scholarly journals Exploring the biosynthetic pathway of lignin in Acorus tatarinowii Schott using de novo leaf and rhizome transcriptome analysis

2021 ◽  
Author(s):  
Shengxiang Zhang ◽  
Liqiang Zhao ◽  
Chunmiao Shan ◽  
Yuanyuan Shi ◽  
Kelong Ma ◽  
...  
Keyword(s):  
Active Sites ◽  
Biosynthetic Pathway ◽  
Lignin Biosynthesis ◽  
Amino Acid Sequences ◽  
Biologically Active ◽  
Pcr Analysis ◽  
Transcriptional Level ◽  
Biosynthesis Pathway ◽  
Lignin Synthesis ◽  
Acorus Tatarinowii

Acorus tatarinowii Schott is a well-known Chinese traditional herb. Lignin is the major biologically active ingredient and exerts a broad range of pharmacological effects: it is an antitumor, antioxidant, and bacteriostatic agent, and protects the cardiovascular system.In this study, the transcriptomes of the leaf and rhizome tissues of A. tatarinowii Schott were obtained using the BGISEQ-500 platform. 141,777 unigenes were successfully assembled, of which 76,714 were annotated in public databases. Further analysis of the lignin biosynthesis pathway revealed a total of 107 unigenes encoding eight key enzymes, which were involved in the lignin biosynthetic pathway. Furthermore, the expression of the key genes involved in lignin synthesis in different tissues was identified by quantitative real-time PCR. Analysis of the differentially expressed genes showed that most of the upregulated unigenes were enriched in rhizome tissues. In addition, 2,426 unigenes were annotated to the transcriptome factor (TF) family. Moreover, 16 TFs regulating the same key enzyme (peroxidase) were involved in the lignin synthesis pathway. The alignment of peroxidase amino acid sequences and the analysis of the structural characteristics revealed that the key peroxidase enzyme had well-conserved sequences, spatial structures, and active sites. This study is the first to provide comprehensive genetic information on A. tatarinowii Schott at the transcriptional level, and will facilitate our understanding of the lignin biosynthesis pathway.

scholarly journals Activation of the Diacetyl/Acetoin Pathway in Lactococcus lactis subsp. lactis bv. diacetylactis CRL264 by Acidic Growth

2008 ◽  
Vol 74 (7) ◽  
pp. 1988-1996 ◽  
Author(s):  
Nieves García-Quintáns ◽  
Guillermo Repizo ◽  
Mauricio Martín ◽  
Christian Magni ◽  
Paloma López
Keyword(s):  
Lactococcus Lactis ◽  
Biosynthetic Pathway ◽  
Growth Conditions ◽  
Aroma Compounds ◽  
Starter Cultures ◽  
Pcr Analysis ◽  
Transcriptional Level ◽  
Ph Homeostasis ◽  
Acid Growth ◽  
The Impact

ABSTRACT Lactococcus lactis subsp. lactis bv. diacetylactis strains are aroma-producing organisms used in starter cultures for the elaboration of dairy products. This species is essentially a fermentative microorganism, which cometabolizes glucose and citrate to yield aroma compounds through the diacetyl/acetoin biosynthetic pathway. Our previous results have shown that under acidic growth Lactococcus bv. diacetylactis CRL264 expresses coordinately the genes responsible for citrate transport and its conversion into pyruvate. In the present work the impact of acidic growth on glucose, citrate, and pyruvate metabolism of Lactococcus bv. diacetylactis CRL264 has been investigated by proteomic analysis. The results indicated that acid growth triggers the conversion of citrate, but not glucose, into α-acetolactate via pyruvate. Moreover, they showed that low pH has no influence on levels of lactate dehydrogenase and pyruvate dehydrogenase. Therefore, the influence of external pH on regulation of the diacetyl/acetoin biosynthetic pathway in Lactococcus bv. diacetylactis CRL264 has been analyzed at the transcriptional level. Expression of the als, aldB, aldC, and butBA genes encoding the enzymes involved in conversion of pyruvate into aroma compounds has been investigated by primer extension, reverse transcription-PCR analysis, and transcriptional fusions. The results support that this biosynthetic pathway is induced at the transcriptional level by acidic growth conditions, presumably contributing to lactococcal pH homeostasis by synthesis of neutral compounds and by decreasing levels of pyruvate.

scholarly journals Novel bHLH and WD40 transcription factors from turmeric (Curcuma longa L.) as putative regulators of curcumin biosynthesis

2021 ◽  
pp. 20-27
Author(s):  
P. Prashina Mol ◽  
R.S. Aparna ◽  
T.E. Sheeja ◽  
K. Deepa
Keyword(s):  
Transcription Factors ◽  
Biosynthetic Pathway ◽  
Curcuma Longa ◽  
Biologically Active ◽  
Pcr Analysis ◽  
Comparative Transcriptome ◽  
Qrt Pcr ◽  
The Family ◽  
Phenylpropanoid Biosynthesis ◽  
Polymerase Chain

Turmeric, the golden spice belonging to the family Zingiberaceae, is enriched with biologically active curcuminoids composed of curcumin, demethoxycurcumin and bisdemethoxycurcumin. Curcuminoids are phenylpropanoid derivatives, and the biosynthetic pathway is controlled by several transcription factors (TFs). bHLH, WD40 and MYB TFs are the most important TFs regulating phenylpropanoid biosynthesis in plants. Through comparative transcriptome analysis of high and low curcumin germplasm accessions, 20 TFs belonging to the classes bHLH, WD 40, NAC, WRKY and bZIP, which showed differential expression with respect to curcumin, were identified. Among these, two bHLH and one WD40 TFs showed maximum comparative fold change and negative correlation vis-a-vis curcumin content in quantitative real-time polymerase chain reaction (qRT-PCR) analysis. The results of comparative transcriptome and qRT-PCR analyses were in congruence, indicating their putative role as negative regulators.

scholarly journals Genetic Characterization of the Carotenoid Biosynthetic Pathway in Methylobacterium extorquens AM1 and Isolation of a Colorless Mutant

2003 ◽  
Vol 69 (12) ◽  
pp. 7563-7566 ◽  
Author(s):  
Stephen J. Van Dien ◽  
Christopher J. Marx ◽  
Brooke N. O'Brien ◽  
Mary E. Lidstrom
Keyword(s):  
Biosynthetic Pathway ◽  
Genetic Characterization ◽  
Carotenoid Biosynthesis ◽  
Biosynthesis Pathway ◽  
Wild Type ◽  
Methylobacterium Extorquens ◽  
Growth Properties ◽  
Carotenoid Biosynthesis Pathway ◽  
Free Strain

ABSTRACT Genomic searches were used to reconstruct the putative carotenoid biosynthesis pathway in the pink-pigmented facultative methylotroph Methylobacterium extorquens AM1. Four genes for putative phytoene desaturases were identified. A colorless mutant was obtained by transposon mutagenesis, and the insertion was shown to be in one of the putative phytoene desaturase genes. Mutations in the other three did not affect color. The tetracycline marker was removed from the original transposon mutant, resulting in a pigment-free strain with wild-type growth properties useful as a tool for future experiments.

scholarly journals A novel site of insertion of IS6110 in the moaB3 gene of a clinical isolate of Mycobacterium tuberculosis

2011 ◽  
Vol 2 (1) ◽  
pp. 7
Author(s):  
Suma Sarojini ◽  
GK Madhavilatha ◽  
Smitha Soman ◽  
R Ajay Kumar ◽  
Sathish Mundayoor
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Clinical Isolate ◽  
Biosynthetic Pathway ◽  
Mobile Genetic Element ◽  
Point Mutations ◽  
Tuberculosis H37rv ◽  
Genomic Variation ◽  
Clinical Isolates ◽  
Pcr Analysis ◽  
Genome Plasticity

In Mycobacterium tuberculosis, genomic variation is generated mainly by insertions and deletions rather than by point mutations. RvD5 is one such deletion in M. tuberculosis H37Rv. Previous studies from our laboratory have shown the presence of moaA3 gene in the RvD5 region in a large number of clinical isolates, that is absent in M. tuberculosis H37Rv and H37Ra. The present study was aimed at investigating the RvD5 locus of the clinical isolates by a detailed PCR analysis. Here we report a new point of insertion of the mobile genetic element, IS6110 in the genome of one clinical isolate of M. tuberculosis. The insertion has disrupted the moaB3 gene, one of the ORFs in the RvD5 region, which is involved in the molybdopterin biosynthetic pathway. This insertion of IS6110 in the moaB3 of the clinical isolate is different when compared to the insertion in the moaB3 gene of M. tuberculosis H37Rv where 4kb RvD5 region has been lost by homologous recombination and only a truncated form of the gene is present. This finding is of relevance since IS6110 is a major element determining the genome plasticity of M. tuberculosis and its numerical and positional polymorphism has always been of special interest.

scholarly journals Bornyl Diphosphate Synthase From Cinnamomum burmanni and Its Application for (+)-Borneol Biosynthesis in Yeast

2021 ◽  
Vol 9 ◽  
Author(s):  
Rui Ma ◽  
Ping Su ◽  
Juan Guo ◽  
Baolong Jin ◽  
Qing Ma ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Biosynthetic Pathway ◽  
Main Product ◽  
Microbial Fermentation ◽  
Biosynthesis Pathway ◽  
Analgesic Effects ◽  
Pathway Reconstruction ◽  
Key Enzyme ◽  
Shake Flasks

(+)-Borneol is a desirable monoterpenoid with effective anti-inflammatory and analgesic effects that is known as soft gold. (+)-bornyl diphosphate synthase is the key enzyme in the (+)-borneol biosynthesis pathway. Despite several reported (+)-bornyl diphosphate synthase genes, relatively low (+)-borneol production hinders the attempts to synthesize it using microbial fermentation. Here, we identified the highly specific (+)-bornyl diphosphate synthase CbTPS1 from Cinnamomum burmanni. An in vitro assay showed that (+)-borneol was the main product of CbTPS1 (88.70% of the total products), and the Km value was 5.11 ± 1.70 μM with a kcat value of 0.01 s–1. Further, we reconstituted the (+)-borneol biosynthetic pathway in Saccharomyces cerevisiae. After tailored truncation and adding Kozak sequences, the (+)-borneol yield was improved by 96.33-fold to 2.89 mg⋅L–1 compared with the initial strain in shake flasks. This work is the first reported attempt to produce (+)-borneol by microbial fermentation. It lays a foundation for further pathway reconstruction and metabolic engineering production of this valuable natural monoterpenoid.

scholarly journals Chronic inflammation in ulcerative colitis causes long term changes in gobletcell function

2021 ◽  
Author(s):  
Varsha Singh ◽  
Kelli Johnson ◽  
Jianyi Yin ◽  
Sunny Lee ◽  
Ruxian Lin ◽  
...  
Keyword(s):  
Ulcerative Colitis ◽  
Active Sites ◽  
Mucus Secretion ◽  
Pcr Analysis ◽  
Mucus Layer ◽  
Percentage Decrease ◽  
Tnf Α ◽  
Long Term Changes ◽  
Reduced Rate

ABSTRACTObjectiveOne of the features of ulcerative colitis (UC) is a defect in the protective mucus layer. This has been attributed to a reduced number of goblet cells (GC). However, it is not known whether abnormal GC mucus secretion also contributes to the reduced mucus layer. Our aims were to test the hypothesis that GC secretion was abnormal in UC with the changes persistent in colonoids even in the absence of immune cells.DesignColonoids were established from intestinal stem cells of healthy subjects (HS) and from patients with UC (inactive and active sites). Colonoids were maintained as undifferentiated (UD) or induced to differentiate (DF) and studied as 3D or monolayers on Transwell filters. Total RNA was extracted for quantitative real-time PCR analysis. Carbachol and PGE2 mediated stimulation followed by examination of mucus layer by MUC2 IF/confocal microscopy and TEM were performed.ResultsColonoids derived from patients with UC can be propagated over many passages; however, they exhibit a reduced rate of growth and TEER compared with colonoids from HS. Differentiated UC colonoid monolayers form a thin and non-continuous mucus layer. UC colonoids have increased expression of secretory lineage markers: ATOH1 and SPDEF, including MUC2 positive GCs and ChgA positive enteroendocrine cells but failed to secrete mucin when exposed to the cholinergic agonist carbachol and PGE2, which caused increased secretion in HS. Exposure to TNF-α (5days), reduced the number of GC with a greater percentage decrease in UC colonoids compared to HS.ConclusionsAbnormal mucus layer in UC is due to long term changes in epithelial cells that lead to abnormal mucus secretion as well as effects of the inflammatory environment to reduce the number of GC. This continued defect in GC mucus secretion may be involved in UC recurrence.

scholarly journals Cloning and Functional Analysis of Lignin Biosynthesis Genes Cf4CL and CfCCoAOMT in Cryptomeria fortunei

Genes ◽  
2019 ◽  
Vol 10 (8) ◽  
pp. 619 ◽  
Author(s):  
Zhenhao Guo ◽  
Hui Hua ◽  
Jin Xu ◽  
Jiaxing Mo ◽  
Hui Zhao ◽  
...  
Keyword(s):  
Gene Editing ◽  
Bioinformatics Analysis ◽  
Southern China ◽  
Lignin Biosynthesis ◽  
Wood Formation ◽  
Primary Component ◽  
Vascular Cambium ◽  
Timber Species ◽  
Wood Production ◽  
Lignin Synthesis

Cryptomeria fortunei, also known as the Chinese cedar, is an important timber species in southern China. The primary component of its woody tissues is lignin, mainly present in secondary cell walls. Therefore, continuous lignin synthesis is crucial for wood formation. In this study, we aimed to discover key genes involved in lignin synthesis expressed in the vascular cambium of C. fortunei. Through transcriptome sequencing, we detected expression of two genes, 4CL and CCoAOMT, known to be homologous to enzymes involved in the lignin synthesis pathway. We studied the function of these genes through bioinformatics analysis, cloning, vascular cambium expression analysis, and transgenic cross-species functional validation studies. Our results show that Cf4CL and CfCCoAOMT do indeed function in the pathway of lignin synthesis and likely perform this function in C. fortunei. They are prime candidates for future (gene-editing) studies aimed at optimizing C. fortunei wood production.

Molecular diversity of KVα- and β-subunit expression in canine gastrointestinal smooth muscles

1999 ◽  
Vol 277 (1) ◽  
pp. G127-G136 ◽  
Author(s):  
Anne Epperson ◽  
Helena P. Bonner ◽  
Sean M. Ward ◽  
William J. Hatton ◽  
Karri K. Bradley ◽  
...  
Keyword(s):  
Smooth Muscle ◽  
Smooth Muscle Cells ◽  
Smooth Muscles ◽  
Muscle Cells ◽  
Pcr Analysis ◽  
Transcriptional Level ◽  
Gi Tract ◽  
Excitable Cells ◽  
Subunit Expression ◽  
Molecular Components

Voltage-activated K+(KV) channels play an important role in regulating the membrane potential in excitable cells. In gastrointestinal (GI) smooth muscles, these channels are particularly important in modulating spontaneous electrical activities. The purpose of this study was to identify the molecular components that may be responsible for the KV currents found in the canine GI tract. In this report, we have examined the qualitative expression of eighteen different KV channel genes in canine GI smooth muscle cells at the transcriptional level using RT-PCR analysis. Our results demonstrate the expression of KV1.4, KV1.5, KV1.6, KV2.2, and KV4.3 transcripts in all regions of the GI tract examined. Transcripts encoding KV1.2, KVβ1.1, and KVβ1.2 subunits were differentially expressed. KV1.1, KV1.3, KV2.1, KV3.1, KV3.2, KV3.4, KV4.1, KV4.2, and KVβ2.1 transcripts were not detected in any GI smooth muscle cells. We have also determined the protein expression for a subset of these KV channel subunits using specific antibodies by immunoblotting and immunohistochemistry. Immunoblotting and immunohistochemistry demonstrated that KV1.2, KV1.4, KV1.5, and KV2.2 are expressed at the protein level in GI tissues and smooth muscle cells. KV2.1 was not detected in any regions of the GI tract examined. These results suggest that the wide array of electrical activity found in different regions of the canine GI tract may be due in part to the differential expression of KV channel subunits.

scholarly journals Transcriptional and Post-transcriptional Regulation of Lignin Biosynthesis Pathway Genes in Populus

2020 ◽  
Vol 11 ◽  
Author(s):  
Jin Zhang ◽  
Gerald A. Tuskan ◽  
Timothy J. Tschaplinski ◽  
Wellington Muchero ◽  
Jin-Gui Chen
Keyword(s):  
Transcriptional Regulation ◽  
Lignin Biosynthesis ◽  
Biosynthesis Pathway ◽  
Post Transcriptional Regulation

scholarly journals Piquiá Shells (Caryocar villosum): A Fruit by-Product with Antioxidant and Antiaging Properties in Caenorhabditis elegans

2020 ◽  
Vol 2020 ◽  
pp. 1-19 ◽  
Author(s):  
Mariana Roxo ◽  
Herbenya Peixoto ◽  
Pille Wetterauer ◽  
Emerson Lima ◽  
Michael Wink
Keyword(s):  
Caenorhabditis Elegans ◽  
Lethal Dose ◽  
Pcr Analysis ◽  
Transcriptional Level ◽  
Dependent Manner ◽  
Wild Type ◽  
Fluorescent Reporter ◽  
Triterpenoid Saponins ◽  
Promising Source

In a context of rising demand for sustainable antiaging interventions, fruit processing by-products are a promising source of bioactive compounds for the production of antiaging dietary supplements. Piquiá (Caryocar villosum) is a native Amazonian fruit consisting of 65% nonedible shells. In the present study, the phytochemical profile of a hydroalcoholic extract of piquiá shells (CV) was characterized by LC-MS/MS analysis. Its antioxidant and antiaging activities were investigated using the nematode Caenorhabditis elegans as an in vivo model. CV is mainly composed by hydrolysable tannins and triterpenoid saponins. The extract enhanced stress resistance of wild-type and mutant worms by reducing the intracellular levels of reactive oxygen species (ROS) and by increasing their survival against a lethal dose of the prooxidant juglone. These effects involved the upregulation of sod-3 and downregulation of gst-4 and hsp-16.2, studied through the GFP fluorescent reporter intensity and at the transcriptional level by qRT-PCR analysis. CV extended the lifespan of wild-type worms in a DAF-16/FoxO- and SKN-1/Nrf-dependent manner. Taken together, our findings indicate piquiá shells as potential candidates for nutraceutical applications. Further studies are needed to validate the relevance of our findings to antiaging interventions in humans.

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