Differentially Accumulated Proteins Research Articles

Comparative proteomic analysis of papaya bud flowers reveals metabolic signatures and pathways driving hermaphrodite development

Papaya (Carica papaya) is a trioecious species with female, male, and hermaphrodite plants. Given the sex segregation, selecting hermaphroditic plants is vital for orchard establishment due to their greater commercial value. However, selecting hermaphrodite plants through sexing is laborious and costly. Moreover, environmental stressors can exacerbate the issue by potentially inducing abnormal flower development, thus affecting fruit quality. Despite these challenges, the molecular mechanisms governing sex development in papaya remain poorly understood. Thus, this study aimed to identify proteins associated with sex development in female and hermaphrodite flowers of papaya through comparative proteomic analysis. Proteins from flower buds at the early and late developmental stages of three papaya genotypes (UENF-CALIMAN 01, JS12, and Sunrise Solo 72/12) were studied via proteomic analysis via the combination of the shotgun method and nanoESI-HDMSE technology. In buds at an early stage of development, 496 (35.9%) proteins exhibited significantly different abundances between sexes for the SS72/12 genotype, 139 (10%) for the JS12 genotype, and 165 (11.9%) for the UC-01 genotype. At the final stage of development, there were 181 (13.5%) for SS72/12, 113 (8.4%) for JS12, and 125 (9.1%) for UC-01. The large group of differentially accumulated proteins (DAPs) between the sexes was related to metabolism, as shown by the observation of only the proteins that exhibited the same pattern of accumulation in the three genotypes. Specifically, carbohydrate metabolism proteins were up-regulated in hermaphrodite flower buds early in development, while those linked to monosaccharide and amino acid metabolism increased during late development. Enrichment of sporopollenin and phenylpropanoid biosynthesis pathways characterizes hermaphrodite samples across developmental stages, with predicted protein interactions highlighting the crucial role of phenylpropanoids in sporopollenin biosynthesis for pollen wall formation. Most of the DAPs played key roles in pectin, cellulose, and lignin synthesis and were essential for cell wall formation and male flower structure development, notably in the pollen coat. These findings suggest that hermaphrodite flowers require more energy for development, likely due to complex pollen wall formation. Overall, these insights illuminate the molecular mechanisms of papaya floral development, revealing complex regulatory networks and energetic demands in the formation of male reproductive structures.

Integrated omics approach reveals the molecular pathways activated in tomato by Kocuria rhizophila, a soil plant growth-promoting bacterium

Plant microbial biostimulants application has become a promising and eco-friendly agricultural strategy to improve crop yields, reducing chemical inputs for more sustainable cropping systems. The soil dwelling bacterium Kocuria rhizophila was previously characterized as Plant Growth Promoting Bacteria (PGPB) for its multiple PGP traits, such as indole-3-acetic acid production, phosphate solubilization capability and salt and drought stress tolerance. Here, we evaluated by a multi-omics approach, the PGP activity of K. rhizophila on tomato, revealing the molecular pathways by which it promotes plant growth. Transcriptomic analysis showed several up-regulated genes mainly related to amino acid metabolism, cell wall organization, lipid and secondary metabolism, together with a modulation in the DNA methylation profile, after PGPB inoculation. In agreement, proteins involved in photosynthesis, cell division, and plant growth were highly accumulated by K. rhizophila. Furthermore, “amino acid and peptides”, “monosaccharides”, and “TCA” classes of metabolites resulted the most affected by PGPB treatment, as well as dopamine, a catecholamine neurotransmitter mediating plant growth through S-adenosylmethionine decarboxylase (SAMDC), a gene enhancing the vegetative growth, up-regulated in tomato by K. rhizophila treatment. Interestingly, eight gene modules well correlated with differentially accumulated proteins (DAPs) and metabolites (DAMs), among which two modules showed the highest correlation with nine proteins, including a nucleoside diphosphate kinase, and cytosolic ascorbate peroxidase, as well as with several amino acids and metabolites involved in TCA cycle. Overall, our findings highlighted that sugars and amino acids, energy regulators, involved in tomato plant growth, were strongly modulated by the K. rhizophila-plant interaction.

Integrated metabolomics and proteomics analyses reveal the molecular mechanism underlying the yellow leaf phenotype of Camellia sinensis

The tea plant cultivar ‘Zhonghuang 2’ (ZH2) possesses albino-induced yellow leaves that contain low levels of catechins but high contents of amino acids. However, the molecular mechanism underlying the yellow leaf phenotype of ZH2 has not been elucidated clearly. In the current research, the yellow shoots (ZH2-Y) and naturally converted green shoots (ZH2-G) of ZH2 were studied using metabolic and proteomic profiling for a better understanding of the mechanism underlying phenotype formation. In total, 107 differentially changed metabolites (DCMs) were identified from the GC‒MS-based metabolomics, and 189 differentially accumulated proteins (DAPs) were identified from the tandem mass tag (TMT)-based quantitative proteomics. Subsequently, integrated analysis revealed that ‘porphyrin and chlorophyll metabolism’, ‘carbon fixation in photosynthetic organisms’, and ‘phenylpropanoid biosynthesis’ pathways were commonly enriched for DAPs and DCMs. We further found that the inhibition of chlorophyll biosynthesis, the deficiency of photosynthetic proteins and the imbalance of the ROS-scavenging system were the crucial reasons responsible for the chlorosis, chloroplast abnormality and photooxidative damage of ZH2 leaves. Altogether, our research combines metabolomics and proteomics approaches to uncover the molecular mechanism leading to the yellow leaf phenotype of tea plants.

Integrated Transcriptomic and Proteomic Characterization of a Chromosome Segment Substitution Line Reveals the Regulatory Mechanism Controlling the Seed Weight in Soybean

Soybean is the major global source of edible oils and vegetable proteins. Seed size and weight are crucial traits determining the soybean yield. Understanding the molecular regulatory mechanism underlying the seed weight and size is helpful for improving soybean genetic breeding. The molecular regulatory pathways controlling the seed weight and size were investigated in this study. The 100-seed weight, seed length, seed width, and seed weight per plant of a chromosome segment substitution line (CSSL) R217 increased compared with those of its recurrent parent ‘Suinong14’ (SN14). Transcriptomic and proteomic analyses of R217 and SN14 were performed at the seed developmental stages S15 and S20. In total, 2643 differentially expressed genes (DEGs) and 208 differentially accumulated proteins (DAPs) were detected at S15, and 1943 DEGs and 1248 DAPs were detected at S20. Furthermore, integrated transcriptomic and proteomic analyses revealed that mitogen-activated protein kinase signaling and cell wall biosynthesis and modification were potential pathways associated with seed weight and size control. Finally, 59 candidate genes that might control seed weight and size were identified. Among them, 25 genes were located on the substituted segments of R217. Two critical pathways controlling seed weight were uncovered in our work. These findings provided new insights into the seed weight-related regulatory network in soybean.

Decoding the effects of drought stress on popcorn (Zea mays var. everta) flowering combining proteomics and physiological analysis

Under conditions of soil water limitation and adequate irrigation, we conducted an investigation into the growth dynamics, gas exchange performance, and proteomic profiles of two inbred popcorn lines—L71, characterized as drought-tolerant, and L61, identified as drought-sensitive. Our goal was to uncover the mechanisms associated with tolerance to soil water limitation during the flowering. The plants were cultivated until grain filling in a substrate composed of perlite and peat within 150cm long lysimeter, subjected to two water conditions (WC): i) irrigated (WW) at lysimeter capacity (LC - 100%), and ii) water-stressed (WS). Under WS conditions, the plants gradually reached 45% of LC and were maintained at this level for 10 days. Irrespective of the WC, L71 exhibited the highest values of dry biomass in both shoot and root systems, signifying its status as the most robust genotype. The imposed water limitation led to early senescence, chlorophyll degradation, and increased anthocyanin levels, with a more pronounced impact observed in L61. Traits related to gas exchange manifested differences between the lines only under WS conditions. A total of 1838 proteins were identified, with 169 differentially accumulated proteins (DAPs) in the tolerant line and 386 DAPs in the sensitive line. Notably, differences in energy metabolism, photosynthesis, oxidative stress response, and protein synthesis pathways were identified as the key distinctions between L71 and L61. Consequently, our findings offer valuable insights into the alterations in proteomic profiles associated with the adaptation to soil water limitation in popcorn.

Quantitative proteomics and metabolomics analysis reveals the response mechanism of alfalfa (Medicago sativa L.) to o-coumaric acid stress

O-coumaric acid (OCA), as a significant phenolic allelochemical found in hairy vetch (Vicia villosa Roth.), that can hinder the growth of alfalfa (Medicago sativa L.), particularly the growth of alfalfa roots. Nonetheless, the mechanism by which OCA inhibits alfalfa root growth remains unclear. In this study, a liquid chromatography tandem mass spectrometry (LC-MS/MS)-based quantitative proteomics analysis was carried out to identify differentially accumulated proteins (DAPs) under OCA treatment. The findings indicated that 680 proteins were DAPs in comparison to the control group. Of those, 333 proteins were up-regulated while 347 proteins were down-regulated. The enrichment analysis unveiled the significance of these DAPs in multiple biological and molecular processes, particularly in ribosome, phenylpropanoid biosynthesis, glutathione metabolism, glycolysis/gluconeogenesis and flavonoid biosynthesis. The majority of DAPs reside in the cytoplasm (36.62%), nucleus (20.59%) and extracellular space (14.12%). In addition, phenylalanine deaminase was identified as a potential chemical-induced regulation target associated with plant lignin formation. DAPs were mainly enriched in flavonoid biosynthesis pathways, which were related to plant root size. Using the UPLC-ESI-MS/MS technique and database, a total of 87 flavonoid metabolites were discovered. The metabolites were predominantly enriched for biosynthesizing naringenin chalcone, which was linked to plant lignin formation, aligning with the enrichment outcomes of DAPs. Consequently, it was deduced that OCA impacted the structure of cell walls by mediating the synthesis of lignin in alfalfa roots, subsequently inducing wilt. Furthermore, a range of proteins have been identified as potential candidates for the breeding of alfalfa strains with enhanced stress tolerance.

Tandem mass tag-based quantitative proteomics elucidates the inactivation mechanisms of high-power pulsed microwave treatment on Pseudomonas aeruginosa PAO1

This study explored the effect of HPPM treatment (200 Hz for 3, 5, 7, 9, and 11 min) on P. aeruginosa PAO1 inactivation using tandem mass tag-based quantitative proteomics. HPPM demonstrated marked nucleic acid and protein constituents (p < 0.05) and inhibited ATPase activity and intercellular ATP concentration time-dependently. Hence, 9 min was selected for proteomic profiling to avoid any potential thermal effect. A total of 452 proteins (309 = down-regulated; 143 = up-regulated) were identified as differentially accumulated proteins (DAPs). The DAPs were primarily related to energy production and conversion; DNA replication, transcription, and translation, cell membrane composition; amino acid (AA) transport and metabolism, and biofilm formation and quorum sensing (QS). HPPM significantly disrupted cell membrane composition, altered AA metabolism, impeded cell energy generation, and drastically inhibited biofilm formation in P. aeruginosa. This study provided insights into the underlying mechanisms of HPPM against P. aeruginosa at the proteomic level. Industrial relevancePseudomonas aeruginosa is a key spoiler implicated in food contamination. High-power pulsed microwave (HPPM) is a potential non-thermal inactivation technology. However, the underlying mechanism to validate its efficacy remains unclear. This study provides the industry with the inactivation efficacy of HPPM against P. aeruginosa, highlighting insights into the molecular and biochemical changes after treatment and its remarkable potential to control cross-contamination in food processing, food services, and clinical environments.

Comparative proteomic analysis of the moderately resistant and susceptible peanut cultivars during infestation by Cylindrocladium parasiticum

Cylindrocladium parasiticum Crous, Wingfield & Alfenas, the causal agent of Cylindrocladium black rot of peanut, has led to economic losses in China. However, the response of peanut plant to C. parasiticum is poorly understood. Here, two contrasting peanut cultivars, T09 (C. parasiticum-moderately resistant) and P562 (C. parasiticum-susceptible) were used for comparative analysis of protein profiles in root segment of plant tissues in responses to C. parasiticum infection. Proteomic profiling identified 1647 and 391 differentially accumulated proteins (DAPs) in P562 and T09 relative to uninoculated control, respectively. A total of 350 and 1095 DAPs were identified between P562 and T09 after 9 day(s) post infection (dpi), respectively. Functional categorization showed that C. parasiticum-responsive proteins were mainly involved in catalytic activity and binding functions. KEGG pathway analysis indicated both moderately resistant and susceptible peanut cultivars can regulate gene expression in the phenylpropanoid pathway, terpenoid backbone biosynthesis, SA, and JA pathways to induce defensive genes and protein expression which enhances plant defence or susceptibility capacity. However, MAPK signal pathway was more pronounced in moderately resistant peanut cultivar T09. We also observed an increase of CYP73A100 involved in phenylpropanoid and flavonoid biosynthesis pathways in susceptible peanut ecotype P562, while decrease in moderately resistant interaction. Additionally, there was a marked activation of brassinosteroid biosynthesis in T09, which indicated a possible involvement of activation of plant immune response in moderately resistant responses of peanut to C. parasiticum. This study provides some insights into molecular networks involved in cellular and physiological responses to C. parasiticum in peanut.

Analysis of the apoplast fluid proteome during the induction of systemic acquired resistance in Arabidopsis thaliana.

Plant-pathogen interactions occur in the apoplast comprising the cell wall matrix and the fluid in the extracellular space outside the plasma membrane. However, little is known regarding the contribution of the apoplastic proteome to systemic acquired resistance (SAR). Specifically, SAR was induced by inoculating plants with Pst DC3000 avrRps4. The apoplast washing fluid (AWF) was collected from the systemic leaves of the SAR-induced or mock-treated plants. A label free quantitative proteomic analysis was performed to identified the proteins related to SAR in AWF. A total of 117 proteins were designated as differentially accumulated proteins (DAPs), including numerous pathogenesis-related proteins, kinases, glycosyl hydrolases, and redox-related proteins. Functional enrichment analyses shown that these DAPs were mainly enriched in carbohydrate metabolic process, cell wall organization, hydrogen peroxide catabolic process, and positive regulation of catalytic activity. Comparative analysis of proteome data indicated that these DAPs were selectively enriched in the apoplast during the induction of SAR. The findings of this study indicate the apoplastic proteome is involved in SAR. The data presented herein may be useful for future investigations on the molecular mechanism mediating the establishment of SAR.

Mapping the gene of a maize leaf senescence mutant and understanding the senescence pathways by expression analysis.

Narrowing down to a single putative target gene behind a leaf senescence mutant and constructing the regulation network by proteomic method. Leaf senescence mutant is an important resource for exploring molecular mechanism of aging. To dig for potential modulation networks during maize leaf aging process, we delimited the gene responsible for a premature leaf senescence mutant els5 to a 1.1Mb interval in the B73 reference genome using a BC1F1 population with 40,000 plants, and analyzed the leaf proteomics of the mutant and its near-isogenic wild type line. A total of 1355 differentially accumulated proteins (DAP) were mainly enriched in regulation pathways such as "photosynthesis", "ribosome", and "porphyrin and chlorophyll metabolism" by the KEGG pathway analysis. The interaction networks constructed by incorporation of transcriptome data showed that ZmELS5 likely repaired several key factors in the photosynthesis system. The putative candidate proteins for els5 were proposed based on DAPs in the fined QTL mapping interval. These results provide fundamental basis for cloning and functional research of the els5 gene, and new insights into the molecular mechanism of leaf senescence in maize.

Analysis of Altered Flowering Related Genes in a Multi-Silique Rapeseed (Brassica napus L.) Line zws-ms Based on Combination of Genome, Transcriptome and Proteome Data

Based on previous researches, we further investigated the multi-silique trait in rapeseed (Brassica napus L.) line zws-ms. In this study, we used a relatively comprehensive list of flowering related genes in rapeseed and compared them between zws-ms and its near-isogenic line (NIL) zws-217. Genes were studied on genome, transcriptome and proteome levels and then we focused on genes with non-synonymous single nucleotide polymorphism (SNP) or frame-shift insertion-deletion (InDel), finding some genes on the list which changes their sequences. Then, combined with their annotation and the information of their orthologs, certain genes such as BnaA09g05900D, ortholog of AGAMOUS-LIKE 42 (AGL42), which encodes an MADS-box protein, were assumed as probably responsible for the multi-silique trait. Also, we analyzed the Differentially Accumulated Proteins (DAPs) between zws-ms and zws-217, revealing some genes involved in homologous recombination and mismatch repair pathways. Since the development of flowers/siliques is crucial to crops and it influences the yield of rapeseed, this study paved a way to deeply understand the mechanism of the multi-pistil flower formation, which may facilitate researches on rapeseed production in future.

Proteomics Identified UDP-Glycosyltransferase Family Members as Pro-Viral Factors for Turnip Mosaic Virus Infection in Nicotiana benthamiana.

Viruses encounter numerous host factors that facilitate or suppress viral infection. Although some host factors manipulated by viruses were uncovered, we have limited knowledge of the pathways hijacked to promote viral replication and activate host defense responses. Turnip mosaic virus (TuMV) is one of the most prevalent viral pathogens in many regions of the world. Here, we employed an isobaric tag for relative and absolute quantitation (iTRAQ)-based proteomics approach to characterize cellular protein changes in the early stages of infection of Nicotiana benthamiana by wild type and replication-defective TuMV. A total of 225 differentially accumulated proteins (DAPs) were identified (182 increased and 43 decreased). Bioinformatics analysis showed that a few biological pathways were associated with TuMV infection. Four upregulated DAPs belonging to uridine diphosphate-glycosyltransferase (UGT) family members were validated by their mRNA expression profiles and their effects on TuMV infection. NbUGT91C1 or NbUGT74F1 knockdown impaired TuMV replication and increased reactive oxygen species production, whereas overexpression of either promoted TuMV replication. Overall, this comparative proteomics analysis delineates the cellular protein changes during early TuMV infection and provides new insights into the role of UGTs in the context of plant viral infection.

Comparative proteomic and physiological analyses reveal tribenuron-methyl phytotoxicity and nontarget-site resistance mechanisms in Brassicanapus.

The application of herbicides is the most effective strategy for weed control and the development of herbicide-resistant crops will facilitate the weed management. The acetolactate synthase-inhibiting herbicide, tribenuron-methyl (TBM), is broadly used for weed control. However, its application in rapeseed field is restricted since rapeseed is sensitive to TBM. Herein, an integrated study of cytological, physiological and proteomic analysis of the TBM-resistant rapeseed mutant M342 and its wild-type (WT) plants was conducted. After TBM spraying, M342 showed improved tolerance to TBM, and proteins implicated in non-target-site resistance (NTSR) to herbicides had a significantly higher level in M342 as compared with the WT. Differentially accumulated proteins (DAPs) between these two genotypes were enriched in glutathione metabolism and oxidoreduction coenzyme metabolic process, which protected the mutant from oxidative stress triggered by TBM. Important DAPs related to stress or defence response were up-accumulated in M342regardless of the TBM treatment, which might serve as the constitutive part of NTSR to TBM. These results provide new clues for further exploration of the NTSR mechanism in plants and establish a theoretical basis for the development of herbicide-resistant crops.

Proteomics Reveals Damaging Effect of Alpha-Cypermethrin Exposure in a Non-Target Freshwater Microalga Chlorella sp. NC-MKM

Alpha-cypermethrin, a pyrethroid pesticide, is frequently used on crops to prevent insect attacks. However, occasionally, due to drift, leaching, or with rainwater, it enters the aquatic environment and poses a serious threat to the growth of non-target aquatic organisms. In the current study, we were interested in investigating the damaging effect of alpha-cypermethrin on a local freshwater non-target green alga Chlorella sp. NC-MKM in terms of its protein levels. This was achieved by exposing Chlorella sp. NC-MKM to an EC50 concentration of alpha-cypermethrin for 1day, followed by the two-dimensional (2-D) gel electrophoresis and MALDI-TOF MS. Fifty-three proteins, which had showed significant differential accumulation (> 1.5 fold, P < 0.05) after exposure to alpha-cypermethrin, were considered as differentially accumulated proteins (DAPs). These DAPs were further divided into several functional categories, and the expressions of each in control and treatment samples were compared. Comparison revealed that alpha-cypermethrin exposure affects the accumulation of proteins related with photosynthesis, stress response, carbohydrate metabolism, signal transduction and transporters, translation, transcription, cell division, lipid metabolism, amino acid and nucleotide biosynthesis, secondary metabolites production, and post-translational modification, and thus rendered the tested algal isolate sensitive toward this pesticide. The overall findings of this research thus offer a fundamental understanding of the possible mechanism of action of the insecticide alpha-cypermethrin on the microalga Chlorella sp. NC-MKM and also suggest potential biomarkers for the investigation of pesticide exposed microalgae.

Physiology and proteomics analyses reveal the response mechanisms of Rhizophora mucronata seedlings to prolonged complete submergence.

Mangrove seedlings are subject to natural tidal inundation, while occasional flooding may lead to complete submergence. Complete submergence reduces light availability and limits gas exchange, affecting several plant metabolic processes. The present study focuses on Rhizophora mucronata, a common mangrove species found along the coasts of Thailand and the Malay Peninsula. To reveal response mechanisms of R. mucronata seedlings to submergence, a physiological investigation coupled with proteomic analyses of leaf and root tissues was carried out in plants subjected to 20 days of control (drained) or submerged conditions. Submerged seedlings showed decreased photosynthetic activity, lower stomatal conductance, higher total antioxidant capacity in leaves and higher lipid peroxidation in roots than control plants. At the same time, tissue nutrient ion content displayed organ-specific responses. Proteome analysis revealed a significant change in 240 proteins in the leaves and 212 proteins in the roots. In leaves, most differentially accumulated proteins (DAPs) are associated with nucleic acids, stress response, protein transport, signal transduction, development and photosynthesis. In roots, most DAPs are associated with protein metabolic process, response to abiotic stimulus, nucleic acid metabolism and transport. Our study provides a comprehensive understanding of submergence responses in R. mucronata seedlings. The results suggest that submergence induced multifaceted stresses related to light limitation, oxidative stress and osmotic stress, but the responses are organ specific. The results revealed many candidate proteins which may be essential for survival of R. mucronata under prolonged submergence.

Comparative proteomic analysis identified proteins and the phenylpropanoid biosynthesis pathway involved in the response to ABA treatment in cotton fiber development

Abscisic acid (ABA) is a plant hormone that plays an important role in cotton fiber development. In this study, the physiological changes and proteomic profiles of cotton (Gossypium hirsutum) ovules were analyzed after 20 days of ABA or ABA inhibitor (ABAI) treatment. The results showed that compared to the control (CK), the fiber length was significantly decreased under ABA treatment and increased under ABAI treatment. Using a tandem mass tags-based quantitative technique, the proteomes of cotton ovules were comprehensively analyzed. A total of 7321 proteins were identified, of which 365 and 69 differentially accumulated proteins (DAPs) were identified in ABA versus CK and ABAI versus CK, respectively. Specifically, 345 and 20 DAPs were up- and down-regulated in the ABA group, and 65 and 4 DAPs were up- and down-regulated in the ABAI group, respectively. The DAPs in the ABA group were mainly enriched in the biosynthesis of secondary metabolites, phenylpropanoid biosynthesis and flavonoid secondary metabolism, whereas the DAPs in the ABAI group were mainly enriched in the indole alkaloid biosynthesis and phenylpropanoid biosynthesis pathways. Moreover, 9 proteins involved in phenylpropanoid biosynthesis were upregulated after ABA treatment, suggesting that this pathway might play important roles in the response to ABA, and 3 auxin-related proteins were upregulated, indicating that auxin might participate in the regulation of fiber development under ABAI treatment.

Cd-induced cytosolic proteome changes in the cyanobacterium Anabaena sp. PCC7120 are mediated by LexA as one of the regulatory proteins

LexA, a well-characterized transcriptional repressor of SOS genes in heterotrophic bacteria, has been shown to regulate diverse genes in cyanobacteria. An earlier study showed that LexA overexpression in a cyanobacterium, Anabaena sp. PCC7120 reduces its tolerance to Cd stress. This was later shown to be due to modulation of photosynthetic redox poising by LexA under Cd stress. However, due to the global regulatory nature of LexA and the prior prediction of AnLexA-box in a few heavy metal-responsive genes, we speculated that LexA has a broad role in Cd tolerance, with regulation over a variety of Cd stress-responsive genes in addition to photosynthetic genes. Thus, to further expand the knowledge on the regulatory role of LexA in Cd stress tolerance, a cytosolic proteome profiling of Anabaena constitutively overexpressing LexA upon Cd stress was performed. The proteomic study revealed 25 differentially accumulated proteins (DAPs) in response to the combined effect of LexA overexpression and Cd stress, and the other 11 DAPs exclusively in response to either LexA overexpression or Cd stress. The 36 identified proteins were related with a variety of functions, including photosynthesis, C-metabolism, antioxidants, protein turnover, post-transcriptional modifications, and a few unknown and hypothetical proteins. The regulation of LexA on corresponding genes, and six previously reported Cd efflux transporters, was further validated by the presence of AnLexA-boxes, transcript, and/or promoter analyses. In a nutshell, this study identifies the regulation of Anabaena LexA on several Cd stress-responsive genes of various functions, hence expanding the regulatory role of LexA under Cd stress.

Transcriptome and proteome analyses reveal a critical role of the sucrose anabolic pathway in regulating Quercus fabri Hance axillary bud outgrowth

Shoot branching is an important aspect of plant architecture because it greatly affects both plant biomass and crop yield. Sucrose is not only a nutrient but also a key signal regulator in bud outgrowth and development. Yet little is known about the mechanisms underlying the shoot branching development of Quercus fabri Hance. In this study, transcriptomics and proteomics analysis of Q. fabri FB and MB mutants were performed. A total of 23 054 differentially expressed genes (DEGs) and 5925 differentially accumulated proteins (DAPs) were identified. The KEGG enrichment analysis revealed that sucrose anabolism pathways were the most active biological pathways associated with downregulated DEGs and DAPs of the SZ-vs.-DZ comparison group. Finally, from the two omics, nine candidate genes having the same trend in expression were selected from among the sucrose anabolism pathways. Their correlation and protein interaction network analysis revealed that these nine genes were most closely related to tryptophan metabolism, plant hormone signal transduction, and cysteine and methionine metabolism. Taken together, these findings can help to elucidate the molecular mechanism and regulatory network of sucrose metabolism and branch development in Quercus trees.

ApGA20ox1, a key gibberellin biosynthesis gene, regulates somatic embryogenesis and plant height in Agapanthus praecox

Agapanthus praecox is cultivated worldwide as an ornamental plant, and a dwarf ideotype has become more popular due to its superior lodging resistance and its suitability for use in cut flowers. The main bioactive gibberellin (GA) controlling scape height in A. praecox is GA4. A GA biosynthesis gene, ApGA20ox1, controls GA4 biosynthesis in this species. Here, we report the development of an A. praecox dwarf phenotype, which was generated by targeted suppression of the biosynthetic pathway for GAs. We utilized Agrobacterium-mediated genetic transformation using embryogenic callus with RNA interference (RNAi) to selectively reduce the expression of the ApGA20ox1 gene. Interestingly, suppression of ApGA20ox1 resulted in poor somatic embryogenesis potential in A. praecox, which was accompanied by a higher accumulation of hydrogen peroxide and poorer catalase activity. Subsequently, the RNAi plantlets showed lower GA levels, leading to inhibition of cell longitudinal size in leaves, which reduced plant height. Furthermore, the dwarf (RNAi) plantlets accumulated higher levels of saccharides and plant hormones such as indole acetic acid (IAA) and abscisic acid (ABA) than the wild type accumulated. However, the levels of endogenous hormones such as GAs, brassinosteroids (BRs), cytokinins (CTKs), which respond to cell proliferation and cell expansion, were significantly decreased. Isobaric tags for relative and absolute quantification (iTRAQ) proteomics revealed that differentially accumulated proteins (DAPs) were enriched differently between control and RNAi plantlets in the categories of cell wall, hormone metabolism, carbohydrate metabolism and stress response. This study provides new insights into the role of GAs in the process of somatic embryogenesis and plant height control in A. praecox.

Physiological Characteristics and Proteome of Dalbergia odorifera in Loam and Gravel Substrates

Dalbergia odorifera, a crucial medicinal and commercial plant, shows great potential for ecological restoration in karst rocky desertification (KRD) areas. However, no studies have examined its adaptation mechanism to barren KRD environments. We focused on the physiological and protein variations of D. odorifera grown under loam substrate (LS), composite substrate (CS, 50% gravel), and gravel substrate (GS, 100% gravel). Results showed that volume, surface area, and dry weight of root in CS were the highest. Proteomic analysis revealed 516 and 443 differentially accumulated proteins (DAPs) in CS compared with LS and GS, respectively. Functional analysis showed that epidermal morphogenesis, organic substrate transport, lipid transport, and detection of abiotic stimulus were enriched in the overlapped DAPs. In addition, compared to LS, specific DAPs in CS were enriched to Gene Ontology (GO) terms such as root hair cell differentiation, ATP, carbohydrate metabolism, and also to pathways including carbohydrate digestion and absorption, starch and sucrose metabolism, HIF-1 signaling, mineral absorption, and lysosome. However, specific DAPs in CS relative to GS were clustered to hydrogen peroxide, fatty acid biosynthesis, and lipid metabolism. Furthermore, a series of transcripts encoding crucial DAPs were confirmed by RT-qPCR. In conclusion, the physiological characteristics and proteomic landscape showed that CS substrate was more favorable to the adaptation of D. odorifera to KRD than LS and GS substrates. The protein evaluation related to substrates in this study provides further evidence for ecological management of D. odorifera in KRD areas.