AtPGL3 is an Arabidopsis BURP domain protein that is localized to the cell wall and promotes cell enlargement

Cloning and functional verification of the male sterile gene BrQRT3 in Chinese cabbage

Chinese cabbage is a cross-pollinated crop with significant heterosis, and male sterile lines are an important way to produce hybrid seeds. In this study, a male sterile mutant msm0795 was identified in an EMS-mutagenized population of Chinese cabbage. Cytological observations revealed that the microspores failed to separate after the tetrad stage, and thus developed into abnormal pollen grains, resulting in anther abortion. MutMap combined with Kompetitive Allele Specific PCR genotyping showed that BraA01g011280.3.5 C was identified as the candidate gene, which encodes polygalacturonase QRT3 and plays a direct role in the degradation of pollen mother cell wall during microspore development, named BrQRT3. Subcellular localization and expression analyses demonstrated that BrQRT3 was localized in the cell membrane and was ubiquitously expressed in roots, stems, leaves, flower buds, and flowers, but the expression of BrQRT3 was gradually suppressed with the anther development. Ectopic expression confirmed that over-expression of BrQRT3 in qrt3 background Arabidopsis mutant can rescue the pollen defects caused by loss of AtQRT3 function. It is the first time to achieve a male sterile mutant caused by the mutation of BrQRT3 in Chinese cabbage. These findings contribute to elucidate the mechanism of BrQRT3 in regulating stamen development of Chinese cabbage.

Independent genetic factors control floret number and spikelet number in Triticum turgidum ssp

Wheat grain yield is a complex trait resulting from a trade-off among many distinct components. During wheat evolution, domestication events and then modern breeding have strongly increased the yield potential of wheat plants, by enhancing spike fertility. To address the genetic bases of spike fertility in terms of spikelet number per spike and floret number per spikelet, a population of 110 recombinant inbred lines (RILS) obtained crossing a Triticum turgidum ssp. durum cultivar (Latino) and a T. dicoccum accession (MG5323) was exploited. Being a modern durum and a semi-domesticated genotype, respectively, the two parents differ for spike architecture and fertility, and thus the corresponding RIL population is the ideal genetic material to dissect genetic bases of yield components. The RIL population was phenotyped in four environments. Using a high-density SNP genetic map and taking advantage of several genome sequencing available for Triticeae, a total of 94 QTLs were identified for the eight traits considered; these QTLs were further reduced to 17 groups, based on their genetic and physical co-location. QTLs controlling floret number per spikelet and spikelet number per spike mapped in non-overlapping chromosomal regions, suggesting that independent genetic factors determine these fertility-related traits. The physical intervals of QTL groups were considered for possible co-location with known genes functionally involved in spike fertility traits and with yield-related QTLs previously mapped in tetraploid wheat. The most interesting result concerns a QTL group on chromosome 5B, associated with spikelet number per spike, since it could host genes still uncharacterized for their association to spike fertility. Finally, we identified two different regions where the trade-off between fertility related traits and kernel weight is overcome. Further analyses of these regions could pave the way for a future identification of new genetic loci contributing to fertility traits essential for yield improvement in durum wheat.

Network interactions with functional roles and evolutionary relationships for BURP domain-containing proteins in chickpea and model species

The functional significance and evolutionary relationships of BURP domain-containing genes unique to plants is of interest. Network analysis reveals different associations of BURP proteins with other proteins and functional terms, throwing light on their involvement in various biological processes and pathways. The gene expression data reveals that BURP genes are affected by salinity stress, reflecting diverse expression patterns in roots and shoots.

Coastal Wild Grapevine Accession (Vitis vinifera L. ssp. sylvestris) Shows Distinct Late and Early Transcriptome Changes under Salt Stress in Comparison to Commercial Rootstock Richter 110

Increase in soil salinity, driven by climate change, is a widespread constrain for viticulture across several regions, including the Mediterranean basin. The implementation of salt-tolerant varieties is sought after to reduce the negative impact of salinity in grape production. An accession of wild grapevine (Vitis vinifera L. ssp. sylvestris), named AS1B, found on the coastline of Asturias (Spain), could be of interest toward the achievement of salt-tolerant varieties, as it demonstrated the ability to survive and grow under high levels of salinity. In the present study, AS1B is compared against widely cultivated commercial rootstock Richter 110, regarding their survival capabilities, and transcriptomic profiles analysis allowed us to identify the genes by employing RNA-seq and gene ontology analyses under increasing salinity and validate (via RT-qPCR) seven salinity-stress-induced genes. The results suggest contrasting transcriptomic responses between AS1B and Richter 110. AS1B is more responsive to a milder increase in salinity and builds up specific mechanisms of tolerance over a sustained salt stress, while Richter 110 maintains a constitutive expression until high and prolonged saline inputs, when it mainly shows responses to osmotic stress. The genetic basis of AS1B's strategy to confront salinity could be valuable in cultivar breeding programs, to expand the current range of salt-tolerant rootstocks, aiming to improve the adaptation of viticulture against climate change.

Identification and expression analysis of BURP domain-containing genes in jujube and their involvement in low temperature and drought response

Background

Plant-specific BURP domain-containing genes are involved in plant development and stress responses. However, the role of BURP family in jujube (Ziziphus jujuba Mill.) has not been investigated.

Results

In this study, 17 BURP genes belonging to four subfamilies were identified in jujube based on homology analysis, gene structures, and conserved motif confirmation. Gene duplication analysis indicated both tandem duplication and segmental duplication had contributed to ZjBURP expansion. The ZjBURPs were extensively expressed in flowers, young fruits, and jujube leaves. Transcriptomic data and qRT-PCR analysis further revealed that ZjBURPs also significantly influence fruit development, and most genes could be induced by low temperature, salinity, and drought stresses. Notably, several BURP genes significantly altered expression in response to low temperature (ZjPG1) and drought stresses (ZjBNM7, ZjBNM8, and ZjBNM9).

Conclusions

These results provided insights into the possible roles of ZjBURPs in jujube development and stress response. These findings would help selecting candidate ZjBURP genes for cold- and drought-tolerant jujube breeding.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08907-9.

Arabidopsis ETHYLENE INSENSITIVE 3 directly regulates the expression of PG1β-like family genes in response to aluminum stress

The genes in the subfamily PG1β (beta subunit of poly-galacturonase isoenzyme 1) have a clear effect on the biosynthesis pathway of pectin, a main component of the cell wall. However, the detailed functions of the PG1β-like gene members in Arabidopsis (AtPG1-3) have not yet been determined. In this study, we investigated their functional roles in response to aluminum (Al) stress. Our results indicate that the PG1β-like gene members are indeed involved in the Al-stress response and they can modulate its accumulation in roots to achieve optimum root elongation and hence better seedling growth. We found that transcription factor EIN3 (ETHYLENE INSENSITIVE 3) alters pectin metabolism and the EIN3 gene responds to Al stress to affect the pectin content in the root cell walls, leading to exacerbation of the inhibition of root growth, as reflected by the phenotypes of overexpressing lines. We determined that EIN3 can directly bind to the promoter regions of PG1-3, which act downstream of EIN3. Thus, our results show that EIN3 responds to Al stress in Arabidopsis directly through regulating the expression of PG1-3. Hence, EIN3 mediates their functions by acting as a biomarker in their molecular biosynthesis pathways, and consequently orchestrates their biological network in response to Al stress.

Transcriptome Analysis of Air Space-Type Variegation Formation in Trifolium pratense

Air space-type variegation is the most diverse among the species of known variegated leaf plants and is caused by conspicuous intercellular spaces between the epidermal and palisade cells and among the palisade cells at non-green areas. Trifolium pratense, a species in Fabaceae with V-shaped air space-type variegation, was selected to explore the application potential of variegated leaf plants and accumulate basic data on the molecular regulatory mechanism and evolutionary history of leaf variegation. We performed comparative transcriptome analysis on young and adult leaflets of variegated and green plants and identified 43 candidate genes related to air space-type variegation formation. Most of the genes were related to cell-wall structure modification (CESA, CSL, EXP, FLA, PG, PGIP, PLL, PME, RGP, SKS, and XTH family genes), followed by photosynthesis (LHCB subfamily, RBCS, GOX, and AGT family genes), redox (2OG and GSH family genes), and nitrogen metabolism (NodGS family genes). Other genes were related to photooxidation, protein interaction, and protease degradation systems. The downregulated expression of light-responsive LHCB subfamily genes and the upregulated expression of the genes involved in cell-wall structure modification were important conditions for air space-type variegation formation in T. pratense. The upregulated expression of the ubiquitin-protein ligase enzyme (E3)-related genes in the protease degradation systems were conducive to air space-type variegation formation. Because these family genes are necessary for plant growth and development, the mechanism of the leaf variegation formation in T. pratense might be a widely existing regulation in air space-type variegation in nature.

Crop genetic diversity uncovers metabolites, elements, and gene networks predicted to be associated with high plant biomass yields in maize

Rapid population growth and increasing demand for food, feed, and bioenergy in these times of unprecedented climate change require breeding for increased biomass production on the world's croplands. To accelerate breeding programs, knowledge of the relationship between biomass features and underlying gene networks is needed to guide future breeding efforts. To this end, large-scale multiomics datasets were created with genetically diverse maize lines, all grown in long-term organic and conventional cropping systems. Analysis of the datasets, integrated using regression modeling and network analysis revealed key metabolites, elements, gene transcripts, and gene networks, whose contents during vegetative growth substantially influence the build-up of plant biomass in the reproductive phase. We found that S and P content in the source leaf and P content in the root during the vegetative stage contributed the most to predicting plant performance at the reproductive stage. In agreement with the Gene Ontology enrichment analysis, the cis-motifs and identified transcription factors associated with upregulated genes under phosphate deficiency showed great diversity in the molecular response to phosphate deficiency in selected lines. Furthermore, our data demonstrate that genotype-dependent uptake, assimilation, and allocation of essential nutrient elements (especially C and N) during vegetative growth under phosphate starvation plays an important role in determining plant biomass by controlling root traits related to nutrient uptake. These integrative multiomics results revealed key factors underlying maize productivity and open new opportunities for efficient, rapid, and cost-effective plant breeding to increase biomass yield of the cereal crop maize under adverse environmental factors.

Exploring key developmental phases and phase-specific genes across the entirety of anther development in maize

Anther development from stamen primordium to pollen dispersal is complex and essential to sexual reproduction. How this highly dynamic and complex developmental process is controlled genetically is not well understood, especially for genes involved in specific key developmental phases. Here we generated RNA sequencing libraries spanning 10 key stages across the entirety of anther development in maize (Zea mays). Global transcriptome analyses revealed distinct phases of cell division and expansion, meiosis, pollen maturation, and mature pollen, for which we detected 50, 245, 42, and 414 phase-specific marker genes, respectively. Phase-specific transcription factor genes were significantly enriched in the phase of meiosis. The phase-specific expression of these marker genes was highly conserved among the maize lines Chang7-2 and W23, indicating they might have important roles in anther development. We explored a desiccation-related protein gene, ZmDRP1, which was exclusively expressed in the tapetum from the tetrad to the uninucleate microspore stage, by generating knockout mutants. Notably, mutants in ZmDRP1 were completely male-sterile, with abnormal Ubisch bodies and defective pollen exine. Our work provides a glimpse into the gene expression dynamics and a valuable resource for exploring the roles of key phase-specific genes that regulate anther development.

Agrobacterium-mediated cassava transformation for the Asian elite variety KU50

Cassava genetic transformation has mostly been reported for African cassava varieties, but not for Asian varieties. This is the first report of cassava transformation in Asian elite varieties using friable embryogenic calli. Agrobacterium-mediated cassava transformation via friable embryogenic calli (FEC) has enabled the robust production of transgenic cassava. So far, mostly the model cassava variety 60444 and African varieties have been transformed because of their good production and regeneration from embryogenic tissues. It is important to develop transformation methods for elite Asian cassava varieties to meet the changing needs in one of the world's major cassava production areas. However, a suitable transformation method for the Asian elite variety Kasetsart 50 (KU50) has not been developed. Here, we report a transformation method for KU50, the cultivar with the highest planting area in Thailand and Vietnam. In cassava transformation, the preparation of FEC as the target tissue for transgene integration is a key step. FEC induction from KU50 was improved by using media with reduced nutrients and excess vitamin B1, and somatic embryo and plant regeneration optimized by manipulation of naphthalene acetic acid (NAA), and benzylamino purine (BAP). The transformation efficiency for KU50 was 22%, approximately half that of 60444 at 45%. Transcriptome analysis indicated that the expression of genes related to cell-wall loosening was upregulated in FEC from KU50 compared with 60444, indicating that cell-wall production and assembly were disproportionate in the Asian variety. The transformation system for KU50 reported here will contribute to the molecular breeding of cassava plants for Asian farmers using transgenic and genome-editing technologies.

In silico analysis and expression profiling of Expansin A4, BURP domain protein RD22-like and E6-like genes associated with fiber quality in cotton

BACKGROUND

To supply high-quality cotton fibre for the textile industry, the development of long, strong and fine fibre cotton varieties is imperative. An interlinked approach was used to comprehend the role of fibre genes by analyzing interspecific progenies of cotton species. Wild Gossypium species and races are rich source of genetic polymorphism due to environmental dispersal and continuous natural selection. These genetic resources hold mass of outclass genes that can be used in cotton improvement breeding programs to exploit possible traits such as fibre quality, abiotic stress tolerance, and disease and insect resistance. Therefore, use of new molecular techniques such as genomics, transcriptomics and bioinformatics is very important to utilize the genetic potential of wild species in cotton improvement programs.

METHODS

Interspecific lines and Gossypium species used in the study were grown at Central Cotton Research Institute (CCRI), Multan. After retrieving DNA sequence of the genes from NCBI, the primers for gene expression and full-length gene sequence were designed. Expression profiling of Expansin A4, BURP Domain protein RD22-like and E6-like fibre genes was performed through Real Time PCR. BLAST and DNA sequence alignment was conducted for sequence comparison of interspecific lines and Gossypium species. Different in silico analysis were used for characterization of fibre genes and identification of cis acting promoter elements in promoter region.

RESULTS

Variable expression of genes related to fibre development was observed at different stages. BLAST and DNA sequence alignment demonstrated resemblance of interspecific lines with G. hirsutum. In silico analysis on the sequence data also confirmed the role of Expansin A4, BURP Domain protein RD22-like and E6-like fibre genes in fibre development. Genetic engineering is also recommended by transferring E6-like, Expansin A4 and BURP Domain RD22-like genes in local cotton cultivars. Similarly, several stress tolerant and light responsive cis acting elements were identified through promotor analysis, which may contribute for fibre development in the breeding programs.

CONCLUSION

Expansin A4, BURP Domain RD22-like and E6-like have positive role in fibre development with variable expression at fiber length and strength associated stages.

Overexpressing PpBURP2 in Rice Increases Plant Defense to Abiotic Stress and Bacterial Leaf Blight

Mosses are one of the earliest diverging land plants that adapted to living on land. The BURP domain-containing proteins (BURP proteins) are plant-specific proteins that appeared when plants shifted from aquatic environments to land. Phylogenetic analysis revealed that the BURP domain of higher plants is originated from lower land plants and divergent because of motif conversion. To discover the function of BURP protein in moss, rice transgenics with ectopic expression of PpBURP2 were subjected to different abiotic stresses treatments. The results revealed that the ectopic expression of PpBURP2 enhanced the tolerance to osmotic and saline stresses at the seedling stage and drought stress at the adult stage. Further ectopic expression of PpBURP2 improved the cadmium (2+) (Cd2+) tolerance and reduced Cd2+ accumulation in rice leaves. Transcriptomic analysis of the transgenic PpBURP2 plants showed that the differentially expressed genes were involved in the metabolism of secondary metabolites, energy, oxidation-reduction process, and defense-related genes. Further experiments showed that the photosynthetic efficiency and resistance against bacterial leaf blight were obviously improved in transgenic plants. Yeast two-hybrid and bimolecular fluorescence complementation (BiFC) assays revealed the physical interaction of BURP domain protein from rice and moss with mitogen-activated protein kinase kinase (MKK) from rice. Therefore, our findings demonstrate that overexpressing PpBURP2 in rice confers resistance to abiotic stresses and bacterial leaf blight. They also suggested that the regulatory role of BURP-like proteins across lower and higher plants was evolutionary conservation of responses of different classes of plants to different environmental challenges.

Cannabis Glandular Trichome Cell Walls Undergo Remodeling to Store Specialized Metabolites

The valuable cannabinoid and terpenoid metabolites of Cannabis sativa L. are produced by floral glandular trichomes. The trichomes consist of secretory disk cells, which produce the abundant lipidic metabolites, and an extracellular storage cavity. The mechanisms of apoplastic cavity formation to accumulate and store metabolites in cannabis glandular trichomes remain wholly unexplored. Here, we identify key wall components and how they change during cannabis trichome development. While glycome and monosaccharide analyses revealed that glandular trichomes have loosely bound xyloglucans and pectic polysaccharides, quantitative immunolabeling with wall-directed antibodies revealed precise spatiotemporal distributions of cell wall epitopes. An epidermal-like identity of early trichome walls matured into specialized wall domains over development. Cavity biogenesis was marked by separation of the subcuticular wall from the underlying surface wall in a homogalacturonan and α-1,5 arabinan epitope-rich zone and was associated with a reduction in fucosylated xyloglucan epitopes. As the cavity filled, a matrix with arabinogalactan and α-1,5 arabinan epitopes enclosed the metabolite droplets. At maturity, the disk cells' apical wall facing the storage cavity accumulated rhamnogalacturonan-I epitopes near the plasma membrane. Together, these data indicate that cannabis glandular trichomes undergo spatiotemporal remodeling at specific wall subdomains to facilitate storage cavity formation and metabolite storage.

Plant Copper Metalloenzymes As Prospects for New Metabolism Involving Aromatic Compounds

Copper is an important transition metal cofactor in plant metabolism, which enables diverse biocatalysis in aerobic environments. Multiple classes of plant metalloenzymes evolved and underwent genetic expansions during the evolution of terrestrial plants and, to date, several representatives of these copper enzyme classes have characterized mechanisms. In this review, we give an updated overview of chemistry, structure, mechanism, function and phylogenetic distribution of plant copper metalloenzymes with an emphasis on biosynthesis of aromatic compounds such as phenylpropanoids (lignin, lignan, flavonoids) and cyclic peptides with macrocyclizations via aromatic amino acids. We also review a recent addition to plant copper enzymology in a copper-dependent peptide cyclase called the BURP domain. Given growing plant genetic resources, a large pool of copper biocatalysts remains to be characterized from plants as plant genomes contain on average more than 70 copper enzyme genes. A major challenge in characterization of copper biocatalysts from plant genomes is the identification of endogenous substrates and catalyzed reactions. We highlight some recent and future trends in filling these knowledge gaps in plant metabolism and the potential for genomic discovery of copper-based enzymology from plants.

Transcriptome Analysis of the Fruit of Two Strawberry Cultivars "Sunnyberry" and "Kingsberry" That Show Different Susceptibility to Botrytis cinerea after Harvest

Gray mold (Botrytis cinerea) is a fungal plant pathogen causing postharvest decay in strawberry fruit. Here, we conducted a comparative transcriptome analysis to identify differences in gene expression between the immature-green (IG) and mature-red (MR) stages of the “Sunnyberry” (gray mold-resistant) and “Kingsberry” (gray mold susceptible) strawberry cultivars. Most of the genes involved in lignin and alkane-type wax biosynthesis were relatively upregulated in “Sunnyberry”. However, pathogenesis-related proteins encoding R- and antioxidant-related genes were comparatively upregulated in “Kingsberry”. Analysis of gene expression and physiological traits in the presence and absence of B. cinerea inoculation revealed that the defense response patterns significantly differed between IG and MR rather than the cultivars. “Kingsberry” showed higher antioxidant induction at IG and upregulated hemicellulose-strengthening and R genes at MR. Hence, “Sunnyberry” and “Kingsberry” differed mainly in terms of the expression levels of the genes forming cuticle, wax, and lignin and controlling the defense responses. These discrepancies might explain the relative difference between these strawberry cultivars in terms of their postharvest responses to B. cinerea.

Molecular mechanisms for magnesium-deficiency-induced leaf vein lignification, enlargement and cracking in Citrus sinensis revealed by RNA-Seq

Citrus sinensis (L.) Osbeck seedlings were fertigated with nutrient solution containing 2 [magnesium (Mg)-sufficiency] or 0 mM (Mg-deficiency) Mg(NO3)2 for 16 weeks. Thereafter, RNA-Seq was used to investigate Mg-deficiency-responsive genes in the veins of upper and lower leaves in order to understand the molecular mechanisms for Mg-deficiency-induced vein lignification, enlargement and cracking, which appeared only in the lower leaves. In this study, 3065 upregulated and 1220 downregulated, and 1390 upregulated and 375 downregulated genes were identified in Mg-deficiency veins of lower leaves (MDVLL) vs Mg-sufficiency veins of lower leaves (MSVLL) and Mg-deficiency veins of upper leaves (MDVUL) vs Mg-sufficiency veins of upper leaves (MSVUL), respectively. There were 1473 common differentially expressed genes (DEGs) between MDVLL vs MSVLL and MDVUL vs MSVUL, 1463 of which displayed the same expression trend. Magnesium-deficiency-induced lignification, enlargement and cracking in veins of lower leaves might be related to the following factors: (i) numerous transciption factors and genes involved in lignin biosynthesis pathways, regulation of cell cycle and cell wall metabolism were upregulated; and (ii) reactive oxygen species, phytohormone and cell wall integrity signalings were activated. Conjoint analysis of proteome and transcriptome indicated that there were 287 and 56 common elements between DEGs and differentially abundant proteins (DAPs) identified in MDVLL vs MSVLL and MDVUL vs MSVUL, respectively, and that among these common elements, the abundances of 198 and 55 DAPs matched well with the transcript levels of the corresponding DEGs in MDVLL vs MSVLL and MDVUL vs MSVUL, respectively, indicating the existence of concordances between protein and transcript levels.

Genome-wide identification and expression analysis of the BURP domain-containing genes in Gossypium hirsutum

Background

Many BURP domain-containing proteins, which are unique to plants, have been identified. They performed diverse functions in plant development and the stress response. To date, only a few BURP domain-containing genes have been studied, and no comprehensive analysis of the gene family in cotton has been reported.

Results

In this study, 18, 17 and 30 putative BURP genes were identified in G. raimondii (D₅), G. arboreum (A₂) and G. hirsutum (AD₁), respectively. These BURP genes were phylogenetically classified into eight subfamilies, which were confirmed by analyses of gene structures, motifs and protein domains. The uneven distribution of BURPs in chromosomes and gene duplication analysis indicated that segmental duplication might be the main driving force of the GhBURP family expansion. Promoter regions of all GhBURPs contained at least one putative stress-related cis-elements. Analysis of transcriptomic data and qRT-PCR showed that GhBURPs showed different expression patterns in different organs, and all of them, especially the members of the RD22-like subfamily, could be induced by different stresses, such as abscisic acid (ABA) and salicylic acid (SA), which indicated that the GhBURPs may performed important functions in cotton’s responses to various abiotic stresses.

Conclusions

Our study comprehensively analyzed BURP genes in G. hirsutum, providing insight into the functions of GhBURPs in cotton development and adaptation to stresses.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5948-y) contains supplementary material, which is available to authorized users.

Thylakoid-Bound Polysomes and a Dynamin-Related Protein, FZL, Mediate Critical Stages of the Linear Chloroplast Biogenesis Program in Greening Arabidopsis Cotyledons

Biogenesis of the complex 3D architecture of plant thylakoids remains an unsolved problem. Here, we analyzed this process in chloroplasts of germinating Arabidopsis thaliana cotyledons using 3D electron microscopy and gene expression analyses of chloroplast proteins. Our study identified a linear developmental sequence with five assembly stages: tubulo-vesicular prothylakoids (24 h after imbibition [HAI]), sheet-like pregranal thylakoids that develop from the prothylakoids (36 HAI), proliferation of pro-grana stacks with wide tubular connections to the originating pregrana thylakoids (60 HAI), structural differentiation of pro-grana stacks and expanded stroma thylakoids (84 HAI), and conversion of the pro-grana stacks into mature grana stacks (120 HAI). Development of the planar pregranal thylakoids and the pro-grana membrane stacks coincides with the appearance of thylakoid-bound polysomes and photosystem II complex subunits at 36 HAI. ATP synthase, cytochrome b6f, and light-harvesting complex II proteins are detected at 60 HAI, while PSI proteins and the curvature-inducing CURT1A protein appear at 84 HAI. If stromal ribosome biogenesis is delayed, prothylakoids accumulate until stromal ribosomes are produced, and grana-forming thylakoids develop after polysomes bind to the thylakoid membranes. In fzo-like (fzl) mutants, in which thylakoid organization is perturbed, pro-grana stacks in cotyledons form discrete, spiral membrane compartments instead of organelle-wide membrane networks, suggesting that FZL is involved in fusing membrane compartments together. Our data demonstrate that the assembly of thylakoid protein complexes, CURT1 proteins, and FZL proteins mediate distinct and critical steps in thylakoid biogenesis.

Gene Expression Patterns in Roots of Camelina sativa With Enhanced Salinity Tolerance Arising From Inoculation of Soil With Plant Growth Promoting Bacteria Producing 1-Aminocyclopropane-1-Carboxylate Deaminase or Expression the Corresponding acdS Gene

Camelina sativa treated with plant growth-promoting bacteria (PGPB) producing 1-aminocyclopropane-1-carboxylate deaminase (acdS) or transgenic lines expressing acdS exhibit increased salinity tolerance. AcdS reduces the level of stress ethylene to below the point where it is inhibitory to plant growth. The study determined that several mechanisms appear to be responsible for the increased salinity tolerance and that the effect of acdS on gene expression patterns in C. sativa roots during salt stress is a function of how it is delivered. Growth in soil treated with the PGPB (Pseudomonas migulae 8R6) mostly affected ethylene- and abscisic acid-dependent signaling in a positive way, while expression of acdS in transgenic lines under the control of the broadly active CaMV 35S promoter or the root-specific rolD promoter affected auxin, jasmonic acid and brassinosteroid signaling and/biosynthesis. The expression of genes involved in minor carbohydrate metabolism were also up-regulated, mainly in roots of lines expressing acdS. Expression of acdS also affected the expression of genes involved in modulating the level of reactive oxygen species (ROS) to prevent cellular damage, while permitting ROS-dependent signal transduction. Though the root is not a photosynthetic tissue, acdS had a positive effect on the expression of genes involved in photosynthesis.

Transcriptomic analysis of boron hyperaccumulation mechanisms in Puccinellia distans

Puccinellia distans, common alkali grass, is found throughout the world and can survive in soils with boron concentrations that are lethal for other plant species. Indeed, P. distans accumulates very high levels of this element. Despite these interesting features, very little research has been performed to elucidate the boron tolerance mechanism in this species. In this study, P. distans samples were treated for three weeks with normal (0.5 mg L^-1) and elevated (500 mg L^-1) boron levels in hydroponic solution. Expressed sequence tags (ESTs) derived from shoot tissue were analyzed by RNA sequencing to identify genes up and down-regulated under boron stress. In this way, 3312 differentially expressed transcripts were detected, 67.7% of which were up-regulated and 32.3% of which were down-regulated in boron-treated plants. To partially confirm the RNA sequencing results, 32 randomly selected transcripts were analyzed for their expression levels in boron-treated plants. The results agreed with the expected direction of change (up or down-regulation). A total of 1652 transcripts had homologs in A. thaliana and/or O. sativa and mapped to 1107 different proteins. Functional annotation of these proteins indicated that the boron tolerance and hyperaccumulation mechanisms of P. distans involve many transcriptomic changes including: alterations in the malate pathway, changes in cell wall components that may allow sequestration of excess boron without toxic effects, and increased expression of at least one putative boron transporter and two putative aquaporins. Elucidation of the boron accumulation mechanism is important in developing approaches for bioremediation of boron contaminated soils.

Melonet-DB, a Grand RNA-Seq Gene Expression Atlas in Melon (Cucumis melo L.)

Melon (Cucumis melo L.) is an important Cucurbitaceae crop produced worldwide, exhibiting wide genetic variations and comprising both climacteric and non-climacteric fruit types. The muskmelon cultivar "'Earl's favorite Harukei-3 (Harukei-3)"' known for its sweetness and rich aroma is used for breeding of high-grade muskmelon in Japan. We conducted RNA sequencing (RNA-seq) transcriptome studies in 30 different tissues of the 'Harukei-3' melon. These included root, stems, leaves, flowers, regenerating callus and ovaries, in addition to the flesh and peel sampled at seven stages of fruit development. The expression patterns of 20,752 genes were determined with fragments per kilobase of transcript per million fragments sequenced (FPKM) >1 in at least one tissue. Principal component analysis distinguished 30 melon tissues based on the global gene expression profile and, further, the weighted gene correlation network analysis classified melon genes into 45 distinct coexpression groups. Some coexpression groups exhibited tissue-specific gene expression. Furthermore, we developed and published web application tools designated "'Gene expression map viewer"' and "'Coexpression viewer"' on our website Melonet-DB (http://melonet-db.agbi.tsukuba.ac.jp/) to promote functional genomics research in melon. By using both tools, we analyzed melon homologs of tomato fruit ripening regulators such as E8, RIPENING-INHIBITOR (RIN) and NON-RIPENING (NOR). The "'Coexpression viewer"' clearly distinguished fruit ripening-associated melon RIN/NOR/CNR homologs from those expressed in other tissues. In addition, several other MADS-box, NAM/ATAF/CUC (NAC) and homeobox transcription factor genes were identified as fruit ripening-associated genes. Our tools provide useful information for research not only on melon but also on other fleshy fruit plants.

An endoplasmic reticulum-localized Coffea arabica BURP domain-containing protein affects the response of transgenic Arabidopsis plants to diverse abiotic stresses

The Coffea arabica BURP domain-containing gene plays an important role in the response of transgenic Arabidopsis plants to abiotic stresses via regulating the level of diverse proteins. Although the functions of plant-specific BURP domain-containing proteins (BDP) have been determined for a few plants, their roles in the growth, development, and stress responses of most plant species, including coffee plant (Coffea arabica), are largely unknown. In this study, the function of a C. arabica BDP, designated CaBDP1, was investigated in transgenic Arabidopsis plants. The expression of CaBDP1 was highly modulated in coffee plants subjected to drought, cold, salt, or ABA. Confocal analysis of CaBDP1-GFP fusion proteins revealed that CaBDP1 is localized in the endoplasmic reticulum. The ectopic expression of CaBDP1 in Arabidopsis resulted in delayed germination of the transgenic plants under abiotic stress and in the presence of ABA. Cotyledon greening and seedling growth of the transgenic plants were inhibited in the presence of ABA due to the upregulation of ABA signaling-related genes like ABI3, ABI4, and ABI5. Proteome analysis revealed that the levels of several proteins are modulated in CaBDP1-expressing transgenic plants. The results of this study underscore the importance of BURP domain proteins in plant responses to diverse abiotic stresses.

Didehydrophenylalanine, an abundant modification in the beta subunit of plant polygalacturonases

The structure and the activity of proteins are often regulated by transient or stable post- translational modifications (PTM). Different from well-known, abundant modifications such as phosphorylation and glycosylation some modifications are limited to one or a few proteins across a broad range of related species. Although few examples of the latter type are known, the evolutionary conservation of these modifications and the enzymes responsible for their synthesis suggest an important physiological role. Here, the first observation of a new, fold-directing PTM is described. During the analysis of alfalfa cell wall proteins a -2Da mass shift was observed on phenylalanine residues in the repeated tetrapeptide FxxY of the beta-subunit of polygalacturonase. This modular protein is known to be involved in developmental and stress-responsive processes. The presence of this modification was confirmed using in-house and external datasets acquired by different commonly used techniques in proteome studies. Based on these analyses it was found that all identified phenylalanine residues in the sequence FxxY of this protein were modified to α,β-didehydro-Phe (ΔPhe). Besides showing the reproducible identification of ΔPhe in different species arguments that substantiate the fold-determining role of ΔPhe are given.

A Global Analysis of the Polygalacturonase Gene Family in Soybean (Glycine max)

Polygalacturonase is one of the pectin hydrolytic enzymes involved in various developmental and physiological processes such as seed germination, organ abscission, pod and anther dehiscence, and xylem cell formation. To date, no systematic analysis of polygalacturonase incorporating genome organization, gene structure, and expression profiling has been conducted in soybean (Glycine max var. Williams 82). In this study, we identified 112 GmPG genes from the soybean Wm82.a2v1 genome. These genes were classified into three groups, group I (105 genes), group II (5 genes), and group III (2 genes). Fifty-four pairs of duplicate paralogous genes were preferentially identified from duplicated regions of the soybean genome, which implied that long segmental duplications significantly contributed to the expansion of the GmPG gene family. Moreover, GmPG transcripts were analyzed in various tissues using RNA-seq data. The results showed the differential expression of 64 GmPGs in the tissue and partially redundant expression of some duplicate genes, while others showed functional diversity. These findings suggested that the GmPGs were retained by substantial subfunctionalization during the soybean evolutionary processes. Finally, evolutionary analysis based on single nucleotide polymorphisms (SNPs) in wild and cultivated soybeans revealed that 107 GmPGs had selected site(s), which indicated that these genes may have undergone strong selection during soybean domestication. Among them, one non-synonymous SNP of GmPG031 affected floral development during selection, which was consistent with the results of RNA-seq and evolutionary analyses. Thus, our results contribute to the functional characterization of GmPG genes in soybean.