Systematic Annotation Reveals CEP Function in Tomato Root Development and Abiotic Stress Response.

Tomato (Solanum lycopersicum) is one of the most important vegetable crops worldwide; however, environmental stressors severely restrict tomato growth and yield. Therefore, it is of great interest to discover novel regulators to improve tomato growth and environmental stress adaptions. Here, we applied a comprehensive bioinformatics approach to identify putative tomato C-TERMINALLY ENCODED PEPTIDE (CEP) genes and to explore their potential physiological function in tomato root development and abiotic stress responses. A total of 17 tomato CEP genes were identified and grouped into two subgroups based on the similarity of CEP motifs. The public RNA-Seq data revealed that tomato CEP genes displayed a diverse expression pattern in tomato tissues. Additionally, CEP genes expression was differentially regulated by nitrate or ammonium status in roots and shoots, respectively. The differences in expression levels of CEP genes induced by nitrogen indicate a potential involvement of CEPs in tomato nitrogen acquisition. The synthetic CEP peptides promoted tomato primary root growth, which requires nitric oxide (NO) and calcium signaling. Furthermore, we also revealed that CEP peptides improved tomato root resistance to salinity. Overall, our work will contribute to provide novel genetic breeding strategies for tomato cultivation under adverse environments.

Trans-kingdom expression of an insect endogenous microRNA in rice enhances resistance to striped stem borer Chilo suppressalis.

BACKGROUND: The striped stem borer (SSB), Chilo suppressalis Walker, is a major pest of rice worldwide. Breeding of transgenic rice expressing Bacillus thuringiensis (Bt) toxins is a powerful strategy to control SSB. However, pests may evolve certain resistance to Bt toxins in transgenic plants. Hence, new controlling strategies must be continuously developed. RESULTS: We successfully generated SSB-resistant rice (csu-53) expressing the artificial microRNA (amiRNA) of SSB endogenous miRNA (csu-novel-miR53) through the RNAi-based technology. Feeding assays demonstrated that csu-53 rice inhibited larval growth, delayed pupation time, and reduced pupal weight and eclosion rate of SSB larva. In a 10-day feeding experiment, the miRNA mimic of csu-novel-miR53 also suppressed larval growth and more importantly increased larval mortality. Transcriptome analysis identified 28 differentially expressed unigenes (DEGs) in the midgut between SSB larvae fed on csu-53 rice and the wild type. One DEG (DN90065_c0_g12) validated by qRT-PCR had a predicted target site of csu-novel-miR53. In addition, in vitro double-stranded RNA synthesis and further feeding assay proved that DN90065_c0_g12 is most likely the target of csu-novel-miR53. CONCLUSION: amiRNA-mediated strategy can be applied to the development of insect-resistant crops, and the novel amiRNA csu-novel-miR53 of SSB has important application potential in developing SSB resistant rice. © 2021 Society of Chemical Industry.

Identification and Expression Analysis of Stress-Associated Proteins (SAPs) Containing A20/AN1 Zinc Finger in Cucumber.

Stress-associated proteins (SAPs) are a class of zinc finger proteins that confer tolerance to a variety of abiotic and biotic stresses in diverse plant species. However, in cucumber (Cucumis sativus L.), very little is known about the roles of SAP gene family members in regulating plant growth, development, and stress responses. In this study, a total of 12 SAP genes (named as CsSAP1-CsSAP12) were identified in the cucumber genome, which were unevenly distributed on six chromosomes. Gene duplication analysis detected one tandem duplication and two segmental duplication events. Phylogenetic analysis of SAP proteins from cucumber and other plants suggested that they could be divided into seven groups (sub-families), and proteins in the same group generally had the same arrangement of AN1 (ZnF-AN1) and A20 (ZnF-A20) domains. Most of the CsSAP genes were intronless and harbored a number of stress- and hormone-responsive cis-elements in their promoter regions. Tissue expression analysis showed that the CsSAP genes had a broad spectrum of expression in different tissues, and some of them displayed remarkable alteration in expression during fruit development. RT-qPCR results indicated that all the selected CsSAP genes displayed transcriptional responses to cold, drought, and salt stresses. These results enable the first comprehensive description of the SAP gene family in cucumber and lay a solid foundation for future research on the biological functions of CsSAP genes.

Translocation of Drought-Responsive Proteins from the Chloroplasts.

Some chloroplast proteins are known to serve as messengers to transmit retrograde signals from chloroplasts to the nuclei in response to environmental stresses. However, whether particular chloroplast proteins respond to drought stress and serve as messengers for retrograde signal transduction are unclear. Here, we used isobaric tags for relative and absolute quantitation (iTRAQ) to monitor the proteomic changes in tobacco (Nicotiana benthamiana) treated with drought stress/re-watering. We identified 3936 and 1087 differentially accumulated total leaf and chloroplast proteins, respectively, which were grouped into 16 categories. Among these, one particular category of proteins, that includes carbonic anhydrase 1 (CA1), exhibited a great decline in chloroplasts, but a remarkable increase in leaves under drought stress. The subcellular localizations of CA1 proteins from moss (Physcomitrella patens), Arabidopsis thaliana and rice (Oryza sativa) in P. patens protoplasts consistently showed that CA1 proteins gradually diminished within chloroplasts but increasingly accumulated in the cytosol under osmotic stress treatment, suggesting that they could be translocated from chloroplasts to the cytosol and act as a signal messenger from the chloroplast. Our results thus highlight the potential importance of chloroplast proteins in retrograde signaling pathways and provide a set of candidate proteins for further research.

Comprehensive Analysis of TIFY Transcription Factors and Their Expression Profiles under Jasmonic Acid and Abiotic Stresses in Watermelon.

The TIFY gene family is plant-specific and encodes proteins involved in the regulation of multiple biological processes. Here, we identified 15 TIFY genes in the watermelon genome, which were divided into four subfamilies (eight JAZs, four ZMLs, two TIFYs, and one PPD) in the phylogenetic tree. The ClTIFY genes were unevenly located on eight chromosomes, and three segmental duplication events and one tandem duplication event were identified, suggesting that gene duplication plays a vital role in the expansion of the TIFY gene family in watermelon. Further analysis of the protein architectures, conserved domains, and gene structures provided additional clues for understanding the putative functions of the TIFY family members. Analysis of qRT-PCR and RNA-seq data revealed that the detected ClTIFY genes had preferential expression in specific tissues. qRT-PCR analysis revealed that nine selected TIFY genes were responsive to jasmonic acid (JA) and abiotic stresses including salt and drought. JA activated eight genes and suppressed one gene, among which ClJAZ1 and ClJAZ7 were the most significantly induced. Salt and drought stress activated nearly all the detected genes to different degrees. These results lay a foundation for further functional characterization of TIFY family genes in Citrullus lanatus.

Physiological and Transcriptome Analyses Reveal Short-Term Responses and Formation of Memory Under Drought Stress in Rice.

In some plants, exposure to stress can induce a memory response, which appears to play an important role in adaptation to recurrent stress environments. However, whether rice exhibits drought stress memory and the molecular mechanisms that might underlie this process have remained unclear. Here, we ensured that rice drought memory was established after cycles of mild drought and re-watering treatment, and studied gene expression by whole-transcriptome strand-specific RNA sequencing (ssRNA-seq). We detected 6,885 transcripts and 238 lncRNAs involved in the drought memory response, grouped into 16 distinct patterns. Notably, the identified genes of dosage memory generally did not respond to the initial drought treatment. Our results demonstrate that stress memory can be developed in rice under appropriate water deficient stress, and lncRNA, DNA methylation and endogenous phytohormones (especially abscisic acid) participate in rice short-term drought memory, possibly acting as memory factors to activate drought-related memory transcripts in pathways such as photosynthesis and proline biosynthesis, to respond to the subsequent stresses.

The overexpression of insect endogenous small RNAs in transgenic rice inhibits growth and delays pupation of striped stem borer (Chilo suppressalis).

BACKGROUND: The striped stem borer (SSB), Chilo suppressalis Walker, is a major rice insect pest worldwide. RNA interference (RNAi) has become a promising strategy for developing insect-resistant crops. In a previous study, five double-stranded RNAs (dsRNAs) targeting important SSB housekeeping genes were overexpressed in rice, but none of the acquired dsRNA-transgenic rice plants showed significant effects on SSB. RESULTS: Thirteen selected SSB endogenous small RNAs, predicted as SSB novel microRNAs (miRNAs), were overexpressed in rice using artificial miRNA (amiRNA) expression technology. Feeding tests showed that two out of 13 selected SSB novel miRNAs caused significant growth inhibition for feeding SSB larvae based on transgenic rice expression. Pupation was delayed 4 days when SSB larvae consecutively fed on transgenic rice expressing the SSB novel miRNA candidate csu-novel-miR15 (csu-15 rice). Gene expression analysis confirmed that the expression levels of at least six SSB unigenes significantly changed (i.e., were up- or down-regulated) after feeding on csu-15 rice. CONCLUSIONS: Our research demonstrated a novel RNAi strategy using SSB endogenous small RNAs to develop RNAi crops for pest management; this strategy is different from the common RNAi resulting from transgenic dsRNAs or amiRNAs targeting certain insect endogenous genes. © 2016 Society of Chemical Industry.

W-box and G-box elements play important roles in early senescence of rice flag leaf.

Plant cis-elements play important roles in global regulation of gene expression. Based on microarray data from rice flag leaves during early senescence, we identified W-box and G-box cis-elements as positive regulators of senescence in the important rice variety Minghui 63. Both cis-elements were bound by leaf senescence-specific proteins in vitro and influenced senescence in vivo. Furthermore, combination of the two elements drove enhanced expression during leaf senescence, and copy numbers of the cis-elements significantly affected the levels of expression. The W-box is the cognate cis-element for WRKY proteins, while the G-box is the cognate cis-element for bZIP, bHLH and NAC proteins. Consistent with this, WRKY, bZIP, bHLH and NAC family members were overrepresented among transcription factor genes up-regulated according during senescence. Crosstalk between ABA, CTK, BR, auxin, GA and JA during senescence was uncovered by comparing expression patterns of senescence up-regulated transcription factors. Together, our results indicate that hormone-mediated signaling could converge on leaf senescence at the transcriptional level through W-box and G-box elements. Considering that there are very few documented early senescence-related cis-elements, our results significantly contribute to understanding the regulation of flag leaf senescence and provide prioritized targets for stay-green trait improvement.

[Active components of Ligustrum lucidum inhibiting hepatitis C virus replicase activity].

Based on previous report that the Chinese herb Ligustrum lucidum (LL) extract directly inhibited hepatitis C virus (HCV) replicase (NS5B) activity, the active components of LL extract to inhibit HCV NS5B activity and their inhibition mode were investigated in this study. LL extract was separated using ethyl acetate and thin layer chromatography (TLC). The inhibitory activity of separated fractions on HCV NS5B was analyzed by the inhibitory assay of NS5B activity. The results showed that only fractions 1 and 2 inhibited NS5B activity, and fraction 2 possessed higher inhibitory activity than fraction 1. HPLC analysis combined with inhibitory assays indicated that ursolic acid and oleanolic acid are the active components within fractions 1 and 2 to inhibit NS5B activity, separately. Moreover, oleanolic acid possessed higher inhibitory activity than ursolic acid. Further inhibition mode analysis found that both oleanolic acid and ursolic acid suppressed NS5B activity as noncompetitive inhibitors. The Ki values of ursolic acid and oleanolic acid were about 4.7 microg x mL(-1) (10 micromol x kg(-1)) and 2.5 microg x mL(-1) (5.5 micromol x kg(-1)), respectively. Taken together, these results demonstrated that oleanolic acid and ursolic acid suppressed NS5B activity as noncompetitive inhibitors, implying that the two natural products have potential value for HCV therapy.

Comparative assessment of the methanogenic steps of single and two-stage processes without or with a previous hydrolysis of cassava distillage.

In this study, cassava distillage with a high solid content was digested in an anaerobic sequencing batch reactor (ASBR) without or with a previous hydrolytic step by a cellulolytic microbial consortium (i.e., single or two-stage process). The methanogenic steps of these processes were compared and evaluated through observation of the methanogenic stability and methane yield under different organic loading rates (OLRs). It was found the methanogenic reactor can be stably performed with the OLRs lower than 20 g COD L(-1) d(-1) in the two-stage process, where a specific methane yield (0.147 L CH4 g(-1) CODremoved) could be achieved, which was 17.6% higher than that of the single-stage process (0.125 L CH4 g(-1) CODremoved). The above results indicated that the degradation of cassava distillage in a two-stage process with a previous hydrolytic step can assure the methanogenic process proceeds with greater stability and generates higher methane yield.

Hepatitis C virus NS4B induces unfolded protein response and endoplasmic reticulum overload response-dependent NF-kappaB activation.

Hepatitis C virus nonstructural protein 4B (NS4B) is an endoplasmic reticulum (ER) membrane associated protein and a potent causative factor of ER stress. Here we reported that unfolded protein response (UPR) can be activated by HCV NS4B through inducing both XBP1 mRNA splicing and ATF6 cleavage in human hepatic cells. Flow cytometric analysis revealed that HCV NS4B stimulates the production of reactive oxygen species (ROS) by perturbing intracellular Ca(2+) homeostasis. Luciferase assay showed that HCV NS4B also activates the multifunctional transcription factor, NF-kappaB, in a dose-dependent manner through Ca(2+) signaling and ROS. Further immunoblot analysis showed that HCV NS4B promotes NF-kappaB translocation into the nucleus via protein-tyrosine kinase (PTK) mediated phosphorylation and subsequent degradation of IkappaBalpha. These studies provide an important insight into the implication of NS4B in HCV life cycle and HCV-associated liver disease by affecting host intracellular signal transduction pathways.