scholarly journals Genome-Wide Survey of Invertase Encoding Genes and Functional Characterization of an Extracellular Fungal Pathogen-Responsive Invertase in Glycine max

2018 ◽  
Vol 19 (8) ◽  
pp. 2395 ◽  
Author(s):  
Tao Su ◽  
Mei Han ◽  
Jie Min ◽  
Peixian Chen ◽  
Yuxin Mao ◽  
...  
Keyword(s):  
Glycine Max ◽  
Molecular Mechanisms ◽  
Soluble Sugar ◽  
Functional Characterization ◽  
Regulatory Elements ◽  
Plant Performance ◽  
Sugar Accumulation ◽  
Stress Regime ◽  
Diverse Range ◽  
Encoding Genes

Invertases are essential enzymes that irreversibly catalyze the cleavage of sucrose into glucose and fructose. Cell wall invertase (CWI) and vacuolar invertase (VI) are glycosylated proteins and exert fundamental roles in plant growth as well as in response to environmental cues. As yet, comprehensive insight into invertase encoding genes are lacking in Glycine max. In the present study, the systematic survey of gene structures, coding regions, regulatory elements, conserved motifs, and phylogenies resulted in the identification of thirty–two putative invertase genes in soybean genome. Concomitantly, impacts on gene expression, enzyme activities, proteins, and soluble sugar accumulation were explored in specific tissues upon stress perturbation. In combination with the observation of subcellular compartmentation of the fluorescent fusion protein that indeed exported to apoplast, heterologous expression, and purification in using Pichia pastoris system revealed that GmCWI4 was a typical extracellular invertase. We postulated that GmCWI4 may play regulatory roles and be involved in pathogenic fungi defense. The experimental evaluation of physiological significance via phenotypic analysis of mutants under stress exposure has been initiated. Moreover, our paper provides theoretical basis for elucidating molecular mechanisms of invertase in association with inhibitors underlying the stress regime, and will contribute to the improvement of plant performance to a diverse range of stressors.

scholarly journals Mortierella elongata Increases Plant Biomass among Non-Leguminous Crop Species

Agronomy ◽  
2020 ◽  
Vol 10 (5) ◽  
pp. 754 ◽  
Author(s):  
Kaile Zhang ◽  
Gregory Bonito ◽  
Chih-Ming Hsu ◽  
Khalid Hameed ◽  
Rytas Vilgalys ◽  
...  
Keyword(s):  
Glycine Max ◽  
Leaf Area ◽  
Plant Height ◽  
Molecular Mechanisms ◽  
Plant Biomass ◽  
Citrullus Lanatus ◽  
Plant Performance ◽  
Future Research ◽  
Crop Species ◽  
Leguminous Crop

Recent studies have shown that M. elongata (M. elongata) isolated from Populus field sites has a dual endophyte–saprotroph lifestyle and is able to promote the growth of Populus. However, little is known about the host fidelity of M. elongata and whether M. elongata strains differ from one another in their ability to promote plant growth. Here, we compared the impacts of three Populus-associated M. elongata isolates (PMI 77, PMI 93, and PMI 624) on the growth of seven different crop species by measuring plant height, plant dry biomass, and leaf area. M. elongata isolates PMI 624 and PMI 93 increased the plant height, leaf area, and plant dry weight of Citrullus lanatus, Zea mays, Solanum lycopersicum, and Cucurbita to a much greater degree than PMI 77 (33.9% to 14.1%). No significant impacts were observed for any isolate on the growth of Abelmoschus esculentus or Glycine max. On the contrary, Glycine max significantly decreased in height by 30.6% after the inoculation of M. elongata PMI 77. In conclusion, this study demonstrates that M. elongata generally promoted metrics of the plant performance among a diverse set of importantly non-leguminous crop species. Future research on understanding the molecular mechanisms that underlie strain and host variability is warranted.

scholarly journals Identification and Functional Characterization of a Soybean (Glycine max) Thioesterase that Acts on Intermediates of Fatty Acid Biosynthesis

Plants ◽  
2019 ◽  
Vol 8 (10) ◽  
pp. 397
Author(s):  
Huong Thi Diem Tran ◽  
Nhan Trong Le ◽  
Vy Le Uyen Khuat ◽  
Thuong Thi Hong Nguyen
Keyword(s):  
Glycine Max ◽  
Stress Responses ◽  
Fatty Acid Biosynthesis ◽  
Acyl Carrier Protein ◽  
Functional Characterization ◽  
In Silico Analysis ◽  
Transcript Level ◽  
Regulatory Elements ◽  
Dodecanoic Acid ◽  
Wide Range

(1) Background: Plants possess many acyl-acyl carrier protein (acyl-ACP) thioesterases (TEs) with unique specificity. One such TE is methylketone synthase 2 (MKS2), an enzyme with a single-hotdog-fold structure found in several tomato species that hydrolyzes 3-ketoacyl-ACPs to give free 3-ketoacids. (2) Methods: In this study, we identified and characterized a tomato MKS2 homolog gene, namely, GmMKS2, in the genome of soybean (Glycine max). (3) Results: GmMKS2 underwent alternative splicing to produce three alternative transcripts, but only one encodes a protein with thioesterase activity when recombinantly expressed in Escherichia coli. Heterologous expression of the main transcript of GmMKS2, GmMKS2-X2, in E. coli generated various types of fatty acids, including 3-ketoacids—with 3-ketotetradecenoic acid (14:1) being the most abundant—cis-Δ5-dodecanoic acid, and 3-hydroxyacids, suggesting that GmMKS2 acts as an acyl-ACP thioesterase. In plants, the GmMKS2-X2 transcript level was found to be higher in the roots compared to other examined organs. In silico analysis revealed that there is a substantial enrichment of putative cis-regulatory elements related to disease-resistance responses and abiotic stress responses in the promoter of this gene. (4) Conclusions: GmMKS2 showed broad substrate specificities toward a wide range of acyl-ACPs that varied in terms of chain length, oxidation state, and saturation degree. Our results suggest that GmMKS2 might have a stress-related physiological function in G. max.

scholarly journals Characterization and Expression of KT/HAK/KUP Transporter Family Genes in Willow under Potassium Deficiency, Drought, and Salt Stresses

2020 ◽  
Vol 2020 ◽  
pp. 1-12 ◽  
Author(s):  
Meixia Liang ◽  
Yachao Gao ◽  
Tingting Mao ◽  
Xiaoyan Zhang ◽  
Shaoying Zhang ◽  
...  
Keyword(s):  
Salt Stress ◽  
Molecular Mechanisms ◽  
Functional Characterization ◽  
Regulatory Elements ◽  
Forest Trees ◽  
Transporter Family ◽  
Whole Plant ◽  
Drought And Salt Stress ◽  
Drought And Salt Stresses ◽  
Plant Level

The K+ transporter/high-affinity K+/K+ uptake (KT/HAK/KUP) transporters dominate K+ uptake, transport, and allocation that play a pivotal role in mineral homeostasis and plant adaptation to adverse abiotic stresses. However, molecular mechanisms towards K+ nutrition in forest trees are extremely rare, especially in willow. In this study, we identified 22 KT/HAK/KUP transporter genes in purple osier willow (designated as SpuHAK1 to SpuHAK22) and examined their expression under K+ deficiency, drought, and salt stress conditions. Both transcriptomic and quantitative real-time PCR (qRT-PCR) analyses demonstrated that SpuHAKs were predominantly expressed in stems, and the expression levels of SpuHAK1, SpuHAK2, SpuHAK3, SpuHAK7, and SpuHAK8 were higher at the whole plant level, whereas SpuHAK9, SpuHAK11, SpuHAK20, and SpuHAK22 were hardly detected in tested tissues. In addition, both K+ deficiency and salt stress decreased the tissue K+ content, while drought increased the tissue K+ content in purple osier plant. Moreover, SpuHAK genes were differentially responsive to K+ deficiency, drought, and salt stresses in roots. K+ deficiency and salt stress mainly enhanced the expression level of responsive SpuHAK genes. Fifteen putative cis-acting regulatory elements, including the stress response, hormone response, circadian regulation, and nutrition and development, were identified in the promoter region of SpuHAK genes. Our findings provide a foundation for further functional characterization of KT/HAK/KUP transporters in forest trees and may be useful for breeding willow rootstocks that utilize potassium more efficiently.

scholarly journals Light Regulation of Two New Manganese Peroxidase-Encoding Genes in Trametes polyzona KU-RNW027

2020 ◽  
Vol 8 (6) ◽  
pp. 852
Author(s):  
Piyangkun Lueangjaroenkit ◽  
Emi Kunitake ◽  
Makiko Sakka ◽  
Tetsuya Kimura ◽  
Churapa Teerapatsakul ◽  
...  
Keyword(s):  
Blue Light ◽  
Enzyme Production ◽  
Molecular Mechanisms ◽  
Light Regulation ◽  
Ligninolytic Enzyme ◽  
Regulatory Elements ◽  
White Rot ◽  
White Rot Fungus ◽  
Gene Expressions ◽  
Encoding Genes

To better understand the light regulation of ligninolytic systems in Trametes polyzona KU-RNW027, ligninolytic enzymes-encoding genes were identified and analyzed to determine their transcriptional regulatory elements. Elements of light regulation were investigated in submerged culture. Three ligninolytic enzyme-encoding genes, mnp1, mnp2, and lac1, were found. Cloning of the genes encoding MnP1 and MnP2 revealed distinct deduced amino acid sequences with 90% and 86% similarity to MnPs in Lenzites gibbosa, respectively. These were classified as new members of short-type hybrid MnPs in subfamily A.2 class II fungal secretion heme peroxidase. A light responsive element (LRE), composed of a 5′-CCRCCC-3′ motif in both mnp promoters, is reported. Light enhanced MnP activity 1.5 times but not laccase activity. The mnp gene expressions under light condition increased 6.5- and 3.8-fold, respectively. Regulation of laccase gene expression by light was inconsistent with the absence of LREs in their promoter. Blue light did not affect gene expressions but impacted their stability. Reductions of MnP and laccase production under blue light were observed. The details of the molecular mechanisms underlying enzyme production in this white-rot fungus provide useful knowledge for wood degradation relative to illumination condition. These novel observations demonstrate the potential of enhancing ligninolytic enzyme production by this fungus for applications with an eco-friendly approach to bioremediation.

scholarly journals Modifying Carbohydrate Supply to Fruit during Development Changes the Composition and Flavour of Actinidia chinensis var. chinensis ‘Zesy002’ Kiwifruit

Plants ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 1328
Author(s):  
Danielle Le Lievre ◽  
Rachelle Anderson ◽  
Helen Boldingh ◽  
Janine Cooney ◽  
Richard Seelye ◽  
...  
Keyword(s):  
Soluble Sugar ◽  
Consumer Acceptance ◽  
Sugar Accumulation ◽  
Actinidia Chinensis ◽  
Ripe Fruit ◽  
High Carbohydrate ◽  
Control Fruit ◽  
Low Carbohydrate ◽  
Final Weight ◽  
Metabolite Accumulation

Consumer acceptance of fruit is determined by size, flavour and ripeness. In this study we investigated how altering the carbohydrate supply to Actinidia chinensis var. chinensis ‘Zesy002′ kiwifruit altered the balance between growth and accumulation of metabolites. Canes were phloem girdled and fruit thinned to a leaf-to-fruit ratio (L:F) of either 2 (Low carbohydrate) or 6 (High carbohydrate) at either 38 (Early) or 86 (Late) days after anthesis (DAA) and compared with ungirdled control canes with a L:F of 3. Fruit growth, metabolite accumulation, cytokinin concentrations and maturation were monitored and the sensory attributes of ripe fruit were assessed. The final weight of Early-High and Late-High carbohydrate fruit was 38% and 16% greater compared with control fruit. High carbohydrate fruit had increased starch,soluble sugar and cytokinin concentrations and fruit began to mature earlier and those with a Low carbohydrate had decreased concentrations and matured later compared with control fruit. Control fruit were described by consumers as more acidic and under-ripe compared with those from Early-High carbohydrate canes, but as sweeter than those from Low carbohydrate canes. This study showed that carbohydrate supply can have a major impact on the growth, sugar accumulation and maturity of ‘Zesy002′ fruit sinks.

scholarly journals Mapping chromatin accessibility and active regulatory elements reveals pathological mechanisms in human gliomas

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Karolina Stępniak ◽  
Magdalena A. Machnicka ◽  
Jakub Mieczkowski ◽  
Anna Macioszek ◽  
Bartosz Wojtaś ◽  
...  
Keyword(s):  
Gene Expression ◽  
Chromatin Structure ◽  
Molecular Mechanisms ◽  
Genome Mapping ◽  
Malignant Gliomas ◽  
Regulatory Elements ◽  
Chromatin Accessibility ◽  
Multiple Tumor ◽  
Genes Encoding ◽  
Methylation Patterns

AbstractChromatin structure and accessibility, and combinatorial binding of transcription factors to regulatory elements in genomic DNA control transcription. Genetic variations in genes encoding histones, epigenetics-related enzymes or modifiers affect chromatin structure/dynamics and result in alterations in gene expression contributing to cancer development or progression. Gliomas are brain tumors frequently associated with epigenetics-related gene deregulation. We perform whole-genome mapping of chromatin accessibility, histone modifications, DNA methylation patterns and transcriptome analysis simultaneously in multiple tumor samples to unravel epigenetic dysfunctions driving gliomagenesis. Based on the results of the integrative analysis of the acquired profiles, we create an atlas of active enhancers and promoters in benign and malignant gliomas. We explore these elements and intersect with Hi-C data to uncover molecular mechanisms instructing gene expression in gliomas.

Characterization of Nucleotide Binding ­Site-Encoding Genes in Sweetpotato, Ipomoea batatas(L.) Lam., and Their Response to Biotic and Abiotic Stresses

2021 ◽  
pp. 1-15
Author(s):  
Zengzhi Si ◽  
Yake Qiao ◽  
Kai Zhang ◽  
Zhixin Ji ◽  
Jinling Han
Keyword(s):  
Binding Site ◽  
Abiotic Stresses ◽  
Ipomoea Batatas ◽  
Expression Profiles ◽  
Nucleotide Binding ◽  
Regulatory Elements ◽  
Nucleotide Binding Site ◽  
Biotic And Abiotic Stresses ◽  
Encoding Genes

Sweetpotato, <i>Ipomoea batatas</i> (L.) Lam., is an important and widely grown crop, yet its production is affected severely by biotic and abiotic stresses. The nucleotide binding site (NBS)-encoding genes have been shown to improve stress tolerance in several plant species. However, the characterization of NBS-encoding genes in sweetpotato is not well-documented to date. In this study, a comprehensive analysis of NBS-encoding genes has been conducted on this species by using bioinformatics and molecular biology methods. A total of 315 NBS-encoding genes were identified, and 260 of them contained all essential conserved domains while 55 genes were truncated. Based on domain architectures, the 260 NBS-encoding genes were grouped into 6 distinct categories. Phylogenetic analysis grouped these genes into 3 classes: TIR, CC (I), and CC (II). Chromosome location analysis revealed that the distribution of NBS-encoding genes in chromosomes was uneven, with a number ranging from 1 to 34. Multiple stress-related regulatory elements were detected in the promoters, and the NBS-encoding genes’ expression profiles under biotic and abiotic stresses were obtained. According to the bioinformatics analysis, 9 genes were selected for RT-qPCR analysis. The results revealed that <i>IbNBS75</i>, <i>IbNBS219</i>, and <i>IbNBS256</i> respond to stem nematode infection; <i>Ib­NBS240</i>, <i>IbNBS90</i>, and <i>IbNBS80</i> respond to cold stress, while <i>IbNBS208</i>, <i>IbNBS71</i>, and <i>IbNBS159</i> respond to 30% PEG treatment. We hope these results will provide new insights into the evolution of NBS-encoding genes in the sweetpotato genome and contribute to the molecular breeding of sweetpotato in the future.

scholarly journals Identification of the specific long-noncoding RNAs involved in night-break mediated flowering retardation in Chenopodium quinoa

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Qi Wu ◽  
Yiming Luo ◽  
Xiaoyong Wu ◽  
Xue Bai ◽  
Xueling Ye ◽  
...  
Keyword(s):  
Expression Profiles ◽  
Functional Characterization ◽  
Chenopodium Quinoa ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Rna Seq ◽  
Short Day ◽  
Homologous Genes ◽  
The Relationship ◽  
Encoding Genes

Abstract Background Night-break (NB) has been proven to repress flowering of short-day plants (SDPs). Long-noncoding RNAs (lncRNAs) play key roles in plant flowering. However, investigation of the relationship between lncRNAs and NB responses is still limited, especially in Chenopodium quinoa, an important short-day coarse cereal. Results In this study, we performed strand-specific RNA-seq of leaf samples collected from quinoa seedlings treated by SD and NB. A total of 4914 high-confidence lncRNAs were identified, out of which 91 lncRNAs showed specific responses to SD and NB. Based on the expression profiles, we identified 17 positive- and 7 negative-flowering lncRNAs. Co-expression network analysis indicated that 1653 mRNAs were the common targets of both types of flowering lncRNAs. By mapping these targets to the known flowering pathways in model plants, we found some pivotal flowering homologs, including 2 florigen encoding genes (FT (FLOWERING LOCUS T) and TSF (TWIN SISTER of FT) homologs), 3 circadian clock related genes (EARLY FLOWERING 3 (ELF3), LATE ELONGATED HYPOCOTYL (LHY) and ELONGATED HYPOCOTYL 5 (HY5) homologs), 2 photoreceptor genes (PHYTOCHROME A (PHYA) and CRYPTOCHROME1 (CRY1) homologs), 1 B-BOX type CONSTANS (CO) homolog and 1 RELATED TO ABI3/VP1 (RAV1) homolog, were specifically affected by NB and competed by the positive and negative-flowering lncRNAs. We speculated that these potential flowering lncRNAs may mediate quinoa NB responses by modifying the expression of the floral homologous genes. Conclusions Together, the findings in this study will deepen our understanding of the roles of lncRNAs in NB responses, and provide valuable information for functional characterization in future.

scholarly journals Deciphering the Mounting Complexity of the p53 Regulatory Network in Correlation to Long Non-Coding RNAs (lncRNAs) in Ovarian Cancer

Cells ◽  
2020 ◽  
Vol 9 (3) ◽  
pp. 527 ◽  
Author(s):  
Sonali Pal ◽  
Manoj Garg ◽  
Amit Kumar Pandey
Keyword(s):  
Ovarian Cancer ◽  
Molecular Mechanisms ◽  
Human Cancer ◽  
Critical Role ◽  
Functional Characterization ◽  
Great Promise ◽  
Altered Expression ◽  
Disease Biology ◽  
Non Coding Rnas ◽  
Post Transcriptional Regulation

Amongst the various gynecological malignancies affecting female health globally, ovarian cancer is one of the predominant and lethal among all. The identification and functional characterization of long non-coding RNAs (lncRNAs) are made possible with the advent of RNA-seq and the advancement of computational logarithm in understanding human disease biology. LncRNAs can interact with deoxyribonucleic acid (DNA), ribonucleic acid (RNA), proteins and their combinations. Moreover, lncRNAs regulate orchestra of diverse functions including chromatin organization and transcriptional and post-transcriptional regulation. LncRNAs have conferred their critical role in key biological processes in human cancer including tumor initiation, proliferation, cell cycle, apoptosis, necroptosis, autophagy, and metastasis. The interwoven function of tumor-suppressor protein p53-linked lncRNAs in the ovarian cancer paradigm is of paramount importance. Several lncRNAs operate as p53 regulators or effectors and modulates a diverse array of functions either by participating in various signaling cascades or via interaction with different proteins. This review highlights the recent progress made in the identification of p53 associated lncRNAs while elucidating their molecular mechanisms behind the altered expression in ovarian cancer tumorigenesis. Moreover, the development of novel clinical and therapeutic strategies for targeting lncRNAs in human cancers harbors great promise.

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