scholarly journals Transcriptome Profile of the Variegated Ficus microcarpa c.v. Milky Stripe Fig Leaf

2019 ◽  
Vol 20 (6) ◽  
pp. 1338 ◽  
Author(s):  
Tin-Han Shih ◽  
Szu-Hsien Lin ◽  
Meng-Yuan Huang ◽  
Wen-Dar Huang ◽  
Chi-Ming Yang
Keyword(s):  
Transcriptome Profile ◽  
Chlorophyll Metabolism ◽  
Chlorophyll Breakdown ◽  
Core Proteins ◽  
Transcription Termination Factor ◽  
N Assimilation ◽  
Genes Encoding ◽  
Ficus Microcarpa ◽  
Differential Expressed Gene ◽  
Photosynthetic Properties

Photosynthetic properties and transcriptomic profiles of green and white sectors of Ficus microcarpa (c.v. milky stripe fig) leaves were examined in naturally variegated plants. An anatomic analysis indicated that chloroplasts of the white sectors contained a higher abundance of starch granules and lacked stacked thylakoids. Moreover, no photosynthetic rate was detected in the white sectors. Transcriptome profile and differential expressed gene (DEG) analysis showed that genes encoding PSII core proteins were down-regulated in the white sectors. In genes related to chlorophyll metabolism, no DEGs were identified in the biosynthesis pathway of chlorophyll. However, genes encoding the first step of chlorophyll breakdown were up-regulated. The repression of genes involved in N-assimilation suggests that the white sectors were deprived of N. The mutation in the transcription factor mitochondrial transcription termination factor (mTERF) suggests that it induces colorlessness in leaves of the milky stripe fig.

scholarly journals Roles of Si and SiNPs in Improving Thermotolerance of Wheat Photosynthetic Machinery via Upregulation of PsbH, PsbB and PsbD Genes Encoding PSII Core Proteins

Horticulturae ◽  
2021 ◽  
Vol 7 (2) ◽  
pp. 16
Author(s):  
Heba Hassan ◽  
Aishah Alatawi ◽  
Awatif Abdulmajeed ◽  
Manal Emam ◽  
Hemmat Khattab
Keyword(s):  
Photosystem Ii ◽  
Global Climate ◽  
Soluble Sugars ◽  
Triticum Aestivum L ◽  
Pcr Analysis ◽  
Silicon Dioxide Nanoparticles ◽  
System Productivity ◽  
Photosynthetic System ◽  
Core Proteins ◽  
Genes Encoding

Photosystem II is extremely susceptible to environmental alterations, particularly high temperatures. The maintenance of an efficient photosynthetic system under stress conditions is one of the main issues for plants to attain their required energy. Nowadays, searching for stress alleviators is the main goal for maintaining photosynthetic system productivity and, thereby, crop yield under global climate change. Potassium silicate (K2SiO3, 1.5 mM) and silicon dioxide nanoparticles (SiO2NPs, 1.66 mM) were used to mitigate the negative impacts of heat stress (45 °C, 5 h) on wheat (Triticum aestivum L.) cv. (Shandawelly) seedlings. The results showed that K2SiO3 and SiO2NPs diminished leaf rolling symptoms and electrolyte leakage (EL) of heat-stressed wheat leaves. Furthermore, the maximum quantum yield of photosystem II (Fv/Fm) and the performance index (PIabs), as well as the photosynthetic pigments and organic solutes including soluble sugars, sucrose, and proline accumulation, were increased in K2SiO3 and SiO2NPs stressed leaves. At the molecular level, RT-PCR analysis showed that K2SiO3 and SiO2NPs treatments stimulated the overexpression of PsbH, PsbB, and PsbD genes. Notably, this investigation indicated that K2SiO3 was more effective in improving wheat thermotolerance compared to SiO2NPs. The application of K2SiO3 and SiO2NPs may be one of the proposed approaches to improve crop growth and productivity to tolerate climatic change.

scholarly journals Cause and Effectors: Whole-Genome Comparisons Reveal Shared but Rapidly Evolving Effector Sets among Host-Specific Plant-Castrating Fungi

mBio ◽  
2019 ◽  
Vol 10 (6) ◽  
Author(s):  
William C. Beckerson ◽  
Ricardo C. Rodríguez de la Vega ◽  
Fanny E. Hartmann ◽  
Marine Duhamel ◽  
Tatiana Giraud ◽  
...  
Keyword(s):  
Positive Selection ◽  
Plant Pathogens ◽  
Pfam Domain ◽  
Rapid Evolution ◽  
Host Specialization ◽  
Secreted Proteins ◽  
Smut Fungi ◽  
Core Proteins ◽  
Genes Encoding ◽  
Species Specific

ABSTRACT Plant pathogens utilize a portfolio of secreted effectors to successfully infect and manipulate their hosts. It is, however, still unclear whether changes in secretomes leading to host specialization involve mostly effector gene gains/losses or changes in their sequences. To test these hypotheses, we compared the secretomes of three host-specific castrating anther smut fungi (Microbotryum), two being sister species. To address within-species evolution, which might involve coevolution and local adaptation, we compared the secretomes of strains from differentiated populations. We experimentally validated a subset of signal peptides. Secretomes ranged from 321 to 445 predicted secreted proteins (SPs), including a few species-specific proteins (42 to 75), and limited copy number variation, i.e., little gene family expansion or reduction. Between 52% and 68% of the SPs did not match any Pfam domain, a percentage that reached 80% for the small secreted proteins, indicating rapid evolution. In comparison to background genes, we indeed found SPs to be more differentiated among species and strains, more often under positive selection, and highly expressed in planta; repeat-induced point mutations (RIPs) had no role in effector diversification, as SPs were not closer to transposable elements than background genes and were not more RIP affected. Our study thus identified both conserved core proteins, likely required for the pathogenic life cycle of all Microbotryum species, and proteins that were species specific or evolving under positive selection; these proteins may be involved in host specialization and/or coevolution. Most changes among closely related host-specific pathogens, however, involved rapid changes in sequences rather than gene gains/losses. IMPORTANCE Plant pathogens use molecular weapons to successfully infect their hosts, secreting a large portfolio of various proteins and enzymes. Different plant species are often parasitized by host-specific pathogens; however, it is still unclear whether the molecular basis of such host specialization involves species-specific weapons or different variants of the same weapons. We therefore compared the genes encoding secreted proteins in three plant-castrating pathogens parasitizing different host plants, producing their spores in plant anthers by replacing pollen. We validated our predictions for secretion signals for some genes and checked that our predicted secreted proteins were often highly expressed during plant infection. While we found few species-specific secreted proteins, numerous genes encoding secreted proteins showed signs of rapid evolution and of natural selection. Our study thus found that most changes among closely related host-specific pathogens involved rapid adaptive changes in shared molecular weapons rather than innovations for new weapons.

scholarly journals A docked mutation phenocopies dumpy oblique alleles via altered vesicle trafficking

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12175
Author(s):  
Suresh Kandasamy ◽  
Kiley Couto ◽  
Justin Thackeray
Keyword(s):  
Matrix Protein ◽  
Vesicle Trafficking ◽  
Notch Pathway ◽  
Vesicle Transport ◽  
Snare Proteins ◽  
Extracellular Matrix Protein ◽  
Functional Connection ◽  
Core Proteins ◽  
Genes Encoding

The Drosophila extracellular matrix protein Dumpy (Dpy) is one of the largest proteins encoded by any animal. One class of dpy mutations produces a characteristic shortening of the wing blade known as oblique (dpyo), due to altered tension in the developing wing. We describe here the characterization of docked (doc), a gene originally named because of an allele producing a truncated wing. We show that doc corresponds to the gene model CG5484, which encodes a homolog of the yeast protein Yif1 and plays a key role in ER to Golgi vesicle transport. Genetic analysis is consistent with a similar role for Doc in vesicle trafficking: docked alleles interact not only with genes encoding the COPII core proteins sec23 and sec13, but also with the SNARE proteins synaptobrevin and syntaxin. Further, we demonstrate that the strong similarity between the doc1 and dpyo wing phenotypes reflects a functional connection between the two genes; we found that various dpy alleles are sensitive to changes in dosage of genes encoding other vesicle transport components such as sec13 and sar1. Doc’s effects on trafficking are not limited to Dpy; for example, reduced doc dosage disturbed Notch pathway signaling during wing blade and vein development. These results suggest a model in which the oblique wing phenotype in doc1 results from reduced transport of wild-type Dumpy protein; by extension, an additional implication is that the dpyo alleles can themselves be explained as hypomorphs.

scholarly journals Co-culturing Hyphomicrobium nitrativorans strain NL23 and Methylophaga nitratireducenticrescens strain JAM1 allows sustainable denitrifying activities under marine conditions

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12424
Author(s):  
Alexandra Cucaita ◽  
Marianne Piochon ◽  
Richard Villemur
Keyword(s):  
Expression Profiles ◽  
Lag Phase ◽  
Rna Seq ◽  
Expression Of Genes ◽  
N Assimilation ◽  
Genes Encoding ◽  
Potential Synergy ◽  
Pure Cultures

Background Hyphomicrobium nitrativorans strain NL23 and Methylophaga nitratireducenticrescens strain JAM1 are the principal bacteria involved in the denitrifying activities of a methanol-fed, fluidized-bed marine denitrification system. Strain NL23 possesses the complete denitrification pathway, but cannot grow under marine conditions in pure cultures. Strain JAM1 is a marine bacterium that lacks genes encoding a dissimilatory nitrite (NO2−) reductase and therefore cannot reduce NO2−. Here, we report the characterization of some of their physiological traits that could influence their co-habitation. We also perform co-cultures to assess the potential synergy between the two strains under marine and denitrifying conditions. Methodology Anoxic planktonic pure cultures of both strains were grown with different concentrations of nitrate (NO3−). Anoxic planktonic co-cultures could only be cultured on low NaCl concentrations for strain NL23 to grow. Biofilm co-cultures were achieved in a 500-mL bioreactor, and operated under denitrifying conditions with increasing concentrations of NaCl. NO3− and NO2− concentrations and the protein content were measured to derive the denitrification rates. The concentrations of both strains in co-cultures were determined by quantitative PCR (qPCR). Ectoine concentration was measured by mass spectrometry in the biofilm co-culture. The biofilm was visualized by fluorescence in situ hybridization. Reverse-transcription-qPCR and RNA-seq approaches were used to assess changes in the expression profiles of genes involved in the nitrogen pathways in the biofilm cultures. Results Planktonic pure cultures of strain JAM1 had a readiness to reduce NO3− with no lag phase for growth in contrast to pure cultures of strain NL23, which had a 2-3 days lag phase before NO3− starts to be consumed and growth to occur. Compared to strain NL23, strain JAM1 has a higher µmax for growth and higher specific NO3− reduction rates. Denitrification rates were twice higher in the planktonic co-cultures than those measured in strain NL23 pure cultures. The biofilm co-cultures showed sustained denitrifying activities and surface colonization by both strains under marine conditions. Increase in ectoine concentrations was observed in the biofilm co-culture with the increase of NaCl concentrations. Changes in the relative transcript levels were observed in the biofilm culture with genes encoding NapA and NapGH in strain NL23. The type of medium had a great impact on the expression of genes involved in the N-assimilation pathways in both strains. Conclusions These results illustrate the capacity of both strains to act together in performing sustainable denitrifying activities under marine conditions. Although strain JAM1 did not contribute in better specific denitrifying activities in the biofilm co-cultures, its presence helped strain NL23 to acclimate to medium with NaCl concentrations >1.0%.

scholarly journals Skeletal Dysplasias Caused by Sulfation Defects

2020 ◽  
Vol 21 (8) ◽  
pp. 2710
Author(s):  
Chiara Paganini ◽  
Chiara Gramegna Tota ◽  
Andrea Superti-Furga ◽  
Antonio Rossi
Keyword(s):  
Extracellular Matrix ◽  
Negative Charge ◽  
Future Research ◽  
Panoramic View ◽  
Skeletal Dysplasias ◽  
Core Proteins ◽  
Extracellular Matrix Molecules ◽  
Genes Encoding ◽  
Sulfate Metabolism ◽  
And Function

Proteoglycans (PGs) are macromolecules present on the cell surface and in the extracellular matrix that confer specific mechanical, biochemical, and physical properties to tissues. Sulfate groups present on glycosaminoglycans, linear polysaccharide chains attached to PG core proteins, are fundamental for correct PG functions. Indeed, through the negative charge of sulfate groups, PGs interact with extracellular matrix molecules and bind growth factors regulating tissue structure and cell behavior. The maintenance of correct sulfate metabolism is important in tissue development and function, particularly in cartilage where PGs are fundamental and abundant components of the extracellular matrix. In chondrocytes, the main sulfate source is the extracellular space, then sulfate is taken up and activated in the cytosol to the universal sulfate donor to be used in sulfotransferase reactions. Alteration in each step of sulfate metabolism can affect macromolecular sulfation, leading to the onset of diseases that affect mainly cartilage and bone. This review presents a panoramic view of skeletal dysplasias caused by mutations in genes encoding for transporters or enzymes involved in macromolecular sulfation. Future research in this field will contribute to the understanding of the disease pathogenesis, allowing the development of targeted therapies aimed at alleviating, preventing, or modifying the disease progression.

scholarly journals Identification of Rf9, a Gene Contributing to the Genetic Complexity of Fertility Restoration in Hybrid Wheat

2020 ◽  
Vol 11 ◽  
Author(s):  
Fahimeh Shahinnia ◽  
Manuel Geyer ◽  
Annette Block ◽  
Volker Mohler ◽  
Lorenz Hartl
Keyword(s):  
Fertility Restoration ◽  
Snp Markers ◽  
Genetic Maps ◽  
Hybrid Seed Production ◽  
Hybrid Wheat ◽  
Pentatricopeptide Repeat ◽  
Male Sterile ◽  
Transcription Termination Factor ◽  
Restorer Of Fertility ◽  
Genes Encoding

Wheat (Triticum aestivum L.) is a self-pollinating crop whose hybrids offer the potential to provide a major boost in yield. Male sterility induced by the cytoplasm of Triticum timopheevii is a powerful method for hybrid seed production. Hybrids produced by this method are often partially sterile, and full fertility restoration is crucial for wheat production using hybrid cultivars. To identify the genetic loci controlling fertility restoration in wheat, we produced two cytoplasmic male-sterile (CMS) backcross (BC1) mapping populations. The restorer lines Gerek 79 and 71R1203 were used to pollinate the male-sterile winter wheat line CMS-Sperber. Seed set and numbers of sterile spikelets per spike were evaluated in 340 and 206 individuals of the populations derived from Gerek 79 and 71R1203, respectively. Genetic maps were constructed using 930 and 994 single nucleotide polymorphism (SNP) markers, spanning 2,160 and 2,328 cM over 21 linkage groups in the two populations, respectively. Twelve quantitative trait loci (QTL) controlled fertility restoration in both BC1 populations, including a novel restorer-of-fertility (Rf) locus flanked by the SNP markers IWB72413 and IWB1550 on chromosome 6AS. The locus was mapped as a qualitative trait in the BC1 Gerek 79 population and was designated Rf9. One hundred-nineteen putative candidate genes were predicted within the QTL region on chromosome 6AS. Among them were genes encoding mitochondrial transcription termination factor and pentatricopeptide repeat-containing proteins that are known to be associated with fertility restoration. This finding is a promising step to better understand the functions of genes for improving fertility restoration in hybrid wheat.

scholarly journals Genes encoding the core proteins of adenovirus type 2.

1984 ◽  
Vol 259 (22) ◽  
pp. 13980-13985 ◽  
Author(s):  
P Aleström ◽  
G Akusjärvi ◽  
M Lager ◽  
L Yeh-kai ◽  
U Pettersson
Keyword(s):  
Adenovirus Type ◽  
The Core ◽  
Core Proteins ◽  
Genes Encoding ◽  
Adenovirus Type 2

scholarly journals Analysis of the regulation networks in grapevine reveals response to waterlogging stress and candidate gene-marker selection for damage severity

2018 ◽  
Vol 5 (6) ◽  
pp. 172253 ◽  
Author(s):  
Xudong Zhu ◽  
Xiaopeng Li ◽  
Songtao Jiu ◽  
Kekun Zhang ◽  
Chen Wang ◽  
...  
Keyword(s):  
Climate Change Impacts ◽  
Grape Berry ◽  
Marker Genes ◽  
Gene Marker ◽  
Waterlogging Tolerance ◽  
Wine Production ◽  
Chlorophyll Metabolism ◽  
Waterlogging Stress ◽  
Marker Selection ◽  
Genes Encoding

Owing to the climate change impacts, waterlogging is one of the most hazardous abiotic stresses to crops, which also can result in a serious reduction in the quantity and quality of grape berry and wine production during the rainy season. Therefore, the exploration of the response mechanism of grape to waterlogging is necessary, for which the analysis of the transcriptomic regulation networks of grapevine leaves in response to waterlogging stress was carried out. In this study, 12 634 genes were detected in both waterlogging stress and control grapevine plants, out of which 6837 genes were differentially expressed. A comparative analysis revealed that genes functioning in the antioxidant system, glycolysis and fermentation pathway, chlorophyll metabolism, amino acid metabolism and hormones were activated to reduce injury to grapes under the waterlogging stress. Meanwhile, genes encoding class-2 non-symbiotic haemoglobin were determined as important in waterlogging acclimation. Additionally, the expression variations of three marker genes were found to be informative and can be used to predict the viability of the grapevines subjected to waterlogging. This research not only probes the molecular mechanism underlying grapevine waterlogging tolerance but also puts forward an idea about the application of gene expression information to practical management.

Unravelling chlorophyll catabolism in higher plants

2002 ◽  
Vol 30 (4) ◽  
pp. 625-630 ◽  
Author(s):  
B. Kräutler
Keyword(s):  
Higher Plants ◽  
Structural Features ◽  
Spectroscopic Methods ◽  
Chlorophyll Metabolism ◽  
Chlorophyll Breakdown ◽  
Chlorophyll Catabolites

Chlorophyll metabolism is probably the most visible manifestation of life. In spite of this, chlorophyll catabolism has remained something of a mystery until about 10 years ago. At that time, the first non-green tetrapyrrolic chlorophyll breakdown products from higher plants were discovered, and the structure of the first one of them was elucidated by modern spectroscopic methods. In the meantime, the essential structural features of chlorophyll catabolites and some of the biochemistry of chlorophyll breakdown in higher plants have been uncovered, as outlined in this article.

scholarly journals Continuous inflorescence removal changes parameters, lignin and saponin a content and alters the transcriptome of root of Bupleurum chinense DC

2020 ◽  
Author(s):  
Hui Wang ◽  
Gaixia Zhang ◽  
Zhihui Gao ◽  
Chun Sui ◽  
Jianhe Wei
Keyword(s):  
Molecular Mechanisms ◽  
Signal Transduction Pathway ◽  
Fold Increase ◽  
Transcriptome Profile ◽  
Root Numbers ◽  
Yield And Quality ◽  
Genes Encoding ◽  
Radix Bupleuri ◽  
Yield Quality

Abstract BackgroundBupleurum chinense DC. is an important traditional medicinal plant, and its root as the only medicinal part named Radix Bupleuri is used widely for the treatments of influenza, fever, inflammation, etc. in China, Japan and Korea. As a bulk herb, this herbal medicine occupies a comparatively big market share and is widely cultivated. However, because of the vigorous flowering and fruiting, the root growth is influenced seriously. ResultsWe assessed the effect of the continuous inflorescence removal (CIR) on improving the yield and quality of Radix Bupleuri. The results showed that the taproot length, root head diameter, and lateral root numbers were significantly elevated by CIR. We also found an average 1.71-fold increase in root biomass, and the lower lignin and higher saponin a content were detected in roots of CIR-treated plants. Based on a comparative transcriptome analysis, 172, 243, 1974 and 3024 differentially expressed genes (DEGs) were respectively identified in the CIR-treated roots. Gene Ontology and KEGG pathway functional annotation analysis of the DEGs showed that multiple genes were involved sugars metabolism pathway, lignin and terpenoids biosynthesis pathway, and the plant hormones signal transduction pathway. In addition, 295 genes encoding transcription factors (TFs), including members of the ERF, MYB-related, bHLH, NAC, MYB, AUX/IAA and bZIP families etc, were identified as CIR responsive. ConclusionThe CIR treatment could improve the yield, quality and market value of B. chinense DC. medicine, and the first transcriptome profile of CIR-treated roots of B. chinense DC. provides a series of clues of the molecular mechanisms of these phenotype changes induced by CIR.

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