Transcriptome Profiling of Two Ornamental and Medicinal Papaver Herbs

The Papaver spp. (Papaver rhoeas (Corn poppy) and Papaver nudicaule (Iceland poppy)) genera are ornamental and medicinal plants that are used for the isolation of alkaloid drugs. In this study, we generated 700 Mb of transcriptome sequences with the PacBio platform. They were assembled into 120,926 contigs, and 1185 (82.2%) of the benchmarking universal single-copy orthologs (BUSCO) core genes were completely present in our assembled transcriptome. Furthermore, using 128 Gb of Illumina sequences, the transcript expression was assessed at three stages of Papaver plant development (30, 60, and 90 days), from which we identified 137 differentially expressed transcripts. Furthermore, three co-occurrence heat maps are generated from 51 different plant genomes along with the Papaver transcriptome, i.e., secondary metabolite biosynthesis, isoquinoline alkaloid biosynthesis (BIA) pathway, and cytochrome. Sixty-nine transcripts in the BIA pathway along with 22 different alkaloids (quantified with LC-QTOF-MS/MS) were mapped into the BIA KEGG map (map00950). Finally, we identified 39 full-length cytochrome transcripts and compared them with other genomes. Collectively, this transcriptome data, along with the expression and quantitative metabolite profiles, provides an initial recording of secondary metabolites and their expression related to Papaver plant development. Moreover, these profiles could help to further detail the functional characterization of the various secondary metabolite biosynthesis and Papaver plant development associated problems.

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Characterization of novel regulators for heat stress tolerance in tomato from Indian sub-continent

10.1101/800607 ◽

2019 ◽

Author(s):

Sonia Balyan ◽

Sombir Rao ◽

Sarita Jha ◽

Chandni Bansal ◽

Jaishri Rubina Das ◽

...

Keyword(s):

Transcription Factors ◽

Heat Stress ◽

Functional Characterization ◽

Transcriptome Profiling ◽

Negative Regulator ◽

Comparative Transcriptome ◽

Regulatory Pathways ◽

Cool Region ◽

Promoter Swapping

AbstractThe footprint of tomato cultivation, a cool region crop that exhibits heat stress (HS) sensitivity, is increasing in the tropics/sub-tropics. Knowledge of novel regulatory hot-spots from varieties growing in the Indian sub-continent climatic zones could be vital for developing HS-resilient crops. Comparative transcriptome-wide signatures of a tolerant (CLN1621L) and sensitive (CA4) cultivar-pair short-listed from a pool of varieties exhibiting variable thermo-sensitivity using physiological, survival and yield-related traits revealed redundant to cultivar-specific HS-regulation with more up-regulated genes for CLN1621L than CA4. The anatgonisiticly-expressing genes include enzymes; have roles in plant defense and response to different abiotic stresses. Functional characterization of three antagonistic genes by overexpression and TRV-VIGS silencing established Solyc09g014280 (Acylsugar acyltransferase) and Solyc07g056570 (Notabilis), that are up-regulated in tolerant cultivar, as positive regulators of HS-tolerance and Solyc03g020030 (Pin-II proteinase inhibitor), that is down-regulated in CLN1621L, as negative regulator of thermotolerance. Transcriptional assessment of promoters of these genes by SNPs in stress-responsive cis-elements and promoter swapping experiments in opposite cultivar background showed inherent cultivar-specific orchestration of transcription factors in regulating transcription. Moreover, overexpression of three ethylene response transcription factors (ERF.C1/F4/F5) also improved HS-tolerance in tomato. This study identifies several novel HS-tolerance genes and provides proof of their utility in tomato-thermotolerance.HighlightNovel heat stress regulatory pathways uncovered by comparative transcriptome profiling between contrasting tomato cultivars from Indian sub-continent for improving thermotolerance. (20/30)

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Functional Characterization of the Versatile MYB Gene Family Uncovered Their Important Roles in Plant Development and Responses to Drought and Waterlogging in Sesame

Genes ◽

10.3390/genes8120362 ◽

2017 ◽

Vol 8 (12) ◽

pp. 362 ◽

Cited By ~ 22

Author(s):

Marie Mmadi ◽

Komivi Dossa ◽

Linhai Wang ◽

Rong Zhou ◽

Yanyan Wang ◽

...

Keyword(s):

Gene Family ◽

Plant Development ◽

Functional Characterization ◽

Myb Gene

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A Mycobacterial Systems Resource for the Research Community

mBio ◽

10.1128/mbio.02401-20 ◽

2021 ◽

Vol 12 (2) ◽

Author(s):

J. A. Judd ◽

J. Canestrari ◽

R. Clark ◽

A. Joseph ◽

P. Lapierre ◽

...

Keyword(s):

Mycobacterium Smegmatis ◽

Protein Localization ◽

Functional Characterization ◽

Model Organism ◽

Research Community ◽

Mycobacterial Species ◽

Biological Resource ◽

Content Type ◽

Core Genes

ABSTRACT Functional characterization of bacterial proteins lags far behind the identification of new protein families. This is especially true for bacterial species that are more difficult to grow and genetically manipulate than model systems such as Escherichia coli and Bacillus subtilis. To facilitate functional characterization of mycobacterial proteins, we have established a Mycobacterial Systems Resource (MSR) using the model organism Mycobacterium smegmatis. This resource focuses specifically on 1,153 highly conserved core genes that are common to many mycobacterial species, including Mycobacterium tuberculosis, in order to provide the most relevant information and resources for the mycobacterial research community. The MSR includes both biological and bioinformatic resources. The biological resource includes (i) an expression plasmid library of 1,116 genes fused to a fluorescent protein for determining protein localization; (ii) a library of 569 precise deletions of nonessential genes; and (iii) a set of 843 CRISPR-interference (CRISPRi) plasmids specifically targeted to silence expression of essential core genes and genes for which a precise deletion was not obtained. The bioinformatic resource includes information about individual genes and a detailed assessment of protein localization. We anticipate that integration of these initial functional analyses and the availability of the biological resource will facilitate studies of these core proteins in many Mycobacterium species, including the less experimentally tractable pathogens M. abscessus, M. avium, M. kansasii, M. leprae, M. marinum, M. tuberculosis, and M. ulcerans. IMPORTANCE Diseases caused by mycobacterial species result in millions of deaths per year globally, and present a substantial health and economic burden, especially in immunocompromised patients. Difficulties inherent in working with mycobacterial pathogens have hampered the development and application of high-throughput genetics that can inform genome annotations and subsequent functional assays. To facilitate mycobacterial research, we have created a biological and bioinformatic resource (https://msrdb.org/) using Mycobacterium smegmatis as a model organism. The resource focuses specifically on 1,153 proteins that are highly conserved across the mycobacterial genus and, therefore, likely perform conserved mycobacterial core functions. Thus, functional insights from the MSR will apply to all mycobacterial species. We believe that the availability of this mycobacterial systems resource will accelerate research throughout the mycobacterial research community.

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Functional characterization of the sterigmatocystin secondary metabolite gene cluster in the filamentous fungusPodospora anserina: involvement in oxidative stress response, sexual development, pigmentation and interspecific competitions

Environmental Microbiology ◽

10.1111/1462-2920.14698 ◽

2019 ◽

Vol 21 (8) ◽

pp. 3011-3026 ◽

Cited By ~ 3

Author(s):

Ling Shen ◽

François‐Hugues Porée ◽

Thomas Gaslonde ◽

Hervé Lalucque ◽

Florence Chapeland‐Leclerc ◽

...

Keyword(s):

Oxidative Stress ◽

Stress Response ◽

Gene Cluster ◽

Secondary Metabolite ◽

Sexual Development ◽

Functional Characterization ◽

Oxidative Stress Response ◽

Secondary Metabolite Gene Cluster

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Overexpression of Trypanosoma rangeli trypanothione reductase increases parasite survival under oxidative stress

Parasitology Open ◽

10.1017/pao.2016.14 ◽

2016 ◽

Vol 2 ◽

Author(s):

I.T. BELTRAME-BOTELHO ◽

P.H. STOCO ◽

M. STEINDEL ◽

B. ANDERSSON ◽

E.F. PELOSO ◽

...

Keyword(s):

Oxidative Stress ◽

Functional Characterization ◽

Nicotinamide Adenine Dinucleotide Phosphate ◽

Single Copy ◽

Trypanothione Reductase ◽

Trypanosoma Rangeli ◽

Reading Frame ◽

Key Enzyme

SUMMARYThe infectivity and virulence of pathogenic trypanosomatids are directly associated with the efficacy of their antioxidant system. Among the molecules involved in the trypanosomatid response to reactive oxygen or nitrogen species, trypanothione reductase (TRed) is a key enzyme. In this study, we performed a molecular and functional characterization of the TRed enzyme fromTrypanosoma rangeli(TrTRed), an avirulent trypanosome of mammals. TheTrTRed gene has an open reading frame (ORF) of 1473 bp (~490 aa, 53 kDa) and occurs as a single-copy gene in the haploid genome. The predicted protein contains two oxidoreductase domains, which are equally expressed in the cytosol of epimastigotes and trypomastigotes. Nicotinamide adenine dinucleotide phosphate (NADPH) generation is reduced and endogenous H2O2production is elevated inT. rangeliChoachí strain compared withT. cruziY strain epimastigotes. Oxidative stress induced by H2O2does not induce significant alterations inTrTRed expression. Overexpression ofTrTRed did not influencein vitrogrowth or differentiation into trypomastigotes, but mutant parasites showed increased resistance to H2O2-induced stress. Our results indicate thatT. rangeliconstitutively expresses TRed during the entire life cycle, with reduced levels during infective and non-replicative trypomastigote stages.

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Structure prediction and functional characterization of secondary metabolite proteins of Ocimum

Bioinformation ◽

10.6026/97320630006315 ◽

2011 ◽

Vol 6 (8) ◽

pp. 315-319 ◽

Cited By ~ 21

Author(s):

Sudeep Roy ◽

Nidhi Maheshwari ◽

Rashi Chauhan ◽

Naresh Kumar Sen ◽

Ashok Sharma

Keyword(s):

Secondary Metabolite ◽

Structure Prediction ◽

Functional Characterization

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Genome-wide analysis of gibberellin-dioxygenases gene family and their responses to GA applications in maize

PLoS ONE ◽

10.1371/journal.pone.0250349 ◽

2021 ◽

Vol 16 (5) ◽

pp. e0250349

Author(s):

Jiabin Ci ◽

Xingyang Wang ◽

Qi Wang ◽

Fuxing Zhao ◽

Wei Yang ◽

...

Keyword(s):

Gene Family ◽

Plant Development ◽

Functional Characterization ◽

Tissue Expression ◽

Leaf Sheath ◽

Solid Base ◽

Specific Expression ◽

Genome Wide ◽

Almost All

Gibberellin-dioxygenases genes plays important roles in the regulating plant development. However, Gibberellin-dioxygenases genes are rarely reported in maize, especially response to gibberellin (GA). In present study, 27 Gibberellin-dioxygenases genes were identified in the maize and they were classified into seven subfamilies (I-VII) based on phylogenetic analysis. This result was also further confirmed by their gene structure and conserved motif characteristics. And gibberellin-dioxygenases genes only occurred segmental duplication that occurs most frequently in plants. Furthermore, the gibberellin-dioxygenases genes showed different tissue expression pattern in different tissues and most of the gibberellin-dioxygenases genes showed tissue specific expression. Moreover, almost all the gibberellin-dioxygenases genes were significantly elevated in response to GA except for ZmGA2ox2 and ZmGA20ox10 of 15 gibberellin-dioxygenases genes normally expressed in leaves while 10 and 11 gibberellin-dioxygenases genes showed up and down regulated under GA treatment than that under normal condition in leaf sheath. In addition, we found that ZmGA2ox1, ZmGA2ox4, ZmGA20ox7, ZmGA3ox1 and ZmGA3ox3 might be potential genes for regulating balance of GAs which play essential roles in plant development. These findings will increase our understanding of Gibberellin-dioxygenases gene family in response to GA and will provide a solid base for further functional characterization of Gibberellin-dioxygenases genes in maize.

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Functional Characterization of Two Clusters of Brachypodium distachyon UDP-Glycosyltransferases Encoding Putative Deoxynivalenol Detoxification Genes

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi-08-12-0205-r ◽

2013 ◽

Vol 26 (7) ◽

pp. 781-792 ◽

Cited By ~ 45

Author(s):

Wolfgang Schweiger ◽

Jean-Claude Pasquet ◽

Thomas Nussbaumer ◽

Maria Paula Kovalsky Paris ◽

Gerlinde Wiesenberger ◽

...

Keyword(s):

Brachypodium Distachyon ◽

Functional Characterization ◽

Rapid Evolution ◽

Gene Clusters ◽

Single Copy ◽

Wild Type ◽

Vast Number ◽

Putative Orthologs ◽

Endogenous Substances

Plant small-molecule UDP-glycosyltransferases (UGT) glycosylate a vast number of endogenous substances but also act in detoxification of metabolites produced by plant-pathogenic microorganisms. The ability to inactivate the Fusarium graminearum mycotoxin deoxynivalenol (DON) into DON-3-O-glucoside is crucial for resistance of cereals. We analyzed the UGT gene family of the monocot model species Brachypodium distachyon and functionally characterized two gene clusters containing putative orthologs of previously identified DON-detoxification genes from Arabidopsis thaliana and barley. Analysis of transcription showed that UGT encoded in both clusters are highly inducible by DON and expressed at much higher levels upon infection with a wild-type DON-producing F. graminearum strain compared with infection with a mutant deficient in DON production. Expression of these genes in a toxin-sensitive strain of Saccharomyces cerevisiae revealed that only two B. distachyon UGT encoded by members of a cluster of six genes homologous to the DON-inactivating barley HvUGT13248 were able to convert DON into DON-3-O-glucoside. Also, a single copy gene from Sorghum bicolor orthologous to this cluster and one of three putative orthologs of rice exhibit this ability. Seemingly, the UGT genes undergo rapid evolution and changes in copy number, making it difficult to identify orthologs with conserved substrate specificity.

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