Lupeol Accumulation Correlates with Auxin in the Epidermis of Castor

Lupeol, a natural lupane-type pentacyclic triterpene, possesses various pharmacological properties, and its production attracts attention. Significant quantities of lupeol are deposited on the castor aerial organ surface and are easily extractable as a predominant wax constituent. Thus, castor might be considered as a potential bioreactor for the production of lupeol. The lupeol biosynthesis pathway is well known, but how it is regulated remains largely unknown. Among large numbers of castor cultivars, we targeted one accession line (337) with high levels of lupeol on its stem surface and low levels thereof on its hypocotyl surface, implicating that lupeol synthesis is differentially regulated in the two organs. To explore the underlying mechanisms, we did comparative transcriptome analysis of the first internode of 337 stem and the upper hypocotyl. Our results show that large amounts of auxin-related genes are differentially expressed in both parts, implying some possible interactions between auxin and lupeol production. We also found that several auxin-responsive cis-elements are present in promoter regions of HMGR and LUS genes encoding two key enzymes involved in lupeol production. Furthermore, auxin treatments apparently induced the expression levels of RcHMGR and RcLUS. Furthermore, we observed that auxin treatment significantly increased lupeol contents, whereas inhibiting auxin transport led to an opposite phenotype. Our study reveals some relationships between hormone activity and lupeol synthesis and might provide a promising way for improving lupeol yields in castor.

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Integration of Transcriptome and Methylome Analyses Provides Insight Into the Pathway of Floral Scent Biosynthesis in Prunus mume

Frontiers in Genetics ◽

10.3389/fgene.2021.779557 ◽

2021 ◽

Vol 12 ◽

Author(s):

Xi Yuan ◽

Kaifeng Ma ◽

Man Zhang ◽

Jia Wang ◽

Qixiang Zhang

Keyword(s):

Dna Methylation ◽

Epigenetic Modification ◽

Floral Scent ◽

Methylation Status ◽

Enrichment Analysis ◽

Biosynthesis Pathway ◽

Prunus Mume ◽

Promoter Regions ◽

Differentially Methylated Genes ◽

Genes Encoding

DNA methylation is a common epigenetic modification involved in regulating many biological processes. However, the epigenetic mechanisms involved in the formation of floral scent have rarely been reported within a famous traditional ornamental plant Prunus mume emitting pleasant fragrance in China. By combining whole-genome bisulfite sequencing and RNA-seq, we determined the global change in DNA methylation and expression levels of genes involved in the biosynthesis of floral scent in four different flowering stages of P. mume. During flowering, the methylation status in the “CHH” sequence context (with H representing A, T, or C) in the promoter regions of genes showed the most significant change. Enrichment analysis showed that the differentially methylated genes (DMGs) were widely involved in eight pathways known to be related to floral scent biosynthesis. As the key biosynthesis pathway of the dominant volatile fragrance of P. mume, the phenylpropane biosynthesis pathway contained the most differentially expressed genes (DEGs) and DMGs. We detected 97 DMGs participated in the most biosynthetic steps of the phenylpropane biosynthesis pathway. Furthermore, among the previously identified genes encoding key enzymes in the biosynthesis of the floral scent of P. mume, 47 candidate genes showed an expression pattern matching the release of floral fragrances and 22 of them were differentially methylated during flowering. Some of these DMGs may or have already been proven to play an important role in biosynthesis of the key floral scent components of P. mume, such as PmCFAT1a/1c, PmBEAT36/37, PmPAL2, PmPAAS3, PmBAR8/9/10, and PmCNL1/3/5/6/14/17/20. In conclusion, our results for the first time revealed that DNA methylation is widely involved in the biosynthesis of floral scent and may play critical roles in regulating the floral scent biosynthesis of P. mume. This study provided insights into floral scent metabolism for molecular breeding.

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Genes encoding components of the olfactory signal transduction cascade contain a DNA binding site that may direct neuronal expression.

Molecular and Cellular Biology ◽

10.1128/mcb.13.9.5805 ◽

1993 ◽

Vol 13 (9) ◽

pp. 5805-5813 ◽

Cited By ~ 52

Author(s):

M M Wang ◽

R Y Tsai ◽

K A Schrader ◽

R R Reed

Keyword(s):

Signal Transduction ◽

Dna Binding ◽

Binding Site ◽

Binding Sites ◽

Consensus Sequence ◽

Initiation Site ◽

Olfactory Neuron ◽

Promoter Regions ◽

Transcriptional Initiation ◽

Genes Encoding

Genes which mediate odorant signal transduction are expressed at high levels in neurons of the olfactory epithelium. The molecular mechanism governing the restricted expression of these genes likely involves tissue-specific DNA binding proteins which coordinately activate transcription through sequence-specific interactions with olfactory promoter regions. We have identified binding sites for the olfactory neuron-specific transcription factor, Olf-1, in the sequences surrounding the transcriptional initiation site of five olfactory neuron-specific genes. The Olf-1 binding sites described define the consensus sequence YTCCCYRGGGAR. In addition, we have identified a second binding site, the U site, in the olfactory cyclic nucleotide gated channel and type III cyclase promoters, which binds factors present in all tissue examined. These experiments support a model in which expression of Olf-1 in the sensory neurons coordinately activates a set of olfactory neuron-specific genes. Furthermore, expression of a subset of these genes may be modulated by additional binding factors.

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Elucidation of the core betalain biosynthesis pathway in Amaranthus tricolor

Scientific Reports ◽

10.1038/s41598-021-85486-x ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Yu-Cheng Chang ◽

Yi-Ching Chiu ◽

Nai-Wen Tsao ◽

Yuan-Lin Chou ◽

Choon-Meng Tan ◽

...

Keyword(s):

Transcriptome Analysis ◽

Natural Antioxidants ◽

Biosynthesis Pathway ◽

Comparative Transcriptome ◽

Amaranthus Tricolor ◽

Enzymatic Assays ◽

Comparative Transcriptome Analysis ◽

Elevated Expression ◽

Green Coloration

AbstractAmaranthus tricolor L., a vegetable Amaranthus species, is an economically important crop containing large amounts of betalains. Betalains are natural antioxidants and can be classified into betacyanins and betaxanthins, with red and yellow colors, respectively. A. tricolor cultivars with varying betalain contents, leading to striking red to green coloration, have been commercially produced. However, the molecular differences underlying betalain biosynthesis in various cultivars of A. tricolor remain largely unknown. In this study, A. tricolor cultivars with different colors were chosen for comparative transcriptome analysis. The elevated expression of AmCYP76AD1 in a red-leaf cultivar of A. tricolor was proposed to play a key role in producing red betalain pigments. The functions of AmCYP76AD1, AmDODAα1, AmDODAα2, and AmcDOPA5GT were also characterized through the heterologous engineering of betalain pigments in Nicotiana benthamiana. Moreover, high and low L-DOPA 4,5-dioxygenase activities of AmDODAα1 and AmDODAα2, respectively, were confirmed through in vitro enzymatic assays. Thus, comparative transcriptome analysis combined with functional and enzymatic studies allowed the construction of a core betalain biosynthesis pathway of A. tricolor. These results not only provide novel insights into betalain biosynthesis and evolution in A. tricolor but also provide a basal framework for examining genes related to betalain biosynthesis among different species of Amaranthaceae.

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RegA, an AraC-Like Protein, Is a Global Transcriptional Regulator That Controls Virulence Gene Expression in Citrobacter rodentium

Infection and Immunity ◽

10.1128/iai.00770-08 ◽

2008 ◽

Vol 76 (11) ◽

pp. 5247-5256 ◽

Cited By ~ 44

Author(s):

Emily Hart ◽

Ji Yang ◽

Marija Tauschek ◽

Michelle Kelly ◽

Matthew J. Wakefield ◽

...

Keyword(s):

Mammalian Cells ◽

Virulence Gene ◽

Virulence Determinants ◽

Intestinal Colonization ◽

Citrobacter Rodentium ◽

Promoter Regions ◽

Reading Frame ◽

Virulence Gene Expression ◽

Genes Encoding ◽

Colonization Factors

ABSTRACT Citrobacter rodentium is an attaching and effacing pathogen which causes transmissible colonic hyperplasia in mice. Infection with C. rodentium serves as a model for infection of humans with enteropathogenic and enterohemorrhagic Escherichia coli. To identify novel colonization factors of C. rodentium, we screened a signature-tagged mutant library of C. rodentium in mice. One noncolonizing mutant had a single transposon insertion in an open reading frame (ORF) which we designated regA because of its homology to genes encoding members of the AraC family of transcriptional regulators. Deletion of regA in C. rodentium resulted in markedly reduced colonization of the mouse intestine. Examination of lacZ transcriptional fusions using promoter regions of known and putative virulence-associated genes of C. rodentium revealed that RegA strongly stimulated transcription of two newly identified genes located close to regA, which we designated adcA and kfcC. The cloned adcA gene conferred autoaggregation and adherence to mammalian cells to E. coli strain DH5α, and a kfc mutation led to a reduction in the duration of intestinal colonization, but the kfc mutant was far less attenuated than the regA mutant. These results indicated that other genes of C. rodentium whose expression required activation by RegA were required for colonization. Microarray analysis revealed a number of RegA-regulated ORFs encoding proteins homologous to known colonization factors. Transcription of these putative virulence determinants was activated by RegA only in the presence of sodium bicarbonate. Taken together, these results show that RegA is a global regulator of virulence in C. rodentium which activates factors that are required for intestinal colonization.

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An amphibian cytoskeletal-type actin gene is expressed exclusively in muscle tissue

Development ◽

10.1242/dev.101.2.393 ◽

1987 ◽

Vol 101 (2) ◽

pp. 393-402 ◽

Cited By ~ 1

Author(s):

T.J. Mohun ◽

N. Garrett

Keyword(s):

Nucleotide Sequence ◽

Protein Isoforms ◽

Actin Gene ◽

Promoter Regions ◽

Conserved Sequence ◽

Beta Actin ◽

Genes Encoding ◽

Actin Mrna ◽

Ccaat Box ◽

Equivalent Region

The complete nucleotide sequence of two Xenopus actin genes encoding cytoskeletal protein isoforms has been determined. Transcripts from these genes are remarkably similar in nucleotide sequence throughout their length and code for type-5 and type-8 cytoskeletal actins. Both share some sequence homology with human gamma-actin mRNA within the 3′ untranslated region but none with the equivalent region of any vertebrate beta-actin transcript. The promoter regions of the two Xenopus genes are virtually identical from the cap site to the CCAAT box and show extensive homology further upstream. Despite such similarity, the two genes are divergently expressed during embryonic development. The type-5 actin gene is expressed in all regions of the developing embryo whilst the type-8 gene is coregulated with the muscle-specific skeletal actin gene. In common with mammalian and avian cytoskeletal actin counterparts, the Xenopus genes possess a conserved sequence within their promoter that has previously been identified as a transcription-factor-binding site.

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SNPs in genes encoding for IL-10, TNF-α, and NFκB p105/p50 are associated with clinical prognostic factors for patients with Hodgkin lymphoma

PLoS ONE ◽

10.1371/journal.pone.0248259 ◽

2021 ◽

Vol 16 (3) ◽

pp. e0248259

Author(s):

Rafael Dezen Gaiolla ◽

Marcelo Padovani de Toledo Moraes ◽

Deilson Elgui de Oliveira

Keyword(s):

Hodgkin Lymphoma ◽

Univariate Analysis ◽

Stage Iv ◽

Inflammatory Cells ◽

Cytokine Gene Expression ◽

Nucleotide Polymorphisms ◽

Promoter Regions ◽

Tnf Α ◽

Mediastinal Disease ◽

Genes Encoding

Classical Hodgkin lymphoma (cHL) is a B-cell-derived malignant neoplasia that has a unique histological distribution, in which the scarce malignant Hodgkin and Reed-Sternberg cells are surrounded by nonmalignant inflammatory cells. The interactions between the malignant and inflammatory cells are mediated by aberrantly produced cytokines, which play an important role in tumor immunopathogenesis. Single nucleotide polymorphisms (SNPs) in genes encoding cytokines and their regulatory proteins may influence the peripheral levels of these molecules and affect disease’s pathobiology. In this study, we evaluate SNPs in the promoter regions of the genes encoding for two key cytokines in Hodgkin lymphoma: IL-10 (SNP/pIL10–592, rs1800872; and SNP/pIL10–1082, rs1800896) and TNF-α (SNP/pTNF -238, rs361525; and SNP/pTNF -862, rs1800630), as well as an SNP in the intronic region of the NFκB1 gene (SNP/iNFKB1, rs1585215), an important regulator of cytokine gene expression. We then look to their possible association with clinical and laboratory features in cHL patients. Seventy-three patients with cHL are genotyped by qPCR-high resolution melting. The SNPs’ genotypes are analyzed individually for each SNP, and when more than two allelic combinations are identified, the genotypes are also divided into two groups according to proposed biological relevance. By univariate analysis, patients harboring SNP/pTNF -238 AG genotype more frequently have EBV-associated cHL compared to homozygous GG, whereas the presence of mediastinal disease (bulky and nonbulky) is more common in the pIL10–592 AC/CC group compared to the AA homozygous group. Patients with SNP/iNFKB1 AA genotype more frequently have stage IV and extranodal disease at diagnosis. These results indicate that some SNPs’ genotypes for IL-10 and TNF-α genes are associated with prognostic parameters in cHL. For the first time, the SNP/iNFKB1 is described in association with clinical features of the disease.

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EPR study of thylakoid membrane dynamics in mutants of the carotenoid biosynthesis pathway of Synechocystis sp. PCC6803.

Acta Biochimica Polonica ◽

10.18388/abp.2012_2178 ◽

2012 ◽

Vol 59 (1) ◽

Cited By ~ 4

Author(s):

Kinga Kłodawska ◽

Przemysław Malec ◽

Mihály Kis ◽

Zoltán Gombos ◽

Kazimierz Strzałka

Keyword(s):

Optimal Growth ◽

Carotenoid Biosynthesis ◽

Growth Conditions ◽

Thylakoid Membranes ◽

Membrane Dynamics ◽

Biosynthesis Pathway ◽

Light Regimes ◽

Genes Encoding ◽

Splitting Parameter ◽

Carotenoid Biosynthesis Pathway

EPR spectroscopy using 5-doxylstearic acid (5-SASL) and 16-doxylstearic acid (16-SASL) spin probes was used to study the fluidity of thylakoid membranes. These were isolated from wild type Synechocystis and from several mutants in genes encoding selected enzymes of the carotenoid biosynthesis pathway and/or acyl-lipid desaturases. Cyanobacteria were cultivated at 25°C and 35°C under different light regimes: photoautotrophically (PAG) and/or in light-activated heterotrophic conditions (LAHG). The relative fluidity of membranes was estimated from EPR spectra based on the empirical outermost splitting parameter in a temperature range from 15°C to 40°C. Our findings demonstrate that in native thylakoid membranes the elimination of xanthophylls decreased fluidity in the inner membrane region under optimal growth conditions (25°C) and increased it under sublethal heat stress (35°C). This indicated that the overall fluidity of native photosynthetic membranes in cyanobacteria may be influenced by the ratio of polar to non-polar carotenoid pools under different environmental conditions.

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Deficiency in Vitamin B12 and Ferritin Is Associated With Epigenetic Alterations in Cancer Patients

10.21203/rs.3.rs-251474/v1 ◽

2021 ◽

Author(s):

Khaled A. Elawdan ◽

Sabah Farouk ◽

Salah Araf ◽

Hany Khalil

Keyword(s):

Dna Methylation ◽

Vitamin B12 ◽

Cancer Patients ◽

Promoter Region ◽

Dna Methyltransferases ◽

Epigenetic Alterations ◽

Promoter Regions ◽

Methylation Sensitive Restriction Enzyme ◽

Low Levels ◽

Dna Methylation Analysis

Abstract Background: Cancer is the second-leading cause of death worldwide, caused by several mutations in DNA within the cells including epigenetic alteration. The epigenetic changes are external modifications to the DNA that switch “on” or “off” gene expression. The present study was conducted to investigate the epigenetic modifications and its correlation with the levels of vitamin B12 and ferritin in cancer patients with hepatocellular carcinoma (HCC), breast cancer (BC), lung cancer (LC), or colon cancer (CC). Methods and Results: A total of 200 blood samples were obtained from cancer patients and healthy individuals. The relative expression of DNA methyltransferases (DNMTs), Ten-Eleven translocation (TET), and methionine synthase (MS) was evaluated in patients with the normal level of vitamin B12/ferritin and patients with the deficient levels of them. DNA methylation within the promoter regions was investigated of each indicated genes using the methylation-sensitive restriction enzyme HpaII and bisulfite PCR. Interestingly, the expression of DNMT1, DNMT3a, and DNMT3b was increased in patients with low levels of vitamin B12 and ferritin, while the expression of MS, TET1, and TET3 was significantly decreased. DNA methylation analysis in patients with deficient levels of vitamin B12/ferritin showed a methylated-cytosine within the location 318/CG and 385/CG in the promoter region of TET1 and TET3, respectively. Moreover, the bisulfite PCR assay further confirmed the methylation changes in the promoter region of TET1 and TET3 at the indicated locations. Conclusion: These data indicate that the deficiency in vitamin B12 and ferritin in cancer patients plays a key role in the epigenetic exchanges during cancer development.

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Genetic Analysis of the Methanol- and Methylamine-Specific Methyltransferase 2 Genes of Methanosarcina acetivorans C2A

Journal of Bacteriology ◽

10.1128/jb.00117-08 ◽

2008 ◽

Vol 190 (11) ◽

pp. 4017-4026 ◽

Cited By ~ 29

Author(s):

Arpita Bose ◽

Matthew A. Pritchett ◽

William W. Metcalf

Keyword(s):

Genetic Analysis ◽

Methane Production ◽

Untranslated Region ◽

Gene Fusions ◽

Methanosarcina Acetivorans ◽

Concerted Effort ◽

Genes Encoding ◽

Low Levels ◽

Reduced Rate

ABSTRACT The entry of methanol into the methylotrophic pathway of methanogenesis is mediated by the concerted effort of two methyltransferases, namely, methyltransferase 1 (MT1) and methyltransferase 2 (MT2). The mtaA1, mtaA2, and mtbA genes of Methanosarcina acetivorans C2A encode putative methanol- or methylamine-specific MT2 enzymes. To address the in vivo roles of these genes in growth and methanogenesis from known substrates, we constructed and characterized mutants with deletions of each of these genes. The mtaA1 gene is required for growth on methanol, whereas mtaA2 was dispensable. However, the mtaA2 mutant had a reduced rate of methane production from methanol. Surprisingly, deletion of mtaA1 in combination with deletions of the genes encoding three methanol-specific MT1 isozymes led to lack of growth on acetate, suggesting that MT1 and MT2 enzymes might play an important role during growth on this substrate. The mtbA gene was required for dimethylamine and monomethylamine (MMA) utilization and was important, but not required, for trimethylamine utilization. Analysis of reporter gene fusions revealed that both mtaA1 and mtbA were expressed on all methanogenic substrates tested. However, mtaA1 expression was induced on methanol, while mtbA expression was down-regulated on MMA and acetate. mtaA2 was expressed at very low levels on all substrates. The mtaA1 transcript had a large 5′ untranslated region (UTR) (275 bp), while the 5′ UTR of the mtbA transcript was only 28 bp long.

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Petal abscission in fragrant roses is associated with large scale differential regulation of the abscission zone transcriptome

Scientific Reports ◽

10.1038/s41598-020-74144-3 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Priya Singh ◽

Neeraj Bharti ◽

Amar Pal Singh ◽

Siddharth Kaushal Tripathi ◽

Saurabh Prakash Pandey ◽

...

Keyword(s):

Transcription Factors ◽

Large Scale ◽

Scale Up ◽

Differential Regulation ◽

Regulatory Proteins ◽

Comparative Transcriptome ◽

Ethylene Sensitivity ◽

Core Set ◽

Genes Encoding ◽

Rosa Bourboniana

Abstract Flowers of fragrant roses such as Rosa bourboniana are ethylene-sensitive and undergo rapid petal abscission while hybrid roses show reduced ethylene sensitivity and delayed abscission. To understand the molecular mechanism underlying these differences, a comparative transcriptome of petal abscission zones (AZ) of 0 h and 8 h ethylene-treated flowers from R. bourboniana was performed. Differential regulation of 3700 genes (1518 up, 2182 down) representing 8.5% of the AZ transcriptome was observed between 0 and 8 h ethylene-treated R. bourboniana petal AZ. Abscission was associated with large scale up-regulation of the ethylene pathway but prominent suppression of the JA, auxin and light-regulated pathways. Regulatory genes encoding kinases/phosphatases/F-box proteins and transcription factors formed the major group undergoing differential regulation besides genes for transporters, wall modification, defense and phenylpropanoid pathways. Further comparisons with ethylene-treated petals of R. bourboniana and 8 h ethylene-treated AZ (R. hybrida) identified a core set of 255 genes uniquely regulated by ethylene in R. bourboniana AZ. Almost 23% of these encoded regulatory proteins largely conserved with Arabidopsis AZ components. Most of these were up-regulated while an entire set of photosystem genes was prominently down-regulated. The studies provide important information on regulation of petal abscission in roses.

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