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 Long non-coding RNAs in plants: emerging modulators of gene activity in development and stress responses

Planta ◽  
2020 ◽  
Vol 252 (5) ◽  
Author(s):  
Li Chen ◽  
Qian-Hao Zhu ◽  
Kerstin Kaufmann
Keyword(s):  
Stress Responses ◽  
Translational Regulation ◽  
Molecular Mechanisms ◽  
Functional Characterization ◽  
Reproductive Organs ◽  
Gene Activity ◽  
Protein Coding ◽  
Wide Range ◽  
Non Coding Rnas ◽  
Coding Potential

Abstract Main conclusion Long non-coding RNAs modulate gene activity in plant development and stress responses by various molecular mechanisms. Abstract Long non-coding RNAs (lncRNAs) are transcripts larger than 200 nucleotides without protein coding potential. Computational approaches have identified numerous lncRNAs in different plant species. Research in the past decade has unveiled that plant lncRNAs participate in a wide range of biological processes, including regulation of flowering time and morphogenesis of reproductive organs, as well as abiotic and biotic stress responses. LncRNAs execute their functions by interacting with DNA, RNA and protein molecules, and by modulating the expression level of their targets through epigenetic, transcriptional, post-transcriptional or translational regulation. In this review, we summarize characteristics of plant lncRNAs, discuss recent progress on understanding of lncRNA functions, and propose an experimental framework for functional characterization.

scholarly journals Characterization of PPTNs, a Cyanobacterial Phosphopantetheinyl Transferase from Nodularia spumigena NSOR10

2007 ◽  
Vol 189 (8) ◽  
pp. 3133-3139 ◽  
Author(s):  
J. N. Copp ◽  
A. A. Roberts ◽  
M. A. Marahiel ◽  
B. A. Neilan
Keyword(s):  
Acyl Carrier Protein ◽  
Functional Characterization ◽  
Bioactive Metabolites ◽  
Sequence Motifs ◽  
Phosphopantetheinyl Transferase ◽  
Carrier Proteins ◽  
Nodularia Spumigena ◽  
Conserved Sequence ◽  
Wide Range

ABSTRACT The phosphopantetheinyl transferases (PPTs) are a superfamily of essential enzymes required for the synthesis of a wide range of compounds, including fatty acids, polyketides, and nonribosomal peptide metabolites. These enzymes activate carrier proteins in specific biosynthetic pathways by transfer of a phosphopantetheinyl moiety. The diverse PPT superfamily can be divided into two families based on specificity and conserved sequence motifs. The first family is typified by the Escherichia coli acyl carrier protein synthase (AcpS), which is involved in fatty acid synthesis. The prototype of the second family is the broad-substrate-range PPT Sfp, which is required for surfactin biosynthesis in Bacillus subtilis. Most cyanobacteria do not encode an AcpS-like PPT, and furthermore, some of their Sfp-like PPTs belong to a unique phylogenetic subgroup defined by the PPTs involved in heterocyst differentiation. Here, we describe the first functional characterization of a cyanobacterial PPT based on a structural analysis and subsequent functional analysis of the Nodularia spumigena NSOR10 PPT. Southern hybridizations suggested that this enzyme may be the only PPT encoded in the N. spumigena NSOR10 genome. Expression and enzyme characterization showed that this PPT was capable of modifying carrier proteins resulting from both heterocyst glycoplipid synthesis and nodularin toxin synthesis. Cyanobacteria are a unique and vast source of bioactive metabolites; therefore, an understanding of cyanobacterial PPTs is important in order to harness the biotechnological potential of cyanobacterial natural products.

The role of phenylalanine hydroxylase in lipogenesis in the oleaginous fungus Mortierella alpina

Microbiology ◽  
2021 ◽  
Vol 167 (8) ◽  
Author(s):  
Hongchao Wang ◽  
Chunmei Wang ◽  
Weiwei Yuan ◽  
Haiqin Chen ◽  
Wenwei Lu ◽  
...  
Keyword(s):  
Fatty Acid Biosynthesis ◽  
Phenylalanine Hydroxylase ◽  
Transcript Level ◽  
Cellular Fatty Acid ◽  
Industrial Applications ◽  
Mortierella Alpina ◽  
Limiting Factor ◽  
Wide Range ◽  
Oleaginous Fungus

Phenylalanine hydroxylase (PAH) catalyses the irreversible hydroxylation of phenylalanine to tyrosine, which is the rate-limiting reaction in phenylalanine metabolism in animals. A variety of polyunsaturated fatty acids can be synthesized by the lipid-producing fungus Mortierella alpina, which has a wide range of industrial applications in the production of arachidonic acid. In this study, RNA interference (RNAi) with the gene PAH was used to explore the role of phenylalanine hydroxylation in lipid biosynthesis in M. alpina. Our results indicated that PAH knockdown decreased the PAH transcript level by approximately 55% and attenuated cellular fatty acid biosynthesis. Furthermore, the level of NADPH, which is a critical reducing agent and the limiting factor in lipogenesis, was decreased in response to PAH RNAi, in addition to the downregulated transcription of other genes involved in NADPH production. Our study indicates that PAH is part of an overall enzymatic and regulatory mechanism supplying NADPH required for lipogenesis in M. alpina.

scholarly journals TOR represses stress responses through global regulation of H3K27 trimethylation in plants

2021 ◽  
Author(s):  
Yihan Dong ◽  
Veli Vural Uslu ◽  
Alexandre Berr ◽  
Gaurav Singh ◽  
Csaba Papdi ◽  
...  
Keyword(s):  
Stress Responses ◽  
In Silico ◽  
In Silico Analysis ◽  
Tor Signaling ◽  
Chromatin Domains ◽  
Transcriptional Reprogramming ◽  
Wide Range ◽  
High Level ◽  
External Stimuli

Combinations of epigenetic modifications H3K4me3 and H3K27me3 implicate bistable feature which alternates between on and off state allowing rapid transcriptional changes upon external stimuli. Target of Rapamycin (TOR) functions as a central sensory hub to link a wide range of external stimuli to gene expression. However, the mechanisms underlying stimulus-specific transcriptional reprogramming by TOR remains elusive. Our in silico analysis in Arabidopsis demonstrates that TOR-repressed genes are associated with either bistable or silent chromatin domains. Both domains regulated by TOR signaling pathway are associated with high level of H3K27me3 deposited by CURLY LEAF (CLF) in specific context with LIKE HETEROCHROMATIN PROTEIN1 (LHP1). Chromatin remodeler SWI2/SNF2 ATPase BRAHMA (BRM) activates TOR-repressed genes only at bistable chromatin domains to rapidly induce biotic stress responses. Here we demonstrated both in silico and in vivo that TOR represses transcriptional stress responses through global maintenance of H3K27me3.

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 Transcriptional and functional characterization of the gene encoding acyl carrier protein in Bacillus subtilis

Microbiology ◽  
2010 ◽  
Vol 156 (2) ◽  
pp. 484-495 ◽  
Author(s):  
Mariano A. Martinez ◽  
Diego de Mendoza ◽  
Gustavo E. Schujman
Keyword(s):  
Bacillus Subtilis ◽  
Fatty Acid ◽  
Molecular Mechanisms ◽  
Fatty Acid Biosynthesis ◽  
Acyl Carrier Protein ◽  
Functional Characterization ◽  
Carrier Protein ◽  
Normal Fatty Acid ◽  
Gram Positive

Acyl carrier protein (ACP) is a universal and highly conserved carrier of acyl intermediates during fatty acid biosynthesis. The molecular mechanisms of regulation of the acpP structural gene, as well as the function of its gene product, are poorly characterized in Bacillus subtilis and other Gram-positive organisms. Here, we report that transcription of acpP takes place from two different promoters: PfapR and PacpP. Expression of acpP from PfapR is coordinated with a cluster of genes involved in lipid synthesis (the fapR operon); the operon consists of fapR-plsX-fabD-fabG-acpP. PacpP is located immediately upstream of the acpP coding sequence, and is necessary and sufficient for normal fatty acid synthesis. We also report that acpP is essential for growth and differentiation, and that ACP localizes in the mother-cell compartment of the sporangium during spore formation. These results provide the first detailed characterization of the expression of the ACP-encoding gene in a Gram-positive bacterium, and highlight the importance of this protein in B. subtilis physiology.

CDF transcription factors: plant regulators to deal with extreme environmental conditions

2020 ◽  
Vol 71 (13) ◽  
pp. 3803-3815 ◽  
Author(s):  
Begoña Renau-Morata ◽  
Laura Carrillo ◽  
Jose Dominguez-Figueroa ◽  
Jesús Vicente-Carbajosa ◽  
Rosa V Molina ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Plant Species ◽  
Stress Responses ◽  
Environmental Conditions ◽  
Functional Characterization ◽  
Plant Responses ◽  
Large Set ◽  
Cell Integrity ◽  
Wide Range ◽  
Adverse Environmental Conditions

Abstract In terrestrial environments, water and nutrient availabilities and temperature conditions are highly variable, and especially in extreme environments limit survival, growth, and reproduction of plants. To sustain growth and maintain cell integrity under unfavourable environmental conditions, plants have developed a variety of biochemical and physiological mechanisms, orchestrated by a large set of stress-responsive genes and a complex network of transcription factors. Recently, cycling DOF factors (CDFs), a group of plant-specific transcription factors (TFs), were identified as components of the transcriptional regulatory networks involved in the control of abiotic stress responses. The majority of the members of this TF family are activated in response to a wide range of adverse environmental conditions in different plant species. CDFs regulate different aspects of plant growth and development such as photoperiodic flowering-time control and root and shoot growth. While most of the functional characterization of CDFs has been reported in Arabidopsis, recent data suggest that their diverse roles extend to other plant species. In this review, we integrate information related to structure and functions of CDFs in plants, with special emphasis on their role in plant responses to adverse environmental conditions.

scholarly journals Genome-Wide Identification and Function of Aquaporin Genes During Dormancy and Sprouting Periods of Kernel-Using Apricot (Prunus armeniaca L.)

2021 ◽  
Vol 12 ◽  
Author(s):  
Shaofeng Li ◽  
Lin Wang ◽  
Yaoxiang Zhang ◽  
Gaopu Zhu ◽  
Xuchun Zhu ◽  
...  
Keyword(s):  
Cold Stress ◽  
Cold Tolerance ◽  
Resistance Genes ◽  
Stress Responses ◽  
Expression Patterns ◽  
Functional Characterization ◽  
Regulatory Elements ◽  
Prunus Armeniaca ◽  
Protein Accumulation ◽  
Flower Buds

Aquaporins (AQPs) are essential channel proteins that play a major role in plant growth and development, regulate plant water homeostasis, and transport uncharged solutes across biological membranes. In this study, 33 AQP genes were systematically identified from the kernel-using apricot (Prunus armeniaca L.) genome and divided into five subfamilies based on phylogenetic analyses. A total of 14 collinear blocks containing AQP genes between P. armeniaca and Arabidopsis thaliana were identified by synteny analysis, and 30 collinear blocks were identified between P. armeniaca and P. persica. Gene structure and conserved functional motif analyses indicated that the PaAQPs exhibit a conserved exon-intron pattern and that conserved motifs are present within members of each subfamily. Physiological mechanism prediction based on the aromatic/arginine selectivity filter, Froger’s positions, and three-dimensional (3D) protein model construction revealed marked differences in substrate specificity between the members of the five subfamilies of PaAQPs. Promoter analysis of the PaAQP genes for conserved regulatory elements suggested a greater abundance of cis-elements involved in light, hormone, and stress responses, which may reflect the differences in expression patterns of PaAQPs and their various functions associated with plant development and abiotic stress responses. Gene expression patterns of PaAQPs showed that PaPIP1-3, PaPIP2-1, and PaTIP1-1 were highly expressed in flower buds during the dormancy and sprouting stages of P. armeniaca. A PaAQP coexpression network showed that PaAQPs were coexpressed with 14 cold resistance genes and with 16 cold stress-associated genes. The expression pattern of 70% of the PaAQPs coexpressed with cold stress resistance genes was consistent with the four periods [Physiological dormancy (PD), ecological dormancy (ED), sprouting period (SP), and germination stage (GS)] of flower buds of P. armeniaca. Detection of the transient expression of GFP-tagged PaPIP1-1, PaPIP2-3, PaSIP1-3, PaXIP1-2, PaNIP6-1, and PaTIP1-1 revealed that the fusion proteins localized to the plasma membrane. Predictions of an A. thaliana ortholog-based protein–protein interaction network indicated that PaAQP proteins had complex relationships with the cold tolerance pathway, PaNIP6-1 could interact with WRKY6, PaTIP1-1 could interact with TSPO, and PaPIP2-1 could interact with ATHATPLC1G. Interestingly, overexpression of PaPIP1-3 and PaTIP1-1 increased the cold tolerance of and protein accumulation in yeast. Compared with wild-type plants, PaPIP1-3- and PaTIP1-1-overexpressing (OE) Arabidopsis plants exhibited greater tolerance to cold stress, as evidenced by better growth and greater antioxidative enzyme activities. Overall, our study provides insights into the interaction networks, expression patterns, and functional analysis of PaAQP genes in P. armeniaca L. and contributes to the further functional characterization of PaAQPs.

scholarly journals Genome-wide characterization and expression analysis suggested diverse functions of the mechanosensitive channel of small conductance-like (MSL) genes in cereal crops

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Amandeep Kaur ◽  
Mehak Taneja ◽  
Shivi Tyagi ◽  
Alok Sharma ◽  
Kashmir Singh ◽  
...  
Keyword(s):  
Expression Analysis ◽  
Stress Responses ◽  
Developmental Stages ◽  
Functional Characterization ◽  
Aegilops Tauschii ◽  
Defense Responses ◽  
Regulatory Elements ◽  
Mechanical Stimuli ◽  
Altered Expression ◽  
Genome Wide

Abstract Mechanosensitive ion channels are pore-forming transmembrane proteins that allow ions to move down their electrochemical gradient in response to mechanical stimuli. They participate in many plant developmental processes including the maintenance of plastid shape, pollen tube growth, etc. Herein, a total of 11, 10, 6, 30, 9, and 8 MSL genes were identified in Aegilops tauschii, Hordeum vulgare, Sorghum bicolor, Triticum aestivum, Triticum urartu, and Zea mays, respectively. These genes were located on various chromosomes of their respective cereal, while MSLs of T. urartu were found on scaffolds. The phylogenetic analysis, subcellular localization, and sequence homology suggested clustering of MSLs into two classes. These genes consisted of cis-regulatory elements related to growth and development, responsive to light, hormone, and stress. Differential expression of various MSL genes in tissue developmental stages and stress conditions revealed their precise role in development and stress responses. Altered expression during CaCl2 stress suggested their role in Ca2+ homeostasis and signaling. The co-expression analysis suggested their interactions with other genes involved in growth, defense responses etc. A comparative expression profiling of paralogous genes revealed either retention of function or pseudo-functionalization. The present study unfolded various characteristics of MSLs in cereals, which will facilitate their in-depth functional characterization in future studies.

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