Cytochrome P450 mono-oxygenases in conifer genomes: discovery of members of the terpenoid oxygenase superfamily in spruce and pine

2006 ◽  
Vol 34 (6) ◽  
pp. 1209-1214 ◽  
Author(s):  
B. Hamberger ◽  
J. Bohlmann
Keyword(s):  
Cytochrome P450 ◽  
Loblolly Pine ◽  
Large Scale ◽  
Expressed Sequence Tag ◽  
Resin Acid ◽  
Functional Characterization ◽  
Structural Diversity ◽  
Resin Acids ◽  
Full Length Sequence ◽  
Diterpene Resin Acids

Diterpene resin acids, together with monoterpenes and sesquiterpenes, are the most prominent defence chemicals in conifers. These compounds belong to the large group of structurally diverse terpenoids formed by enzymes known as terpenoid synthases. CYPs (cytochrome P450-dependent mono-oxygenases) can further increase the structural diversity of these terpenoids. While most terpenoids are characterized as specialized or secondary metabolites, some terpenoids, such as the phytohormones GA (gibberellic acid), BRs (brassinosteroids) and ABA (abscisic acid), have essential functions in plant growth and development. To date, very few CYP genes involved in conifer terpenoid metabolism have been functionally characterized and were limited to two systems, yew (Taxus) and loblolly pine (Pinus taeda). The characterized yew CYP genes are involved in taxol diterpene biosynthesis, while the only characterized pine terpenoid CYP gene is part of DRA (diterpene resin acid) biosynthesis. These CYPs from yew and pine are members of two apparently conifer-specific CYP families within the larger CYP85 clan, one of four plant CYP multifamily clans. Other CYP families within the CYP85 clan were characterized from a variety of angiosperms with functions in terpenoid phytohormone metabolism of GA, BR, and ABA. The recent development of EST (expressed sequence tag) and FLcDNA (where FL is full-length) sequence databases and cDNA collections for species of two conifers, spruce (Picea) and pine, allows for the discovery of new terpenoid CYPs in gymnosperms by means of large-scale sequence mining, phylogenetic analysis and functional characterization. Here, we present a snapshot of conifer CYP data mining, discovery of new conifer CYPs in all but one family within the CYP85 clan, and suggestions for their functional characterization. This paper will focus on the discovery of conifer CYPs associated with diterpene metabolism and CYP with possible functions in the formation of GA, BR, and ABA in conifers.

scholarly journals In Silico Identification and Functional Characterization of Conserved miRNAs in the Genome of Cryptosporidium parvum

2021 ◽  
Vol 15 ◽  
pp. 117793222110276
Author(s):  
Md. Irtija Ahsan ◽  
Md. Shahidur Rahman Chowdhury ◽  
Moumita Das ◽  
Sharmin Akter ◽  
Sawrab Roy ◽  
...  
Keyword(s):  
Cryptosporidium Parvum ◽  
Target Genes ◽  
Expressed Sequence Tag ◽  
Functional Characterization ◽  
Childhood Mortality ◽  
Homology Search ◽  
Health Concern ◽  
Nutrient Metabolism ◽  
Screening Process ◽  
Computational Screening

Cryptosporidium parvum, a predominant causal agent of a fatal zoonotic protozoan diarrhoeal disease called cryptosporidiosis, bears a worldwide public health concern for childhood mortality and poses a key threat to the dairy and water industries. MicroRNAs (miRNAs), small but powerful posttranscriptional gene silencing RNA molecules, regulate a variety of molecular, biological, and cellular processes in animals and plants. As to the present date, there is a paucity of information regarding miRNAs of C. parvum; hence, this study was used to identify miRNAs in the organism using a comprehensible expressed sequence tag–based homology search approach consisting of a series of computational screening process from the identification of putative miRNA candidates to the functional annotation of the important gene targets in C. parvum. The results revealed a conserved miRNA that targeted 487 genes in the model organism ( Drosophila melanogaster) and 85 genes in C. parvum, of which 11 genes had direct involvements in several crucial virulence factors such as environmental oocyst protection, excystation, locomotion, adhesion, invasion, stress protection, intracellular growth, and survival. Besides, 20 genes showed their association with various major pathways dedicated for the ribosomal biosynthesis, DNA repair, transportation, protein production, gene expression, cell cycle, cell proliferation, development, immune response, differentiation, and nutrient metabolism of the organism in the host. Thus, this study provides a strong evidence of great impact of identified miRNA on the biology, virulence, and pathogenesis of C. parvum. Furthermore, the study suggests that the detected miRNA could be a potential epigenomic tool for controlling the protozoon through silencing those virulent and pathway-related target genes.

scholarly journals Functional Characterization of Spliceosomal Introns and Identification of U2, U4, and U5 snRNAs in the Deep-Branching Eukaryote Entamoeba histolytica

2007 ◽  
Vol 6 (6) ◽  
pp. 940-948 ◽  
Author(s):  
Carrie A. Davis ◽  
Michael P. S. Brown ◽  
Upinder Singh
Keyword(s):  
Entamoeba Histolytica ◽  
Splice Site ◽  
Expressed Sequence Tag ◽  
Functional Characterization ◽  
Molecular Evidence ◽  
Spliceosomal Introns ◽  
Accurate Expression ◽  
Eukaryotic Organisms

ABSTRACT Pre-mRNA splicing is essential to ensure accurate expression of many genes in eukaryotic organisms. In Entamoeba histolytica, a deep-branching eukaryote, approximately 30% of the annotated genes are predicted to contain introns; however, the accuracy of these predictions has not been tested. In this study, we mined an expressed sequence tag (EST) library representing 7% of amoebic genes and found evidence supporting splicing of 60% of the testable intron predictions, the majority of which contain a GUUUGU 5′ splice site and a UAG 3′ splice site. Additionally, we identified several splice site misannotations, evidence for the existence of 30 novel introns in previously annotated genes, and identified novel genes through uncovering their spliced ESTs. Finally, we provided molecular evidence for the E. histolytica U2, U4, and U5 snRNAs. These data lay the foundation for further dissection of the role of RNA processing in E. histolytica gene expression.

Anchored Reference Loci in Loblolly Pine (Pinus taeda L.) for Integrating Pine Genomics

Genetics ◽  
2001 ◽  
Vol 159 (2) ◽  
pp. 799-809 ◽  
Author(s):  
Garth R Brown ◽  
Edward E Kadel ◽  
Daniel L Bassoni ◽  
Kristine L Kiehne ◽  
Berhanu Temesgen ◽  
...  
Keyword(s):  
Pinus Taeda ◽  
Loblolly Pine ◽  
Comparative Mapping ◽  
Expressed Sequence Tag ◽  
Single Species ◽  
Douglas Fir ◽  
Genetic Maps ◽  
Multiple Sources ◽  
Primer Sets ◽  
Pinus Taeda L

Abstract Anchored reference loci provide a framework for comparative mapping. They are landmarks to denote conserved chromosomal segments, allowing the synthesis of genetic maps from multiple sources. We evaluated 90 expressed sequence tag polymorphisms (ESTPs) from loblolly pine (Pinus taeda L.) for this function. Primer sets were assayed for amplification and polymorphism in six pedigrees, representing two subgenera of Pinus and a distant member of the Pinaceae, Douglas-fir (Pseudotsuga menziesii [Mirb.] Franco). On average, 89% of primer sets amplified in four species of subgenus Pinus, 49% in one species of subgenus Strobus, and 22% in Douglas-fir. Polymorphisms were detected for 37–61% of the ESTPs within each pedigree. Comparative mapping in loblolly and slash pine (P. elliottii Englm.) revealed that ESTPs mapped to the same location. Disrupted synteny or significant disruptions in colinearity were not detected. Thirty-five ESTPs met criteria established for anchor loci. The majority of those that did not meet these criteria were excluded when map location was known in only a single species. Anchor loci provide a unifying tool for the community, facilitating the creation of a “generic” pine map and serving as a foundation for studies on genome organization and evolution.

scholarly journals Identification and functional characterization of two bamboo FD gene homologs having contrasting effects on shoot growth and flowering

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Smritikana Dutta ◽  
Anwesha Deb ◽  
Prasun Biswas ◽  
Sukanya Chakraborty ◽  
Suman Guha ◽  
...  
Keyword(s):  
Large Scale ◽  
Forest Ecology ◽  
Phylogenetic Analyses ◽  
Functional Characterization ◽  
Constitutive Expression ◽  
Transcript Level ◽  
In Planta ◽  
Mobility Shift ◽  
Vegetative Development ◽  
Sequence Comparisons

AbstractBamboos, member of the family Poaceae, represent many interesting features with respect to their fast and extended vegetative growth, unusual, yet divergent flowering time across species, and impact of sudden, large scale flowering on forest ecology. However, not many studies have been conducted at the molecular level to characterize important genes that regulate vegetative and flowering habit in bamboo. In this study, two bamboo FD genes, BtFD1 and BtFD2, which are members of the florigen activation complex (FAC) have been identified by sequence and phylogenetic analyses. Sequence comparisons identified one important amino acid, which was located in the DNA-binding basic region and was altered between BtFD1 and BtFD2 (Ala146 of BtFD1 vs. Leu100 of BtFD2). Electrophoretic mobility shift assay revealed that this alteration had resulted into ten times higher binding efficiency of BtFD1 than BtFD2 to its target ACGT motif present at the promoter of the APETALA1 gene. Expression analyses in different tissues and seasons indicated the involvement of BtFD1 in flower and vegetative development, while BtFD2 was very lowly expressed throughout all the tissues and conditions studied. Finally, a tenfold increase of the AtAP1 transcript level by p35S::BtFD1 Arabidopsis plants compared to wild type confirms a positively regulatory role of BtFD1 towards flowering. However, constitutive expression of BtFD1 had led to dwarfisms and apparent reduction in the length of flowering stalk and numbers of flowers/plant, whereas no visible phenotype was observed for BtFD2 overexpression. This signifies that timely expression of BtFD1 may be critical to perform its programmed developmental role in planta.

SYNTHETIC PHEROMONES DISRUPT MALE DIORYCTRIA SPP. MOTHS IN A LOBLOLLY PINE SEED ORCHARD

2000 ◽  
Vol 132 (3) ◽  
pp. 345-351 ◽  
Author(s):  
Gary L. DeBarr ◽  
James L. Hanula ◽  
Christine G. Niwa ◽  
John C. Nord
Keyword(s):  
Loblolly Pine ◽  
Large Scale ◽  
Sex Pheromones ◽  
Mating Disruption ◽  
Seed Orchard ◽  
Control Treatment ◽  
Tetradecenyl Acetate ◽  
Lepidoptera Pyralidae ◽  
Trap Catches ◽  
Large Scale Tests

AbstractSynthetic sex pheromones released in a loblolly pine, Pinus taeda L. (Pinaceae), seed orchard interfered with the ability of male coneworm moths, Dioryctria Zeller spp. (Lepidoptera: Pyralidae), to locate traps baited with sex pheromones or live females. Pherocon 1C® traps baited with synthetic pheromones or live conspecific females were hung near the center of two 1.2-ha circular plots during emergence of Dioryctria amatella (Hulst), Dioryctria disclusa (Heinrich), and Dioryctria merkeli (Mutuura and Munroe). In a paired design, trap catches for the mating-disruption treatment with synthetic pheromone dispensers consisting of three polyvinyl chloride rods placed in every tree were compared with the control treatment. Treatments were alternated at intervals of 2–3 d. Trap catches of D. amatella were reduced by 91% when plots were treated with 2.5 g/ha of Z-11-hexadencenyl acetate. Catches were reduced by 99.5% for D. disclusa and by 97% for D. merkeli when plots were treated with 12.5 g/ha of Z-9-tetradecenyl acetate, whereas catches of D. amatella were unaffected by this mating-disruption treatment. Daily disappearance of Z-9-tetradecenyl acetate from the dispensers averaged 0.46 g/ha or less. Manually placing dispensers on nylon lines in the tops of trees was an effective method for releasing synthetic Dioryctria pheromones in the orchard. These data suggest it may be feasible to prevent mating of Dioryctria spp. in pine seed orchards by using synthetic pheromones for mating disruption, but large-scale tests will be required to demonstrate cone protection.

Biomass logistics analysis for large scale biofuel production: Case study of loblolly pine and switchgrass

2015 ◽  
Vol 183 ◽  
pp. 1-9 ◽  
Author(s):  
Xiaoming Lu ◽  
Mitch R. Withers ◽  
Navid Seifkar ◽  
Randall P. Field ◽  
Steven R.H. Barrett ◽  
...  
Keyword(s):  
Loblolly Pine ◽  
Large Scale ◽  
Biofuel Production ◽  
Biomass Logistics

Identification and functional characterization of novel feline cytochrome P450 2A

Xenobiotica ◽  
2014 ◽  
Vol 45 (6) ◽  
pp. 503-510 ◽  
Author(s):  
Gaku Okamatsu ◽  
Tetsuya Komatsu ◽  
Akira Kubota ◽  
Takenori Onaga ◽  
Tsuyoshi Uchide ◽  
...  
Keyword(s):  
Cytochrome P450 ◽  
Functional Characterization

scholarly journals Poly(ADP-ribose) polymerase 1 in genome-wide expression control in Drosophila

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Guillaume Bordet ◽  
Niraj Lodhi ◽  
Danping Guo ◽  
Andrew Kossenkov ◽  
Alexei V. Tulin
Keyword(s):  
Cytochrome P450 ◽  
Transcription Factors ◽  
Transcription Regulation ◽  
Large Scale ◽  
Mobile Elements ◽  
Expression Control ◽  
Genome Wide ◽  
Cytochrome P450 Family ◽  
Parp 1

AbstractPoly(ADP-ribose) polymerase 1 (PARP-1) is a nuclear enzyme involved in DNA repair and transcription regulation, among other processes. Malignant transformations, tumor progression, the onset of some neuropathies and other disorders have been linked to misregulation of PARP-1 activity. Despite intensive studies during the last few decades, the role of PARP-1 in transcription regulation is still not well understood. In this study, a transcriptomic analysis in Drosophila melanogaster third instar larvae was carried out. A total of 602 genes were identified, showing large-scale changes in their expression levels in the absence of PARP-1 in vivo. Among these genes, several functional gene groups were present, including transcription factors and cytochrome family members. The transcription levels of genes from the same functional group were affected by the absence of PARP-1 in a similar manner. In the absence of PARP-1, all misregulated genes coding for transcription factors were downregulated, whereas all genes coding for members of the cytochrome P450 family were upregulated. The cytochrome P450 proteins contain heme as a cofactor and are involved in oxidoreduction. Significant changes were also observed in the expression of several mobile elements in the absence of PARP-1, suggesting that PARP-1 may be involved in regulating the expression of mobile elements.

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