scholarly journals Scenarios of Genes-to-Terpenoids Network Led to the Identification of a Novel α/β-Farnesene/β-Ocimene Synthase in Camellia sinensis

2020 ◽  
Vol 21 (2) ◽  
pp. 655
Author(s):  
Jieyang Jin ◽  
Shangrui Zhang ◽  
Mingyue Zhao ◽  
Tingting Jing ◽  
Na Zhang ◽  
...  
Keyword(s):  
Function Analysis ◽  
Pearson Correlation ◽  
Integrated Approach ◽  
In Planta ◽  
Terpene Synthases ◽  
Gene Transcripts ◽  
Pearson Correlation Analysis ◽  
Tea Plants ◽  
And Function

Terpenoids play vital roles in tea aroma quality and plants defense performance determination, whereas the scenarios of genes to metabolites of terpenes pathway remain uninvestigated in tea plants. Here, we report the use of an integrated approach combining metabolites, target gene transcripts and function analyses to reveal a gene-to-terpene network in tea plants. Forty-one terpenes including 26 monoterpenes, 14 sesquiterpenes and one triterpene were detected and 82 terpenes related genes were identified from five tissues of tea plants. Pearson correlation analysis resulted in genes to metabolites network. One terpene synthases whose expression positively correlated with farnesene were selected and its function was confirmed involved in the biosynthesis of α-farnesene, β-ocimene and β-farnesene, a very important and conserved alarm pheromone in response to aphids by both in vitro enzymatic assay in planta function analysis. In summary, we provided the first reliable gene-to-terpene network for novel genes discovery.

scholarly journals Platelet Phenotyping and Function Testing in Thrombocytopenia

2021 ◽  
Vol 10 (5) ◽  
pp. 1114
Author(s):  
Kerstin Jurk ◽  
Yavar Shiravand
Keyword(s):  
Function Analysis ◽  
Point Of Care ◽  
Bleeding Complications ◽  
Diagnostic Significance ◽  
Blood Samples ◽  
Skilled Personnel ◽  
Life Threatening ◽  
And Function ◽  
Function Testing

Patients who suffer from inherited or acquired thrombocytopenia can be also affected by platelet function defects, which potentially increase the risk of severe and life-threatening bleeding complications. A plethora of tests and assays for platelet phenotyping and function analysis are available, which are, in part, feasible in clinical practice due to adequate point-of-care qualities. However, most of them are time-consuming, require experienced and skilled personnel for platelet handling and processing, and are therefore well-established only in specialized laboratories. This review summarizes major indications, methods/assays for platelet phenotyping, and in vitro function testing in blood samples with reduced platelet count in relation to their clinical practicability. In addition, the diagnostic significance, difficulties, and challenges of selected tests to evaluate the hemostatic capacity and specific defects of platelets with reduced number are addressed.

scholarly journals HC-Pro protein of sugar cane mosaic virus interacts specifically with maize ferredoxin-5 in vitro and in planta

2008 ◽  
Vol 89 (8) ◽  
pp. 2046-2054 ◽  
Author(s):  
Yu-Qin Cheng ◽  
Zhong-Mei Liu ◽  
Jian Xu ◽  
Tao Zhou ◽  
Meng Wang ◽  
...  
Keyword(s):  
Mosaic Virus ◽  
Sugar Cane ◽  
Transit Peptide ◽  
Viral Disease ◽  
Middle Part ◽  
Symptom Development ◽  
In Planta ◽  
Maize Plants ◽  
And Function

Symptom development of a plant viral disease is a result of molecular interactions between the virus and its host plant; thus, the elucidation of specific interactions is a prerequisite to reveal the mechanism of viral pathogenesis. Here, we show that the chloroplast precursor of ferredoxin-5 (Fd V) from maize (Zea mays) interacts with the multifunctional HC-Pro protein of sugar cane mosaic virus (SCMV) in yeast, Nicotiana benthamiana cells and maize protoplasts. Our results demonstrate that the transit peptide rather than the mature protein of Fd V precursor could interact with both N-terminal (residues 1–100) and C-terminal (residues 301–460) fragments, but not the middle part (residues 101–300), of HC-Pro. In addition, SCMV HC-Pro interacted only with Fd V, and not with the other two photosynthetic ferredoxin isoproteins (Fd I and Fd II) from maize plants. SCMV infection significantly downregulated the level of Fd V mRNA in maize plants; however, no obvious changes were observed in levels of Fd I and Fd II mRNA. These results suggest that SCMV HC-Pro interacts specifically with maize Fd V and that this interaction may disturb the post-translational import of Fd V into maize bundle-sheath cell chloroplasts, which could lead to the perturbation of chloroplast structure and function.

Multimerization and tubulin binding are required for the SPIRAL2 protein to localize to and stabilize microtubule minus ends

2021 ◽  
Author(s):  
YUANWEI FAN ◽  
Natasha Bilkey ◽  
Ram Dixit
Keyword(s):  
Coiled Coil ◽  
Spatial Arrangement ◽  
In Planta ◽  
Structural Determinants ◽  
Coiled Coil Domain ◽  
Tubulin Binding ◽  
And Function ◽  
Necessary And Sufficient ◽  
Basic Region

Accruing evidence points to the control of microtubule minus-end dynamics as being crucial for the spatial arrangement and function of the microtubule cytoskeleton. In plants, the SPIRAL2 (SPR2) protein has emerged as a microtubule minus-end regulator that is structurally distinct from the animal minus-end regulators. Previously, SPR2 was shown to autonomously localize to microtubule minus ends and decrease their depolymerization rate. Here, we used in vitro and in planta experiments to identify the structural determinants required for SPR2 to recognize and stabilize microtubule minus ends. We show that SPR2 contains a single N-terminal TOG domain that binds to soluble tubulin. The TOG domain, a basic region, and coiled-coil domain are necessary and sufficient to target and stabilize microtubule minus ends. We demonstrate that the coiled-coil domain mediates multimerization of SPR2 that provides avidity for microtubule binding and is essential for binding to soluble tubulin. While TOG domain-containing proteins are traditionally thought to function as microtubule plus-end regulators, our results reveal that nature has repurposed the TOG domain of SPR2 to regulate microtubule minus ends.

scholarly journals Hopanoids confer robustness to physicochemical variability in the niche of the plant symbiont Bradyrhizobium diazoefficiens

2021 ◽  
Author(s):  
Elise M Tookmanian ◽  
Lisa Junghans ◽  
Gargi Kulkarni ◽  
Raphael Ledermann ◽  
James Peter Saenz ◽  
...  
Keyword(s):  
Climate Change ◽  
Environmental Variability ◽  
Root Nodules ◽  
Soil Health ◽  
In Planta ◽  
Growth Defects ◽  
Plant Symbiont ◽  
Fitness Advantage ◽  
And Function

Climate change poses a threat to soil health and agriculture, but the potential effects of climate change on soil bacteria that can help maintain soil health are understudied. Rhizobia are a group of bacteria that increase soil nitrogen content through a symbiosis with legume plants. The soil and symbiosis are potentially stressful environments, and the soil will likely become even more stressful as the climate changes. Many rhizobia within the bradyrhizobia clade, like Bradyrhizobium diazoefficiens, possess the genetic capacity to synthesize hopanoids, steroid-like lipids similar in structure and function to cholesterol. Hopanoids are known to protect against stresses relevant to the niche of B. diazoefficiens. Paradoxically, mutants unable to synthesize the extended class of hopanoids participate in similarly successful symbioses compared to the wild type, despite being delayed in root nodule initiation. Here, we show that in B. diazoefficiens, the in vitro growth defects of extended hopanoid deficient mutants can be at least partially compensated for by the physicochemical environment, specifically by optimal osmotic and divalent cation concentrations. Through biophysical measurements, we show that extended hopanoids confer robustness to environmental variability. These results help explain the discrepancy between previous in vitro and in planta results and indicate that hopanoids may provide a greater fitness advantage to rhizobia in the variable soil environment than the more controlled environment within root nodules. To improve the legume-rhizobia symbiosis through either bioengineering or strain selection, it will be important to consider the full lifecycle of rhizobia, from the soil to the symbiosis.

scholarly journals Function of the HYDROXYCINNAMOYL-CoA:SHIKIMATE HYDROXYCINNAMOYL TRANSFERASE is evolutionarily conserved in embryophytes

2020 ◽  
Author(s):  
Lucie Kriegshauser ◽  
Samuel Knosp ◽  
Etienne Grienenberger ◽  
Kanade Tatsumi ◽  
Desirée D. Gütle ◽  
...  
Keyword(s):  
Phenylpropanoid Pathway ◽  
Evolutionary Significance ◽  
Marchantia Polymorpha ◽  
Loss Of Function ◽  
In Planta ◽  
Critical Function ◽  
Acyl Acceptor ◽  
Bona Fide ◽  
And Function

ABSTRACTThe plant phenylpropanoid pathway generates a major class of specialized metabolites and precursors of essential extracellular polymers that initially appeared upon plant terrestrialization. Despite its evolutionary significance, little is known about the complexity and function of this major metabolic pathway in extant bryophytes, the ancestors of which were the first land plants. Here, we report that the HYDROXYCINNAMOYL-CoA:SHIKIMATE HYDROXYCINNAMOYL TRANSFERASE (HCT) gene, which plays a critical function in the phenylpropanoid pathway during seed plant development, is functionally conserved in Physcomitrium patens (Physcomitrella), in the moss lineage of bryophytes. Phylogenetic analysis indicates that bona fide HCT function emerged in the progenitor of embryophytes. In vitro enzyme assays, moss phenolic pathway reconstitution in yeast and in planta gene inactivation coupled to targeted metabolic profiling, collectively indicate that P. patens HCT (PpHCT), similar to tracheophyte HCT orthologs, uses shikimate as a native acyl acceptor to produce a p-coumaroyl-5-O-shikimate intermediate. Phenotypic and metabolic analyses of loss-of-function mutants show that PpHCT is necessary for the production of caffeate derivatives, including previously reported caffeoyl-threonate esters, and for the formation of an intact cuticle. Deep conservation of HCT function in embryophytes is further suggested by the ability of HCT genes from P. patens and the liverwort Marchantia polymorpha to complement an Arabidopsis thaliana CRISPR/Cas9 hct mutant, and by the presence of phenolic esters of shikimate in representative species of the three bryophyte lineages.

scholarly journals Formation of α-Farnesene in Tea (Camellia sinensis) Leaves Induced by Herbivore-Derived Wounding and Its Effect on Neighboring Tea Plants

2019 ◽  
Vol 20 (17) ◽  
pp. 4151 ◽  
Author(s):  
Xuewen Wang ◽  
Lanting Zeng ◽  
Yinyin Liao ◽  
Jianlong Li ◽  
Jinchi Tang ◽  
...  
Keyword(s):  
Camellia Sinensis ◽  
Nicotiana Benthamiana ◽  
Plant Volatiles ◽  
Tea Leaves ◽  
Related Factors ◽  
Geranyl Diphosphate ◽  
Herbivore Induced Plant Volatiles ◽  
Tea Plants ◽  
And Function

Herbivore-induced plant volatiles (HIPVs) play important ecological roles in defense against stresses. In contrast to model plants, reports on HIPV formation and function in crops are limited. Tea (Camellia sinensis) is an important crop in China. α-Farnesene is a common HIPV produced in tea plants in response to different herbivore attacks. In this study, a C. sinensis α-farnesene synthase (CsAFS) was isolated, cloned, sequenced, and functionally characterized. The CsAFS recombinant protein produced in Escherichia coli was able to transform farnesyl diphosphate (FPP) into α-farnesene and also convert geranyl diphosphate (GPP) to β-ocimene in vitro. Furthermore, transient expression analysis in Nicotiana benthamiana plants indicated that CsAFS was located in the cytoplasm and could convert FPP to α-farnesene in plants. Wounding, to simulate herbivore damage, activated jasmonic acid (JA) formation, which significantly enhanced the CsAFS expression level and α-farnesene content. This suggested that herbivore-derived wounding induced α-farnesene formation in tea leaves. Furthermore, the emitted α-farnesene might act as a signal to activate antibacterial-related factors in neighboring undamaged tea leaves. This research advances our understanding of the formation and signaling roles of common HIPVs in crops such as tea plants.

scholarly journals Downregulation of miR-193a-3p is involved in the pathogenesis of hepatocellular carcinoma by targeting CCND1

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8409 ◽  
Author(s):  
Shi-shuo Wang ◽  
Zhi-guang Huang ◽  
Hua-yu Wu ◽  
Rong-quan He ◽  
Li-hua Yang ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Correlation Analysis ◽  
Kegg Pathway ◽  
Pearson Correlation ◽  
Luciferase Reporter ◽  
Kegg Pathway Analysis ◽  
Reporter Assays ◽  
Pearson Correlation Analysis ◽  
Hcc Cells

Background Hepatocellular carcinoma (HCC) is the second-highest cause of malignancy-related death worldwide, and many physiological and pathological processes, including cancer, are regulated by microRNAs (miRNAs). miR-193a-3p is an anti-oncogene that plays an important part in health and disease biology by interacting with specific targets and signals. Methods In vitro assays were performed to explore the influences of miR-193a-3p on the propagation and apoptosis of HCC cells. The sequencing data for HCC were obtained from The Cancer Genome Atlas (TCGA), and the expression levels of miR-193a-3p in HCC and non-HCC tissues were calculated. The differential expression of miR-193a-3p in HCC was presented as standardized mean difference (SMD) with 95% confidence intervals (CIs) in Stata SE. The impact of miR-193a-3p on the prognoses of HCC patients was determined by survival analysis. The potential targets of miR-193a-3p were then predicted using miRWalk 2.0 and subjected to enrichment analyses, including Gene Ontology (GO) annotation, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, and Protein-Protein Interaction (PPI) network analysis. The interaction between miR-193a-3p and one predicted target, Cyclin D1 (CCND1), was verified by dual luciferase reporter assays and Pearson correlation analysis. Results MiR-193a-3p inhibited the propagation and facilitated the apoptosis of HCC cells in vitro. The pooled SMD indicated that miR-193a-3p had a low level of expression in HCC (SMD: −0.88, 95% CI [−2.36 −0.59]). Also, HCC patients with a higher level of miR-193a-3p expression tended to have a favorable overall survival (OS: HR = 0.7, 95% CI [0.43–1.13], P = 0.14). For the KEGG pathway analysis, the most related pathway was “proteoglycans in cancer”, while the most enriched GO term was “protein binding”. The dual luciferase reporter assays demonstrated the direct interaction between miR-193a-3p and CCND1, and the Pearson correlation analysis suggested that miR-193a-3p was negatively correlated with CCND1 in HCC tissues (R =  − 0.154, P = 0.002). Conclusion miR-193a-3p could suppress proliferation and promote apoptosis by targeting CCND1 in HCC cells. Further, miR-193a-3p can be used as a promising biomarker for the diagnosis and treatment of HCC in the future.

scholarly journals Non-Canonical G-quadruplexes cause the hCEB1 minisatellite instability in Saccharomyces cerevisiae

eLife ◽  
2017 ◽  
Vol 6 ◽  
Author(s):  
Aurèle Piazza ◽  
Xiaojie Cui ◽  
Michael Adrian ◽  
Frédéric Samazan ◽  
Brahim Heddi ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Structure Function ◽  
Genomic Instability ◽  
Function Analysis ◽  
Structural Features ◽  
Detectable Effect ◽  
Definition Of ◽  
And Function

G-quadruplexes (G4) are polymorphic four-stranded structures formed by certain G-rich nucleic acids in vitro, but the sequence and structural features dictating their formation and function in vivo remains uncertain. Here we report a structure-function analysis of the complex hCEB1 G4-forming sequence. We isolated four G4 conformations in vitro, all of which bear unusual structural features: Form 1 bears a V-shaped loop and a snapback guanine; Form 2 contains a terminal G-triad; Form 3 bears a zero-nucleotide loop; and Form 4 is a zero-nucleotide loop monomer or an interlocked dimer. In vivo, Form 1 and Form 2 differently account for 2/3rd of the genomic instability of hCEB1 in two G4-stabilizing conditions. Form 3 and an unidentified form contribute to the remaining instability, while Form 4 has no detectable effect. This work underscores the structural polymorphisms originated from a single highly G-rich sequence and demonstrates the existence of non-canonical G4s in cells, thus broadening the definition of G4-forming sequences.

scholarly journals Structure-guided disruption of pseudopilus tip inhibits Type II secretion in Pseudomonas aeruginosa

2018 ◽  
Author(s):  
Zongchao Jia ◽  
Yichen Zhang ◽  
Frederick Faucher ◽  
Wenwen Zhang ◽  
Shu Wang ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Function Analysis ◽  
Type Ii Secretion ◽  
Type Ii ◽  
Core Complex ◽  
Wide Range ◽  
Interaction Interface ◽  
And Function

Pseudomonas aeruginosa utilizes the Type II secretion system (T2SS) to translocate a wide range of large, structured protein virulence factors through the periplasm to the extracellular environment for infection. In the T2SS, five pseudopilins assemble into the pseudopilus that acts as a piston to extrude exoproteins out of cells. Through structure determination of the pseudopilin complexes of XcpVWX and XcpVW and function analysis, we have confirmed that two minor pseudopilins, XcpV and XcpW, constitute a core complex indispensable to the pseudopilus tip. The absence of either XcpV or -W resulted in the non-functional T2SS. Our small-angle X-ray scattering experiment for the first time revealed the architecture of the entire pseudopilus tip and established the working model. Based on the interaction interface of complexes, we have developed inhibitory peptides. The structure-based peptides not only disrupted of the XcpVW core complex and the entire pseudopilus tip in vitro but also inhibited the T2SS in vivo. More importantly, these peptides effectively reduced the virulence of P. aeruginosa towards Caenorhabditis elegans.

scholarly journals Efficacy based ginger fingerprinting reveals potential antiproliferative analytes for triple negative breast cancer

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Lihan Zhao ◽  
Manali Rupji ◽  
Ishita Choudhary ◽  
Remus Osan ◽  
Shobhna Kapoor ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Triple Negative Breast Cancer ◽  
Triple Negative ◽  
Pearson Correlation ◽  
Principal Component ◽  
Zingiber Officinale ◽  
Ginger Extract ◽  
Anticancer Efficacy ◽  
Pearson Correlation Analysis

Abstract Ginger (Zingiber officinale) is one of the most widely consumed dietary supplements worldwide. Its anticancer potential has been demonstrated in various studies. However, ginger roots obtained from different geographical locations showed extensive variability in their activities, mainly due to differences in the levels of bioactive compounds. Here we evaluated the effect of these differences on the anticancer activity of ginger by performing efficacy-based fingerprinting. We characterized the fingerprint profiles of 22 ginger samples using liquid chromatography-mass spectroscopy, followed by a principal component analysis (PCA) and pearson correlation analysis. We also evaluated the anti-proliferative effects (IC50) of these samples on triple-negative breast cancer cells using the MTT assays. The supervised PCA identified a subset of analytes whose abundance strongly associated with the IC50 values of the ginger extracts, providing a link between ginger extract composition and in vitro anticancer efficacy. This study demonstrated that variation in the ginger fingerprint profiles resulting from differences in their chemical composition could have a significant impact on efficacy and bioactivity of ginger extracts. Also, this first-of-a-kind efficacy-based fingerprinting approach proposed here can identify potent anticancer candidates from the ginger fingerprint without the need for isolating individual components from the extracts.

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