Journal articles: 'Specialized metabolite'

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Panda, Sayantan, Yana Kazachkova, and Asaph Aharoni. "Catch-22 in specialized metabolism: balancing defense and growth." Journal of Experimental Botany 72, no. 17 (July 22, 2021): 6027–41. http://dx.doi.org/10.1093/jxb/erab348.

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Abstract Plants are unsurpassed biochemists that synthesize a plethora of molecules in response to an ever-changing environment. The majority of these molecules, considered as specialized metabolites, effectively protect the plant against pathogens and herbivores. However, this defense most probably comes at a great expense, leading to reduction of growth (known as the ‘growth–defense trade-off’). Plants employ several strategies to reduce the high metabolic costs associated with chemical defense. Production of specialized metabolites is tightly regulated by a network of transcription factors facilitating its fine-tuning in time and space. Multifunctionality of specialized metabolites—their effective recycling system by re-using carbon, nitrogen, and sulfur, thus re-introducing them back to the primary metabolite pool—allows further cost reduction. Spatial separation of biosynthetic enzymes and their substrates, and sequestration of potentially toxic substances and conversion to less toxic metabolite forms are the plant’s solutions to avoid the detrimental effects of metabolites they produce as well as to reduce production costs. Constant fitness pressure from herbivores, pathogens, and abiotic stressors leads to honing of specialized metabolite biosynthesis reactions to be timely, efficient, and metabolically cost-effective. In this review, we assess the costs of production of specialized metabolites for chemical defense and the different plant mechanisms to reduce the cost of such metabolic activity in terms of self-toxicity and growth.

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Rai, Megha, Amit Rai, Tetsuya Mori, Ryo Nakabayashi, Manami Yamamoto, Michimi Nakamura, Hideyuki Suzuki, Kazuki Saito, and Mami Yamazaki. "Gene-Metabolite Network Analysis Revealed Tissue-Specific Accumulation of Therapeutic Metabolites in Mallotus japonicus." International Journal of Molecular Sciences 22, no. 16 (August 17, 2021): 8835. http://dx.doi.org/10.3390/ijms22168835.

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Mallotus japonicus is a valuable traditional medicinal plant in East Asia for applications as a gastrointestinal drug. However, the molecular components involved in the biosynthesis of bioactive metabolites have not yet been explored, primarily due to a lack of omics resources. In this study, we established metabolome and transcriptome resources for M. japonicus to capture the diverse metabolite constituents and active transcripts involved in its biosynthesis and regulation. A combination of untargeted metabolite profiling with data-dependent metabolite fragmentation and metabolite annotation through manual curation and feature-based molecular networking established an overall metabospace of M. japonicus represented by 2129 metabolite features. M. japonicus de novo transcriptome assembly showed 96.9% transcriptome completeness, representing 226,250 active transcripts across seven tissues. We identified specialized metabolites biosynthesis in a tissue-specific manner, with a strong correlation between transcripts expression and metabolite accumulations in M. japonicus. The correlation- and network-based integration of metabolome and transcriptome datasets identified candidate genes involved in the biosynthesis of key specialized metabolites of M. japonicus. We further used phylogenetic analysis to identify 13 C-glycosyltransferases and 11 methyltransferases coding candidate genes involved in the biosynthesis of medicinally important bergenin. This study provides comprehensive, high-quality multi-omics resources to further investigate biological properties of specialized metabolites biosynthesis in M. japonicus.

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Chen, Si, Jun Lin, Huihui Liu, Zhihong Gong, Xiaxia Wang, Meihong Li, Asaph Aharoni, Zhenbiao Yang, and Xiaomin Yu. "Insights into Tissue-specific Specialized Metabolism in Tieguanyin Tea Cultivar by Untargeted Metabolomics." Molecules 23, no. 7 (July 21, 2018): 1817. http://dx.doi.org/10.3390/molecules23071817.

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Tea plants produce extremely diverse and abundant specialized metabolites, the types and levels of which are developmentally and environmentally regulated. However, little is known about how developmental cues affect the synthesis of many of these molecules. In this study, we conducted a comparative profiling of specialized metabolites from six different tissues in a premium oolong tea cultivar, Tieguanyin, which is gaining worldwide popularity due to its uniquely rich flavors and health benefits. UPLC-QTOF MS combined with multivariate analyses tentatively identified 68 metabolites belonging to 11 metabolite classes, which exhibited sharp variations among tissues. Several metabolite classes, such as flavonoids, alkaloids, and hydroxycinnamic acid amides were detected predominantly in certain plant tissues. In particular, tricoumaroyl spermidine and dicoumaroyl putrescine were discovered as unique tea flower metabolites. This study offers novel insights into tissue-specific specialized metabolism in Tieguanyin, which provides a good reference point to explore gene-metabolite relationships in this cultivar.

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Nguyen, Don D., Veronika Saharuka, Vitaly Kovalev, Lachlan Stuart, Massimo Del Prete, Kinga Lubowiecka, René De Mot, Vittorio Venturi, and Theodore Alexandrov. "Facilitating Imaging Mass Spectrometry of Microbial Specialized Metabolites with METASPACE." Metabolites 11, no. 8 (July 23, 2021): 477. http://dx.doi.org/10.3390/metabo11080477.

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Metabolite annotation from imaging mass spectrometry (imaging MS) data is a difficult undertaking that is extremely resource intensive. Here, we adapted METASPACE, cloud software for imaging MS metabolite annotation and data interpretation, to quickly annotate microbial specialized metabolites from high-resolution and high-mass accuracy imaging MS data. Compared with manual ion image and MS1 annotation, METASPACE is faster and, with the appropriate database, more accurate. We applied it to data from microbial colonies grown on agar containing 10 diverse bacterial species and showed that METASPACE was able to annotate 53 ions corresponding to 32 different microbial metabolites. This demonstrates METASPACE to be a useful tool to annotate the chemistry and metabolic exchange factors found in microbial interactions, thereby elucidating the functions of these molecules.

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Clark, Chase M., Maria S. Costa, Laura M. Sanchez, and Brian T. Murphy. "Coupling MALDI-TOF mass spectrometry protein and specialized metabolite analyses to rapidly discriminate bacterial function." Proceedings of the National Academy of Sciences 115, no. 19 (April 23, 2018): 4981–86. http://dx.doi.org/10.1073/pnas.1801247115.

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For decades, researchers have lacked the ability to rapidly correlate microbial identity with bacterial metabolism. Since specialized metabolites are critical to bacterial function and survival in the environment, we designed a data acquisition and bioinformatics technique (IDBac) that utilizes in situ matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to analyze protein and specialized metabolite spectra recorded from single bacterial colonies picked from agar plates. We demonstrated the power of our approach by discriminating between twoBacillus subtilisstrains in <30 min solely on the basis of their differential ability to produce cyclic peptide antibiotics surfactin and plipastatin, caused by a single frameshift mutation. Next, we used IDBac to detect subtle intraspecies differences in the production of metal scavenging acyl-desferrioxamines in a group of eight freshwaterMicromonosporaisolates that share >99% sequence similarity in the 16S rRNA gene. Finally, we used IDBac to simultaneously extract protein and specialized metabolite MS profiles from unidentified Lake Michigan sponge-associated bacteria isolated from an agar plate. In just 3 h, we created hierarchical protein MS groupings of 11 environmental isolates (10 MS replicates each, for a total of 110 spectra) that accurately mirrored phylogenetic groupings. We further distinguished isolates within these groupings, which share nearly identical 16S rRNA gene sequence identity, based on interspecies and intraspecies differences in specialized metabolite production. IDBac is an attempt to couple in situ MS analyses of protein content and specialized metabolite production to allow for facile discrimination of closely related bacterial colonies.

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Nicault, Matthieu, Abdoul-Razak Tidjani, Anthony Gauthier, Stéphane Dumarcay, Eric Gelhaye, Cyril Bontemps, and Pierre Leblond. "Mining the Biosynthetic Potential for Specialized Metabolism of a Streptomyces Soil Community." Antibiotics 9, no. 5 (May 23, 2020): 271. http://dx.doi.org/10.3390/antibiotics9050271.

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The diversity and distribution of specialized metabolite gene clusters within a community of bacteria living in the same soil habitat are poorly documented. Here we analyzed the genomes of 8 Streptomyces isolated at micro-scale from a forest soil that belong to the same species or to different species. The results reveal high levels of diversity, with a total of 261 biosynthesis gene clusters (BGCs) encoding metabolites such as terpenes, polyketides (PKs), non-ribosomal peptides (NRPs) and ribosomally synthesized and post-translationally modified peptides (RiPPs) with potential bioactivities. A significant part of these BGCs (n = 53) were unique to only one strain when only 5 were common to all strains. The metabolites belong to very diverse chemical families and revealed that a large diversity of metabolites can potentially be produced in the community. Although that analysis of the global metabolome using GC-MS revealed that most of the metabolites were shared between the strains, they exhibited a specific metabolic pattern. We also observed that the presence of these accessory pathways might result from frequent loss and gain of genes (horizontal transfer), showing that the potential of metabolite production is a dynamic phenomenon in the community. Sampling Streptomyces at the community level constitutes a good frame to discover new biosynthetic pathways and it appears as a promising reservoir for the discovery of new bioactive compounds.

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Nagel, Raimund. "Pyrethrin Biosynthesis: From a Phytohormone to Specialized Metabolite." Plant Physiology 181, no. 3 (November 2019): 836–37. http://dx.doi.org/10.1104/pp.19.01210.

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Du, Yi-Ling, Melanie A. Higgins, Guiyun Zhao, and Katherine S. Ryan. "Convergent biosynthetic transformations to a bacterial specialized metabolite." Nature Chemical Biology 15, no. 11 (August 12, 2019): 1043–48. http://dx.doi.org/10.1038/s41589-019-0331-5.

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Shaikh, Arshad Ali, Louis-Felix Nothias, Santosh K. Srivastava, Pieter C. Dorrestein, and Kapil Tahlan. "Specialized Metabolites from Ribosome Engineered Strains of Streptomyces clavuligerus." Metabolites 11, no. 4 (April 13, 2021): 239. http://dx.doi.org/10.3390/metabo11040239.

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Bacterial specialized metabolites are of immense importance because of their medicinal, industrial, and agricultural applications. Streptomyces clavuligerus is a known producer of such compounds; however, much of its metabolic potential remains unknown, as many associated biosynthetic gene clusters are silent or expressed at low levels. The overexpression of ribosome recycling factor (frr) and ribosome engineering (induced rpsL mutations) in other Streptomyces spp. has been reported to increase the production of known specialized metabolites. Therefore, we used an overexpression strategy in combination with untargeted metabolomics, molecular networking, and in silico analysis to annotate 28 metabolites in the current study, which have not been reported previously in S. clavuligerus. Many of the newly described metabolites are commonly found in plants, further alluding to the ability of S. clavuligerus to produce such compounds under specific conditions. In addition, the manipulation of frr and rpsL led to different metabolite production profiles in most cases. Known and putative gene clusters associated with the production of the observed compounds are also discussed. This work suggests that the combination of traditional strain engineering and recently developed metabolomics technologies together can provide rapid and cost-effective strategies to further speed up the discovery of novel natural products.

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Vicente, Cláudia, Annabelle Thibessard, Jean-Noël Lorenzi, Mabrouka Benhadj, Laurence Hôtel, Djamila Gacemi-Kirane, Olivier Lespinet, Pierre Leblond, and Bertrand Aigle. "Comparative Genomics among Closely Related Streptomyces Strains Revealed Specialized Metabolite Biosynthetic Gene Cluster Diversity." Antibiotics 7, no. 4 (October 2, 2018): 86. http://dx.doi.org/10.3390/antibiotics7040086.

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Specialized metabolites are of great interest due to their possible industrial and clinical applications. The increasing number of antimicrobial resistant infectious agents is a major health threat and therefore, the discovery of chemical diversity and new antimicrobials is crucial. Extensive genomic data from Streptomyces spp. confirm their production potential and great importance. Genome sequencing of the same species strains indicates that specialized metabolite biosynthetic gene cluster (SMBGC) diversity is not exhausted, and instead, a pool of novel specialized metabolites still exists. Here, we analyze the genome sequence data from six phylogenetically close Streptomyces strains. The results reveal that the closer strains are phylogenetically, the number of shared gene clusters is higher. Eight specialized metabolites comprise the core metabolome, although some strains have only six core gene clusters. The number of conserved gene clusters common between the isolated strains and their closest phylogenetic counterparts varies from nine to 23 SMBGCs. However, the analysis of these phylogenetic relationships is not affected by the acquisition of gene clusters, probably by horizontal gene transfer events, as each strain also harbors strain-specific SMBGCs. Between one and 15 strain-specific gene clusters were identified, of which up to six gene clusters in a single strain are unknown and have no identifiable orthologs in other species, attesting to the existing SMBGC novelty at the strain level.

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Millán-Aguiñaga, Natalie, Sylvia Soldatou, Sarah Brozio, John T. Munnoch, John Howe, Paul A. Hoskisson, and Katherine R. Duncan. "Awakening ancient polar Actinobacteria: diversity, evolution and specialized metabolite potential." Microbiology 165, no. 11 (November 1, 2019): 1169–80. http://dx.doi.org/10.1099/mic.0.000845.

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Schweiger, Rabea, Eva Castells, Luca Da Sois, Jordi Martínez-Vilalta, and Caroline Müller. "Highly Species-Specific Foliar Metabolomes of Diverse Woody Species and Relationships with the Leaf Economics Spectrum." Cells 10, no. 3 (March 13, 2021): 644. http://dx.doi.org/10.3390/cells10030644.

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Plants show an extraordinary diversity in chemical composition and are characterized by different functional traits. However, relationships between the foliar primary and specialized metabolism in terms of metabolite numbers and composition as well as links with the leaf economics spectrum have rarely been explored. We investigated these relationships in leaves of 20 woody species from the Mediterranean region grown as saplings in a common garden, using a comparative ecometabolomics approach that included (semi-)polar primary and specialized metabolites. Our analyses revealed significant positive correlations between both the numbers and relative composition of primary and specialized metabolites. The leaf metabolomes were highly species-specific but in addition showed some phylogenetic imprints. Moreover, metabolomes of deciduous species were distinct from those of evergreens. Significant relationships were found between the primary metabolome and nitrogen content and carbon/nitrogen ratio, important traits of the leaf economics spectrum, ranging from acquisitive (mostly deciduous) to conservative (evergreen) leaves. A comprehensive understanding of various leaf traits and their coordination in different plant species may facilitate our understanding of plant functioning in ecosystems. Chemodiversity is thereby an important component of biodiversity.

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Padilla-González, Guillermo F., Evelyn Amrehn, Maximilian Frey, Javier Gómez-Zeledón, Alevtina Kaa, Fernando B. Da Da Costa, and Otmar Spring. "Metabolomic and Gene Expression Studies Reveal the Diversity, Distribution and Spatial Regulation of the Specialized Metabolism of Yacón (Smallanthus sonchifolius, Asteraceae)." International Journal of Molecular Sciences 21, no. 12 (June 26, 2020): 4555. http://dx.doi.org/10.3390/ijms21124555.

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Smallanthus sonchifolius, also known as yacón, is an Andean crop species commercialized for its nutraceutical and medicinal properties. The tuberous roots of yacón accumulate a diverse array of probiotic and bioactive metabolites including fructooligosaccharides and caffeic acid esters. However, the metabolic diversity of yacón remains unexplored, including the site of biosynthesis and accumulation of key metabolite classes. We report herein a multidisciplinary approach involving metabolomics, gene expression and scanning electron microscopy, to provide a comprehensive analysis of the diversity, distribution and spatial regulation of the specialized metabolism in yacón. Our results demonstrate that different metabolic fingerprints and gene expression patterns characterize specific tissues, organs and cultivars of yacón. Manual inspection of mass spectrometry data and molecular networking allowed the tentative identification of 71 metabolites, including undescribed structural analogues of known bioactive compounds. Imaging by scanning electron microscopy revealed the presence of a new type of glandular trichome in yacón bracts, with a distinctive metabolite profile. Furthermore, the high concentration of sesquiterpene lactones in capitate glandular trichomes and the restricted presence of certain flavonoids and caffeic acid esters in underground organs and internal tissues suggests that these metabolites could be involved in protective and ecological functions. This study demonstrates that individual organs and tissues make specific contributions to the highly diverse and specialized metabolome of yacón, which is proving to be a reservoir of previously undescribed molecules of potential significance in human health.

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Nadi, Roya, Behrouz Golein, Aurelio Gómez-Cadenas, and Vicent Arbona. "Developmental Stage- and Genotype-Dependent Regulation of Specialized Metabolite Accumulation in Fruit Tissues of Different Citrus Varieties." International Journal of Molecular Sciences 20, no. 5 (March 12, 2019): 1245. http://dx.doi.org/10.3390/ijms20051245.

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Flavor traits in citrus are the result of a blend of low molecular weight metabolites including sugars, acids, flavonoids and limonoids, these latter being mainly responsible for the characteristic bitter flavor in citrus. In this work, the genotype- and developmental stage-dependent accumulation of flavonoids and limonoids is addressed. To fulfill this goal, three models for citrus bitterness: bitter Duncan grapefruit, bittersweet Thomson orange and sweet Wase mandarin were selected from a total of eight different varieties. Compounds were annotated from LC/ESI-QqTOF-MS non-targeted metabolite profiles from albedo and pulp tissues. Results indicated that the specific blend of compounds providing the characteristic flavor trait is genotype-specific and hence under genetic control, but it is also regulated at the developmental level. Metabolite profiles in albedo mirrored those found in pulp, the edible part of the fruit, despite differences in the concentration and accumulation/depletion rates being found. This is particularly relevant for polymethoxylated flavones and glycosylated limonoids that showed a clear partitioning towards albedo and pulp tissues, respectively. Fruit ripening was characterized by a reduction in flavonoids and the accumulation of limonoid glycosides. However, bitter grapefruit showed higher levels of limonin A-ring lactone and naringin in contrast to sweeter orange and mandarin. Data indicated that the accumulation profile was compound class-specific and conserved among the studied varieties despite differing in the respective accumulation and/or depletion rate, leading to different specialized metabolite concentration at the full ripe stage, consistent with the flavor trait output.

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Visser, Wouter F., Carlo W. T. van Roermund, Lodewijk Ijlst, Hans R. Waterham, and Ronald J. A. Wanders. "Metabolite transport across the peroxisomal membrane." Biochemical Journal 401, no. 2 (December 21, 2006): 365–75. http://dx.doi.org/10.1042/bj20061352.

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In recent years, much progress has been made with respect to the unravelling of the functions of peroxisomes in metabolism, and it is now well established that peroxisomes are indispensable organelles, especially in higher eukaryotes. Peroxisomes catalyse a number of essential metabolic functions including fatty acid β-oxidation, ether phospholipid biosynthesis, fatty acid α-oxidation and glyoxylate detoxification. The involvement of peroxisomes in these metabolic pathways necessitates the transport of metabolites in and out of peroxisomes. Recently, considerable progress has been made in the characterization of metabolite transport across the peroxisomal membrane. Peroxisomes posses several specialized transport systems to transport metabolites. This is exemplified by the identification of a specific transporter for adenine nucleotides and several half-ABC (ATP-binding cassette) transporters which may be present as hetero- and homo-dimers. The nature of the substrates handled by the different ABC transporters is less clear. In this review we will describe the current state of knowledge of the permeability properties of the peroxisomal membrane.

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Strauch, Renee C., Elisabeth Svedin, Brian Dilkes, Clint Chapple, and Xu Li. "Discovery of a novel amino acid racemase through exploration of natural variation inArabidopsis thaliana." Proceedings of the National Academy of Sciences 112, no. 37 (August 31, 2015): 11726–31. http://dx.doi.org/10.1073/pnas.1503272112.

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Plants produce diverse low-molecular-weight compounds via specialized metabolism. Discovery of the pathways underlying production of these metabolites is an important challenge for harnessing the huge chemical diversity and catalytic potential in the plant kingdom for human uses, but this effort is often encumbered by the necessity to initially identify compounds of interest or purify a catalyst involved in their synthesis. As an alternative approach, we have performed untargeted metabolite profiling and genome-wide association analysis on 440 natural accessions ofArabidopsis thaliana. This approach allowed us to establish genetic linkages between metabolites and genes. Investigation of one of the metabolite–gene associations led to the identification ofN-malonyl-d-allo-isoleucine, and the discovery of a novel amino acid racemase involved in its biosynthesis. This finding provides, to our knowledge, the first functional characterization of a eukaryotic member of a large and widely conserved phenazine biosynthesis protein PhzF-like protein family. Unlike most of known eukaryotic amino acid racemases, the newly discovered enzyme does not require pyridoxal 5′-phosphate for its activity. This study thus identifies a newd-amino acid racemase gene family and advances our knowledge of plantd-amino acid metabolism that is currently largely unexplored. It also demonstrates that exploitation of natural metabolic variation by integrating metabolomics with genome-wide association is a powerful approach for functional genomics study of specialized metabolism.

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Cruz-Rivera, Edwin, and Valerie J. Paul. "Chemical Deterrence of a Cyanobacterial Metabolite against Generalized and Specialized Grazers." Journal of Chemical Ecology 33, no. 1 (October 25, 2006): 213–17. http://dx.doi.org/10.1007/s10886-006-9212-y.

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Li, Dapeng, Sven Heiling, Ian T. Baldwin, and Emmanuel Gaquerel. "Illuminating a plant’s tissue-specific metabolic diversity using computational metabolomics and information theory." Proceedings of the National Academy of Sciences 113, no. 47 (November 7, 2016): E7610—E7618. http://dx.doi.org/10.1073/pnas.1610218113.

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Secondary metabolite diversity is considered an important fitness determinant for plants’ biotic and abiotic interactions in nature. This diversity can be examined in two dimensions. The first one considers metabolite diversity across plant species. A second way of looking at this diversity is by considering the tissue-specific localization of pathways underlying secondary metabolism within a plant. Although these cross-tissue metabolite variations are increasingly regarded as important readouts of tissue-level gene function and regulatory processes, they have rarely been comprehensively explored by nontargeted metabolomics. As such, important questions have remained superficially addressed. For instance, which tissues exhibit prevalent signatures of metabolic specialization? Reciprocally, which metabolites contribute most to this tissue specialization in contrast to those metabolites exhibiting housekeeping characteristics? Here, we explore tissue-level metabolic specialization in Nicotiana attenuata, an ecological model with rich secondary metabolism, by combining tissue-wide nontargeted mass spectral data acquisition, information theory analysis, and tandem MS (MS/MS) molecular networks. This analysis was conducted for two different methanolic extracts of 14 tissues and deconvoluted 895 nonredundant MS/MS spectra. Using information theory analysis, anthers were found to harbor the most specialized metabolome, and most unique metabolites of anthers and other tissues were annotated through MS/MS molecular networks. Tissue–metabolite association maps were used to predict tissue-specific gene functions. Predictions for the function of two UDP-glycosyltransferases in flavonoid metabolism were confirmed by virus-induced gene silencing. The present workflow allows biologists to amortize the vast amount of data produced by modern MS instrumentation in their quest to understand gene function.

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Hamberger, Björn, and Søren Bak. "Plant P450s as versatile drivers for evolution of species-specific chemical diversity." Philosophical Transactions of the Royal Society B: Biological Sciences 368, no. 1612 (February 19, 2013): 20120426. http://dx.doi.org/10.1098/rstb.2012.0426.

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The irreversible nature of reactions catalysed by P450s makes these enzymes landmarks in the evolution of plant metabolic pathways. Founding members of P450 families are often associated with general (i.e. primary) metabolic pathways, restricted to single copy or very few representatives, indicative of purifying selection. Recruitment of those and subsequent blooms into multi-member gene families generates genetic raw material for functional diversification, which is an inherent characteristic of specialized (i.e. secondary) metabolism. However, a growing number of highly specialized P450s from not only the CYP71 clan indicate substantial contribution of convergent and divergent evolution to the observed general and specialized metabolite diversity. We will discuss examples of how the genetic and functional diversification of plant P450s drives chemical diversity in light of plant evolution. Even though it is difficult to predict the function or substrate of a P450 based on sequence similarity, grouping with a family or subfamily in phylogenetic trees can indicate association with metabolism of particular classes of compounds. Examples will be given that focus on multi-member gene families of P450s involved in the metabolic routes of four classes of specialized metabolites: cyanogenic glucosides, glucosinolates, mono- to triterpenoids and phenylpropanoids.

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Sugiyama, Ryosuke, Rui Li, Ayuko Kuwahara, Ryo Nakabayashi, Naoyuki Sotta, Tetsuya Mori, Takehiro Ito, et al. "Retrograde sulfur flow from glucosinolates to cysteine in Arabidopsis thaliana." Proceedings of the National Academy of Sciences 118, no. 22 (May 25, 2021): e2017890118. http://dx.doi.org/10.1073/pnas.2017890118.

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Specialized (secondary) metabolic pathways in plants have long been considered one-way routes of leading primary metabolite precursors to bioactive end products. Conversely, endogenous degradation of such “end” products in plant tissues has been observed following environmental stimuli, including nutrition stress. Therefore, it is of general interest whether specialized metabolites can be reintegrated into primary metabolism to recover the invested resources, especially in the case of nitrogen- or sulfur-rich compounds. Here, we demonstrate that endogenous glucosinolates (GLs), a class of sulfur-rich plant metabolites, are exploited as a sulfur source by the reallocation of sulfur atoms to primary metabolites such as cysteine in Arabidopsis thaliana. Tracer experiments using 34S- or deuterium-labeled GLs depicted the catabolic processing of GL breakdown products in which sulfur is mobilized from the thioglucoside group in GL molecules, potentially accompanied by the release of the sulfate group. Moreover, we reveal that beta-glucosidases BGLU28 and BGLU30 are the major myrosinases that initiate sulfur reallocation by hydrolyzing particular GL species, conferring sulfur deficiency tolerance in A. thaliana, especially during early development. The results delineate the physiological function of GL as a sulfur reservoir, in addition to their well-known functions as defense chemicals. Overall, our findings demonstrate the bidirectional interaction between primary and specialized metabolism, which enhances our understanding of the underlying metabolic mechanisms via which plants adapt to their environments.

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Kamdem, Ramsay Soup Teoua, Omonike Ogbole, Pascal Wafo, F. Uzor Philip, Zulfiqar Ali, Fidele Ntie-Kang, Ikhlas A. Khan, and Peter Spiteller. "Rational engineering of specialized metabolites in bacteria and fungi." Physical Sciences Reviews 6, no. 5 (May 1, 2021): 9–26. http://dx.doi.org/10.1515/psr-2018-0170.

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Abstract Bacteria and fungi have a high potential to produce compounds that display large structural change and diversity, thus displaying an extensive range of biological activities. Secondary metabolism or specialized metabolism is a term for pathways and small molecule products of metabolism that are not mandatory for the subsistence of the organism but improve and control their phenotype. Their interesting biological activities have occasioned their application in the fields of agriculture, food, and pharmaceuticals. Metabolic engineering is a powerful approach to improve access to these treasured molecules or to rationally engineer new ones. A thorough overview of engineering methods in secondary metabolism is presented, both in heterologous and epigenetic modification. Engineering methods to modify the structure of some secondary metabolite classes in their host are also intensively assessed.

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Lockhart, Jennifer. "Chasing Scattered Genes: Identifying Specialized Metabolite Pathway Genes through Global Coexpression Analysis." Plant Cell 29, no. 5 (April 13, 2017): 915. http://dx.doi.org/10.1105/tpc.17.00303.

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Celano, Rita, Teresa Docimo, Anna Lisa Piccinelli, Serena Rizzo, Luca Campone, Rosa Di Sanzo, Sonia Carabetta, Luca Rastrelli, and Mariateresa Russo. "Specialized metabolite profiling of different Glycyrrhiza glabra organs by untargeted UHPLC-HRMS." Industrial Crops and Products 170 (October 2021): 113688. http://dx.doi.org/10.1016/j.indcrop.2021.113688.

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Horten, Patrick, Lilia Colina-Tenorio, and Heike Rampelt. "Biogenesis of Mitochondrial Metabolite Carriers." Biomolecules 10, no. 7 (July 7, 2020): 1008. http://dx.doi.org/10.3390/biom10071008.

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Metabolite carriers of the mitochondrial inner membrane are crucial for cellular physiology since mitochondria contribute essential metabolic reactions and synthesize the majority of the cellular ATP. Like almost all mitochondrial proteins, carriers have to be imported into mitochondria from the cytosol. Carrier precursors utilize a specialized translocation pathway dedicated to the biogenesis of carriers and related proteins, the carrier translocase of the inner membrane (TIM22) pathway. After recognition and import through the mitochondrial outer membrane via the translocase of the outer membrane (TOM) complex, carrier precursors are ushered through the intermembrane space by hexameric TIM chaperones and ultimately integrated into the inner membrane by the TIM22 carrier translocase. Recent advances have shed light on the mechanisms of TOM translocase and TIM chaperone function, uncovered an unexpected versatility of the machineries, and revealed novel components and functional crosstalk of the human TIM22 translocase.

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Masullo, Milena, Antonietta Cerulli, Cosimo Pizza, and Sonia Piacente. "Pouteria lucuma Pulp and Skin: In Depth Chemical Profile and Evaluation of Antioxidant Activity." Molecules 26, no. 17 (August 29, 2021): 5236. http://dx.doi.org/10.3390/molecules26175236.

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Pouteria lucuma Ruiz and Pav., known as the ‘Gold of the Incas’ or ‘lucuma’, is a subtropical fruit belonging to the Sapotaceae family, with a very sweet flavor, used to prepare cakes, ice creams as well as in the baking and dairy industries. To date, the content of primary metabolites is known, but little information is reported about the composition in specialized metabolites. Moreover, no study is reported on skin which represent an important agricultural waste due to the high demand for lucuma. In order to have a preliminary metabolite profile of Pouteria lucuma, the extracts of pulp and skin have been analyzed by LC-ESI/LTQOrbitrap/MS/MS in negative ion mode. The careful analysis of the accurate masses, of the molecular formulas and of the ESI/MS spectra allowed to identify specialized metabolites belonging to phenolic, flavonoid and polar lipid classes. The LC-MS/MS analysis guided the isolation of compounds occurring in the pulp extract whose structures have been characterized by spectroscopic methods including 1D- and 2D-NMR experiments and ESI-MS analysis. Furthermore, the phenolic content of the extracts along with the antioxidant activity of extracts and isolated compounds was evaluated.

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Chevalier, Wilfried, Sitti-Anlati Moussa, Miguel Medeiros Netto Ottoni, Cécile Dubois-Laurent, Sébastien Huet, Christophe Aubert, Elsa Desnoues, et al. "Multisite evaluation of phenotypic plasticity for specialized metabolites, some involved in carrot quality and disease resistance." PLOS ONE 16, no. 4 (April 2, 2021): e0249613. http://dx.doi.org/10.1371/journal.pone.0249613.

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Renewed consumer demand motivates the nutritional and sensory quality improvement of fruits and vegetables. Specialized metabolites being largely involved in nutritional and sensory quality of carrot, a better knowledge of their phenotypic variability is required. A metabolomic approach was used to evaluate phenotypic plasticity level of carrot commercial varieties, over three years and a wide range of cropping environments spread over several geographical areas in France. Seven groups of metabolites have been quantified by HPLC or GC methods: sugars, carotenoids, terpenes, phenolic compounds, phenylpropanoids and polyacetylenes. A large variation in root metabolic profiles was observed, in relation with environment, variety and variety by environment interaction effects in decreasing order of importance. Our results show a clear diversity structuration based on metabolite content. Polyacetylenes, β-pinene and α-carotene were identified mostly as relatively stable varietal markers, exhibiting static stability. Nevertheless, environment effect was substantial for a large part of carrot metabolic profile and various levels of phenotypic plasticity were observed depending on metabolites and varieties. A strong difference of environmental sensitivity between varieties was observed for several compounds, particularly myristicin, 6MM and D-germacrene, known to be involved in responses to biotic and abiotic stress. This work provides useful information about plasticity in the perspective of carrot breeding and production. A balance between constitutive content and environmental sensitivity for key metabolites should be reached for quality improvement in carrot and other vegetables.

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Sonawane, Prashant D., Uwe Heinig, Sayantan Panda, Netta Segal Gilboa, Meital Yona, S. Pradeep Kumar, Noam Alkan, et al. "Short-chain dehydrogenase/reductase governs steroidal specialized metabolites structural diversity and toxicity in the genus Solanum." Proceedings of the National Academy of Sciences 115, no. 23 (May 21, 2018): E5419—E5428. http://dx.doi.org/10.1073/pnas.1804835115.

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Thousands of specialized, steroidal metabolites are found in a wide spectrum of plants. These include the steroidal glycoalkaloids (SGAs), produced primarily by most species of the genus Solanum, and metabolites belonging to the steroidal saponins class that are widespread throughout the plant kingdom. SGAs play a protective role in plants and have potent activity in mammals, including antinutritional effects in humans. The presence or absence of the double bond at the C-5,6 position (unsaturated and saturated, respectively) creates vast structural diversity within this metabolite class and determines the degree of SGA toxicity. For many years, the elimination of the double bond from unsaturated SGAs was presumed to occur through a single hydrogenation step. In contrast to this prior assumption, here, we show that the tomato GLYCOALKALOID METABOLISM25 (GAME25), a short-chain dehydrogenase/reductase, catalyzes the first of three prospective reactions required to reduce the C-5,6 double bond in dehydrotomatidine to form tomatidine. The recombinant GAME25 enzyme displayed 3β-hydroxysteroid dehydrogenase/Δ5,4 isomerase activity not only on diverse steroidal alkaloid aglycone substrates but also on steroidal saponin aglycones. Notably, GAME25 down-regulation rerouted the entire tomato SGA repertoire toward the dehydro-SGAs branch rather than forming the typically abundant saturated α-tomatine derivatives. Overexpressing the tomato GAME25 in the tomato plant resulted in significant accumulation of α-tomatine in ripe fruit, while heterologous expression in cultivated eggplant generated saturated SGAs and atypical saturated steroidal saponin glycosides. This study demonstrates how a single scaffold modification of steroidal metabolites in plants results in extensive structural diversity and modulation of product toxicity.

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de Man, Tom J. B., Jason E. Stajich, Christian P. Kubicek, Clotilde Teiling, Komal Chenthamara, Lea Atanasova, Irina S. Druzhinina, et al. "Small genome of the fungus Escovopsis weberi, a specialized disease agent of ant agriculture." Proceedings of the National Academy of Sciences 113, no. 13 (March 14, 2016): 3567–72. http://dx.doi.org/10.1073/pnas.1518501113.

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Many microorganisms with specialized lifestyles have reduced genomes. This is best understood in beneficial bacterial symbioses, where partner fidelity facilitates loss of genes necessary for living independently. Specialized microbial pathogens may also exhibit gene loss relative to generalists. Here, we demonstrate that Escovopsis weberi, a fungal parasite of the crops of fungus-growing ants, has a reduced genome in terms of both size and gene content relative to closely related but less specialized fungi. Although primary metabolism genes have been retained, the E. weberi genome is depleted in carbohydrate active enzymes, which is consistent with reliance on a host with these functions. E. weberi has also lost genes considered necessary for sexual reproduction. Contrasting these losses, the genome encodes unique secondary metabolite biosynthesis clusters, some of which include genes that exhibit up-regulated expression during host attack. Thus, the specialized nature of the interaction between Escovopsis and ant agriculture is reflected in the parasite’s genome.

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Semwal, Ankit, Raghav Dogra, Kritika Verma, and Rohit Bhatia. "Impact of UPLC-MS in Food and Drug/Metabolite Analysis." Current Pharmaceutical Analysis 17, no. 1 (November 23, 2020): 10–30. http://dx.doi.org/10.2174/1573412915666190923105355.

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The hyphenation of Ultra-Performance Liquid performance (UPLC) with mass spectrometry (MS) has emerged as a powerful tool in analytical research due to its advanced sensitivity, resolution and speed. Its advanced instrumentation, specialized columns, separation at ultra-high pressure and sophisticated software are the distinguishing features as compared to the traditional separating techniques. It has a wide range of applications in various fields such as analysis of food stuffs, drug metabolites, beverages, toxicology, soil samples and micronutrient analysis. In the present compilation, authors have highlighted the applicability of UPLC-MS in the analysis of food stuffs and drug metabolites along with the various optimized analytical conditions and obtained results.

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Nielsen, Morten T., Johan Andersen Ranberg, Ulla Christensen, Hanne Bjerre Christensen, Scott J. Harrison, Carl Erik Olsen, Björn Hamberger, Birger Lindberg Møller, and Morten H. H. Nørholm. "Microbial Synthesis of the Forskolin Precursor Manoyl Oxide in an Enantiomerically Pure Form." Applied and Environmental Microbiology 80, no. 23 (September 19, 2014): 7258–65. http://dx.doi.org/10.1128/aem.02301-14.

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ABSTRACTForskolin is a promising medicinal compound belonging to a plethora of specialized plant metabolites that constitute a rich source of bioactive high-value compounds. A major obstacle for exploitation of plant metabolites is that they often are produced in small amounts and in plants difficult to cultivate. This may result in insufficient and unreliable supply leading to fluctuating and high sales prices. Hence, substantial efforts and resources have been invested in developing sustainable and reliable supply routes based on microbial cell factories. Here, we report microbial synthesis of (13R)-manoyl oxide, a proposed intermediate in the biosynthesis of forskolin and other medically important labdane-type terpenoids. Process optimization enabled synthesis of enantiomerically pure (13R)-manoyl oxide as the sole metabolite, providing a pure compound in just two steps with a yield of 10 mg/liter. The work presented here demonstrates the value of a standardized bioengineering pipeline and the large potential of microbial cell factories as sources for sustainable synthesis of complex biochemicals.

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Chanda, Anindya, Ludmila V. Roze, and John E. Linz. "A Possible Role for Exocytosis in Aflatoxin Export in Aspergillus parasiticus." Eukaryotic Cell 9, no. 11 (September 24, 2010): 1724–27. http://dx.doi.org/10.1128/ec.00118-10.

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ABSTRACT Filamentous fungi synthesize bioactive secondary metabolites with major human health and economic impacts. Little is known about the mechanisms that mediate the export of these metabolites to the cell exterior. Aspergillus parasiticus synthesizes aflatoxin, a secondary metabolite that is one of the most potent naturally occurring carcinogens known. We previously demonstrated that aflatoxin is synthesized and compartmentalized in specialized vesicles called aflatoxisomes and that these subcellular organelles also play a role in the export process. In the current study, we tested the hypothesis that aflatoxisomes fuse with the cytoplasmic membrane to facilitate the release of aflatoxin into the growth environment. Microscopic analysis of A. parasiticus grown under aflatoxin-inducing and non-aflatoxin-inducing conditions generated several lines of experimental evidence that supported the hypothesis. On the basis of the evidence, we propose that export of the mycotoxin aflatoxin in Aspergillus parasiticus occurs by exocytosis, and we present a model to illustrate this export mechanism.

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Wilson, Wilken, van der Nest, Wingfield, and Wingfield. "It’s All in the Genes: The Regulatory Pathways of Sexual Reproduction in Filamentous Ascomycetes." Genes 10, no. 5 (April 30, 2019): 330. http://dx.doi.org/10.3390/genes10050330.

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Sexual reproduction in filamentous ascomycete fungi results in the production of highly specialized sexual tissues, which arise from relatively simple, vegetative mycelia. This conversion takes place after the recognition of and response to a variety of exogenous and endogenous cues, and relies on very strictly regulated gene, protein, and metabolite pathways. This makes studying sexual development in fungi an interesting tool in which to study gene–gene, gene–protein, and protein–metabolite interactions. This review provides an overview of some of the most important genes involved in this process; from those involved in the conversion of mycelia into sexually-competent tissue, to those involved in the development of the ascomata, the asci, and ultimately, the ascospores.

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Hayashi, Shunya, Mutsumi Watanabe, Makoto Kobayashi, Takayuki Tohge, Takashi Hashimoto, and Tsubasa Shoji. "Genetic Manipulation of Transcriptional Regulators Alters Nicotine Biosynthesis in Tobacco." Plant and Cell Physiology 61, no. 6 (March 19, 2020): 1041–53. http://dx.doi.org/10.1093/pcp/pcaa036.

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Abstract The toxic alkaloid nicotine is produced in the roots of Nicotiana species and primarily accumulates in leaves as a specialized metabolite. A series of metabolic and transport genes involved in the nicotine pathway are coordinately upregulated by a pair of jasmonate-responsive AP2/ERF-family transcription factors, NtERF189 and NtERF199, in the roots of Nicotiana tabacum (tobacco). In this study, we explored the potential of manipulating the expression of these transcriptional regulators to alter nicotine biosynthesis in tobacco. The transient overexpression of NtERF189 led to alkaloid production in the leaves of Nicotiana benthamiana and Nicotiana alata. This ectopic production was further enhanced by co-overexpressing a gene encoding a basic helix-loop-helix-family MYC2 transcription factor. Constitutive and leaf-specific overexpression of NtERF189 increased the accumulation of foliar alkaloids in transgenic tobacco plants but negatively affected plant growth. By contrast, in a knockout mutant of NtERF189 and NtERF199 obtained through CRISPR/Cas9-based genome editing, alkaloid levels were drastically reduced without causing major growth defects. Metabolite profiling revealed the impact of manipulating the nicotine pathway on a wide range of nitrogen- and carbon-containing metabolites. Our findings provide insights into the biotechnological applications of engineering metabolic pathways by targeting transcription factors.

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Kopsell, Dean A., Carl E. Sams, and Robert C. Morrow. "Blue Wavelengths from LED Lighting Increase Nutritionally Important Metabolites in Specialty Crops." HortScience 50, no. 9 (September 2015): 1285–88. http://dx.doi.org/10.21273/hortsci.50.9.1285.

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Light is one of the most important environmental stimuli impacting plant growth and development. Plants have evolved specialized pigment-protein complexes, commonly referred to as photoreceptors, to capture light energy to drive photosynthetic processes, as well as to respond to changes in light quality and quantity. Blue light can act as a powerful environmental signal regulating phototropisms, suppression of stem elongation, chloroplast movements, stomatal regulation, and cell membrane transport activity. An emerging application of light-emitting diode (LED) technology is for horticultural plant production in controlled environments. Work by our research group is measuring important plant responses to different wavelengths of light from LEDs. We have demonstrated positive impacts of blue wavelengths on primary and secondary metabolism in microgreen and baby leafy green brassica crops. Results show significant increases in shoot tissue pigments, glucosinolates, and essential mineral elements following exposure to higher percentages of blue wavelengths from LED lighting. The perception of energy-rich blue light by specialized plant photoreceptors appears to trigger a cascade of metabolic responses, which is supported by current research showing stimulation of primary and secondary metabolite biosynthesis following exposure to blue wavelengths. Management of the light environment may be a viable means to improve concentrations of nutritionally important primary and secondary metabolites in specialty vegetable crops.

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Kang, Kyo Bin, Sunmin Woo, Madeleine Ernst, Justin J. J. van der Hooft, Louis-Félix Nothias, Ricardo R. da Silva, Pieter C. Dorrestein, Sang Hyun Sung, and Mina Lee. "Assessing specialized metabolite diversity of Alnus species by a digitized LC–MS/MS data analysis workflow." Phytochemistry 173 (May 2020): 112292. http://dx.doi.org/10.1016/j.phytochem.2020.112292.

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Lybbert, Andrew C., Justin L. Williams, Ruma Raghuvanshi, A. Daniel Jones, and Robert A. Quinn. "Mining Public Mass Spectrometry Data to Characterize the Diversity and Ubiquity of P. aeruginosa Specialized Metabolites." Metabolites 10, no. 11 (November 5, 2020): 445. http://dx.doi.org/10.3390/metabo10110445.

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Pseudomonas aeruginosa is a ubiquitous environmental bacterium that causes chronic infections of burn wounds and in the lungs of cystic fibrosis (CF) patients. Vital to its infection is a myriad of specialized metabolites that serve a variety of biological roles including quorum sensing, metal chelation and inhibition of other competing bacteria. This study employed newly available algorithms for searching individual tandem mass (MS/MS) spectra against the publicly available Global Natural Product Social Molecular Networking (GNPS) database to identify the chemical diversity of these compounds and their presence in environmental, laboratory and clinical samples. For initial characterization, the metabolomes of eight clinical isolates of P. aeruginosa were analyzed using liquid chromatography-tandem mass spectrometry (LC-MS/MS) and uploaded to GNPS for spectral searching. Quinolones, rhamnolipids, phenazines and siderophores were identified and characterized; including the discovery of modified forms of the iron chelator pyochelin. Quinolones were highly diverse with the three base forms Pseudomonas quinolone signal 2-heptyl-3-hydroxy-4(1H)-quinolone (PQS), 4-heptyl-4(1H)-quinolone (HHQ) and 2-heptyl-4-quinolone-N-oxide (HQNO) having extensive variation in the length of their acyl chain from as small as 3 carbons to as large as 17. Rhamnolipids were limited to either one or two sugars with a limited set of fatty acyl chains, but the base lipid form without the rhamnose was also detected. These specialized metabolites were identified from diverse sources including ant-fungal mutualist dens, soil, plants, human teeth, feces, various lung mucus samples and cultured laboratory isolates. Their prevalence in fecal samples was particularly notable as P. aeruginosa is not known as a common colonizer of the human gut. The chemical diversity of the compounds identified, particularly the quinolones, demonstrates a broad spectrum of chemical properties within these the metabolite groups with likely significant impacts on their biological functions. Mining public data with GNPS enables a new approach to characterize the chemical diversity of biological organisms, which includes enabling the discovery of new chemistry from pathogenic bacteria.

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Johnson, M. A., and M. Le Pennec. "The development of the female gamete in the endosymbiont-bearing bivalve Loripes lucinalis." Journal of the Marine Biological Association of the United Kingdom 74, no. 1 (February 1994): 233–42. http://dx.doi.org/10.1017/s0025315400035797.

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The development of the female gonad in Loripes lucinalis (Lamarck) from Brest Harbour (Brittany, France) was examined over a one-year period. Throughout the year, several size classes of eggs were observed, and spawning was seen to occur twice. A major spawning occurred in May leaving the gonad completely empty in June. A minor spawning is also thought to have occurred between the November and December sampling periods. These spawnings do not seem to correlate with the classical environmental factors often associated with gametogenesis and spawning, namely temperature and chlorophyll a levels. The energy for gametogenesis seems to be obtained from the transfer of metabolites to the oocytes via specialized follicle cells. These metabolites are believed to be of heterosynthetic origin. An inverse relationship exists between the thickness of the follicle cell epithelium and the occupancy level of the gametes. During periods of gonadal proliferation, these cells represent the nutritive cells of the gonad, but during periods of non-proliferation they make up a somatic tissue used for metabolite storage until conditions are adequate for gonadal development.

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Darghouth, Dhouha, Bérengère Koehl, Geoffrey Madalinski, Jean-François Heilier, Petra Bovee, Ying Xu, Marie-Françoise Olivier, et al. "Pathophysiology of sickle cell disease is mirrored by the red blood cell metabolome." Blood 117, no. 6 (February 10, 2011): e57-e66. http://dx.doi.org/10.1182/blood-2010-07-299636.

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Abstract Emerging metabolomic tools can now be used to establish metabolic signatures of specialized circulating hematopoietic cells in physiologic or pathologic conditions and in human hematologic diseases. To determine metabolomes of normal and sickle cell erythrocytes, we used an extraction method of erythrocytes metabolites coupled with a liquid chromatography-mass spectrometry–based metabolite profiling method. Comparison of these 2 metabolomes identified major changes in metabolites produced by (1) endogenous glycolysis characterized by accumulation of many glycolytic intermediates; (2) endogenous glutathione and ascorbate metabolisms characterized by accumulation of ascorbate metabolism intermediates, such as diketogulonic acid and decreased levels of both glutathione and glutathione disulfide; (3) membrane turnover, such as carnitine, or membrane transport characteristics, such as amino acids; and (4) exogenous arginine and NO metabolisms, such as spermine, spermidine, or citrulline. Finally, metabolomic analysis of young and old normal red blood cells indicates metabolites whose levels are directly related to sickle cell disease. These results show the relevance of metabolic profiling for the follow-up of sickle cell patients or other red blood cell diseases and pinpoint the importance of metabolomics to further depict the pathophysiology of human hematologic diseases.

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Khaniani, Yeganeh, Matthias Lipfert, Dipanjan Bhattacharyya, Rolando Perez Pineiro, Jiamin Zheng, and David Wishart. "A Simple and Convenient Synthesis of Unlabeled and 13C-Labeled 3-(3-Hydroxyphenyl)-3-Hydroxypropionic Acid and Its Quantification in Human Urine Samples." Metabolites 8, no. 4 (November 21, 2018): 80. http://dx.doi.org/10.3390/metabo8040080.

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An improved method to synthesize the highly abundant and biomedically important urinary metabolite 3-(3-hydroxyphenyl)-3-hydroxypropionic acid (HPHPA) is reported. The modified protocol is based on an indium-mediated sonochemical Reformatsky reaction. The synthesis is a simple two-step route as opposed to a complex four-step route previously reported in the literature that requires specialized equipment, flammable materials, and high-pressure reaction vessels. The described procedure also provides an expedient route to prepare a 13C isotopically labeled HPHPA that can be used as a standard for quantitative LC-MS analysis. This report also illustrates how the synthesized metabolite standard was used to detect and accurately quantify its presence in human urine samples using both NMR and LC-MS techniques.

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Ritmejerytė, Edita, Berin A. Boughton, Michael J. Bayly, and Rebecca E. Miller. "Unique and highly specific cyanogenic glycoside localization in stigmatic cells and pollen in the genus Lomatia (Proteaceae)." Annals of Botany 126, no. 3 (March 11, 2020): 387–400. http://dx.doi.org/10.1093/aob/mcaa038.

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Abstract Background and Aims Floral chemical defence strategies remain understudied despite the significance of flowers to plant fitness, and the fact that many flowers contain secondary metabolites that confer resistance to herbivores. Optimal defence and apparency theories predict that the most apparent plant parts and/or those most important to fitness should be most defended. To test whether within-flower distributions of chemical defence are consistent with these theories we used cyanogenic glycosides (CNglycs), which are constitutive defence metabolites that deter herbivores by releasing hydrogen cyanide upon hydrolysis. Methods We used cyanogenic florets of the genus Lomatia to investigate at what scale there may be strategic allocation of CNglycs in flowers, what their localization reveals about function, and whether levels of floral CNglycs differ between eight congeneric species across a climatic gradient. Within-flower distributions of CNglycs during development were quantified, CNglycs were identified and their localization was visualized in cryosectioned florets using matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI-MSI). Key Results Florets of all congeneric species studied were cyanogenic, and concentrations differed between species. Within florets there was substantial variation in CNglyc concentrations, with extremely high concentrations (up to 14.6 mg CN g−1 d. wt) in pollen and loose, specialized surface cells on the pollen presenter, among the highest concentrations reported in plant tissues. Two tyrosine-derived CNglycs, the monoglycoside dhurrin and diglycoside proteacin, were identified. MALDI-MSI revealed their varying ratios in different floral tissues; proteacin was primarily localized to anthers and ovules, and dhurrin to specialized cells on the pollen presenter. The mix of transient specialized cells and pollen of L. fraxinifolia was ~11 % dhurrin and ~1.1 % proteacin by mass. Conclusions Tissue-specific distributions of two CNglycs and substantial variation in their concentrations within florets suggests their allocation is under strong selection. Localized, high CNglyc concentrations in transient cells challenge the predictions of defence theories, and highlight the importance of fine-scale metabolite visualization, and the need for further investigation into the ecological and metabolic roles of CNglycs in floral tissues.

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Brown, Stephanie, Marc Clastre, Vincent Courdavault, and Sarah E. O’Connor. "De novo production of the plant-derived alkaloid strictosidine in yeast." Proceedings of the National Academy of Sciences 112, no. 11 (February 9, 2015): 3205–10. http://dx.doi.org/10.1073/pnas.1423555112.

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The monoterpene indole alkaloids are a large group of plant-derived specialized metabolites, many of which have valuable pharmaceutical or biological activity. There are ∼3,000 monoterpene indole alkaloids produced by thousands of plant species in numerous families. The diverse chemical structures found in this metabolite class originate from strictosidine, which is the last common biosynthetic intermediate for all monoterpene indole alkaloid enzymatic pathways. Reconstitution of biosynthetic pathways in a heterologous host is a promising strategy for rapid and inexpensive production of complex molecules that are found in plants. Here, we demonstrate how strictosidine can be produced de novo in a Saccharomyces cerevisiae host from 14 known monoterpene indole alkaloid pathway genes, along with an additional seven genes and three gene deletions that enhance secondary metabolism. This system provides an important resource for developing the production of more complex plant-derived alkaloids, engineering of nonnatural derivatives, identification of bottlenecks in monoterpene indole alkaloid biosynthesis, and discovery of new pathway genes in a convenient yeast host.

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Li, Dapeng, and Emmanuel Gaquerel. "Next-Generation Mass Spectrometry Metabolomics Revives the Functional Analysis of Plant Metabolic Diversity." Annual Review of Plant Biology 72, no. 1 (June 17, 2021): 867–91. http://dx.doi.org/10.1146/annurev-arplant-071720-114836.

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The remarkable diversity of specialized metabolites produced by plants has inspired several decades of research and nucleated a long list of theories to guide empirical ecological studies. However, analytical constraints and the lack of untargeted processing workflows have long precluded comprehensive metabolite profiling and, consequently, the collection of the critical currencies to test theory predictions for the ecological functions of plant metabolic diversity. Developments in mass spectrometry (MS) metabolomics have revolutionized the large-scale inventory and annotation of chemicals from biospecimens. Hence, the next generation of MS metabolomics propelled by new bioinformatics developments provides a long-awaited framework to revisit metabolism-centered ecological questions, much like the advances in next-generation sequencing of the last two decades impacted all research horizons in genomics. Here, we review advances in plant (computational) metabolomics to foster hypothesis formulation from complex metabolome data. Additionally, we reflect on how next-generation metabolomics could reinvigorate the testing of long-standing theories on plant metabolic diversity.

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Arya, Sagar S., James E. Rookes, David M. Cahill, and Sangram K. Lenka. "Next-generation metabolic engineering approaches towards development of plant cell suspension cultures as specialized metabolite producing biofactories." Biotechnology Advances 45 (December 2020): 107635. http://dx.doi.org/10.1016/j.biotechadv.2020.107635.

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Cheng, Sihua, Xiumin Fu, Yinyin Liao, Xinlan Xu, Lanting Zeng, Jinchi Tang, Jianlong Li, Jianhong Lai, and Ziyin Yang. "Differential accumulation of specialized metabolite l-theanine in green and albino-induced yellow tea (Camellia sinensis) leaves." Food Chemistry 276 (March 2019): 93–100. http://dx.doi.org/10.1016/j.foodchem.2018.10.010.

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Gabotti, Damiano, Franca Locatelli, Erica Cusano, Elena Baldoni, Annamaria Genga, Laura Pucci, Roberto Consonni, and Monica Mattana. "Cell Suspensions of Cannabis sativa (var. Futura): Effect of Elicitation on Metabolite Content and Antioxidant Activity." Molecules 24, no. 22 (November 9, 2019): 4056. http://dx.doi.org/10.3390/molecules24224056.

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Cannabis sativa L. is one of the most-studied species for its phytochemistry due to the abundance of secondary metabolites, including cannabinoids, terpenes and phenolic compounds. In the last decade, fiber-type hemp varieties have received interest for the production of many specialized secondary metabolites derived from the phenylpropanoid pathway. The interest in these molecules is due to their antioxidant activity. Since secondary metabolite synthesis occurs at a very low level in plants, the aim of this study was to develop a strategy to increase the production of such compounds and to elucidate the biochemical pathways involved. Therefore, cell suspensions of industrial hemp (C. sativa L. var. Futura) were produced, and an advantageous elicitation strategy (methyl jasmonate, MeJA) in combination with precursor feeding (tyrosine, Tyr) was developed. The activity and expression of phenylalanine ammonia-lyase (PAL) and tyrosine aminotransferase (TAT) increased upon treatment. Through 1H-NMR analyses, some aromatic compounds were identified, including, for the first time, 4-hydroxyphenylpyruvate (4-HPP) in addition to tyrosol. The 4-day MeJA+Tyr elicited samples showed a 51% increase in the in vitro assay (2,2-diphenyl-1-picrylhydrazyl, DPPH) radical scavenging activity relative to the control and a 80% increase in the cellular antioxidant activity estimated on an ex vivo model of human erythrocytes. Our results outline the active metabolic pathways and the antioxidant properties of hemp cell extracts under the effect of specific elicitors.

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Meschede, Ingrid P., Nicholas C. Ovenden, Miguel C. Seabra, Clare E. Futter, Marcela Votruba, Michael E. Cheetham, and Thomas Burgoyne. "Symmetric arrangement of mitochondria:plasma membrane contacts between adjacent photoreceptor cells regulated by Opa1." Proceedings of the National Academy of Sciences 117, no. 27 (June 22, 2020): 15684–93. http://dx.doi.org/10.1073/pnas.2000304117.

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Mitochondria are known to play an essential role in photoreceptor function and survival that enables normal vision. Within photoreceptors, mitochondria are elongated and extend most of the inner-segment length, where they supply energy for protein synthesis and the phototransduction machinery in the outer segment, as well as acting as a calcium store. Here, we examined the arrangement of the mitochondria within the inner segment in detail using three-dimensional (3D) electron microscopy techniques and show they are tethered to the plasma membrane in a highly specialized arrangement. Remarkably, mitochondria and their cristae openings align with those of neighboring inner segments. The pathway by which photoreceptors meet their high energy demands is not fully understood. We propose this to be a mechanism to share metabolites and assist in maintaining homeostasis across the photoreceptor cell layer. In the extracellular space between photoreceptors, Müller glial processes were identified. Due to the often close proximity to the inner-segment mitochondria, they may, too, play a role in the inner-segment mitochondrial arrangement as well as metabolite shuttling. OPA1 is an important factor in mitochondrial homeostasis, including cristae remodeling; therefore, we examined the photoreceptors of a heterozygousOpa1knockout mouse model. The cristae structure in theOpa1+/−photoreceptors was not greatly affected, but the mitochondria were enlarged and had reduced alignment to neighboring inner-segment mitochondria. This indicates the importance of key regulators in maintaining this specialized photoreceptor mitochondrial arrangement.

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Yactayo-Chang, Jessica P., Hoang V. Tang, Jorrel Mendoza, Shawn A. Christensen, and Anna K. Block. "Plant Defense Chemicals against Insect Pests." Agronomy 10, no. 8 (August 8, 2020): 1156. http://dx.doi.org/10.3390/agronomy10081156.

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Insect pests cause significant global agricultural damage and lead to major financial and environmental costs. Crops contain intrinsic defenses to protect themselves from such pests, including a wide array of specialized secondary metabolite-based defense chemicals. These chemicals can be induced upon attack (phytoalexins) or are constitutive (phytoanticipins), and can have a direct impact on the pests or be used indirectly to attract their natural enemies. They form part of a global arms race between the crops and their insect pests, with the insects developing methods of suppression, avoidance, detoxification, or even capture of their hosts defensive chemicals. Harnessing and optimizing the chemical defense capabilities of crops has the potential to aid in the continuing struggle to enhance or improve agricultural pest management. Such strategies include breeding for the restoration of defense chemicals from ancestral varieties, or cross-species transfer of defense metabolite production.

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Ceusters, Nathalie, Stijn Luca, Regina Feil, Johan E. Claes, John E. Lunn, Wim Van den Ende, and Johan Ceusters. "Hierarchical clustering reveals unique features in the diel dynamics of metabolites in the CAM orchid Phalaenopsis." Journal of Experimental Botany 70, no. 12 (April 11, 2019): 3269–81. http://dx.doi.org/10.1093/jxb/erz170.

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Abstract Crassulacean acid metabolism (CAM) is a major adaptation of photosynthesis that involves temporally separated phases of CO2 fixation and accumulation of organic acids at night, followed by decarboxylation and refixation of CO2 by the classical C3 pathway during the day. Transitory reserves such as soluble sugars or starch are degraded at night to provide the phosphoenolpyruvate (PEP) and energy needed for initial carboxylation by PEP carboxylase. The primary photosynthetic pathways in CAM species are well known, but their integration with other pathways of central C metabolism during different phases of the diel light–dark cycle is poorly understood. Gas exchange was measured in leaves of the CAM orchid Phalaenopsis ‘Edessa’ and leaves were sampled every 2 h during a complete 12-h light–12-h dark cycle for metabolite analysis. A hierarchical agglomerative clustering approach was employed to explore the diel dynamics and relationships of metabolites in this CAM species, and compare these with those in model C3 species. High levels of 3-phosphoglycerate (3PGA) in the light activated ADP-glucose pyrophosphorylase, thereby enhancing production of ADP-glucose, the substrate for starch synthesis. Trehalose 6-phosphate (T6P), a sugar signalling metabolite, was also correlated with ADP-glucose, 3PGA and PEP, but not sucrose, over the diel cycle. Whether or not this indicates a different function of T6P in CAM plants is discussed. T6P levels were low at night, suggesting that starch degradation is regulated primarily by circadian clock-dependent mechanisms. During the lag in starch degradation at dusk, carbon and energy could be supplied by rapid consumption of a large pool of aconitate that accumulates in the light. Our study showed similarities in the diel dynamics and relationships between many photosynthetic metabolites in CAM and C3 plants, but also revealed some major differences reflecting the specialized metabolic fluxes in CAM plants, especially during light–dark transitions and at night.

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Bode, Edna, Antje K. Heinrich, Merle Hirschmann, Desalegne Abebew, Yan‐Ni Shi, Tien Duy Vo, Frank Wesche, et al. "Promoter Activation in Δ hfq Mutants as an Efficient Tool for Specialized Metabolite Production Enabling Direct Bioactivity Testing." Angewandte Chemie International Edition 58, no. 52 (December 19, 2019): 18957–63. http://dx.doi.org/10.1002/anie.201910563.

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Phelan, V. V., W. J. Moree, J. Aguilar, D. S. Cornett, A. Koumoutsi, S. M. Noble, K. Pogliano, C. A. Guerrero, and P. C. Dorrestein. "Impact of a Transposon Insertion in phzF2 on the Specialized Metabolite Production and Interkingdom Interactions of Pseudomonas aeruginosa." Journal of Bacteriology 196, no. 9 (February 14, 2014): 1683–93. http://dx.doi.org/10.1128/jb.01258-13.

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Journal articles on the topic 'Specialized metabolite'

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