trichocarpa.Eight genes encoding ACBP proteins were identified,and they are distributed on eight chromosomes in P.trichocarpa.These PtACBP genes were divided into four subgroups according to gene structure,conserved motifs and phylogenetic relationship.Promoter analysis revealed that cis-elements were related to stress response,phytohormone response,and physical and reproductive growth regulation.Expression levels of PtACBP genes varied among different organs,with the highest expression in leaves and the lowest in stems.Quantitative real-time PCR(qRT-PCR)analysis showed that under salinity-alkali stresses(i.e.,200 mM NaCl,75 mM Na2CO3,and 100 mM NaHCO3),four(PtACBP1,PtACBP3,PtACBP4 and PtACBP8)of eight PtACBP genes were significantly induced in roots and leaves.These data provide a comprehensive analysis of the ACBPs family in P.trichocarpa,which could be useful for gene function analyses.

A survey of FLS2 genes from multiple citrus species identifies candidates for enhancing disease resistance to Xanthomonas citri ssp. citri.

Pathogen-associated molecular patterns(PAMPs)-triggered immunity(PTI)is an important component of plant innate immunity.In a previous study,we showed that the PAMP flg22 from Xanthomonas citri ssp.citri(Xflg22),the causal agent of citrus canker,induced PTI in citrus,which correlated with the observed levels of canker resistance.Here,we identified and sequenced two bacterial flagellin/flg22 receptors(FLS2-1 and FLS2-2)from‘Duncan’grapefruit(Citrus paradisi,CpFLS2-1 and CpFLS2-2)and‘Sun Chu Sha’mandarin(C.reticulata,CrFLS2-1 and CrFLS2-2).We were able to isolate only one FLS2 from‘Nagami’kumquat(Fortunella margarita,FmFLS2-1)and gene flanking sequences suggest a rearrangement event that resulted in the deletion of FLS2-2 from the genome.Phylogenetic analysis,gene structure and presence of critical amino acid domains all indicate we identified the true FLS2 genes in citrus.FLS2-2 was more transcriptionally responsive to Xflg22 than FLS2-1,with induced expression levels higher in canker-resistant citrus than in susceptible ones.Interestingly,‘Nagami’kumquat showed the highest FLS2-1 steady-state expression levels,although it was not induced by Xflg22.We selected FmFLS2-1,CrFLS2-2 and CpFLS2-2 to further evaluate their capacity to enhance bacterial resistance using Agrobacterium-mediated transient expression assays.Both FmFLS2-1 and CrFLS2-2,the two proteins from canker-resistant species,conferred stronger Xflg22 responses and reduced canker symptoms in leaves of the susceptible grapefruit genotype.These two citrus genes will be useful resources to enhance PTI and achieve resistance against canker and possibly other bacterial pathogens in susceptible citrus types.

Inhibitors of glucose transport and glycolysis as novel anticancer therapeutics

Metabolic reprogramming and altered energetics have become an emerging hallmark of cancer and an active area of basic, translational, and clinical cancer research in the recent decade. Development of effective anticancer therapeutics may depend on improved understanding of the altered cancer metabolism compared to that of normal cells. Changes in glucose transport and glycolysis, which are drastically upregulated in most can-cers and termed the Warburg effect, are one of major focuses of this new research area. By taking advantage of the new knowledge and understanding of cancer's mechanisms, numerous therapeutic agents have been developed to target proteins and enzymes involved in glucose transport and metabolism, with promising results in cancer cells, animal tumor models and even clinical trials. It has also been hypothesized that targeting a pathway or a process, such as glucose transport or glucose metabolism, rather than a specific protein or enzyme in a signaling pathway may be more effective. This is based on the observation that cancer somehow can always bypass the inhibition of a target drug by switching to a redundant or compensatory pathway. In addition, cancer cells have higher dependence on glucose. This review will provide background information on glucose transport and metabolism in cancer, and summarize new therapeutic developments in basic and translational research in these areas, with a focus on glucose transporter inhibitors and glycolysis inhibitors. The daunting challenges facing both basic and clinical researchers of the field are also presented and discussed.

Cytochrome P450 monooxygenase-mediated eicosanoid pathway:A potential mechanistic linkage between dietary fatty acid consumption and colon cancer risk

Human consumption of linoleic acid(LA,18:2ω-6,abundant in vegetable oils)is very high.Animal experiments showed that excessive LA intake increased azoxymethane-induced colon tumorigenesis,however,the impact of excessive LA on colon cancer in human is not conclusive,making it difficult to make dietary recommendations for optimal intake of LA.Understanding the molecular mechanisms of LA on colon tumorigenesis could help to clarify its health effect,and facilitate development of mechanismbased strategies for preventing colon cancer.Recent studies show that the previously unappreciated cytochrome P450 monooxygenase-mediated eicosanoid pathway is upregulated in colon cancer and plays critical roles in its pathogenesis,and could contribute to the effects of dietary LA,as well asω-3 fatty acids,on colon tumorigenesis.In this review,we will discuss recent studies about the roles of cytochrome P450 monooxygenases in fatty acid metabolism and its roles in colonic inflammation and colon cancer,and how this information could help us to clarify the health impacts of dietary fatty acids.

Redox proteomics of tomato in response to Pseudomonas syringae infection

Unlike mammals with adaptive immunity,plants rely on their innate immunity based on pattern-triggered immunity(PTI)and effector-triggered immunity(ETI)for pathogen defense.Reactive oxygen species,known to play crucial roles in PTI and ETI,can perturb cellular redox homeostasis and lead to changes of redox-sensitive proteins through modification of cysteine sulfhydryl groups.Although redox regulation of protein functions has emerged as an important mechanism in several biological processes,little is known about redox proteins and how they function in PTI and ETI.In this study,cysTMT proteomics technology was used to identify similarities and differences of protein redox modifications in tomato resistant(PtoR)and susceptible(prf3)genotypes in response to Pseudomonas syringae pv tomato(Pst)infection.In addition,the results of the redox changes were compared and corrected with the protein level changes.A total of 90 potential redox-regulated proteins were identified with functions in carbohydrate and energy metabolism,biosynthesis of cysteine,sucrose and brassinosteroid,cell wall biogenesis,polysaccharide/starch biosynthesis,cuticle development,lipid metabolism,proteolysis,tricarboxylic acid cycle,protein targeting to vacuole,and oxidation–reduction.This inventory of previously unknown protein redox switches in tomato pathogen defense lays a foundation for future research toward understanding the biological significance of protein redox modifications in plant defense responses.

Identifying genomic regions controlling ratoon stunting disease resistance in sugarcane(Saccharum spp.) clonal F_(1) population

The ratoon stunting disease (RSD) of sugarcane,caused by the bacterium Leifsonia xyli subsp.xyli,is one of the major concerns to sugarcane production and breeding programs worldwide.Due to no obvious external symptoms,RSD cannot be easily detected by the growers,hence has reduced the world’s sugarcane production significantly.This study aimed to identify quantitative trait loci (QTL) associated with RSD resistance and to assist in the development of linked molecular markers for marker-assisted breeding to minimize the reduction in sugarcane yield by the RSD infection.A set of 146 individuals derived from a self-crossing of CP80-1827 were evaluated for RSD resistance in a mechanically duplicated inoculated field trial from 2014 to 2017 using tissue blot immunoassay.Leveraging the genetic data and the four years phenotyping data of CP80-1827 selfing population,linkage map construction and QTL analysis were conducted based on clonal F_1 and F_2 mapping population types with GACD V.1.2 and Ici Mapping V.3.3,respectively.A total of 23 QTL associated with RSD resistance were identified,which explained 6%to13%of the phenotypic variation with the two types of software.A total of 82 disease resistance genes were identified by searching these 23 QTL regions on their corresponding regions on the Sorghum bicolor genome (44 genes),sugarcane R570 genome (20 genes),and S.spontaneum genome (18 genes),respectively.Compared with Ici Mapping V.3.3,GACD V.1.2 identified more major (6 vs.3) and stable QTL (2vs.0),and more disease resistance genes (51 vs.31),indicating GACD V.1.2 (clonal F_1 mapping type) is most likely to be more efficient than Ici Mapping (F_2 mapping type) for QTL analysis of a sefling population or clonal F_1 population in clonal species.The identified QTL controlling RSD resistance along with the associated SNP markers will assist sugarcane molecular breeding programs in combating this disease.

Glioblastoma-derived tumor cells induce vasculogenic mimicry through Flk-1 protein activation

Glioblastoma(GBM)is extremely aggressive and essentially incurable.Its malignancy is characterized by vigorous microvascular proliferations.Recent evidence has shown that tumor cells display the ability to drive blood-perfused vasculogenic mimicry(VM),an alternative microvascular circulation independent of endothelial cell angiogenesis.However,molecular mechanisms underlying this vascular

Prot-Class: A bioinformatics tool for protein classification based on amino acid signatures

Knowledge about characteristics shared across known members of a protein family enables their identification within the complete set of proteins in an organism. Shared features are usually expressed through motifs, which can incorporate specific patterns and even amino acid (AA) biases. Based on a set of classification patterns and biases it can be determined which additional proteins may belong to a specific family and share its functionality. A bioinformatics tool (Prot-Class) was implemented to examine protein sequences and characterize them based upon user-defined AA composition percentages and user defined AA patterns. In addition the tool allows for the identification of repeated AA patterns, biased AA compositions within windows of user-defined length, and the characteristics of putative signal peptides and glycosylphosphatidylinositol (GPI) lipid anchors. ProtClass is general purpose and can be applied to analyze protein sequences from any organism. The Prot-Class source code is available through the GNU General Public License v3 and can be accessed via the Google Code Repository: http://code.google.com/p/prot-class/.

IRX14 and IRX14-LIKE, Two Glycosyl Transferases Involved in Glucuronoxylan Biosynthesis and Drought Tolerance in Arabidopsis

IRX14 and IRX14-LIKE （IRX14L） are two closely related glycosyl transferases in the glycosyl transferase 43 （GT43） family of Arabidopsis. A T-DNA insertion mutant for IRX14 results in comparatively minor changes, such as irregular xylem, while a mutation for IRX14L results in no changes. However, an irx14 and irx14L double mutant severely affects growth and development, with the dwarf plants failing to produce an inflorescence stem. Plants that are homozygous for IRX14 but heterozygous for IRX14L （irx14 irx14L（±）） exhibit an intermediate phenotype, including noticeably smaller leaves, stems, and underdeveloped siliques. Additionally, the T-DNA insertion mutant for IRX14 was found to result in a drought-tolerant phenotype. Carbohydrate analysis of total cell wall extracts revealed a reduction in xylose for the irx14 and irx14 irx14L（±） mutants, consistent with a defect in glucuronoxylan biosynthesis. Immunolocalization of xylan with the LM10 antibody revealed a loss of xylan in irx14 mutants and a further reduction in the irx14 irx14L（±） mutants. IRX14L likely functions redundantly with IRX14 in glucuronoxylan biosynthesis, with IRX14 having a more important role in the process.

rhe Mitochondrion-Targeted PENTATRICOPEPTIDE REPEAT78 Protein Is Required for nad5 Mature mRNA Stability and Development in Maize

Pentatricopepetide repeat （PPR） proteins are a large family of RNA-binding proteins involved in RNA meta- bolism in plant organelles. Although many PPR proteins have been functionally studied, few of them are identified with a function in mitochondrial RNA stability. By using a reverse genetic approach, we characterized the role of the mitochondrion-targeted PPR78 protein in nad5 mature mRNA stability and maize （Zea mays） seed development. Loss of PPR78 function leads to a dramatic reduction in the steady-state level of mitochondrial nad5 mature mRNA, blocks the assembly of complex I in the electron transport chain, and causes an arrest in embryogenesis and endosperm development. Characterization of a second strong allele confirms the function of PPR78 in nad5 mRNA accumulation and maize seed development. The generation of mature nad5 requires the assembly of three distinct precursor RNAs via transsplicing reactions, and the accumulation ofnad5T1 precursor is reduced in the ppr78 mutants. However, it is the instability of mature nad5 rather than nad5T1 causing loss of the full-length nad5 transcript, and degradation of nad5 losing both translation start and stop codons is enriched in the mutant. Our data imply the assembly of mature nad5 mRNA precedes the protection of PPR78.

Proteomics and Metabolomics of Arabidopsis Responses to Perturbation of Glucosinolate Biosynthesis

To understand plant molecular networks of glucosinolate metabolism, perturbation of aliphatic glucosinolate biosynthesis was established using inducible RNA interference （RNAi） in Arabidopsis. Two RNAi lines were chosen for examining global protein and metabolite changes using complementary proteomics and metabolomics approaches. Pro- teins involved in metabolism including photosynthesis and hormone metabolism, protein binding, energy, stress, and defense showed marked responses to glucosinolate perturbation. In parallel, metabolomics revealed major changes in the levels of amino acids, carbohydrates, peptides, and hormones. The metabolomics data were correlated with the pro- teomics results and revealed intimate molecular connections between cellular pathways/processes and glucosinolate me- tabolism. This study has provided an unprecedented view of the molecular networks of glucosinolate metabolism and laid a foundation towards rationale glucosinolate engineering for enhanced defense and quality.

G-Quadruplex(G4) Motifs in the Maize(Zea mays L.) Genome Are Enriched at Specific Locations in Thousands of Genes Coupled to Energy Status,Hypoxia,Low Sugar,and Nutrient Deprivation

The G-quadruplex （G4） elements comprise a class of nucleic acid structures formed by stacking of guanine base quartets in a quadruple helix. This （34 DNA can form within or across single-stranded DNA molecules and is mutually exclusive with duplex B-form DNA. The reversibility and structural diversity of G4s make them highly versatile genetic structures, as demonstrated by their roles in various functions including telomere metabolism, genome maintenance, immunoglobulin gene diversification, transcription, and translation. Sequence motifs capable of forming G4 DNA are typically located in telomere repeat DNA and other non-telomeric genomic loci. To investigate their potential roles in a large-genome model plant species, we computationaily identified 149,988 non-telomeric G4 motifs in maize （Zea mays L., B73 AGPv2）, 29% of which were in non-repetitive genomic regions. G4 motif hotspots exhibited non-random enrichment in genes at two locations on the antisense strand, one in the 5~ UTR and the other at the 5~ end of the first intron. Several genic G4 motifs were shown to adopt sequence-specific and potassium-dependent G4 DNA structures in vitro. The G4 motifs were prevalent in key regulatory genes associated with hypoxia （group VII ERFs）, oxidative stress （D J-1/GATasel）, and energy status （AMPK/ SnRK） pathways. They also showed statistical enrichment for genes in metabolic pathways that function in glycolysis, sugar degradation, inositol metabolism, and base excision repair. Collectively, the maize G4 motifs may represent conditional regulatory elements that can aid in energy status gene responses. Such a network of elements could provide a mechanistic basis for linking energy status signals to gene regulation in maize, a model genetic system and major world crop species for feed, food, and fuel.

Na_(2)CO_(3)-responsive Photosynthetic and ROS Scavenging Mechanisms in Chloroplasts of Alkaligrass Revealed by Phosphoproteomics

Alkali-salinity exerts severe osmotic,ionic,and high-p H stresses to plants.To understand the alkali-salinity responsive mechanisms underlying photosynthetic modulation and reactive oxygen species(ROS)homeostasis,physiological and diverse quantitative proteomics analyses of alkaligrass(Puccinellia tenuiflora)under Na_(2)CO_(3)stress were conducted.In addition,Western blot,real-time PCR,and transgenic techniques were applied to validate the proteomic results and test the functions of the Na_(2)CO_(3)-responsive proteins.A total of 104 and 102 Na_(2)CO_(3)-responsive proteins were identified in leaves and chloroplasts,respectively.In addition,84 Na_(2)CO_(3)-responsive phosphoproteins were identified,including 56 new phosphorylation sites in 56 phosphoproteins from chloroplasts,which are crucial for the regulation of photosynthesis,ion transport,signal transduction,and energy homeostasis.A full-length Pt FBA encoding an alkaligrass chloroplastic fructosebisphosphate aldolase(FBA)was overexpressed in wild-type cells of cyanobacterium Synechocystis sp.Strain PCC 6803,leading to enhanced Na_(2)CO_(3)tolerance.All these results indicate that thermal dissipation,state transition,cyclic electron transport,photorespiration,repair of photosystem(PS)Ⅱ,PSI activity,and ROS homeostasis were altered in response to Na_(2)CO_(3)stress,which help to improve our understanding of the Na_(2)CO_(3)-responsive mechanisms in halophytes.

Advances in quantitative proteomics

Large-scale protein quantification has become a major proteomics application in many areas of biological and medical research.During the past years,different techniques have been developed,including gel-based such as differential in-gel electrophoresis(DIGE)and liquid chromatography-based such as isotope labeling and labelfree quantification.These quantitative proteomics tools hold significant promise for biomarker discovery,diagnostic and therapeutic applications.They are also important for research in functional genomics and systems biology towards basic understanding of molecular networks and pathway interactions.In this review,we summarize current technologies in quantitative proteomics and discuss recent applications of the technologies.

Fern spore germination in response to environmental factors

Fern spore germination gives rise to the rhizoid and protonemal cell through asymmetric cell division, and then develops into a gametophyte. Spore germination is also a representative single-cell model for the investigation of nuclear polar movement, asymmetrical cell division, polarity establishment and rhizoid tip-growth. These processes are affected by various environmental factors, such as light, gravity, phytohormones, metal ions, and temperature. Here, we present a catalog of spore germination in response to different environmental factors. They are as follows： （1） Representative modes of light affecting spore germination from different fern species include red light-stimulated and far red light-inhibited spore germination, far red light-uninhibited spore germination, blue light-inhibited spore germination, and spore germination in the dark. The optimal light intensity and illumination time for spore germination are different among various fern species. Light response upon spore germination is initiated from the cell mitosis that regulated by phytochromes （PHYs） and cryptochromes （CRYs）. AcPHY2, AcCRY3 and/or AcCRY4 are hypothesized to be involved in spore germination; （2） Gravity and calcium are crucial to early nuclear movement and polarity establishment of spores; （3） Gibberellin and antheridiogen can initiate and promote spore germination in many species, but abscisic acid, jasmonic acid, and ethylene pose only minor effects; （4） Spores can obtain the maximal germination rate in their favorable growth medium. Moreover, metal ions, pH, and spore density in the culture medium also affect spore germination; （5） Most fern spores germinate at 25℃, and an optimal CO2 concentration is necessary for spore germination of certain fern plants. These provide valuable information for understanding fern spore germination in response to environmental factors.

Proteomics characteristics of rice leaves in response to environmental factors

Rice is an important food crop worldwide.Its productivity has been influenced by various abiotic and biotic factors including temperature,drought,salt,microbe,ozone,hormone and glyphosate.The responses of plants to stress are regulated by multiple signaling pathways,and the mechanisms of leaf growth and development in response to stress remain unclear to date.Recently,proteomics studies have provided new evidence for better understanding the mechanisms.The proteins in response to different stress conditions are mainly involved in photosynthesis,signal transduction,transcription,protein synthesis and destination,defense response,cytoskeleton,energy,cell wall and other metabolism.In addition,some stress type-specific proteins have been identified,such as small heat shock proteins under temperature stress,S-like RNase homolog and actin depolymerizing factor under drought stress,ascorbate peroxidase and lipid peroxidation under salt stress,probenazole-inducible protein and rice pathogenesis-related proteins under blast fungus.Many of the proteins including ribulose-1,5-bisphosphate carboxylase/oxygenase(RuBisCO),molecular chaperones,antioxidases and S-adenosylmethionine synthetase play very important roles in leaves.This paper reviews the proteomic characterization of rice leaves in response to various environmental factors.

Stimulation of in vitro bone formation by canine prostate cancer

Aim:Patients with prostate cancer frequently develop osteoblastic bone metastases.Canine models are important because dogs are the only mammal to develop spontaneous prostate cancer with osteoblastic bone metastases similar to men.The mechanism by which prostate cancer induces bone formation is unclear;however,it depends on the complex interaction between prostate cancer cells and bone microenvironment.This study investigated the effects of three canine prostate cancer cell lines(Ace-1,LuMa,and Probasco)on bone formation and resorption in vitro.Methods:Mouse calvaria were treated with conditioned medium(CM)from cell lines.Calvaria were evaluated by histology,fluorescent calcein uptake at sites of bone mineralization,medium calcium assay,and alkaline phosphatase activity.The expression of bone-related genes was measured using quantitative reverse transcription PCR.Results:A novel calcein uptake assay was developed to measure bone formation and mineralization in vitro.Ace-1 CM induced predominantly bone resorption in calvaria,while Probasco CM induced marked bone formation,mineralization,and healing of calvaria defects.The expression of osteoblast-related genes in calvaria showed that Probasco CM stimulated the maturation and differentiation of osteoblasts and inhibited osteoclastogenesis.Both bone modeling and remodeling were involved in Probasco CM-induced bone formation and mineralization by inhibiting remodeling with zoledronic acid.Inhibition of WNT activity by DKK-1 decreased the osteoblastic activity of Probasco cells.Conclusion:Probasco cells induced bone formation and mineralization in vitro that depended on the WNT signaling pathway.Probasco cells will serve as a valuable model for studying the mechanisms of osteoblastic bone metastasis in prostate cancer.

Long‑read DNA sequencing leads to the more complete sequence characterization of the fruit size reducing region flanking a Fusarium wilt resistance gene

Introduction Fruit size is an important trait for fruit crops including tomato(Solanum lycopersicum).It influences yield,which is the top priority for plant breeding and improvement programs.Studies have shown that introgression of disease resistance,often a necessity for successful cultivar development,impacts negatively on yield(Ning et al.,2017).Therefore,genetic resources,which do not compromise existing traits except for the new trait of interest,are always in high demand as such resources can be highly beneficial for rapidly incorporating new trait(s)into breeding backgrounds.Given this,exploiting knowledge of these negative impacts at the DNA sequence level has been of interest in the(applied)plant science society.