scholarly journals Transcriptome Analysis Provides Insights into the Mechanism of Astaxanthin Enrichment in a Mutant of the Ridgetail White Prawn Exopalaemon carinicauda

Genes ◽  
2021 ◽  
Vol 12 (5) ◽  
pp. 618
Author(s):  
Yue Jin ◽  
Shihao Li ◽  
Yang Yu ◽  
Chengsong Zhang ◽  
Xiaojun Zhang ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Underlying Mechanism ◽  
Biological Processes ◽  
Wild Type ◽  
Expression Levels ◽  
In The Wild ◽  
Cuticle Proteins ◽  
Apolipoprotein D ◽  
High Level ◽  
Lower Expression

A mutant of the ridgetail white prawn, which exhibited rare orange-red body color with a higher level of free astaxanthin (ASTX) concentration than that in the wild-type prawn, was obtained in our lab. In order to understand the underlying mechanism for the existence of a high level of free astaxanthin, transcriptome analysis was performed to identify the differentially expressed genes (DEGs) between the mutant and wild-type prawns. A total of 78,224 unigenes were obtained, and 1863 were identified as DEGs, in which 902 unigenes showed higher expression levels, while 961 unigenes presented lower expression levels in the mutant in comparison with the wild-type prawns. Based on Gene Ontology analysis and Kyoto Encyclopedia of Genes and Genomes analysis, as well as further investigation of annotated DEGs, we found that the biological processes related to astaxanthin binding, transport, and metabolism presented significant differences between the mutant and the wild-type prawns. Some genes related to these processes, including crustacyanin, apolipoprotein D (ApoD), cathepsin, and cuticle proteins, were identified as DEGs between the two types of prawns. These data may provide important information for us to understand the molecular mechanism of the existence of a high level of free astaxanthin in the prawn.

STOP1 regulates the expression of HsfA2 and GDHs that are critical for low-oxygen tolerance in Arabidopsis

2019 ◽  
Vol 70 (12) ◽  
pp. 3297-3311 ◽  
Author(s):  
Takuo Enomoto ◽  
Mutsutomo Tokizawa ◽  
Hiroki Ito ◽  
Satoshi Iuchi ◽  
Masatomo Kobayashi ◽  
...  
Keyword(s):  
Oxygen Sensitivity ◽  
Wild Type ◽  
In Planta ◽  
Low Oxygen ◽  
Expression Levels ◽  
Oxygen Tolerance ◽  
Ph Tolerance ◽  
Genes Encoding ◽  
In The Wild ◽  
Lower Expression

Abstract The SENSITIVE TO PROTON RHIZOTOXICITY 1 (STOP1) transcription factor regulates gene expression associated with multiple stress tolerances in plant roots. In this study, we investigated the mechanism responsible for the sensitivity of the stop1 mutant to low-oxygen stress in Arabidopsis. Transcriptomic analyses revealed that two genes involved in low-oxygen tolerance, namely GLUTAMATE DEHYDROGENASE 1 (GDH1) and GDH2, showed lower expression levels in the stop1 mutant than in the wild-type. Sensitivity of the gdh1gdh2 double-mutant to low-oxygen conditions was partly attributable to the low-oxygen sensitivity of the stop1 mutant. Two transcription factors, STOP2 and HEAT SHOCK FACTOR A2 (HsfA2), were expressed at lower levels in the stop1 mutant. An in planta complementation assay indicated that CaMV35S::STOP2 or CaMV35S::HsfA2 partially rescued the low-oxygen tolerance of the stop1 mutant, which was concomitant with recovered expression of genes regulating low-pH tolerance and genes encoding molecular chaperones. Prediction of cis-elements and in planta promoter assays revealed that STOP1 directly activated the expression of HsfA2. Similar STOP1-dependent low-oxygen sensitivity was detected in tobacco. Suppression of NtSTOP1 induced low-oxygen sensitivity, which was associated with lower expression levels of NtHsfA2 and NtGDHs compared with the wild-type. Our results indicated that STOP1 pleiotropically regulates low-oxygen tolerance by transcriptional regulation.

scholarly journals The PKS4 Gene of Fusarium graminearum Is Essential for Zearalenone Production

2006 ◽  
Vol 72 (6) ◽  
pp. 3924-3932 ◽  
Author(s):  
Erik Lys�e ◽  
Sonja S. Klemsdal ◽  
Karen R. Bone ◽  
Rasmus J. N. Frandsen ◽  
Thomas Johansen ◽  
...  
Keyword(s):  
Fusarium Graminearum ◽  
High Performance ◽  
Polyketide Synthase ◽  
Wild Type ◽  
Root Infection ◽  
Enoyl Reductase ◽  
Transformation Protocol ◽  
Chromatography Analysis ◽  
In The Wild ◽  
High Level

ABSTRACT Zearalenones are produced by several Fusarium species and can cause reproductive problems in animals. Some aurofusarin mutants of Fusarium pseudograminearum produce elevated levels of zearalenone (ZON), one of the estrogenic mycotoxins comprising the zearalenones. An analysis of transcripts from polyketide synthase genes identified in the Fusarium graminearum database was carried out for these mutants. PKS4 was the only gene with an enoyl reductase domain that had a higher level of transcription in the aurofusarin mutants than in the wild type. An Agrobacterium tumefaciens-mediated transformation protocol was used to replace the central part of the PKS4 gene with a hygB resistance gene through double homologous recombination in an F. graminearum strain producing a high level of ZON. PCR and Southern analysis of transformants were used to identify isolates with single insertional replacements of PKS4. High-performance liquid chromatography analysis showed that the PKS4 replacement mutant did not produce ZON. Thus, PKS4 encodes an enzyme required for the production of ZON in F. graminearum. Barley root infection studies revealed no alteration in the pathogenicity of the PKS4 mutant compared to the pathogenicity of the wild type. The expression of PKS13, which is located in the same cluster as PKS4, decreased dramatically in the mutant, while transcription of PKS4 was unchanged. This differential expression may indicate that ZON or its derivatives do not regulate expression of PKS4 and that the PKS4-encoded protein or its product stimulates expression of PKS13. Furthermore, both the lack of aurofusarin and ZON influenced the expression of other polyketide synthases, demonstrating that one polyketide can influence the expression of others.

scholarly journals Alterations of Metabolic and Lipid Profiles in Polymyxin-ResistantPseudomonas aeruginosa

2018 ◽  
Vol 62 (6) ◽  
Author(s):  
Mei-Ling Han ◽  
Yan Zhu ◽  
Darren J. Creek ◽  
Yu-Wei Lin ◽  
Dovile Anderson ◽  
...  
Keyword(s):  
Lipid A ◽  
Therapeutic Option ◽  
Polymyxin B ◽  
Multidrug Resistant ◽  
Wild Type ◽  
Metabolomics Data ◽  
Content Type ◽  
In The Wild ◽  
High Level ◽  
Acyl Coenzyme A

ABSTRACTMultidrug-resistantPseudomonas aeruginosapresents a global medical challenge, and polymyxins are a key last-resort therapeutic option. Unfortunately, polymyxin resistance inP. aeruginosahas been increasingly reported. The present study was designed to define metabolic differences between paired polymyxin-susceptible and -resistantP. aeruginosastrains using untargeted metabolomics and lipidomics analyses. The metabolomes of wild-typeP. aeruginosastrain K ([PAK] polymyxin B MIC, 1 mg/liter) and its pairedpmrBmutant strains, PAKpmrB6and PAKpmrB12(polymyxin B MICs of 16 mg/liter and 64 mg/liter, respectively) were characterized using liquid chromatography-mass spectrometry, and metabolic differences were identified through multivariate and univariate statistics. PAKpmrB6and PAKpmrB12, which displayed lipid A modifications with 4-amino-4-deoxy-l-arabinose, showed significant perturbations in amino acid and carbohydrate metabolism, particularly the intermediate metabolites from 4-amino-4-deoxy-l-arabinose synthesis and the methionine salvage cycle pathways. The genomics result showed a premature termination (Y275stop) inspeE(encoding spermidine synthase) in PAKpmrB6, and metabolomics data revealed a decreased intracellular level of spermidine in PAKpmrB6compared to that in PAKpmrB12. Our results indicate that spermidine may play an important role in high-level polymyxin resistance inP. aeruginosa. Interestingly, bothpmrBmutants had decreased levels of phospholipids, fatty acids, and acyl-coenzyme A compared to those in the wild-type PAK. Moreover, the more resistant PAKpmrB12mutant exhibited much lower levels of phospholipids than the PAKpmrB6mutant, suggesting that the decreased phospholipid level was associated with polymyxin resistance. In summary, this study provides novel mechanistic information on polymyxin resistance inP. aeruginosaand highlights its impacts on bacterial metabolism.

scholarly journals Production and Secretion Stress Caused by Overexpression of Heterologous α-Amylase Leads to Inhibition of Sporulation and a Prolonged Motile Phase in Bacillus subtilis

2007 ◽  
Vol 73 (16) ◽  
pp. 5354-5362 ◽  
Author(s):  
Andrzej T. Lulko ◽  
Jan-Willem Veening ◽  
Girbe Buist ◽  
Wiep Klaas Smits ◽  
Evert Jan Blom ◽  
...  
Keyword(s):  
Bacillus Subtilis ◽  
Protein Secretion ◽  
Dependent Manner ◽  
Wild Type ◽  
Positive Bacterium ◽  
Expression Levels ◽  
High Affinity ◽  
Flow Cytometric ◽  
Secretion Stress ◽  
High Level

ABSTRACT Transcriptome analysis was used to investigate the global stress response of the gram-positive bacterium Bacillus subtilis caused by overproduction of the well-secreted AmyQ α-amylase from Bacillus amyloliquefaciens. Analyses of the control and overproducing strains were carried out at the end of exponential growth and in stationary phase, when protein secretion from B. subtilis is optimal. Among the genes that showed increased expression were htrA and htrB, which are part of the CssRS regulon, which responds to high-level protein secretion and heat stress. The analysis of the transcriptome profiles of a cssS mutant compared to the wild type, under identical secretion stress conditions, revealed several genes with altered transcription in a CssRS-dependent manner, for example, citM, ylxF, yloA, ykoJ, and several genes of the flgB operon. However, high-affinity CssR binding was observed only for htrA, htrB, and, possibly, citM. In addition, the DNA macroarray approach revealed that several genes of the sporulation pathway are downregulated by AmyQ overexpression and that a group of motility-specific (σD-dependent) transcripts were clearly upregulated. Subsequent flow-cytometric analyses demonstrate that, upon overproduction of AmyQ as well as of a nonsecretable variant of the α-amylase, the process of sporulation is severely inhibited. Similar experiments were performed to investigate the expression levels of the hag promoter, a well-established reporter for σD-dependent gene expression. This approach confirmed the observations based on our DNA macroarray analyses and led us to conclude that expression levels of several genes involved in motility are maintained at high levels under all conditions of α-amylase overproduction.

Involvement of the Clock Gene period in the Circadian Rhythm of the Silkmoth Bombyx mori

2019 ◽  
Vol 34 (3) ◽  
pp. 283-292 ◽  
Author(s):  
Kento Ikeda ◽  
Takaaki Daimon ◽  
Hideki Sezutsu ◽  
Hiroko Udaka ◽  
Hideharu Numata
Keyword(s):  
Circadian Rhythm ◽  
Circadian Rhythms ◽  
Bombyx Mori ◽  
Negative Feedback ◽  
Masking Effect ◽  
Wild Type ◽  
Expression Levels ◽  
Knockout Strain ◽  
Behavioral Rhythms ◽  
In The Wild

In Lepidoptera, the roles of period ( per) and the negative feedback involving this gene in circadian rhythm are controversial. In the present study, we established a per knockout strain using TALEN in Bombyx mori, and compared eclosion and hatching rhythms between the per-knockout and wild-type strains to examine whether per is actually involved in these rhythms. The generated per knockout allele was considered null, because it encoded an extensively truncated form of PERIOD (198 aa due to a 64-bp deletion in exon 7, in contrast to 1113 aa in the wild-type protein). In this per knockout strain, circadian rhythms in eclosion and hatching were disrupted. Under LD cycles, however, a steep peak existed at 1 h after lights-on in both eclosion and hatching, and was considered to be produced by a masking effect—a direct response to light. In the per-knockout strain, temporal expression changes of per and timeless ( tim) were also lost. The expression levels of tim were continuously high, probably due to the loss of negative feedback by per and tim. In contrast, the expression levels of per were much lower in the per knockout strain than in the wild type at every time point. From these results, we concluded that per is indispensable for circadian rhythms, and we suggest that the negative feedback loop of the circadian rhythm involving per functions for the production of behavioral rhythms in B. mori.

scholarly journals Antiaging effect of a Jianpi-yangwei formula in Caenorhabditis elegans

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Liling Zeng ◽  
Zhimin Yang ◽  
Tianchan Yun ◽  
Shaoyi Fan ◽  
Zhong Pei ◽  
...  
Keyword(s):  
Caenorhabditis Elegans ◽  
Target Genes ◽  
Underlying Mechanism ◽  
Control Group ◽  
Wild Type ◽  
Survival Times ◽  
Expression Levels ◽  
C Elegans ◽  
Heat Stress Resistance ◽  
Increased Activity

Abstract Background Jianpi-yangwei (JPYW), a traditional Chinese medicine (TCM), helps to nourish the stomach and spleen and is primarily used to treat functional declines related to aging. This study aimed to explore the antiaging effects and mechanism of JPYW by employing a Caenorhabditis elegans model. Methods Wild-type C. elegans N2 worms were cultured in growth medium with or without JPYW, and lifespan analysis, oxidative and heat stress resistance assays, and other aging-related assays were performed. The effects of JPYW on the levels of superoxide dismutase (SOD) and the expression of specific genes were examined to explore the underlying mechanism of JPYW. Results Compared to control worms, JPYW-treated wild-type worms showed increased survival times under both normal and stress conditions (P < 0.05). JPYW-treated worms also exhibited enhanced reproduction, movement and growth and decreased intestinal lipofuscin accumulation compared to controls (P < 0.05). Furthermore, increased activity of SOD, downregulated expression levels of the proaging gene clk-2 and upregulated expression levels of the antiaging genes daf-16, skn-1, and sir-2.1 were observed in the JPYW group compared to the control group. Conclusion Our findings suggest that JPYW extends the lifespan of C. elegans and exerts antiaging effects by increasing the activity of an antioxidant enzyme (SOD) and by regulating the expression of aging-related genes. This study not only indicates that this Chinese compound exerts antiaging effects by activating and repressing target genes but also provides a proven methodology for studying the biological mechanisms of TCMs.

scholarly journals Coiled-coil registry shifts in the F684I mutant of Bicaudal result in cargo-independent activation of dynein motility

2019 ◽  
Author(s):  
Heying Cui ◽  
Kathleen M. Trybus ◽  
M. Yusuf Ali ◽  
Puja Goyal ◽  
Kaiqi Zhang ◽  
...  
Keyword(s):  
Coiled Coil ◽  
Underlying Mechanism ◽  
Structural Flexibility ◽  
Human Homolog ◽  
Wild Type ◽  
Transport Pathways ◽  
X Ray ◽  
In The Wild ◽  
Selection For ◽  
Dependent Transport

ABSTRACTThe dynein adaptor Drosophila Bicaudal D (BicD) is auto-inhibited and activates dynein motility only after cargo is bound, but the underlying mechanism is elusive. In contrast, we show that the full-length BicD/F684I mutant activates dynein processivity even in the absence of cargo. Our X-ray structure of the C-terminal domain of the BicD/F684I mutant reveals a coiled-coil registry shift; in the N-terminal region, the two helices of the homodimer are aligned, whereas they are vertically shifted in the wild-type. One chain is partially disordered and this structural flexibility is confirmed by computations, which reveal that the mutant transitions back and forth between the two registries. We propose that a coiled-coil registry shift upon cargo binding activates BicD for dynein recruitment. Moreover, the human homolog BicD2/F743I exhibits diminished binding of cargo adaptor Nup358, implying that a coiled-coil registry shift may be a mechanism to modulate cargo selection for BicD2–dependent transport pathways.

scholarly journals Genetic Characteristic and RNA-Seq Analysis in Transparent Mutant of Carp–Goldfish Nucleocytoplasmic Hybrid

Genes ◽  
2019 ◽  
Vol 10 (9) ◽  
pp. 704
Author(s):  
Lingling Zhou ◽  
Hongwei Liang ◽  
Xiaoyun Zhou ◽  
Jingyi Jia ◽  
Cheng Ye ◽  
...  
Keyword(s):  
Interaction Analysis ◽  
Pigment Cells ◽  
Hybrid Population ◽  
Biological Processes ◽  
Endothelin Receptor ◽  
Rna Seq ◽  
Wild Type ◽  
Specific Mechanism ◽  
Differential Expression Genes ◽  
In The Wild

In teleost, pigment in the skin and scales played important roles in various biological processes. Iridophores, one of the main pigment cells in teleost, could produce silver pigments to reflect light. However, the specific mechanism of the formation of silver pigments is still unclear. In our previous study, some transparent mutant individuals were found in the carp–goldfish nucleocytoplasmic hybrid (CyCa hybrid) population. In the present study, using transparent mutants (TM) and wild type (WT) of the CyCa hybrid as a model, firstly, microscopic observations showed that the silver pigments and melanin were both lost in the scales of transparent mutants compared to that in wild types. Secondly, genetic study demonstrated that the transparent trait in the CyCa hybrid was recessively inherent, and controlled by an allele in line with Mendelism. Thirdly, RNA-Seq analysis showed that differential expression genes (DEGs) between wild type and transparent mutants were mainly enriched in the metabolism of guanine, such as hydrolase, guanyl nucleotide binding, guanyl ribonucleotide binding, and GTPase activity. Among the DEGs, purine nucleoside phosphorylase 4a (pnp4a) and endothelin receptor B (ednrb) were more highly expressed in the wild type compared to the transparent mutant (p < 0.05). Finally, miRNA-Seq analysis showed that miRNA-146a and miR-153b were both more highly expressed in the transparent mutant compared to that in wild type (p < 0.05). Interaction analysis between miRNAs and mRNAs indicated that miRNA-146a was associated with six DEGs (MGAT5B, MFAP4, GP2, htt, Sema6b, Obscn) that might be involved in silver pigmentation.

scholarly journals Sensitivity of Populations of Botrytis cinerea from Pear-Related Sources to Benzimidazole and Dicarboximide Fungicides

Plant Disease ◽  
2003 ◽  
Vol 87 (6) ◽  
pp. 645-649 ◽  
Author(s):  
Cheryl L. Lennox ◽  
Robert A. Spotts
Keyword(s):  
Botrytis Cinerea ◽  
Pacific Northwest ◽  
Wild Type ◽  
Baseline Sensitivity ◽  
Benzimidazole Fungicides ◽  
Postharvest Application ◽  
The Pacific ◽  
In The Wild ◽  
Type Population ◽  
High Level

Botrytis cinerea is responsible for a major portion of postharvest decay in winter pears in the Pacific Northwest. The baseline sensitivity levels (mean EC50 values) of a wild-type B. cinerea population to thiabendazole and iprodione were 6.66 and 0.56 mg/liter, respectively. B. cinerea from commercial orchards not treated with a benzimidazole had significantly lower incidence of resistance (0.59%) to a discriminatory concentration of thiabendazole at 10 mg/liter than did isolates from orchards in which benomyl had been applied for experimental purposes (16.0%), unsprayed control trees in benomyl-sprayed orchards (5.34%), and isolates from packinghouses where thiabendazole was applied as a prestorage drench or packingline spray (3.23%). The mean EC50 value of isolates in the wild-type population was lower than those of resistant isolates from all other sources. High-level thiabendazole resistance (EC50 > 100 mg/liter) was found in 0.20% of isolates from unsprayed commercial orchards, 9.33% of isolates from benomyl-sprayed orchards, and 2.67% of isolates from unsprayed control trees in these benomyl-sprayed orchards. In isolates from packinghouses where a thiabendazole line spray was applied, 1.52% had high-level thiabendazole resistance. All isolates from all pear-related sources tested were sensitive to iprodione at 10 mg/liter. This study provides evidence supporting current recommendations of a single postharvest application of a benzimidazole to control decay caused by B. cinerea, and no application of benzimidazole fungicides in the orchard.

scholarly journals Role of Maltogenic Amylase and Pullulanase in Maltodextrin and Glycogen Metabolism of Bacillus subtilis 168

2009 ◽  
Vol 191 (15) ◽  
pp. 4835-4844 ◽  
Author(s):  
Jae-Hoon Shim ◽  
Jong-Tae Park ◽  
Jung-Sun Hong ◽  
Ki Woo Kim ◽  
Myo-Jeong Kim ◽  
...  
Keyword(s):  
Bacillus Subtilis ◽  
Glycogen Metabolism ◽  
Outer Side ◽  
Wild Type ◽  
Amylolytic Enzymes ◽  
In The Wild ◽  
Maltogenic Amylase ◽  
Molecular Masses ◽  
Average Molecular Masses ◽  
High Level

ABSTRACT The physiological functions of two amylolytic enzymes, a maltogenic amylase (MAase) encoded by yvdF and a debranching enzyme (pullulanase) encoded by amyX, in the carbohydrate metabolism of Bacillus subtilis 168 were investigated using yvdF, amyX, and yvdF amyX mutant strains. An immunolocalization study revealed that YvdF was distributed on both sides of the cytoplasmic membrane and in the periplasm during vegetative growth but in the cytoplasm of prespores. Small carbohydrates such as maltoheptaose and β-cyclodextrin (β-CD) taken up by wild-type B. subtilis cells via two distinct transporters, the Mdx and Cyc ABC transporters, respectively, were hydrolyzed immediately to form smaller or linear maltodextrins. On the other hand, the yvdF mutant exhibited limited degradation of the substrates, indicating that, in the wild type, maltodextrins and β-CD were hydrolyzed by MAase while being taken up by the bacterium. With glycogen and branched β-CDs as substrates, pullulanase showed high-level specificity for the hydrolysis of the outer side chains of glycogen with three to five glucosyl residues. To investigate the roles of MAase and pullulanase in glycogen utilization, the following glycogen-overproducing strains were constructed: a glg mutant with a wild-type background, yvdF glg and amyX glg mutants, and a glg mutant with a double mutant (DM) background. The amyX glg and glg DM strains accumulated significantly larger amounts of glycogen than the glg mutant, while the yvdF glg strain accumulated an intermediate amount. Glycogen samples from the amyX glg and glg DM strains exhibited average molecular masses two and three times larger, respectively, than that of glycogen from the glg mutant. The results suggested that glycogen breakdown may be a sequential process that involves pullulanase and MAase, whereby pullulanase hydrolyzes the α-1,6-glycosidic linkage at the branch point to release a linear maltooligosaccharide that is then hydrolyzed into maltose and maltotriose by MAase.

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