Dihydrodipicolinate Synthase: Structure, Dynamics, Function, and Evolution

Evidence for novel polycyclic aromatic hydrocarbon degradation pathways in culturable marine isolates

IMPORTANCE

Polycyclic aromatic hydrocarbon (PAH) pollution is widespread throughout marine environments and significantly affects native flora and fauna. Investigating microbes responsible for degrading PAHs in these environments provides a greater understanding of natural attenuation in these systems. In addition, the use of culture-based approaches to inform bioinformatic and omics-based approaches is useful in identifying novel mechanisms of PAH degradation that elude genetic biomarker-based investigations. Furthermore, culture-based approaches allow for the study of PAH co-metabolism, which increasingly appears to be a prominent mechanism for PAH degradation in marine microbes.

Potential Importance of Molybdenum Priming to Metabolism and Nutritive Value of Canavalia spp. Sprouts

Molybdenum ions (Mo) can improve plants' nutritional value primarily by enhancing nitrogenous metabolism. In this study, the comparative effects of seed priming using Mo were evaluated among sproutings of Canavalia species/cultivars, including Canavalia ensiformis var. gladiata (CA1), Canavalia ensiformis var. truncata Ricker (CA2), and Canavalia gladiata var. alba Hisauc (CA3). Mo impacts on growth, metabolism (e.g., nitrogen and phenolic metabolism, pigment and total nutrient profiles), and biological activities were assayed. Principal component analysis (PCA) was used to correlate Mo-mediated impacts. The results showed that Mo induced photosynthetic pigments that resulted in an improvement in growth and increased biomass. The N content was increased 0.3-fold in CA3 and 0.2-fold in CA1 and CA2. Enhanced nitrogen metabolism by Mo provided the precursors for amino acids, protein, and lipid biosynthesis. At the secondary metabolic level, phenolic metabolism-related precursors and enzyme activities were also differentially increased in Canavalia species/cultivars. The observed increase in metabolism resulted in the enhancement of the antioxidant (2,2-diphenyl-1-picryl-hydrazyl-hydrate (DPPH) free radical scavenging, 2,2-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS), ferric reducing antioxidant power (FRAP)) and antidiabetic potential (Glycemic index (GI) and inhibition activity of α-amylase, and α-glucosidase) of species. The antioxidant activity increased 20% in CA3, 14% in CA1, and 8% in CA2. Furthermore, PCA showed significant variations not only between Mo-treated and untreated samples but also among Canavalia species. Overall, this study indicated that the sprouts of Canavalia species have tremendous potential for commercial usage due to their high nutritive value, which can be enhanced further with Mo treatment to accomplish the demand for nutritious feed.

Structure of the 4-hydroxy-tetrahydrodipicolinate synthase from the thermoacidophilic methanotroph Methylacidiphilum fumariolicum SolV and the phylogeny of the aminotransferase pathway

The enzyme 4-hydroxy-tetrahydrodipicolinate synthase (DapA) is involved in the production of lysine and precursor molecules for peptidoglycan synthesis. In a multistep reaction, DapA converts pyruvate and L-aspartate-4-semialdehyde to 4-hydroxy-2,3,4,5-tetrahydrodipicolinic acid. In many organisms, lysine binds allosterically to DapA, causing negative feedback, thus making the enzyme an important regulatory component of the pathway. Here, the 2.1 Å resolution crystal structure of DapA from the thermoacidophilic methanotroph Methylacidiphilum fumariolicum SolV is reported. The enzyme crystallized as a contaminant of a protein preparation from native biomass. Genome analysis reveals that M. fumariolicum SolV utilizes the recently discovered aminotransferase pathway for lysine biosynthesis. Phylogenetic analyses of the genes involved in this pathway shed new light on the distribution of this pathway across the three domains of life.

Role of the Dihydrodipicolinate Synthase DapA1 on Iron Homeostasis During Cyanide Assimilation by the Alkaliphilic Bacterium Pseudomonas pseudoalcaligenes CECT5344

Cyanide is a toxic compound widely used in mining and jewelry industries, as well as in the synthesis of many different chemicals. Cyanide toxicity derives from its high affinity for metals, which causes inhibition of relevant metalloenzymes. However, some cyanide-degrading microorganisms like the alkaliphilic bacterium Pseudomonas pseudoalcaligenes CECT5344 may detoxify hazardous industrial wastewaters that contain elevated cyanide and metal concentrations. Considering that iron availability is strongly reduced in the presence of cyanide, mechanisms for iron homeostasis should be required for cyanide biodegradation. Previous omic studies revealed that in the presence of a cyanide-containing jewelry residue the strain CECT5344 overproduced the dihydrodipicolinate synthase DapA1, a protein involved in lysine metabolism that also participates in the synthesis of dipicolinates, which are excellent metal chelators. In this work, a dapA1 ^- mutant of P. pseudoalcaligenes CECT5344 has been generated and characterized. This mutant showed reduced growth and cyanide consumption in media with the cyanide-containing wastewater. Intracellular levels of metals like iron, copper and zinc were increased in the dapA1 ^- mutant, especially in cells grown with the jewelry residue. In addition, a differential quantitative proteomic analysis by LC-MS/MS was carried out between the wild-type and the dapA1 ^- mutant strains in media with jewelry residue. The mutation in the dapA1 gene altered the expression of several proteins related to urea cycle and metabolism of arginine and other amino acids. Additionally, the dapA1 ^- mutant showed increased levels of the global nitrogen regulator PII and the glutamine synthetase. This proteomic study has also highlighted that the DapA1 protein is relevant for cyanide resistance, oxidative stress and iron homeostasis response, which is mediated by the ferric uptake regulator Fur. DapA1 is required to produce dipicolinates that could act as iron chelators, conferring protection against oxidative stress and allowing the regeneration of Fe-S centers to reactivate cyanide-damaged metalloproteins.

Whirly (Why) transcription factors in tomato (Solanum lycopersicum L.): genome-wide identification and transcriptional profiling under drought and salt stresses

Whirly (Why) transcription factor (TFs) constitute one of the important TF families which plays essential roles in plant metabolism to cope with environmental stresses. In the present study, Why genes were identified at genome-wide scale in tomato (Solanum lycopersicum), and bioinformatics analyses were implemented. Validation of Why genes expressions under drought and salt stresses were also performed using RT-qPCR. The analyses revealed the presence of two Why genes in tomato genome, SlWhy1 (Solyc05g007100.2.1) and SlWhy2 (Solyc11g044750.1.1). Both genes contained Whirly transcription factor domain structure (PF08536), and Why proteins were in basic character (pI ≥ 7). While the lengths of the proteins ranged from 268 to 236 amino acid residues for SlWhy1 and SlWhy2 respectively, exon numbers identified in both genes were seven. According to the digital expression data, SlWhy genes are expressed at medium level in different anatomical parts and developmental stages. In the promotor sequence analysis, 13 types of putative TF binding sites were identified, and the highest motif number was 46, found for GATA TF. Gene co-expression analyses revealed that complex networks for SlWhy genes, which are connected with various metabolic pathways. Based on the RT-qPCR data, both SlWhy1 and SlWhy2 genes were up-regulated under salt and drought stresses. 3D structure analyses revealed that SlWhy1 protein had a more diverged structure than SlWhy2 protein, based on their comparisons in Arabidopsis and potato. The results obtained in the present study could be a useful scientific basis for understanding Why genes in tomato and their functions under abiotic stress conditions.

Proteomic analysis of bacterial response to a 4-hydroxybenzylidene indolinone compound, which re-sensitizes bacteria to traditional antibiotics

Halogenated 4-hydroxybenzylidene indolinones have been shown to re-sensitize methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococcus faecalis (VRE) to methicillin and vancomycin respectively. The mechanism of antibiotic re-sensitization was however not previously studied. Here, we probe the scope of antibiotic re-sensitization and present the global proteomics analysis of S. aureus treated with GW5074, a 4-hydroxybenzylidene indolinone compound. With a minimum inhibitory concentration (MIC) of 8 μg/mL against S. aureus, GW5074 synergized with beta-lactam antibiotics like ampicillin, carbenicillin and cloxacillin, the DNA synthesis inhibitor, ciprofloxacin, the protein synthesis inhibitor, gentamicin and the folate acid synthesis inhibitor, trimethoprim. Global proteomics analysis revealed that GW5074 treatment resulted in significant downregulation of enzymes involved in the purine biosynthesis. S. aureus proteins involved in amino acid metabolism and peptide transport were also observed to be downregulated. Interestingly, anti-virulence targets such as AgrC (a quorum sensing-related histidine kinase), AgrA (a quorum sensing-related response regulator) as well as downstream targets, such as hemolysins, lipases and proteases in S. aureus were also downregulated by GW5074. We observed that the peptidoglycan hydrolase, SceD was significantly upregulated. The activity of GW5074 on S. aureus suggests that the compound primes bacteria for the antibacterial action of ineffective antibiotics. SIGNIFICANCE: Antibiotic resistance continues to present significant challenges to the treatment of bacterial infections. Given that antibiotic resistance is a natural phenomenon and that it has become increasingly difficult to discover novel antibiotics, efforts to improve the activity of existing agents are worth pursuing. A few small molecules that re-sensitize resistant bacteria to traditional antibiotics have been described but the molecular details that underpin how these compounds work to re-sensitize bacteria remain largely unknown. In this report, global label-free quantitative proteomics was used to identify changes in the proteome that occurs when GW5074, a compound that re-sensitize MRSA to methicillin, is administered to S. aureus. The identification of pathways that are impacted by GW5074 could help identify novel targets for antibiotic re-sensitization.

Involvement of a dihydrodipicolinate synthase gene (FaDHDPS1) in fungal development, pathogenesis and stress responses in Fusarium asiaticum

BACKGROUND

Dihydrodipicolinate synthase (DHDPS) is an allosteric enzyme, which catalyzes the first unique step of lysine biosynthesis in prokaryotes, higher plants and some fungi. To date, the biological roles of DHDPS in filamentous fungi are poorly understood.

RESULTS

In this study, on the basis of comparative genome resequencing, a DHDPS gene was found to be specific in Fusarium asiaticum, named FaDHDPS1, which showed high amino acid identity to that of entomopathogenic fungus. Subcellular localization of the FaDHDPS1-GFP fusion protein was mainly concentrated in the cytoplasm of conidia and dispersed in the cytoplasm during conidial germination. To reveal the biological functions, both deletion and complementation mutants of FaDHDPS1 were generated. The results showed that the FaDHDPS1 deletion mutant was defective in conidiation, virulence and DON biosynthesis. In addition, deletion of FaDHDPS1 resulted in tolerance to sodium pyruvate, lysine, low temperature and Congo red.

CONCLUSION

Results of this study indicate that FaDHDPS1 plays an important role in the regulation of vegetative differentiation, pathogenesis and adaption to multiple stresses in F. asiaticum.