The Lipoxygenase Gene Family in Poplar: Identification, Classification, and Expression in Response to MeJA Treatment

Thilmony

et al. 2016

Nucleic Acids Res

PIECE (Plant Intron Exon Comparison and Evolution) is a web-accessible database that houses intron and exon information of plant genes. PIECE serves as a resource for biologists interested in comparing intron–exon organization and provides valuable insights into the evolution of gene structure in plant genomes. Recently, we updated PIECE to a new version, PIECE 2.0 (http://probes.pw.usda.gov/piece or http://aegilops.wheat.ucdavis.edu/piece). PIECE 2.0 contains annotated genes from 49 sequenced plant species as compared to 25 species in the previous version. In the current version, we also added several new features: (i) a new viewer was developed to show phylogenetic trees displayed along with the structure of individual genes; (ii) genes in the phylogenetic tree can now be also grouped according to KOG (The annotation of Eukaryotic Orthologous Groups) and KO (KEGG Orthology) in addition to Pfam domains; (iii) information on intronless genes are now included in the database; (iv) a statistical summary of global gene structure information for each species and its comparison with other species was added; and (v) an improved GSDraw tool was implemented in the web server to enhance the analysis and display of gene structure. The updated PIECE 2.0 database will be a valuable resource for the plant research community for the study of gene structure and evolution.

Section: New Featuresupporting

confidence: 93%

PIECE 2.0: an update for the plant gene structure comparison and evolution database

Thilmony

et al. 2016

Nucleic Acids Res

“…Phylogenetic analysis of the 9-LOX and 13-LOX sequences from date palm, oil palm, banana, and Arabidopsis (Figure 8) shows the divergence of the two groups of LOX sequences from the basal level of the tree. As reported for other plant LOX (Chen et al, 2015) there was also a clear separation of type I and type II 13-LOX sequences. In general, type I LOX proteins share high levels of sequences similarity (>75%) and do not contain predicted plastid targeting sequences and are therefore probably located in a cytosolic compartment(s).…”

Section: Discussionsupporting

confidence: 83%

“…In general, type I LOX proteins share high levels of sequences similarity (>75%) and do not contain predicted plastid targeting sequences and are therefore probably located in a cytosolic compartment(s). In contrast, type II LOX proteins have an N-terminal plastid targeting sequence but have lower levels of similarity one to another (Chen et al, 2015). In contrast, the vast majority of 9-LOX proteins are predicted to have cytosolic locations, and this was borne out by the absence of plastid targeting sequences in the species studied here (see Figure S2 and Table 3).…”

Section: Discussionmentioning

confidence: 99%

“…In this study, six CLO proteins in Elaeis guineensis and two CLO proteins in Musa acuminate were also identified. Using Arabidopsis LOXs as query sequences, LOX sequences were obtained for Phoenix dactylifera, Elaeis guineensis, Musa acuminate from NCBI via local BLAST+ search (Chen et al, 2015). These candidate LOX sequences were analyzed using the InterProScan program (http://www.ebi.ac.uk/interpro/) to confirm the presence of the major LOX domain and PLAT/LH2 (polycystin-1, lipoxygenase, lipoxygenase homology) domain (Jones et al, 2014).…”

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Specific Caleosin/Peroxygenase and Lipoxygenase Activities Are Tissue-Differentially Expressed in Date Palm (Phoenix dactylifera L.) Seedlings and Are Further Induced Following Exposure to the Toxin 2,3,7,8-tetrachlorodibenzo-p-dioxin

et al. 2017

Two caleosin/peroxygenase isoforms from date palm, Phoenix dactylifera L., PdCLO2 and PdCLO4, were characterized with respect to their tissue expression, subcellular localization, and oxylipin pathway substrate specificities in developing seedlings. Both PdCLO2 and PdCLO4 had peroxygenase activities that peaked at the mid-stage (radicle length of 2.5 cm) of seedling growth and were associated with the lipid droplet (LD) and microsomal fractions. Recombinant PdCLO2 and PdCLO4 proteins heterologously expressed in yeast cells were localized in both LD and microsomal fractions. Each of the purified recombinant proteins exhibited peroxygenase activity but they were catalytically distinct with respect to their specificity and product formation from fatty acid epoxide and hydroxide substrates. We recently showed that date palm CLO genes were upregulated following exposure to the potent toxin, 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) (Hanano et al., 2016), and we show here that transcripts of 9- and 13-lipoxygenase (LOX) genes were also induced by TCDD exposure. At the enzyme level, 9-LOX and 13-LOX activities were present in a range of seedling tissues and responded differently to TCDD exposure, as did the 9- and 13-fatty acid hydroperoxide reductase activities. This demonstrates that at least two branches of the oxylipin pathway are involved in responses to the environmental organic toxin, TCDD in date palm.

“…Thus, 150 mM mannitol was use as moderate osmotic stress treatment in this study. For phytohormone treatments, the plants were cultured in 1/2 MS medium with 200 μM ABA55, 100 μM SA56 or 100 μM MeJA57, according to a previous study. Prior to this, we also confirmed the ABA, SA and MeJA concentrations mentioned above, which can reduce growth but not induce wilting or necrosis within 7 d. All media were adjusted to pH 5.8 before addition of 0.6% plant agar (Biotopped, Beijing, China), and then sterilized by autoclaving at 121 °C for 15 min.…”

Section: Methodsmentioning

confidence: 99%

Comprehensive analysis of trihelix genes and their expression under biotic and abiotic stresses in Populus trichocarpa

Liu

et al. 2016

Sci Rep

Trihelix genes play important roles in plant growth and development and responses to biotic and abiotic stresses. Here, we identified 56 full-length trihelix genes in Populus trichocarpa and classified them into five groups. Most genes within a given group had similar gene structures and conserved motifs. The trihelix genes were unequally distributed across 19 different linkage groups. Fifteen paralogous pairs were identified, 14 of which have undergone segmental duplication events. Promoter cis-element analysis indicated that most trihelix genes contain stress- or phytohormone-related cis-elements. The expression profiles of the trihelix genes suggest that they are primarily expressed in leaves and roots. Quantitative real-time reverse transcription polymerase chain reaction analysis indicated that members of the trihelix gene family are significantly induced in response to osmotic, abscisic acid, salicylic acid, methyl jasmonate and pathogen infection. PtrGT10 was identified as a target gene of miR172d, which is involved in the osmotic response. Repression of PtrGT10 could increase reactive oxygen species scavenging ability and decrease cell death. This study provides novel insights into the phylogenetic relationships and functions of the P. trichocarpa trihelix genes, which will aid future functional studies investigating the divergent roles of trihelix genes belonging to other species.