Arabidopsis Chloroplast protein for Growth and Fertility1 (CGF1) and CGF2 are essential for chloroplast development and female gametogenesis.

BACKGROUND: Chloroplasts are essential organelles of plant cells for not only being the energy factory but also making plant cells adaptable to different environmental stimuli. The nuclear genome encodes most of the chloroplast proteins, among which a large percentage of membrane proteins have yet to be functionally characterized. RESULTS: We report here functional characterization of two nuclear-encoded chloroplast proteins, Chloroplast protein for Growth and Fertility (CGF1) and CGF2. CGF1 and CGF2 are expressed in diverse tissues and developmental stages. Proteins they encode are associated with chloroplasts through a N-terminal chloroplast-targeting signal in green tissues but also located at plastids in roots and seeds. Mutants of CGF1 and CGF2 generated by CRISPR/Cas9 exhibited vegetative defects, including reduced leaf size, dwarfism, and abnormal cell death. CGF1 and CGF2 redundantly mediate female gametogenesis, likely by securing local energy supply. Indeed, mutations of both genes impaired chloroplast integrity whereas exogenous sucrose rescued the growth defects of the CGF double mutant. CONCLUSION: This study reports that two nuclear-encoded chloroplast proteins, Chloroplast protein for Growth and Fertility (CGF1) and CGF2, play important roles in vegetative growth, in female gametogenesis, and in embryogenesis likely by mediating chloroplast integrity and development.

The AAA-ATPase MIDASIN 1 Functions in Ribosome Biogenesis and Is Essential for Embryo and Root Development.

Ribosome biogenesis is an orchestrated process that relies on many assembly factors. The AAA-ATPase Midasin 1 (Mdn1) functions as a ribosome assembly factor in yeast (Saccharomyces cerevisiae), but the roles of MDN1 in Arabidopsis (Arabidopsis thaliana) are poorly understood. Here, we showed that the Arabidopsis null mutant of MDN1 is embryo-lethal. Using the weak mutant mdn1-1, which maintains viability, we found that MDN1 is critical for the regular pattern of auxin maxima in the globular embryo and functions in root meristem maintenance. By detecting the subcellular distribution of ribosome proteins, we noted that mdn1-1 impairs nuclear export of the pre-60S ribosomal particle. The processing of ribosomal precusor RNAs, including 35S, 27SB, and 20S, is also affected in this mutant. MDN1 physically interacts with PESCADILLO2 (PES2), an essential assembly factor of the 60S ribosome, and the observed mislocalization of PES2 in mdn1-1 further implied that MDN1 plays an indispensable role in 60S ribosome biogenesis. Therefore, the observed hypersensitivity of mdn1-1 to a eukaryotic translation inhibitor and high-sugar conditions might be associated with the defect in ribosome biogenesis. Overall, this work establishes a role of Arabidopsis MDN1 in ribosome biogenesis, which agrees with its roles in embryogenesis and root development.

A role of GUNs-Involved retrograde signaling in regulating Acetyl-CoA carboxylase 2 in Arabidopsis.

In Arabidopsis thaliana (Arabidopsis), Acetyl-CoA Carboxylase 2 (ACC2) is a nuclear DNA-encoded and plastid-targeted enzyme that catalyzes the conversion of acetyl-CoA to malonyl-CoA. ACC2 improves plant growth and development when chloroplast translation is impaired. However, little is known about the upstream signals that regulate ACC2. Here, through analyzing the transcriptome changes in brz-insensitive-pale green (bpg) 2-2, a pale-green mutant with impaired chloroplast gene expression resulting from loss of the BPG2 function, we found that the level of ACC2 was significantly up-regulated. Through performing genetic analysis, we further demonstrated that loss of the GENOMES UNCOUPLED 1 (GUN1) or GUN5 function partly perturbed the up-regulation of ACC2 in the bpg2-2 mutant, whereas ABA INSENSITIVE 4 (ABI4)-function-loss had no clear effect on the ACC2 expression. Furthermore, when plants were treated with plastid translation inhibitors, such as lincomycin and spectinomycin, the ACC2 transcriptional level was also markedly increased in a GUN-dependent manner. In conclusion, our results suggested that the GUN-involved plastid-to-nucleus retrograde communication played a role in regulating ACC2 in Arabidopsis.

Metabolomics analysis of the nutraceutical diversity and physiological quality of Torreya yunnanensis seeds during cold storage.

This study investigated how cold storage affects the nutraceutical diversity and physiological quality of Torreya yunnanensis seeds, using a widely targeted UPLC-MS/MS-based metabolomics analysis. The 373 identified metabolites were divided into nine categories: lipids, phenolic acids, amino acids and derivatives, organic acids, nucleotides, saccharides, vitamins and alcohols. Among them, 49 metabolites showed significant changes after 3 months of cold storage, affecting 28 metabolic pathways. The content of amino acid-related metabolites significantly increased, while the content of sugar-related metabolites decreased during storage. Notably, the content of proline acid, shikimic acid, α-linolenic acid and branched-chain amino acids showed significant changes, indicating their potential role in seed storage. This study deepens our understanding of the nutraceutical diversity and physiological quality of T. yunnanensis seeds during storage, providing insight for conservation efforts and habitat restoration.

A chitosan induced 9-lipoxygenase in Adelostemma gracillimum seedlings.

Oxylipins generated by the lipoxygenase (LOX) pathway play an important role in plant defense against biotic and abiotic stress. In chitosan-treated Adelostemma gracillimum seedlings, obvious accumulation of 9-LOX-derived oxylipins, namely 9,10,11-trihydroxy-12-octadecenoic acid, was detected. Using degenerate primers, a LOX-specific fragment putatively encoding LOX was obtained by RT-PCR, and a 2.9-kb full-length cDNA named AgLOX1 was isolated by RACE from chitosan-induced A. gracillimum seedlings. Genomic Southern analysis implied that there was only one copy of AgLOX1 in the A. gracillimum genome. AgLOX1 was expressed in Escherichia coli and the recombinant protein was partially purified. The enzyme converted linoleic and linolenic acids almost exclusively to their 9-hydroperoxides. AgLOX1 encoded a 9-lipoxygenase. Northern blot analysis indicated that chitosan-induced AgLOX1 transcript accumulation peaked at 8 h after initiation of treatment, whereas trihydroxy derivatives accumulation was highest at 24 h after elicitation. Results showed that chitosan-induced AgLOX1 encoded a 9-lipoxygenase potentially involved in the defense response through 9-LOX pathway leading to biosynthesis of antimicrobial compounds in A. gracillimum seedlings.

Comparative chloroplast genome and phylogenetic analyses of Chinese Polyspora.

Polyspora Sweet (Theaceae) are winter ornamental landscape plants native to southern and southeastern Asia, some of which have medicinal value. The chloroplast (cp) genome data of Polyspora are scarce, and the gene evolution and interspecific relationship are still unclear. In this study, we sequenced and annotated Polyspora chrysandra cp genome and combined it with previously published genomes for other Chinese Polyspora species. The results showed that cp genomes of six Chinese Polyspora varied in length between 156,452 bp (P. chrysandra) and 157,066 bp (P. speciosa), but all contained 132 genes, with GC content of 37.3%, and highly similar genes distribution and codon usage. A total of eleven intergenic spacer regions were found having the highest levels of divergence, and eight divergence hotspots were identified as molecular markers for Phylogeography and genetic diversity studies in Polyspora. Gene selection pressure suggested that five genes were subjected to positive selection. Phylogenetic relationships among Polyspora species based on the complete cp genomes were supported strongly, indicating that the cp genomes have the potential to be used as super barcodes for further analysis of the phylogeny of the entire genus. The cp genomes of Chinese Polyspora species will provide valuable information for species identification, molecular breeding and evolutionary analysis of genus Polyspora.

Impacts of climate change on species distribution patterns of Polyspora sweet in China.

Climate change is an important driver of species distribution and biodiversity. Understanding the response of plants to climate change is helpful to understand species differentiation and formulate conservation strategies. The genus Polyspora (Theaceae) has an ancient origin and is widely distributed in subtropical evergreen broad-leaved forests. Studies on the impacts of climate change on species geographical distribution of Chinese Polyspora can provide an important reference for exploring the responses of plant groups in subtropical evergreen broad-leaved forests with geological events and climate change in China. Based on the environmental variables, distribution records, and chloroplast genomes, we modeled the potential distribution of Chinese Polyspora in the Last Glacial Maximum, middle Holocene, current, and future by using MaxEnt-ArcGIS model and molecular phylogenetic method. The changes in the species distribution area, centroid shift, and ecological niche in each periods were analyzed to speculate the response modes of Chinese Polyspora to climate change in different periods. The most important environmental factor affecting the distribution of Polyspora was the precipitation of the driest month, ranging from 13 to 25 mm for the highly suitable habitats. At present, highly suitable distribution areas of Polyspora were mainly located in the south of 25°N, and had species-specificity. The main glacial refugia of the Chinese Polyspora might be located in the Ailao, Gaoligong, and Dawei Mountains of Yunnan Province. Jinping County, Pingbian County, and the Maguan County at the border of China and Vietnam might be the species differentiation center of the Chinese Polyspora. Moderate climate warming in the future would be beneficial to the survival of P. axillaris, P. chrysandra, and P. speciosa. However, climate warming under different shared socio-economic pathways would reduce the suitable habitats of P. hainanensis and P. longicarpa.

The complete chloroplast genome of Hydrangea strigosa Rehder (Hydrangeaceae).

Hydrangea strigosa Rehder is a wild flowering shrub with high ornamental value. The complete chloroplast genome sequence of H. strigosa was characterized from Hiseq (Illumina Co., San Diego, CA) sequencing data. The chloroplast genome of H. strigosa is 157,905 bp in length with a pair of inverted repeats (IRs) (26,127 bp) which are separated by a large single-copy (LSC) (86,897 bp) and a small single-copy regions (SSC) (18,754 bp). It contains 131 genes, including 85 protein-coding genes, 38 tRNAs genes, and 8 rRNAs genes. The overall GC content of the whole genome is 37.80%. The maximum-likelihood phylogenetic analysis with the complete chloroplast genomes sequence of 22 species of Hydrangeaceae showed that H. strigosa is closely related to H. davidii.

The complete chloroplast genome sequence of Phalaenopsis wilsonii Rolfe, a vulnerable wild moth orchid species (Orchidaceae).

Phalaenopsis wilsonii Rolfe is a vulnerable wild moth orchid species with important horticultural value. The complete chloroplast genome sequence of P. wilsonii was generated by de novo assembly using whole genome next-generation sequencing to provide genomic data for further conservation genetics, phylogeny and molecular breeding in Phalaenopsis. The complete plastome of P. wilsonii is 145,096 bp in length, containing two inverted repeats (IR) regions (24,787 bp), a large single-copy (LSC) region (84,688 bp), and a small single-copy (SSC) region (10,834 bp). The chloroplast genome encoded 119 unique genes, including 73 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. The overall GC content of the whole genome is 36.9%. Phylogenetic analysis indicated P. wilsonii was closely related to P. lowii.

Characterization of the complete chloroplast genome of Polyspora tiantangensis (Theaceae), an endemic and endangered species in southwestern China.

Polyspora tiantangensis (Theaceae) is an endangered woody plant in southwestern China. In this study, we assembled complete chloroplast (cp) genome of P. tiantangensis based on the Illumina reads. The cp genome of P. tiantangensis is 157,057 bp in length, including a large single-copy (LSC) region of 86,593 bp and a small single-copy (SSC) region of 18,284 bp, separated by two inverted repeat (IR) regions of 26,090 bp each. The cp genome encoded 132 genes including 87 protein-coding genes, 37 tRNA genes, and eight rRNA genes. The GC content of cp genome of P. tiantangensis is 37.3%. A total of 68 SSRs were discovered. Phylogenetic analysis of cp genomes from 26 species of Theaceae revealed that all species of Polyspora formed one monophyletic clade and P. tiantangensis was closely related with its congeneric species P. longicarpa with 100% bootstrap value.

Transcriptional Differences in Peanut (Arachis hypogaea L.) Seeds at the Freshly Harvested, After-ripening and Newly Germinated Seed Stages: Insights into the Regulatory Networks of Seed Dormancy Release and Germination.

Seed dormancy and germination are the two important traits related to plant survival, reproduction and crop yield. To understand the regulatory mechanisms of these traits, it is crucial to clarify which genes or pathways participate in the regulation of these processes. However, little information is available on seed dormancy and germination in peanut. In this study, seeds of the variety Luhua No.14, which undergoes nondeep dormancy, were selected, and their transcriptional changes at three different developmental stages, the freshly harvested seed (FS), the after-ripening seed (DS) and the newly germinated seed (GS) stages, were investigated by comparative transcriptomic analysis. The results showed that genes with increased transcription in the DS vs FS comparison were overrepresented for oxidative phosphorylation, the glycolysis pathway and the tricarboxylic acid (TCA) cycle, suggesting that after a period of dry storage, the intermediates stored in the dry seeds were rapidly mobilized by glycolysis, the TCA cycle, the glyoxylate cycle, etc.; the electron transport chain accompanied by respiration was reactivated to provide ATP for the mobilization of other reserves and for seed germination. In the GS vs DS pairwise comparison, dozens of the upregulated genes were related to plant hormone biosynthesis and signal transduction, including the majority of components involved in the auxin signal pathway, brassinosteroid biosynthesis and signal transduction as well as some GA and ABA signal transduction genes. During seed germination, the expression of some EXPANSIN and XYLOGLUCAN ENDOTRANSGLYCOSYLASE genes was also significantly enhanced. To investigate the effects of different hormones during seed germination, the contents and differential distribution of ABA, GAs, BRs and IAA in the cotyledons, hypocotyls and radicles, and plumules of three seed sections at different developmental stages were also investigated. Combined with previous data in other species, it was suggested that the coordination of multiple hormone signal transduction nets plays a key role in radicle protrusion and seed germination.

Effects of hyperglycaemia and elevated glycosylated haemoglobin on contrast-induced nephropathy after coronary angiography.

In patients undergoing percutaneous coronary intervention after acute myocardial infarction, hyperglycaemia on admission is associated with an increased risk of contrast-induced nephropathy (CIN). However, the effects of hyperglycaemia and elevated glycosylated haemoglobin (HbA1c) on CIN have remained to be fully elucidated. Therefore, a prospective cohort study was performed, comprising 258 patients who underwent coronary angiography between May 2017 and November 2017 at Zhongda Hospital affiliated with Southeast University (Nanjing, China). According to the diagnostic criteria for CIN (increase of serum creatinine by >44.2 µmol/l or by 25% within 48-72 h of using contrast agent), the patients were divided into two groups: CIN (45 cases) and non-CIN (213 cases). For all patients, the baseline data, medical history, laboratory parameters, medication history and intraoperative situation were recorded and assessed using single-factor analysis and multiple logistic regression analysis to analyse the risk factors of CIN. The incidence of CIN in the hyperglycaemia group (blood glucose on admission, >11.1 mmol/l) was 25%, compared with 13.8% in the non-hyperglycaemia group (P=0.026). Furthermore, the incidence of CIN in the elevated HbA1c group (HbA1c on admission, upper limit of normal) was 26.1%, compared with 14.3% in the group without elevated HbA1c (P=0.027). Hyperglycaemia was present on hospital admission in 84 of 258 patients (32.6%). The percentage of patients with elevated HbA1c was 26.7%. Age, estimated glomerular filtration rate, pre-operative blood cholesterol, hyperglycaemia on admission and elevated HbA1c were all identified to be associated with CIN. According to the multivariate logistic regression analysis, hyperglycaemia was an independent predictor of CIN (odds ratio, 2.815; 95% confidence interval, 1.042-4.581; P=0.029). In the acute coronary syndrome (ACS) and diabetes subgroups, hyperglycaemia was significantly associated with CIN. In the ACS subgroup, the incidence of CIN was 38.1%. It was indicated that hyperglycaemia is an independent risk factor for CIN, particularly in patients with ACS or diabetes. Trial registration no. ChiCTR-OOC-17011466.

Combined small RNA and gene expression analysis revealed roles of miRNAs in maize response to rice black-streaked dwarf virus infection.

Maize rough dwarf disease, caused by rice black-streaked dwarf virus (RBSDV), is a devastating disease in maize (Zea mays L.). MicroRNAs (miRNAs) are known to play critical roles in regulation of plant growth, development, and adaptation to abiotic and biotic stresses. To elucidate the roles of miRNAs in the regulation of maize in response to RBSDV, we employed high-throughput sequencing technology to analyze the miRNAome and transcriptome following RBSDV infection. A total of 76 known miRNAs, 226 potential novel miRNAs and 351 target genes were identified. Our dataset showed that the expression patterns of 81 miRNAs changed dramatically in response to RBSDV infection. Transcriptome analysis showed that 453 genes were differentially expressed after RBSDV infection. GO, COG and KEGG analysis results demonstrated that genes involved with photosynthesis and metabolism were significantly enriched. In addition, twelve miRNA-mRNA interaction pairs were identified, and six of them were likely to play significant roles in maize response to RBSDV. This study provided valuable information for understanding the molecular mechanism of maize disease resistance, and could be useful in method development to protect maize against RBSDV.