PDC1, a pyruvate/α-ketoacid decarboxylase, is involved in acetaldehyde, propanal and pentanal biosynthesis in melon (Cucumis melo L.) fruit

Functional annotation of proteins in Catharanthus roseus shoot cultures under biogenic zinc nanotreatment

Nano-interactions are well known for their positive as well as negative impacts on the morphological and physiological systems of plants. Keeping in mind, the conformational changes in plant proteins as one of the key mechanisms for stress adaptation responses, the current project was designed to explore the effect of glutathione-capped and uncapped zinc nano-entities on Catharanthus roseus shoot cultures. Zinc nanotreatment (0.05 μg/mL) significantly induced ester production in C. roseus shoots as detected by Gas Chromatography-Mass spectrometry. These nanotreated shoots were further subjected to peptide-centric nano-LC-MS/MS analysis. Mass spectrometry followed by a Heat map revealed a significant effect of zinc nanoparticles on 59 distinct classes of proteins as compared to control. Proteins involved in regulating stress scavenging, transport, and secondary metabolite biosynthesis were robustly altered under capped zinc nanotreatment. UniProt database identified majority of the localization of the abundantly altered protein in cell membranes and chloroplasts. STRING and Cytoscape analysis assessed inter and intra coordination of triosephosphate isomerase with other identified proteins and highlighted its role in the regulation of protein abundance under applied stress. This study highlights the understanding of complex underlying mechanisms and regulatory networks involved in proteomic alterations and interactions within the plant system to cope with the nano-effect.

Genetic regulation of volatile production in two melon introgression line collections with contrasting ripening behavior

The importance of melon aroma in determining fruit quality has been highlighted in recent years. The fruit volatile profile is influenced by the type of fruit ripening. Non-climacteric fruits contain predominantly aldehydes, while climacteric fruits mainly produce esters. Several genes have been described to participate in volatile organic compounds (VOCs) biosynthesis pathways, but knowledge in this area is still incomplete. In this work we analysed the volatile profile of two reciprocal Introgression Line (IL) collections generated from a cross between 'Piel de Sapo' (PS) and 'Védrantais' (VED) melons, differing in their aroma profile and ripening behaviour. SPME GC-MS was performed to identify genes responsible for VOCs formation. More than 1000 QTLs for many volatiles were detected taken together both populations. Introgressions on chromosomes 3, 5, 6, 7 and 8 modified ester-aldehyde balance and were correlated to ripening changes in both genetic backgrounds. Some previously identified QTLs for fruit ripening might be involved in these phenotypes, such as ETHQV8.1 on chromosome 8 and ETHQV6.3 on chromosome 6. PS alleles on chromosomes 2, 6, 10 and 11 were found to increase ester content when introgressed in VED melons. Terpenes showed to be affected by several genomic regions not related to ripening. In addition, several candidate genes have been hypothesized to be responsible for some of the QTLs detected. The analysis of volatile compounds in two reciprocal IL collections has increased our understanding of the relationship between ripening and aroma and offers valuable plant material to improve food quality in melon breeding programs.

A translation proofreader of archaeal origin imparts multi-aldehyde stress tolerance to land plants

Aldehydes, being an integral part of carbon metabolism, energy generation, and signalling pathways, are ingrained in plant physiology. Land plants have developed intricate metabolic pathways which involve production of reactive aldehydes and its detoxification to survive harsh terrestrial environments. Here, we show that physiologically produced aldehydes, i.e., formaldehyde and methylglyoxal in addition to acetaldehyde, generate adducts with aminoacyl-tRNAs, a substrate for protein synthesis. Plants are unique in possessing two distinct chiral proofreading systems, D-aminoacyl-tRNA deacylase1 (DTD1) and DTD2, of bacterial and archaeal origins, respectively. Extensive biochemical analysis revealed that only archaeal DTD2 can remove the stable D-aminoacyl adducts on tRNA thereby shielding archaea and plants from these system-generated aldehydes. Using Arabidopsis as a model system, we have shown that the loss of DTD2 gene renders plants susceptible to these toxic aldehydes as they generate stable alkyl modification on D-aminoacyl-tRNAs, which are recycled only by DTD2. Bioinformatic analysis identifies the expansion of aldehyde metabolising repertoire in land plant ancestors which strongly correlates with the recruitment of archaeal DTD2. Finally, we demonstrate that the overexpression of DTD2 offers better protection against aldehydes than in wild type Arabidopsis highlighting its role as a multi-aldehyde detoxifier that can be explored as a transgenic crop development strategy.

Discrimination of internal browning in pineapple during storage based on changes in volatile compounds

Internal browning (IB) is a physiological disorder without external symptoms of postharvest pineapples, but whether and how IB influences pineapple volatiles remain unknown. We examined eigenvalues of volatiles in 'Comte de Paris' pineapples with or without IB using electronic nose (E-nose) and gas chromatography-mass spectrometry (GC-MS). Correlation coefficients between the responses of E-nose sensors S7 and S9 and IB were 0.836 and 0.804, respectively. The multilayer perceptron neural network and radial basis function neural network models classified IB degree with accuracy of 94.77% and 91.67%. GC-MS analysis revealed 30 volatile substances upregulated in pineapple with IB compared to those without, of which 15 were esters. IB regulated volatile compound synthesis through the lipoxygenase pathway which involved lipoxygenase, pyruvate decarboxylase 1, alcohol dehydrogenases, acyl-CoA oxidase 1, and alcohol acyltransferase genes and their related enzymes. These results suggested that volatiles regulated by IB could be used to discriminate IB severity in pineapples.

bZIP transcription factor PubZIP914 enhances production of fatty acid-derived volatiles in pear

'Nanguo' pear emitted a rich aroma when entirely ripe. The six-carbon (C6) volatiles, including the aldehydes, 2-hexenal, and hexanal, as well as their corresponding alcohols and esters which are derived from lipoxygenase pathway are the important volatile components in 'Nanguo' pears. However, the transcriptional regulation mechanism of aroma synthesis of 'Nanguo' pears remains largely unknown. bZIP transcription factors (TFs) mediate different developmental processes in plants. In this study, we identified and characterized a bZIP TF that is highly expressed and induced in 'Nanguo' pear fruits at the mature stage. The content of fatty acid-derived volatiles increased significantly in transgenic pears and tomatoes of PubZIP914 overexpression. Meanwhile, PubZIP914 could regulate PuLOX3.1 by binding directly to PuLOX3.1 promoter. The results of this study provide evidence demonstrating how bZIP transcription factors regulate fatty acid-derived volatiles biosynthesis during pear fruit ripening.

A metabolome and transcriptome survey to tap the dynamics of fruit prolonged shelf-life and improved quality within Greek tomato germplasm

Introduction

Tomato is a high economic value crop worldwide with recognized nutritional properties and diverse postharvest potential. Nowadays, there is an emerging awareness about the exploitation and utilization of underutilized traditional germplasm in modern breeding programs. In this context, the existing diversity among Greek accessions in terms of their postharvest life and nutritional value remains largely unexplored.

Methods

Herein, a detailed evaluation of 130 tomato Greek accessions for postharvest and nutritional characteristics was performed, using metabolomics and transcriptomics, leading to the selection of accessions with these interesting traits.

Results

The results showed remarkable differences among tomato Greek accessions for overall ripening parameters (color, firmness) and weight loss. On the basis of their postharvest performance, a balance between short shelf life (SSL) and long shelf life (LSL) accessions was revealed. Metabolome analysis performed on 14 selected accessions with contrasting shelf-life potential identified a total of 206 phytonutrients and volatile compounds. In turn, transcriptome analysis in fruits from the best SSL and the best LSL accessions revealed remarkable differences in the expression profiles of transcripts involved in key metabolic pathways related to fruit quality and postharvest potential.

Discussion

The pathways towards cell wall synthesis, polyamine synthesis, ABA catabolism, and steroidal alkaloids synthesis were mostly induced in the LSL accession, whereas those related to ethylene biosynthesis, cell wall degradation, isoprenoids, phenylpropanoids, ascorbic acid and aroma (TomloxC) were stimulated in the SSL accession. Overall, these data would provide valuable insights into the molecular mechanism towards enhancing shelf-life and improving flavor and aroma of modern tomato cultivars.

Ethanol mediates the interaction between Caenorhabditis elegans and the nematophagous fungus Purpureocillium lavendulum

Accurately recognizing pathogens by the host is vital for initiating appropriate immune response against infecting microorganisms. Caenorhabditis elegans has no known receptor to recognize pathogen-associated molecular pattern. However, recent studies showed that nematodes have a strong specificity for transcriptomes infected by different pathogens, indicating that they can identify different pathogenic microorganisms. However, the mechanism(s) for such specificity remains largely unknown. In this study, we showed that the nematophagous fungus Purpureocillium lavendulum can infect the intestinal tract of the nematode C. elegans and the infection led to the accumulation of reactive oxygen species (ROS) in the infected intestinal tract, which suppressed fungal growth. Co-transcriptional analysis revealed that fungal genes related to anaerobic respiration and ethanol production were up-regulated during infection. Meanwhile, the ethanol dehydrogenase Sodh-1 in C. elegans was also up-regulated. Together, these results suggested that the infecting fungi encounter hypoxia stress in the nematode gut and that ethanol may play a role in the host-pathogen interaction. Ethanol production in vitro during fungal cultivation in hypoxia conditions was confirmed by gas chromatography-mass spectrometry. Direct treatment of C. elegans with ethanol elevated the sodh-1 expression and ROS accumulation while repressing a series of immunity genes that were also repressed during fungal infection. Mutation of sodh-1 in C. elegans blocked ROS accumulation and increased the nematode's susceptibility to fungal infection. Our study revealed a new recognition and antifungal mechanism in C. elegans. The novel mechanism of ethanol-mediated interaction between the fungus and nematode provides new insights into fungal pathogenesis and for developing alternative biocontrol of pathogenic nematodes by nematophagous fungi. IMPORTANCE Nematodes are among the most abundant animals on our planet. Many of them are parasites in animals and plants and cause human and animal health problems as well as agricultural losses. Studying the interaction of nematodes and their microbial pathogens is of great importance for the biocontrol of animal and plant parasitic nematodes. In this study, we found that the model nematode Caenorhabditis elegans can recognize its fungal pathogen, the nematophagous fungus Purpureocillium lavendulum, through fungal-produced ethanol. Then the nematode elevated the reactive oxygen species production in the gut to inhibit fungal growth in an ethanol dehydrogenase-dependent manner. With this mechanism, novel biocontrol strategies may be developed targeting the ethanol receptor or metabolic pathway of nematodes. Meanwhile, as a volatile organic compound, ethanol should be taken seriously as a vector molecule in the microbial-host interaction in nature.

Postharvest chilling diminishes melon flavor via effects on volatile acetate ester biosynthesis

In postharvest handling systems, refrigeration can extend fruit shelf life and delay decay via slowing ripening progress; however, it selectively alters the biosynthesis of flavor-associated volatile organic compounds (VOCs), which results in reduced flavor quality. Volatile esters are major contributors to melon fruit flavor. The more esters, the more consumers enjoy the melon fruit. However, the effects of chilling on melon flavor and volatiles associated with consumer liking are yet to be fully understood. In the present study, consumer sensory evaluation showed that chilling changed the perception of melon fruit. Total ester content was lower after chilling, particularly volatile acetate esters (VAEs). Transcriptomic analysis revealed that transcript abundance of multiple flavor-associated genes in fatty acid and amino acid pathways was reduced after chilling. Additionally, expression levels of the transcription factors (TFs), such as NOR, MYB, and AP2/ERF, also were substantially downregulated, which likely altered the transcript levels of ester-associated pathway genes during cold storage. VAE content and expression of some key genes recover after transfer to room temperature. Therefore, chilling-induced changes of VAE profiles were consistent with expression patterns of some pathway genes that encode specific fatty acid- and amino acid-mobilizing enzymes as well as TFs involved in fruit ripening, metabolic regulation, and hormone signaling.

Quality and Metabolomics Analysis of Houttuynia cordata Based on HS-SPME/GC-MS

Houttuynia cordata is a medicinal and edible plant with a wide biological interest. Many parts were discarded due to various modes of consumption, resulting in resource waste. In this study, a comprehensive study was conducted on various edible indicators and medicinal components of Houttuynia cordata to understand its edible and medicinal value. The edible indexes of each root, stem, and leaf were determined, and the metabolites of different parts were investigated using the headspace solid-phase micro-extraction technique (HS-SPME-GC-MS). The differential metabolites were screened by orthogonal partial least squares discriminant analysis (OPLS-DA) and clustering analysis. The results of the study showed that the parts of Houttuynia cordata with high edibility values as a vegetable were mainly the roots and leaves, with the highest vitamin C content in the roots and the highest total flavonoids, soluble sugars, and total protein in the leaves. The nutrient content of all the stems of Houttuynia cordata was lower and significantly different from the roots and leaves (p < 0.05). In addition, 209 metabolites were isolated from Houttuynia cordata, 135 in the roots, 146 in the stems, 158 in the leaves, and 91 shared metabolites. The clustering analysis and OPLS-DA found that the parts of Houttuynia cordata can be mainly divided into above-ground parts (leaves and stems) and underground parts (roots). When comparing the differential metabolites between the above-ground parts and underground parts, it was found that the most important medicinal component of Houttuynia cordata, 2-undecanone, was mainly concentrated in the underground parts. The cluster analysis resulted in 28 metabolites with up-regulation and 17 metabolites with down-regulation in the underground parts. Most of the main components of the underground part have pharmacological effects such as anti-inflammatory, anti-bacterial and antiviral, which are more suitable for drug development. Furthermore, the above-ground part has more spice components and good antioxidant capacity, which is suitable for the extraction of edible flavors. Therefore, by comparing and analyzing the differences between the edible and medicinal uses of different parts of Houttuynia cordata as a medicinal and food plant, good insights can be obtained into food development, pharmaceutical applications, agricultural development, and the hygiene and cosmetic industries. This paper provides a scientific basis for quality control and clinical use.

Amino acids metabolism as a source for aroma volatiles biosynthesis

Aroma volatiles are essential for plant ecological fitness and reproduction. Plants produce and use volatiles to attract pollinators and seed dispersers, repel herbivores and recruit their natural enemies, and communicate with other plants. Amino acids and their biosynthetic intermediates play key roles as precursors for the biosynthesis of plant volatiles. Different plants utilize different strategies and biosynthetic pathways to meet their specific biological needs. This review focuses on the different biosynthetic pathways that plants utilize to form amino acid-derived aroma volatiles, emphasizing their common and unique aspects and stressing the importance of the limiting enzymes residing in the primary-specialized metabolism interface. We also briefly review how biotechnology has used this interface and point to promising future directions for improving the quality of agricultural produce and the production of key volatiles.

Machine learning discovery of missing links that mediate alternative branches to plant alkaloids

Engineering the microbial production of secondary metabolites is limited by the known reactions of correctly annotated enzymes. Therefore, the machine learning discovery of specialized enzymes offers great potential to expand the range of biosynthesis pathways. Benzylisoquinoline alkaloid production is a model example of metabolic engineering with potential to revolutionize the paradigm of sustainable biomanufacturing. Existing bacterial studies utilize a norlaudanosoline pathway, whereas plants contain a more stable norcoclaurine pathway, which is exploited in yeast. However, committed aromatic precursors are still produced using microbial enzymes that remain elusive in plants, and additional downstream missing links remain hidden within highly duplicated plant gene families. In the current study, machine learning is applied to predict and select plant missing link enzymes from homologous candidate sequences. Metabolomics-based characterization of the selected sequences reveals potential aromatic acetaldehyde synthases and phenylpyruvate decarboxylases in reconstructed plant gene-only benzylisoquinoline alkaloid pathways from tyrosine. Synergistic application of the aryl acetaldehyde producing enzymes results in enhanced benzylisoquinoline alkaloid production through hybrid norcoclaurine and norlaudanosoline pathways.

Producing plant secondary metabolites by microbes is limited by the known enzymatic reactions. Here, the authors apply machine learning to predict missing link enzymes of benzylisoquinoline alkaloid (BIA) biosynthesis in Papaver somniferum, and validate the specialized activities through heterologous production.

Production of Propionate by a Sequential Fermentation-Biotransformation Process via l-Threonine

Bio-based propionate is widely welcome in the food additive industry. The current anaerobic process by Propionibacteria endures low titers and a long fermentation time. In this study, a new route for propionate production from l-threonine was designed. 2-Ketobutyrate, deaminated from l-threonine, is cleaved into propionaldehyde and CO₂ and then be oxidized into propionic acid, which is neutralized by ammonia released from the first deamination step. This CoA-independent pathway with only CO₂ as a byproduct boosts propionate production from l-threonine with high productivity and purity. The key enzyme for 2-ketobutyrate decarboxylation was selected, and its expression was optimized. The engineered Pseudomonas putida strain, harboring 2-ketoisovalerate decarboxylase from Lactococcus lactis could produce 580 mM (43 g/L) pure propionic acid from 600 mM l-threonine in 24 h in the batch biotransformation process. Furthermore, a high titer of 62 g/L propionic acid with a productivity of 1.07 g/L/h and a molar yield of >0.98 was achieved in the fed-batch pattern. Finally, an efficient sequential fermentation-biotransformation process was demonstrated to produce propionate directly from the fermentation broth containing l-threonine, which further reduces the costs since no l-threonine purification step is required.

Unexpected Reactions of α,β-Unsaturated Fatty Acids Provide Insight into the Mechanisms of CYP152 Peroxygenases

CYP152 peroxygenases catalyze decarboxylation and hydroxylation of fatty acids using H₂ O₂ as cofactor. To understand the molecular basis for the chemo- and regioselectivity of these unique P450 enzymes, we analyze the activities of three CYP152 peroxygenases (OleT_JE , P450_SPα , P450_BSβ ) towards cis- and trans-dodecenoic acids as substrate probes. The unexpected 6S-hydroxylation of the trans-isomer and 4R-hydroxylation of the cis-isomer by OleT_JE , and molecular docking results suggest that the unprecedented selectivity is due to OleT_JE 's preference of C2-C3 cis-configuration. In addition to the common epoxide products, undecanal is the unexpected major product of P450_SPα and P450_BSβ regardless of the cis/trans-configuration of substrates. The combined H₂ ¹⁸ O₂ tracing experiments, MD simulations, and QM/MM calculations unravel an unusual mechanism for Compound I-mediated aldehyde formation in which the active site water derived from H₂ O₂ activation is involved in the generation of a four-membered ring lactone intermediate. These findings provide new insights into the unusual mechanisms of CYP152 peroxygenases.

Production of Aldehydes by Biocatalysis

The production of aldehydes, highly reactive and toxic chemicals, brings specific challenges to biocatalytic processes. Absence of natural accumulation of aldehydes in microorganisms has led to a combination of in vitro and in vivo strategies for both, bulk and fine production. Advances in genetic and metabolic engineering and implementation of computational techniques led to the production of various enzymes with special requirements. Cofactor synthesis, post-translational modifications and structure engineering are applied to prepare active enzymes for one-step or cascade reactions. This review presents the highlights in biocatalytical production of aldehydes with the potential to shape future industrial applications.

FaMYB9 is involved in the regulation of C6 volatile biosynthesis in strawberry

The large-scale untargeted proteomic and metabolomic studies were conducted in strawberry (Fragaria × ananassa) cv. Akihime fruit at five developmental stages. We found that some C6 volatiles highly contributed to the enrichment of volatiles at the red stage of strawberry fruit. We found that 12 genes involved in LOX pathway for volatile biosynthesis showed multiple patterns in protein abundance during fruit development and ripening, and 9 out of the 12 genes exhibited a significant increase in their relative expression levels at the red stage of fruit. We also found that the MYB9 gene (FaMYB9) expression level was positively correlated with the content of C6 volatiles (R = 0.989) and with the relative expression level and protein abundance of FaLOX5 at different strawberry fruit developmental stages (R = 0.954). The interaction between FaMYB9 and FaLOX5 was detected by yeast two-hybrid, co-immunoprecipitation (Co-IP), bimolecular fluorescence complementation (BiFC), and immunofluorescence (IF) analyses. Transient silencing of FaMYB9 delayed the fruit development and ripening, resulting in a significant decrease in the contents of C6 volatiles, while overexpression of FaMYB9 increased the fruit development and ripening and the contents of C6 volatiles in Akihime fruit. Therefore, FaMYB9 is positively involved in C6 volatile biosynthesis.

From Central to Specialized Metabolism: An Overview of Some Secondary Compounds Derived From the Primary Metabolism for Their Role in Conferring Nutritional and Organoleptic Characteristics to Fruit

Fruit flavor and nutritional characteristics are key quality traits and ones of the main factors influencing consumer preference. Central carbon metabolism, also known as primary metabolism, contributes to the synthesis of intermediate compounds that act as precursors for plant secondary metabolism. Specific and specialized metabolic pathways that evolved from primary metabolism play a key role in the plant's interaction with its environment. In particular, secondary metabolites present in the fruit serve to increase its attractiveness to seed dispersers and to protect it against biotic and abiotic stresses. As a consequence, several important organoleptic characteristics, such as aroma, color, and fruit nutritional value, rely upon secondary metabolite content. Phenolic and terpenoid compounds are large and diverse classes of secondary metabolites that contribute to fruit quality and have their origin in primary metabolic pathways, while the delicate aroma of ripe fruits is formed by a unique combination of hundreds of volatiles that are derived from primary metabolites. In this review, we show that the manipulation of primary metabolism is a powerful tool to engineer quality traits in fruits, such as the phenolic, terpenoid, and volatile content. The enzymatic reactions responsible for the accumulation of primary precursors are bottlenecks in the transfer of metabolic flux from central to specialized metabolism and should be taken into account to increase the yield of the final products of the biosynthetic pathways. In addition, understanding the connection and regulation of the carbon flow between primary and secondary metabolism is a key factor for the development of fruit cultivars with enhanced organoleptic and nutritional traits.