scholarly journals Defining Color Change in Pitaya: A Close Look at Betacyanin Synthesis Genes in Stenocereus queretaroensis

2021 ◽  
Vol 5 ◽  
Author(s):  
Javier Morales ◽  
Jorge Araujo-Sanchez ◽  
Lizbeth Castro-Concha ◽  
Angela Ku ◽  
Alejandro Pereira-Santana ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Color Change ◽  
Differential Expression Analysis ◽  
Plant Stress ◽  
Aromatic Amino Acids ◽  
Suspension Cells ◽  
Natural Colorants ◽  
Visual Attraction ◽  
Acid Pathway ◽  
Growing Conditions

Betalains are tyrosine-derived plant pigments present in several species of the Caryophyllales order. Betalains are classified in red betacyanins and yellow betaxanthins and are implicated in plant stress tolerance and visual attraction for pollinators. The compounds are used as natural colorants in many industries. Today, there is little information on betalain biosynthesis with several key enzymes that remain unknown on plants of the Caryophyllales order. Omic tools have proven to be very useful in gaining insights into various molecular mechanisms. In this study, we used suspension cells from fruits of the cactus Stenocereus queretaroensis. Two growing conditions were used to perform RNA-seq and differential expression analysis to help identify betalain biosynthesis-related genes. We found 98 differential expressed genes related to aromatic amino acids and betalain biosynthesis pathways. Interestingly, we found that only one gene of the betalain synthesis pathway was differentially expressed. The rest of the genes belong to the aromatic amino acid pathway, including hydroxy phenylpyruvate-related genes, suggesting the possibility of an alternative biosynthetic pathway similar to that observed in legumes.

Cross-species Transcriptomes Reveal Species-specific and Shared Molecular Adaptations for Plants Development on Iron-rich Rocky Outcrops Soils

2021 ◽  
Author(s):  
Mariana Costa Dias ◽  
Cecílio Caldeira ◽  
Markus Gastauer ◽  
Silvio Ramos ◽  
Guilherme Oliveira
Keyword(s):  
Circadian Rhythm ◽  
Differential Expression ◽  
Native Species ◽  
Molecular Mechanisms ◽  
Light Stimulus ◽  
Differential Expression Analysis ◽  
Common Mechanism ◽  
Dependent Manner ◽  
Rocky Outcrops ◽  
Species Specific

Abstract BackgroundCanga is the Brazilian term for the savanna-like vegetation harboring several endemic species on iron-rich rocky outcrops, usually considered for mining activities. Parkia platycephala Benth. and Stryphnodendron pulcherrimum (Willd.) Hochr. naturally occur in the cangas of Serra dos Carajás (eastern Amazonia, Brazil) and the surrounding forest, indicating high phenotypic plasticity. The morphological and physiological mechanisms of the plants’ establishment in the canga environment are well studied, but the molecular adaptative responses are still unknown. We aimed to identify molecular mechanisms that allow the establishment of these plants in the canga environment.ResultsPlants were grown in canga and forest substrates collected in the Carajás Mineral Province. RNA was extracted from pooled leaf tissue, and RNA-seq paired-end reads were assembled into representative transcriptomes for P. platycephala and S. pulcherrimum containing 31,728 and 31,311 primary transcripts, respectively. We identified both species-specific and core molecular responses in plants grown in the canga substrate using differential expression analyses. In the species-specific analysis, we identified 1,112 and 838 differentially expressed genes for P. platycephala and S. pulcherrimum, respectively. Enrichment analyses showed unique biological processes and metabolic pathways affected for each species. Comparative differential expression analysis was based on shared single-copy orthologs. The overall pattern of ortholog expression was species-specific. Even so, almost 300 altered genes were identified between plants in canga and forest substrates, responding the same way in both species. The genes were functionally associated with the response to light stimulus and the circadian rhythm pathway.ConclusionsPlants possess species-specific adaptative responses to cope with the substrates. Our results also suggest that plants adapted to both canga and forest environments can adjust the circadian rhythm in a substrate-dependent manner. The circadian clock gene modulation might be a central mechanism regulating the plants’ development in the canga substrate in the studied legume species. The mechanism may be shared as a common mechanism to abiotic stress compensation in other native species.

scholarly journals A concise review on advances in development of small molecule anti-inflammatory therapeutics emphasising AMPK: An emerging target

2016 ◽  
Vol 29 (4) ◽  
pp. 562-571 ◽  
Author(s):  
Chethan Gejjalagere Honnappa ◽  
Unnikrishnan Mazhuvancherry Kesavan
Keyword(s):  
Drug Targets ◽  
Molecular Mechanisms ◽  
Inflammatory Diseases ◽  
Cyclooxygenase Inhibitors ◽  
Evolutionarily Conserved ◽  
Inflammatory Drugs ◽  
Anti Inflammatory ◽  
Acid Pathway ◽  
Clinical Trial Results ◽  
Amp Activated Protein Kinase

Inflammatory diseases are complex, multi-factorial outcomes of evolutionarily conserved tissue repair processes. For decades, non-steroidal anti-inflammatory drugs and cyclooxygenase inhibitors, the primary drugs of choice for the management of inflammatory diseases, addressed individual targets in the arachidonic acid pathway. Unsatisfactory safety and efficacy profiles of the above have necessitated the development of multi-target agents to treat complex inflammatory diseases. Current anti-inflammatory therapies still fall short of clinical needs and the clinical trial results of multi-target therapeutics are anticipated. Additionally, new drug targets are emerging with improved understanding of molecular mechanisms controlling the pathophysiology of inflammation. This review presents an outline of small molecules and drug targets in anti-inflammatory therapeutics with a summary of a newly identified target AMP-activated protein kinase, which constitutes a novel therapeutic pathway in inflammatory pathology.

scholarly journals Distinct Amino Acid Availability-Dependent Regulatory Mechanisms of MepS and MepM Levels in Escherichia coli

2021 ◽  
Vol 12 ◽  
Author(s):  
Yung Jae Kim ◽  
Byoung Jun Choi ◽  
Si Hyoung Park ◽  
Han Byeol Lee ◽  
Ji Eun Son ◽  
...  
Keyword(s):  
Amino Acid ◽  
Minimal Medium ◽  
Molecular Mechanisms ◽  
Aromatic Amino Acids ◽  
Normal Growth ◽  
Regulatory Mechanisms ◽  
Dependent Manner ◽  
Bacterial Physiology ◽  
Protein Levels ◽  
Amino Acid Availability

Peptidoglycan (PG) hydrolases play important roles in various aspects of bacterial physiology, including cytokinesis, PG synthesis, quality control of PG, PG recycling, and antibiotic resistance. However, the regulatory mechanisms of their expression are poorly understood. In this study, we have uncovered novel regulatory mechanisms of the protein levels of the synthetically lethal PG endopeptidases MepS and MepM, which are involved in PG synthesis. A mutant defective for both MepS and MepM was lethal in an amino acid-rich medium, whereas it exhibited almost normal growth in a minimal medium, suggesting the expendability of MepS and MepM in a minimal medium. Protein levels of MepS and MepM dramatically decreased in the minimal medium. Although MepM was revealed as a substrate of Prc, a periplasmic protease involved in the proteolysis of MepS, only the decrease in the MepS level in the minimal medium was affected by the prc depletion. Phenotypic and biochemical analyses showed that the presence of aromatic amino acids in the medium induced the accumulation of MepS, but not MepM, while the presence of glutamate increased the level of MepM, but not MepS. Together, these results demonstrate that the protein levels of the two major PG endopeptidases are regulated in an amino acid availability-dependent manner, but their molecular mechanisms and signaling are significantly distinct.

scholarly journals Transcriptional, Behavioral and Biochemical Profiling in the 3xTg-AD Mouse Model Reveals a Specific Signature of Amyloid Deposition and Functional Decline in Alzheimer’s Disease

2020 ◽  
Vol 14 ◽  
Author(s):  
Wencheng Yin ◽  
Navei Cerda-Hernández ◽  
Atahualpa Castillo-Morales ◽  
Mayra L. Ruiz-Tejada-Segura ◽  
Jimena Monzón-Sandoval ◽  
...  
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Molecular Mechanisms ◽  
Transcriptional Profiling ◽  
Differential Expression Analysis ◽  
Functional Decline ◽  
Insular Cortex ◽  
Learning Performance ◽  
Significant Enrichment ◽  
Transcriptional Changes

Alzheimer’s disease (AD)-related degenerative decline is associated to the presence of amyloid beta (Aβ) plaque lesions and neuro fibrillary tangles (NFT). However, the precise molecular mechanisms linking Aβ deposition and neurological decline are still unclear. Here we combine genome-wide transcriptional profiling of the insular cortex of 3xTg-AD mice and control littermates from early through to late adulthood (2–14 months of age), with behavioral and biochemical profiling in the same animals to identify transcriptional determinants of functional decline specifically associated to build-up of Aβ deposits. Differential expression analysis revealed differentially expressed genes (DEGs) in the cortex long before observed onset of behavioral symptoms in this model. Using behavioral and biochemical data derived from the same mice and samples, we found that down but not up-regulated DEGs show a stronger average association with learning performance than random background genes in control not seen in AD mice. Conversely, these same genes were found to have a stronger association with Aβ deposition than background genes in AD but not in control mice, thereby identifying these genes as potential intermediaries between abnormal Aβ/NFT deposition and functional decline. Using a complementary approach, gene ontology analysis revealed a highly significant enrichment of learning and memory, associative, memory, and cognitive functions only among down-regulated, but not up-regulated, DEGs. Our results demonstrate wider transcriptional changes triggered by the abnormal deposition of Aβ/NFT occurring well before behavioral decline and identify a distinct set of genes specifically associated to abnormal Aβ protein deposition and cognitive decline.

scholarly journals Differentiation of Tracheary Elements in Sugarcane Suspension Cells Involves Changes in Secondary Wall Deposition and Extensive Transcriptional Reprogramming

2020 ◽  
Vol 11 ◽  
Author(s):  
Marcella Siqueira Simões ◽  
Sávio Siqueira Ferreira ◽  
Adriana Grandis ◽  
Jorge Rencoret ◽  
Staffan Persson ◽  
...  
Keyword(s):  
Regulatory Networks ◽  
Molecular Mechanisms ◽  
Plant Biomass ◽  
Physical Structure ◽  
Grass Species ◽  
Phenylpropanoid Metabolism ◽  
Primary Metabolism ◽  
Tracheary Elements ◽  
Suspension Cells ◽  
Transcriptional Reprogramming

Plant lignocellulosic biomass, mostly composed of polysaccharide-rich secondary cell walls (SCWs), provides fermentable sugars that may be used to produce biofuels and biomaterials. However, the complex chemical composition and physical structure of SCWs hinder efficient processing of plant biomass. Understanding the molecular mechanisms underlying SCW deposition is, thus, essential to optimize bioenergy feedstocks. Here, we establish a xylogenic culture as a model system to study SCW deposition in sugarcane; the first of its kind in a C4 grass species. We used auxin and brassinolide to differentiate sugarcane suspension cells into tracheary elements, which showed metaxylem-like reticulate or pitted SCW patterning. The differentiation led to increased lignin levels, mainly caused by S-lignin units, and a rise in p-coumarate, leading to increased p-coumarate:ferulate ratios. RNAseq analysis revealed massive transcriptional reprogramming during differentiation, with upregulation of genes associated with cell wall biogenesis and phenylpropanoid metabolism and downregulation of genes related to cell division and primary metabolism. To better understand the differentiation process, we constructed regulatory networks of transcription factors and SCW-related genes based on co-expression analyses. Accordingly, we found multiple regulatory modules that may underpin SCW deposition in sugarcane. Our results provide important insights and resources to identify biotechnological strategies for sugarcane biomass optimization.

Regulation of Chloramphenicol Synthesis in Streptomyces sp. 3022a. 3-Deoxy-D-arabino-heptulosonate 7-Phosphate Synthetase

1971 ◽  
Vol 49 (4) ◽  
pp. 448-455 ◽  
Author(s):  
D. A. Lowe ◽  
D. W. S. Westlake
Keyword(s):  
Enzyme Activity ◽  
Shikimic Acid ◽  
Aromatic Amino Acids ◽  
Product Inhibition ◽  
Enzyme Synthesis ◽  
Synthetase Activity ◽  
Shikimic Acid Pathway ◽  
Sugar Phosphates ◽  
Acid Pathway ◽  
Single Enzyme

The repression and end-product inhibition of 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthetase were studied in a chloramphenicol-producing Streptomycetes. Synthesis of DAHP synthetase was repressed by p-hydroxybenzoate, and enzyme activity was inhibited competitively by sugar phosphates, especially D-ribose 5-phosphate. The presence of chloramphenicol, aromatic amino acids, or shikimic acid pathway intermediates did not repress enzyme synthesis nor inhibit enzyme activity. Chloramphenicol production by growing cultures was not affected by the intermediates or end products of the shikimic acid pathway nor by the repression of DAHP synthetase. Purification of DAHP synthetase activity indicated the presence of a single enzyme protein with a molecular weight of 88 000.

scholarly journals Combating stress: the interplay between hormone signaling and autophagy in plants

2019 ◽  
Vol 71 (5) ◽  
pp. 1723-1733 ◽  
Author(s):  
Ching-Yi Liao ◽  
Diane C Bassham
Keyword(s):  
Stress Responses ◽  
Molecular Mechanisms ◽  
Plant Stress ◽  
Stress Conditions ◽  
Hormone Signaling ◽  
Hormone Synthesis ◽  
Energy Sensor ◽  
Sensor Kinases ◽  
Plant Stress Responses ◽  
Cellular Components

Abstract Autophagy is a conserved recycling process in which cellular components are delivered to and degraded in the vacuole/lysosome for reuse. In plants, it assists in responding to dynamic environmental conditions and maintaining metabolite homeostasis under normal or stress conditions. Under stress, autophagy is activated to remove damaged components and to recycle nutrients for survival, and the energy sensor kinases target of rapamycin (TOR) and SNF-related kinase 1 (SnRK1) are key to this activation. Here, we discuss accumulating evidence that hormone signaling plays critical roles in regulating autophagy and plant stress responses, although the molecular mechanisms by which this occurs are often not clear. Several hormones have been shown to regulate TOR activity during stress, in turn controlling autophagy. Hormone signaling can also regulate autophagy gene expression, while, reciprocally, autophagy can regulate hormone synthesis and signaling pathways. We highlight how the interplay between major energy sensors, plant hormones, and autophagy under abiotic and biotic stress conditions can assist in plant stress tolerance.

scholarly journals Genome-wide Identification, characterization and expression analysis of the effector-triggered immunity (ETI) pathway-mediated defense responsive genes in grapes against powdery and downy mildew infections

2020 ◽  
Author(s):  
Neetu Goyal ◽  
Garima Bhatia ◽  
Naina Garewal ◽  
Anuradha Upadhyay ◽  
Kashmir Singh
Keyword(s):  
Expression Analysis ◽  
Molecular Mechanisms ◽  
Differential Expression Analysis ◽  
Differentially Expressed ◽  
Fungal Resistance ◽  
Biotic Stresses ◽  
Sequence Of Events ◽  
Genome Wide ◽  
Effector Triggered Immunity ◽  
Grape Varieties

Abstract Grapevine productivity is severely affected by fungal diseases worldwide and for the diseases control in eco-friendly way, it is essential to understand the molecular mechanisms of fungal resistance in grapes. Therefore, we performed genome-wide identification of various Resistance (R) genes expressed during PM and DM infection in grapevine. Consequently, we identified 6, 21, 2, 5, 3 and 48 EDS1, NDR1, PAD4, NPR, RAR and PR genes respectively in the grapevine genome. Further, differential expression analysis resulted in identification of 2, 4, 7, 2, 4, 1 and 7 differentially expressed PM-responsive Resistance (R) genes (NBS-LRR, EDS1, NDR1, PAD4, NPR, RAR1 and PR) and 28, 2, 5, 4, 1 and 19 differentially expressed DM-responsive Resistance (R) genes (NBS-LRR, EDS1, NDR1, NPR, RAR1 and PR) in V. vinifera. These genes are involved in salicylic acid mediated Effector-triggered immunity (ETI) pathway, therefore, we examined their co-expression to determine the sequence of events that occurs during a signaling cascade in order to respond against PM and DM-infection. Altogether, the PM and DM responsive R genes of ETI pathway found in this study can be used in future to produce new and improved grape varieties that are immune to biotic stresses.

scholarly journals Transcriptome Analysis Identities Key Candidate Genes Mediating Purple Ovary Coloration in Asiatic Hybrid Lilies

2016 ◽  
Author(s):  
Leifeng Xu ◽  
Panpan Yang ◽  
Suxia Yuan ◽  
Yayan Feng ◽  
Hua Xu ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Developmental Stages ◽  
Anthocyanin Biosynthesis ◽  
Differential Expression Analysis ◽  
Transcriptome Data ◽  
Comparative Transcriptome ◽  
Myb Gene ◽  
Short Lifespan ◽  
H Gene ◽  
Pigment Accumulation

Lily tepals have a short lifespan. Once the tepals senesce, the ornamental value of the flower is lost. Some cultivars have attractive purple ovaries and fruits which greatly enhance the ornamental value of Asiatic hybrid lilies. However, little is known about the molecular mechanisms of anthocyanin biosynthesis in Asiatic hybrid lily ovaries. To investigate the transcriptional network that governs purple ovary coloration in Asiatic hybrid lilies, we obtained transcriptome data from green ovaries (S1) and purple ovaries (S2) of Asiatic ‘Tiny Padhye’. Comparative transcriptome analysis revealed 4228 differentially expressed genes. Differential expression analysis revealed that nine unigenes including four CHS genes, one CHI gene, one F3H gene, one F3′H gene, one DFR gene, and one UFGT gene were significantly up-regulated in purple ovaries. One MYB gene, LhMYB12-Lat, was identified as a key transcription factor determining the distribution of anthocyanins in Asiatic hybrid lily ovaries. Further qPCR results showed unigenes related to anthocyanin biosynthesis were highly expressed in purple ovaries of Asiatic ‘Tiny Padhye’ at stages 2 and 3, while they showed an extremely low level of expression in ovaries of Asiatic ‘Yellow Pixels’ during all developmental stages. In addition, shading treatment significantly decreased pigment accumulation by suppressing the expression of several unigenes related to anthocyanin biosynthesis in ovaries of Asiatic ‘Tiny Padhye’. These results could further our understanding of the molecular mechanisms of anthocyanin biosynthesis in Asiatic hybrid lily ovaries.

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