scholarly journals Identification of a Unique Type of Isoflavone O-Methyltransferase, GmIOMT1, Based on Multi-Omics Analysis of Soybean under Biotic Stress

2020 ◽  
Vol 61 (11) ◽  
pp. 1974-1985
Author(s):  
Kai Uchida ◽  
Yuji Sawada ◽  
Koji Ochiai ◽  
Muneo Sato ◽  
Jun Inaba ◽  
...  
Keyword(s):  
Biotic Stress ◽  
Biosynthetic Pathway ◽  
Metabolome Analysis ◽  
Gene Encoding ◽  
Unique Type ◽  
Soybean Seedlings ◽  
Genes Encoding ◽  
Liquid Chromatography Tandem Mass ◽  
Key Enzyme ◽  
Fungal Inoculation

Abstract Isoflavonoids are commonly found in leguminous plants. Glycitein is one of the isoflavones produced by soybean. The genes encoding the enzymes in the isoflavone biosynthetic pathway have mostly been identified and characterized. However, the gene(s) for isoflavone O-methyltransferase (IOMT), which catalyzes the last step of glycitein biosynthesis, has not yet been identified. In this study, we conducted multi-omics analyses of fungal-inoculated soybean and indicated that glycitein biosynthesis was induced in response to biotic stress. Moreover, we identified a unique type of IOMT, which participates in glycitein biosynthesis. Soybean seedlings were inoculated with Aspergillus oryzae or Rhizopus oligosporus and sampled daily for 8 d. Multi-omics analyses were conducted using liquid chromatography–tandem mass spectrometry and RNA sequencing. Metabolome analysis revealed that glycitein derivatives increased following fungal inoculation. Transcriptome co-expression analysis identified two candidate IOMTs that were co-expressed with the gene encoding flavonoid 6-hydroxylase (F6H), the key enzyme in glycitein biosynthesis. The enzymatic assay of the two IOMTs using respective recombinant proteins showed that one IOMT, named as GmIOMT1, produced glycitein. Unlike other IOMTs, GmIOMT1 belongs to the cation-dependent OMT family and exhibited the highest activity with Zn2+ among cations tested. Moreover, we demonstrated that GmIOMT1 overexpression increased the levels of glycitein derivatives in soybean hairy roots when F6H was co-expressed. These results strongly suggest that GmIOMT1 participates in inducing glycitein biosynthesis in response to biotic stress.

scholarly journals Crosstalk among Indoleamines, Neuropeptides and JH/20E in Regulation of Reproduction in the American Cockroach, Periplaneta americana

Insects ◽  
2020 ◽  
Vol 11 (3) ◽  
pp. 155 ◽  
Author(s):  
A. S. M. Kamruzzaman ◽  
Azam Mikani ◽  
Amr A. Mohamed ◽  
Azza M. Elgendy ◽  
Makio Takeda
Keyword(s):  
Oocyte Maturation ◽  
Biosynthetic Pathway ◽  
Periplaneta Americana ◽  
American Cockroach ◽  
Second Step ◽  
Double Stranded Rna ◽  
Vitellogenin Receptor ◽  
Genes Encoding ◽  
Key Enzyme ◽  
Indoleamine Metabolism

Although the regulation of vitellogenesis in insects has been mainly discussed in terms of ‘classical’ lipid hormones, juvenile hormone (JH), and 20-hydroxyecdysone (20E), recent data support the notion that this process must be adjusted in harmony with a nutritional input/reservoir and involvement of certain indoleamines and neuropeptides in regulation of such process. This study focuses on crosstalks among these axes, lipid hormones, monoamines, and neuropeptides in regulation of vitellogenesis in the American cockroach Periplaneta americana with novel aspects in the roles of arylalkylamine N-acetyltransferase (aaNAT), a key enzyme in indoleamine metabolism, and the enteroendocrine peptides; crustacean cardioactive peptide (CCAP) and short neuropeptide F (sNPF). Double-stranded RNA against aaNAT (dsRNAaaNAT) was injected into designated-aged females and the effects were monitored including the expressions of aaNAT itself, vitellogenin 1 and 2 (Vg1 and Vg2) and the vitellogenin receptor (VgR) mRNAs, oocyte maturation and changes in the hemolymph peptide concentrations. Effects of peptides application and 20E were also investigated. Injection of dsRNAaaNAT strongly suppressed oocyte maturation, transcription of Vg1, Vg2, VgR, and genes encoding JH acid- and farnesoate O-methyltransferases (JHAMT and FAMeT, respectively) acting in the JH biosynthetic pathway. However, it did not affect hemolymph concentrations of CCAP and sNPF. Injection of CCAP stimulated, while sNPF suppressed oocyte maturation and Vgs/VgR transcription, i.e., acting as allatomedins. Injection of CCAP promoted, while sNPF repressed ecdysteroid (20E) synthesis, particularly at the second step of Vg uptake. 20E also affected the JH biosynthetic pathway and Vg/VgR synthesis. The results revealed that on the course of vitellogenesis, JH- and 20E-mediated regulation occurs downstream to indoleamines- and peptides-mediated regulations. Intricate mutual interactions of these regulatory routes must orchestrate reproduction in this species at the highest potency.

scholarly journals Occurrence, phylogeny and evolution of ribulose-1,5-bisphosphate carboxylase/oxygenase genes in obligately chemolithoautotrophic sulfur-oxidizing bacteria of the genera Thiomicrospira and Thioalkalimicrobium

Microbiology ◽  
2006 ◽  
Vol 152 (7) ◽  
pp. 2159-2169 ◽  
Author(s):  
Tatjana P. Tourova ◽  
Elizaveta M. Spiridonova ◽  
Ivan A. Berg ◽  
Boris B. Kuznetsov ◽  
Dimitry Yu. Sorokin
Keyword(s):  
16S Rrna ◽  
Large Subunit ◽  
Gene Encoding ◽  
Bisphosphate Carboxylase ◽  
Phylogenetic Cluster ◽  
New Family ◽  
Genes Encoding ◽  
Key Enzyme ◽  
Sulfur Oxidizing ◽  
Phylogeny And Evolution

The occurrence of the different genes encoding ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO), the key enzyme of the Calvin–Benson–Bassham cycle of autotrophic CO2 fixation, was investigated in the members of the genus Thiomicrospira and the relative genus Thioalkalimicrobium, all obligately chemolithoautotrophic sulfur-oxidizing Gammaproteobacteria. The cbbL gene encoding the ‘green-like’ form I RubisCO large subunit was found in all analysed species, while the cbbM gene encoding form II RubisCO was present only in Thiomicrospira species. Furthermore, species belonging to the Thiomicrospira crunogena 16S rRNA-based phylogenetic cluster also possessed two genes of green-like form I RubisCO, cbbL-1 and cbbL-2. Both 16S-rRNA- and cbbL-based phylogenies of the Thiomicrospira–Thioalkalimicrobium–Hydrogenovibrio group were congruent, thus supporting its monophyletic origin. On the other hand, it also supports the necessity for taxonomy reorganization of this group into a new family with four genera.

scholarly journals Purification, Overproduction, and Partial Characterization of β-RFAP Synthase, a Key Enzyme in the Methanopterin Biosynthesis Pathway†

2002 ◽  
Vol 184 (16) ◽  
pp. 4442-4448 ◽  
Author(s):  
Joseph W. Scott ◽  
Madeline E. Rasche
Keyword(s):  
Biosynthetic Pathway ◽  
Methanogenic Archaea ◽  
Methylotrophic Bacteria ◽  
Methylobacterium Extorquens ◽  
Gene Encoding ◽  
Methanosarcina Thermophila ◽  
Inorganic Pyrophosphate ◽  
Sulfate Reducing ◽  
Key Enzyme

ABSTRACT Methanopterin is a folate analog involved in the C1 metabolism of methanogenic archaea, sulfate-reducing archaea, and methylotrophic bacteria. Although a pathway for methanopterin biosynthesis has been described in methanogens, little is known about the enzymes and genes involved in the biosynthetic pathway. The enzyme β-ribofuranosylaminobenzene 5′-phosphate synthase (β-RFAP synthase) catalyzes the first unique step to be identified in the pathway of methanopterin biosynthesis, namely, the condensation of p-aminobenzoic acid with phosphoribosylpyrophosphate to form β-RFAP, CO2, and inorganic pyrophosphate. The enzyme catalyzing this reaction has not been purified to homogeneity, and the gene encoding β-RFAP synthase has not yet been identified. In the present work, we report on the purification to homogeneity of β-RFAP synthase. The enzyme was purified from the methane-producing archaeon Methanosarcina thermophila, and the N-terminal sequence of the protein was used to identify corresponding genes from several archaea, including the methanogen Methanococcus jannaschii and the sulfate-reducing archaeon Archaeoglobus fulgidus. The putative β-RFAP synthase gene from A. fulgidus was expressed in Escherichia coli, and the enzymatic activity of the recombinant gene product was verified. A BLAST search using the deduced amino acid sequence of the β-RFAP synthase gene identified homologs in additional archaea and in a gene cluster required for C1 metabolism by the bacterium Methylobacterium extorquens. The identification of a gene encoding a potential β-RFAP synthase in M. extorquens is the first report of a putative methanopterin biosynthetic gene found in the Bacteria and provides evidence that the pathways of methanopterin biosynthesis in Bacteria and Archaea are similar.

scholarly journals Transcriptome and metabolome analysis to reveal major genes of saikosaponin biosynthesis in Bupleurum chinense

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Yilian He ◽  
Hua Chen ◽  
Jun Zhao ◽  
Yuxia Yang ◽  
Bin Yang ◽  
...  
Keyword(s):  
Medicinal Plant ◽  
Biosynthetic Pathway ◽  
Gene Families ◽  
Integrated Analysis ◽  
Cytochrome P450 Enzymes ◽  
Bioactive Constituents ◽  
Metabolome Analysis ◽  
Coa Transferase ◽  
Liquid Chromatography Tandem Mass ◽  
Coa Reductase

Abstract Background Bupleurum chinense DC. is a widely used traditional Chinese medicinal plant. Saikosaponins are the major bioactive constituents of B. chinense, but relatively little is known about saikosaponin biosynthesis. In the present study, we performed an integrated analysis of metabolic composition and the expressed genes involved in saikosaponin biosynthetic pathways among four organs (the root, flower, stem, and leaf) of B. chinense to discover the genes related to the saikosaponin biosynthetic pathway. Results Transcript and metabolite profiles were generated through high-throughput RNA-sequencing (RNA-seq) data analysis and liquid chromatography tandem mass spectrometry, respectively. Evaluation of saikosaponin contents and transcriptional changes showed 152 strong correlations (P < 0.05) over 3 compounds and 77 unigenes. These unigenes belonged to eight gene families: the acetoacetyl CoA transferase (AACT) (6), HMG-CoA synthase (HMGS) (2), HMG-CoA reductase (HMGR) (2), mevalonate diphosphate decarboxylase (MVD) (1), 1-deoxy-D-xylulose-5-phosphate synthase (DXS) (3), farnesyl diphosphate synthase (FPPS) (11), β-amyrin synthase (β-AS) (13) and cytochrome P450 enzymes (P450s) (39) families. Conclusions Our results investigated the diversity of the saikosaponin triterpene biosynthetic pathway in the roots, stems, leaves and flowers of B. chinese by integrated transcriptomic and metabolomic analysis, implying that manipulation of P450s genes such as Bc95697 and Bc35434 might improve saikosaponin biosynthesis. This is a good candidate for the genetic improvement of this important medicinal plant.

scholarly journals Inactivation of the ampDE Operon Increases Transcription of algD and Affects Morphology and Encystment of Azotobacter vinelandii

2000 ◽  
Vol 182 (17) ◽  
pp. 4829-4835 ◽  
Author(s):  
Cinthia Núñez ◽  
Soledad Moreno ◽  
Luis Cárdenas ◽  
Gloria Soberón-Chávez ◽  
Guadalupe Espín
Keyword(s):  
Escherichia Coli ◽  
Biosynthetic Pathway ◽  
Azotobacter Vinelandii ◽  
Transmembrane Protein ◽  
Nucleotide Sequencing ◽  
Insertion Mutant ◽  
Gene Encoding ◽  
Alginate Production ◽  
Key Enzyme

ABSTRACT Transcription of algD, encoding GDP-mannose dehydrogenase, the key enzyme in the alginate biosynthetic pathway, is highly regulated in Azotobacter vinelandii. We describe here the characterization of a Tn5 insertion mutant (AC28) which shows a higher level of expression of analgD::lacZ fusion. AC28 cells were morphologically abnormal and unable to encyst. The cloning and nucleotide sequencing of the Tn5-disrupted locus in AC28 revealed an operon homologous to the Escherichia coli ampDEoperon. Tn5 was located within the ampD gene, encoding a cytosolicN-acetyl-anhydromuramyl-l-alanine amidase that participates in the intracellular recycling of peptidoglycan fragments. The ampE gene encodes a transmembrane protein, but the function of the protein is not known. We constructed strains carryingampD or ampE mutations and one with anampDE deletion. The strain with a deletion of theampDE operon showed a phenotype similar to that of mutant AC28. The present work demonstrates that both alginate production and bacterial encystment are greatly influenced by the bacterial ability to recycle its cell wall.

scholarly journals Genome Mining Reveals Two Missing CrtP and AldH Enzymes in the C30 Carotenoid Biosynthesis Pathway in Planococcus faecalis AJ003T

Molecules ◽  
2020 ◽  
Vol 25 (24) ◽  
pp. 5892
Author(s):  
Jun Ho Lee ◽  
Jin Won Kim ◽  
Pyung Cheon Lee
Keyword(s):  
Escherichia Coli ◽  
Biosynthetic Pathway ◽  
Genome Mining ◽  
Carotenoid Biosynthesis ◽  
Biosynthesis Pathway ◽  
Gene Encoding ◽  
A Genome ◽  
Genes Encoding ◽  
Carotenoid Biosynthesis Pathway ◽  
Carotenoid Pathway

Planococcus faecalis AJ003T produces glycosyl-4,4′-diaponeurosporen-4′-ol-4-oic acid as its main carotenoid. Five carotenoid pathway genes were presumed to be present in the genome of P. faecalis AJ003T; however, 4,4-diaponeurosporene oxidase (CrtP) was non-functional, and a gene encoding aldehyde dehydrogenase (AldH) was not identified. In the present study, a genome mining approach identified two missing enzymes, CrtP2 and AldH2454, in the glycosyl-4,4′-diaponeurosporen-4′-ol-4-oic acid biosynthetic pathway. Moreover, CrtP2 and AldH enzymes were functional in heterologous Escherichia coli and generated two carotenoid aldehydes (4,4′-diapolycopene-dial and 4,4′-diaponeurosporene-4-al) and two carotenoid carboxylic acids (4,4′-diaponeurosporenoic acid and 4,4′-diapolycopenoic acid). Furthermore, the genes encoding CrtP2 and AldH2454 were located at a distance the carotenoid gene cluster of P. faecalis.

Characterization of three genes encoding enzymes of the folate biosynthetic pathway in Plasmodium falciparum

Parasitology ◽  
2001 ◽  
Vol 122 (1) ◽  
pp. 1-13 ◽  
Author(s):  
C.-S. LEE ◽  
E. SALCEDO ◽  
Q. WANG ◽  
P. WANG ◽  
P.F.G. SIMS ◽  
...  
Keyword(s):  
Biosynthetic Pathway ◽  
Serine Hydroxymethyltransferase ◽  
Gtp Cyclohydrolase I ◽  
Gene Encoding ◽  
New Genes ◽  
Isolation And Characterization ◽  
Genes Encoding ◽  
Antifolate Drugs ◽  
Dihydroneopterin Aldolase

Although the folate metabolic pathway in malaria parasites is a major chemotherapeutic target, resistance to currently available antifolate drugs is an increasing problem. This pathway, however, includes a number of enzymes that, to date, have not been characterized despite their potential for clinical exploitation. As a step towards evaluation of additional targets in this pathway, we report the isolation and characterization of 3 new genes that encode homologues of GTP cyclohydrolase I (GTP-CH), dihydrofolate synthase/folylpolyglutamate synthase (DHFS/FPGS) and serine hydroxymethyltransferase (SHMT). The genes encoding GTP-CH and SHMT are unambiguously assigned to chromosome 12, while that for DHFS/FPGS is tentatively assigned to chromosome 13. All 3 genes are expressed in blood-stage parasites, yielding transcripts of which only ca 60–70% is accounted for by coding sequence. All 3 of the proteins predicted to be encoded by these genes display sequence differences compared to the human host homologues that may be of functional significance. These data bring the complement of cloned genes that encode activities in the pathway to seven, leaving only the gene encoding dihydroneopterin aldolase (DHNA) to be identified in the route from GTP to folate synthesis and folate turnover in the thymidylate cycle.

scholarly journals Regulation of Alginate Biosynthesis inPseudomonas syringae pv. syringae

1999 ◽  
Vol 181 (11) ◽  
pp. 3478-3485 ◽  
Author(s):  
Mohamed K. Fakhr ◽  
Alejandro Peñaloza-Vázquez ◽  
Ananda M. Chakrabarty ◽  
Carol L. Bender
Keyword(s):  
Sigma Factor ◽  
Promoter Region ◽  
Biosynthetic Pathway ◽  
Response Regulator ◽  
Consensus Sequence ◽  
Gene Encoding ◽  
Environmental Signals ◽  
Alginate Production ◽  
Key Enzyme ◽  
Alginate Biosynthesis

ABSTRACT Both Pseudomonas aeruginosa and the phytopathogenP. syringae produce the exopolysaccharide alginate. However, the environmental signals that trigger alginate gene expression in P. syringae are different from those inP. aeruginosa with copper being a major signal in P. syringae. In P. aeruginosa, the alternate sigma factor encoded by algT (ς22) and the response regulator AlgR1 are required for transcription of algD, a gene which encodes a key enzyme in the alginate biosynthetic pathway. In the present study, we cloned and characterized the gene encoding AlgR1 from P. syringae. The deduced amino acid sequence of AlgR1 from P. syringae showed 86% identity to its P. aeruginosa counterpart. Sequence analysis of the region flankingalgR1 in P. syringae revealed the presence ofargH, algZ, and hemC in an arrangement virtually identical to that reported in P. aeruginosa. An algR1 mutant, P. syringaeFF5.32, was defective in alginate production but could be complemented when algR1 was expressed in trans. ThealgD promoter region in P. syringae(PsalgD) was also characterized and shown to diverge significantly from the algD promoter in P. aeruginosa. Unlike P. aeruginosa, algR1was not required for the transcription of algD in P. syringae, and PsalgD lacked the consensus sequence recognized by AlgR1. However, both the algD andalgR1 upstream regions in P. syringae contained the consensus sequence recognized by ς22, suggesting thatalgT is required for transcription of both genes.

Water Stress Enhances Expression of Genes Encoding Plastid Terminal Oxidase and Key Components of Chlororespiration and Alternative Respiration in Soybean Seedlings

2014 ◽  
Vol 69 (7-8) ◽  
pp. 300-308 ◽  
Author(s):  
Xin Sun ◽  
Cui-Qin Yang ◽  
Tao Wen ◽  
Fu-Chun Zeng ◽  
Qiang Wang ◽  
...  
Keyword(s):  
Water Stress ◽  
Water Deficit Stress ◽  
Terminal Oxidase ◽  
Alternative Respiration ◽  
Gene Encoding ◽  
Transcript Levels ◽  
Soybean Seedlings ◽  
Expression Of Genes ◽  
Genes Encoding ◽  
Plastid Terminal Oxidase

Plastid terminal oxidase (PTOX) is a plastid-localized plastoquinone (PQ) oxidase in plants. It functions as the terminal oxidase of chlororespiration, and has the potential ability to regulate the redox state of the PQ pool. Expression of the PTOX gene was up-regulated in soybean seedlings after exposure to water deficit stress for 6 h. Concomitantly expression of the NDH-H gene, encoding a component of the NADPH dehydrogenase (NDH) complex which is a key component of both chlororespiration and NDH-dependent cyclic electron transfer (CET), was also up-regulated. Transcript levels of the proton gradient regulation (PGR5) gene, which encodes an essential component of the PGR5-dependent CET, were not affected by water stress, while the expression of the alternative oxidase (AOX1) gene, which encodes a terminal oxidase of alternative respiration in mitochondria, was also up-regulated under water stress. Therefore, our results indicate that water stress induced the up-regulation of genes encoding key components of chlororespiration and alternative respiration. Transcript levels of the AOX1 gene began to increase in response to water stress before those of PTOX suggesting that alternative respiration may react faster to water stress than chlororespiration.

scholarly journals Effects of a novel variant of the yeast γ-glutamyl kinase Pro1 on its enzymatic activity and sake brewing

2020 ◽  
Vol 47 (9-10) ◽  
pp. 715-723 ◽  
Author(s):  
Naoyuki Murakami ◽  
Atsushi Kotaka ◽  
Shota Isogai ◽  
Keiko Ashida ◽  
Akira Nishimura ◽  
...  
Keyword(s):  
Feedback Inhibition ◽  
Novel Mutation ◽  
Alcoholic Beverage ◽  
Practical Method ◽  
Metabolome Analysis ◽  
Gene Encoding ◽  
Yeast Strains ◽  
Novel Variant ◽  
Key Enzyme ◽  
Proline Overproduction

Abstract Sake is a traditional Japanese alcoholic beverage brewed with the yeast Saccharomyces cerevisiae. Sake taste is affected by sugars, organic acids, and amino acids. We previously isolated mutants resistant to the proline analogue azetidine-2-carboxylate derived from a diploid sake yeast strain. Some of the mutants produced a greater amount of proline in the brewed sake. One of them (strain K-9-AZC) carried a novel mutation in the PRO1 gene encoding the Gln79His variant of the γ-glutamyl kinase Pro1, a key enzyme in proline biosynthesis in S. cerevisiae. This mutation resulted in extreme desensitization to feedback inhibition by proline, leading to proline overproduction. Interestingly, sake brewed with K-9-AZC contained 3.7-fold more proline, but only 25% less succinate than sake brewed with the parent strain. Metabolome analysis suggests that the decrease in succinate was attributable to a lower level of 2-oxoglutarate, which is converted into glutamate. The approach here could be a practical method for breeding of yeast strains involved in the diversity of sake taste.

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