Dipeptide Product Research Articles

Phosphonoalamides Reveal the Biosynthetic Origin of Phosphonoalanine Natural Products and a Convergent Pathway for Their Diversification

AbstractPhosphonate natural products, with their potent inhibitory activity, have found widespread use across multiple industries. Their success has inspired development of genome mining approaches that continue to reveal previously unknown bioactive scaffolds and biosynthetic insights. However, a greater understanding of phosphonate metabolism is required to enable prediction of compounds and their bioactivities from sequence information alone. Here, we expand our knowledge of this natural product class by reporting the complete biosynthesis of the phosphonoalamides, antimicrobial tripeptides with a conserved N‐terminal l‐phosphonoalanine (PnAla) residue produced by Streptomyces. The phosphonoalamides result from the convergence of PnAla biosynthesis and peptide ligation pathways. We elucidate the biochemistry underlying the transamination of phosphonopyruvate to PnAla, a new early branchpoint in phosphonate biosynthesis catalyzed by an aminotransferase with evolved specificity for phosphonate metabolism. Peptide formation is catalyzed by two ATP‐grasp ligases, the first of which produces dipeptides, and a second which ligates dipeptides to PnAla to produce phosphonoalamides. Substrate specificity profiling revealed a dramatic expansion of dipeptide and tripeptide products, while finding PnaC to be the most promiscuous dipeptide ligase reported thus far. Our findings highlight previously unknown transformations in natural product biosynthesis, promising enzyme biocatalysts, and unveil insights into the diversity of phosphonopeptide natural products.

Phosphonoalamides Reveal the Biosynthetic Origin of Phosphonoalanine Natural Products and a Convergent Pathway for Their Diversification.

Phosphonate natural products, with their potent inhibitory activity, have found widespread use across multiple industries. Their success has inspired development of genome mining approaches that continue to reveal previously unknown bioactive scaffolds and biosynthetic insights. However, a greater understanding of phosphonate metabolism is required to enable prediction of compounds and their bioactivities from sequence information alone. Here, we expand our knowledge of this natural product class by reporting the complete biosynthesis of the phosphonoalamides, antimicrobial tripeptides with a conserved N-terminal l-phosphonoalanine (PnAla) residue produced by Streptomyces. The phosphonoalamides result from the convergence of PnAla biosynthesis and peptide ligation pathways. We elucidate the biochemistry underlying the transamination of phosphonopyruvate to PnAla, a new early branchpoint in phosphonate biosynthesis catalyzed by an aminotransferase with evolved specificity for phosphonate metabolism. Peptide formation is catalyzed by two ATP-grasp ligases, the first of which produces dipeptides, and a second which ligates dipeptides to PnAla to produce phosphonoalamides. Substrate specificity profiling revealed a dramatic expansion of dipeptide and tripeptide products, while finding PnaC to be the most promiscuous dipeptide ligase reported thus far. Our findings highlight previously unknown transformations in natural product biosynthesis, promising enzyme biocatalysts, and unveil insights into the diversity of phosphonopeptide natural products.

Cyclization of l-leucyl-l-valine dipeptide in the crystal phase under non-isоthermal conditions

Thermal treatment of linear dipeptides in the solid phase makes it possible to obtain their cyclic analogues in high yield and without additional costs. At the same time, such reactions occurring under the constraints of a crystal lattice with the participation of molecules in the zwitterionic form have not been sufficiently studied. In this work, the cyclization reaction of the dipeptide L-leucyl-L-valine in the crystalline phase upon heating was studied. Using isoconversion kinetics approaches, a kinetic model describing this process is determined, and kinetic parameters are calculated, including activation energy, Arrhenius multiplier, and reaction order. The enantiomeric purity of the resulting cyclic product was assessed. The self-assembly of linear and cyclic dipeptides on a solid support was studied. The results of the study will be useful for establishing the mechanism of the cyclization reaction of dipeptides in the solid phase, and can also be used in the development of effective and cost-effective methods for the production of cyclic dipeptides.

Dual-Color Real-Time Chemosensing of a Compartmentalized Reaction Network Involving Enzyme-Induced Membrane Permeation of Peptides.

The design of synthetic systems with interrelated reaction sequences that model incipient biological complexity is limited by physicochemical tools that allow the direct monitoring of the individual processes in real-time. To mimic a simple digestion-resorption sequence, the authors have designed compartmentalized liposomal systems that incorporate extra- and intravesicular chemosensing ensembles. The extravesicular reporter pair consists of cucurbit[7]uril and methylene blue to monitor the enzymatic cleavage of short enkephalin-related peptides by thermolysin through a switch-off fluorescence response ("digestion"). Because the substrate is membrane-impermeable, but the dipeptide product is permeable, uptake of the latter into the pre-formed liposomes occurs as a follow-up process. The intravesicular chemosensing ensemble consists of i) cucurbit[8]uril, 2-anilinonaphthalene-6-sulfonic acid, and methyl viologen or ii) cucurbit[7]uril and berberine to monitor the uptake ("resorption") of the enzymatic products through the liposomal membranes by i) a switch-on or ii) a switch-off fluorescence response. The dyes are designed to allow selective optical excitation and read-out of the extra- and intravesicular dyes, which allow for dual-color chemosensing and, therefore, kinetic discrimination of the two sequential reactions.

Exploring the changes in microorganisms and metabolites during the fermentation process of traditional Chinese watermelon–soybean paste

Watermelon–soybean paste (WSP) is a traditional Chinese fermented food item. Changes in the microbial community diversity affect the final product quality. However, the correlation between microorganisms and their metabolites in WSP is not clearly understood. In this study, seven bacterial and eight fungal genera were found to be dominant during WSP fermentation using 16S rRNA and ITS gene sequencing. A total of 838 metabolites were identified using UHPLC-TOF-MS; of which, 99 were identified as differential metabolites. Correlation analysis showed that the microbial metabolic activities of Bacillus sp., Candia sp., and Kodamaea sp. were associated with amino acid production. Bacillus sp. and Aspergillus sp. correlated with dipeptide production. Metabolic pathway analysis suggested that amino acid metabolism was the most significant differential metabolic pathway, which may be related to the fermentation quality of WSP. Our study provides a new theoretical basis for improving WSP quality from the perspective of metabolomic and microbial diversity.

NOVEL APPLICATIONS OF BACTERIOCINS IN FOOD AND IMPACT ON HUMAN HEALTH

Background: Bacteriocins are proteins groups, produced by gram-positive bacteria having the potential to use as food preservatives and antibacterial agents. Objectives: This review is aim to provide a comprehensive information on bacteriocins and their application. Methodology: Different databases were searched to find relevant information. Results: The protein of bacteriocins is ribosomal synthesized peptides. These proteins are produced by protein synthesis mechanism within a cell with amino acid composition ranging from 30 to 60 amino acids. The peptides have a narrow to wide spectrum of antibacterial activity against gram-positive bacteria, and their antibacterial properties remain intact even when exposed to heat. Bacteriocins proteins can be used in hot environments, such as cooking and food preparation, without losing their effectiveness. Additionally, the producer strain of Bacteriocins can provide a degree of self-protection against its own antibacterial peptide. Other than bacteriocins, specific LAB may generate antimicrobial peptides aiding in the preservation and safety of food due to production of cyclic dipeptides. Nisin is non-toxic, produced by generally recognized as safe (GRAS) bacteria, and quickly eliminated in the digestive system. Bacteriocins does not adversely affect the gut microflora. Conclusion: The bacteriocins can provide immunity for foods, allowing processors to maintain their desired microbial balance even after manufacture is complete.

Biocatalytic Production of Bioactive Dipeptides

Dipeptides are a promising substance class with a large variety of bioactivities. N‐terminal ar‐ ginyl dipeptides (Arg‐X) have been shown to exhibit both salt‐taste enhancing (Arg‐Ser among others) and antihypertensive properties (Arg‐Phe). A novel biocatalytic strategy for the specific synthesis of these dipeptides is the application of L‐amino acid ligases like RizA from B. subtilis, which enables production of Arg‐X dipeptides directly from their amino acids. However, challenges for an industrial application are the dependence on the expensive cofactor ATP (adenosine triphosphate), low product yields, formation of the undesired side product Arg Arg and the potentially high enzyme costs.In order to reduce the need for ATP, a strategy for ATP regeneration from acetyl phosphate was established using acetate kinase from E. coli (AckA). Up to 5.9 g/L Arg‐Ser were produced, corresponding to an ATP efficiency of 23 g Arg‐Ser per gram ATP (without regeneration max. 0.5 g Arg‐Ser/g ATP). Next, variants of RizA were created to alter the substrate specificity. A total of 21 RizA variants were created by site‐directed mutagenesis of eight positions in the substrate binding pocket. Additional 14 variants were created by combination of different mutations. Variants with improved activity and specificity were identified for all five examined amino acid combinations (Arg + Arg, Asp, Ser, Ala, Phe). The largest change was observed for K83F_S156A, which improved the product formation of Arg‐Phe six‐fold and improved specificity more than tenfold. Finally, co immobilization of RizA and selected variants with AckA was performed to enable reusability of this biocatalytic system. Immobilisates of T81F_A158S produced up to 3.0 g/L Arg Ser and immobilisates of K83F_S156A produced up to 3.8 g/L Arg‐Phe and could both be reused several times.This thesis represents the first extensive scientific investigation into establishing ATP regeneration for an L‐amino acid ligase and co‐immobilization of such a biocatalytic system, and substantially expanded the knowledge about engineering the substrate specificity of L amino acid ligases.

Immunoelectron Microscopic Analysis of Dipeptidyl-Peptidases and Dipeptide Transporter Involved in Nutrient Acquisition in Porphyromonas gingivalis.

Porphyromonas gingivalis is an asaccharolytic, Gram-negative, anaerobic bacterium representing a keystone pathogen in chronic periodontitis. The bacterium's energy production depends on the metabolism of amino acids, which are predominantly incorporated as dipeptides via the proton-dependent oligopeptide transporter (Pot). In this study, the localization of dipeptidyl-peptidases (DPPs) and Pot was investigated for the first time in P. gingivalis using immunoelectron microscopy with specific antibodies for the bacterial molecules and gold-conjugated secondary antibodies on ultrathin sections. High-temperature protein G and hemin-binding protein 35 were used as controls, and the cytoplasmic localization of the former and outer membrane localization of the latter were confirmed. P. gingivalis DPP4, DPP5, DPP7, and DPP11, which are considered sufficient for complete dipeptide production, were detected in the periplasmic space. In contrast, DPP3 was localized in the cytoplasmic space in accord with the absence of a signal sequence. The inner membrane localization of Pot was confirmed. Thus, spatial integration of the nutrient acquisition system exists in P. gingivalis, in which where dipeptides are produced in the periplasmic space by DPPs and readily transported across the inner membrane via Pot.

Chiral analysis of linear protonated dipeptides by complexing with Cyclodextrins using Ion-Mobility Mass-Spectrometry and DFT structural calculations

The functions and applications of dipeptides have been reported to possess unique characteristics compared to that of proteins or amino acids. Naturally occurring amino acids, except for glycine, are chiral molecules; thus, for each type of dipeptide there are four possible isomers. Isomeric structural analysis of dipeptides is important for measuring the quality of dipeptide products, as well as understanding their chemical and biological functions in humans. In the present study, a rapid and simple method for isomeric recognition of protonated dipeptides H-D/l-Phe-D/L-X-OH, where X = hydrophobic amino acids, including alanine (Ala), isoleucine (Ile), leucine (Leu), proline (Pro), tryptophan (Trp), valine (Val), phenylalanine (Phe), and methionine (Met), was developed and investigated. Mixed solutions of dipeptides and cyclodextrins (CDs) were prepared for the production of gas phase, non-covalent complex ions by electrospray ionization (ESI). Trapped ion-mobility mass spectrometry (TIMS-MS) was subsequently used to investigate the corresponding ion mobilities (IM). The TIMS and density functional theory (DFT) results showed that the chiral structure of different dipeptides can be distinguished by β-CD, which indicates that different isomeric complexes have different collision cross sections (CCSs) and spatial conformations. The relative content of isomeric dipeptides mixtures was also obtained in the ratio range from 10:1 to 1:10 to measure the detection limits. Our work provides a direct analytical method for determining isomeric dipeptides, which could potentially have wide applications in the field of chiral recognition.

Improving the enzymatic activity of l-amino acid α-ligase for imidazole dipeptide production by site-directed mutagenesis.

Imidazole dipeptides, histidine-containing dipeptides, including carnosine (β-alanyl-l-histidine), anserine (β-alanyl-3-methyl-l-histidine), and balenine (β-alanyl-1-methyl-l-histidine) in animal muscles have physiological functions, such as significant antioxidant and antifatigue effects. They are obtained by extraction from natural raw materials, including chicken and fish meat. However, using natural raw materials entails stable supply and mass production limitations. l-amino acid α-ligase (Lal) catalyzes the formation of various dipeptides from unprotected l-amino acids by conjugating with adenosine 5'-triphosphate (ATP) hydrolysis reaction. In this study, site-directed mutagenesis of Lal was applied to establish an efficient method for producing imidazole dipeptides by the enzymatic process. We significantly improved the conversion rate from substrate amino acids compared with wild-type Lal.

Stable isotope tracing reveals compartmentalized nitrogen assimilation in scleractinian corals

Corals form symbiotic relationships with dinoflagellate algae of the family Symbiodiniaceae, bacteria, and other microbes. Central to that relationship is the regulation of nutrition flux between the animal host and the photosynthetic Symbiodiniaceae that it is reliant on for the majority of metabolic needs. Nitrogen availability controls the growth and density of Symbiodiniaceae within coral tissues and has been proposed to play a role in host derived symbiosis regulation. Warming ocean temperatures and subsequent increases in dissolved organic carbon can potentially increase nitrogen fixation and lead to bleaching. We investigated the importance of nitrogen metabolism in vivo with LC-MS based stable isotope tracing using nubbins from three species of Hawaiian coral, the more heat tolerant Montipora capitata and Porites compressa and the more heat sensitive Pocillopora acuta, that were collected from reefs in Kāne’ohe Bay, O’ahu. In addition to 15N incorporation into nucleotides, amino acids, and urea cycle metabolites, we also observed significant isotopic labeling in dipeptides, supporting their previous identification as major heat stress response metabolites. Surprisingly, the dipeptides are highly enriched in 15N compared to free amino acids, which are the biosynthetic precursors for dipeptides. This suggests that there is a high turnover of dipeptide pools and distinct biosynthetic mechanisms that separately mediate amino acid and dipeptide production. These preliminary data show that nitrogen assimilation in the coral holobiont is likely compartmentalized, with rapid assimilation and quick dipeptide turnover occurring in one region of the holobiont and slow turnover of other nitrogen containing metabolites in other region(s).

Discovery of an ʟ-amino acid ligase implicated in Staphylococcal sulfur amino acid metabolism

Enzymes involved in Staphylococcus aureus amino acid metabolism have recently gained traction as promising targets for the development of new antibiotics, however, not all aspects of this process are understood. The ATP-grasp superfamily includes enzymes that predominantly catalyze the ATP-dependent ligation of various carboxylate and amine substrates. One subset, ʟ-amino acid ligases (LALs), primarily catalyze the formation of dipeptide products in Gram-positive bacteria, however, their involvement in S. aureus amino acid metabolism has not been investigated. Here, we present the characterization of the putative ATP-grasp enzyme (SAOUHSC_02373) from S. aureus NCTC 8325 and its identification as a novel LAL. First, we interrogated the activity of SAOUHSC_02373 against a panel of ʟ-amino acid substrates. As a result, we identified SAOUHSC_02373 as an LAL with high selectivity for ʟ-aspartate and ʟ-methionine substrates, specifically forming an ʟ-aspartyl–ʟ-methionine dipeptide. Thus, we propose that SAOUHSC_02373 be assigned as ʟ-aspartate–ʟ-methionine ligase (LdmS). To further understand this unique activity, we investigated the mechanism of LdmS by X-ray crystallography, molecular modeling, and site-directed mutagenesis. Our results suggest that LdmS shares a similar mechanism to other ATP-grasp enzymes but possesses a distinctive active site architecture that confers selectivity for the ʟ-Asp and ʟ-Met substrates. Phylogenetic analysis revealed LdmS homologs are highly conserved in Staphylococcus and closely related Gram-positive Firmicutes. Subsequent genetic analysis upstream of the ldmS operon revealed several trans-acting regulatory elements associated with control of Met and Cys metabolism. Together, these findings support a role for LdmS in Staphylococcal sulfur amino acid metabolism.

Co-Immobilization of RizA Variants with Acetate Kinase for the Production of Bioactive Arginyl Dipeptides.

The biocatalytic system comprised of RizA and acetate kinase (AckA) combines the specific synthesis of bioactive arginyl dipeptides with efficient ATP regeneration. Immobilization of this coupled enzyme system was performed and characterized in terms of activity, specificity and reusability of the immobilisates. Co-immobilization of RizA and AckA into a single immobilisate conferred no disadvantage in comparison to immobilization of only RizA, and a small addition of AckA (20:1) was sufficient for ATP regeneration. New variants of RizA were constructed by combining mutations to yield variants with increased biocatalytic activity and specificity. A selection of RizA variants were co-immobilized with AckA and used for the production of the salt-taste enhancers Arg-Ser and Arg-Ala and the antihypertensive Arg-Phe. The best variants yielded final dipeptide concentrations of 11.3 mM Arg-Ser (T81F_A158S) and 11.8 mM Arg-Phe (K83F_S156A), the latter of which represents a five-fold increase in comparison to the wild-type enzyme. T81F_A158S retained more than 50% activity for over 96 h and K83F_S156A for over 72 h. This study provides the first example of the successful co-immobilization of an l-amino acid ligase with an ATP-regenerating enzyme and paves the way towards a bioprocess for the production of bioactive dipeptides.

Expanded substrate specificity supported by P1′ and P2′ residues enables bacterial dipeptidyl-peptidase 7 to degrade bioactive peptides

Dipeptide production from extracellular proteins is crucial for Porphyromonas gingivalis, a pathogen related to chronic periodontitis, because its energy production is entirely dependent on the metabolism of amino acids predominantly incorporated as dipeptides. These dipeptides are produced by periplasmic dipeptidyl-peptidase (DPP)4, DPP5, DPP7, and DPP11. Although the substrate specificities of these four DPPs cover most amino acids at the penultimate position from the N terminus (P1), no DPP is known to cleave penultimate Gly, Ser, Thr, or His. Here, we report an expanded substrate preference of bacterial DPP7 that covers those residues. MALDI-TOF mass spectrometry analysis demonstrated that DPP7 efficiently degraded incretins and other gastrointestinal peptides, which were successively cleaved at every second residue, including Ala, Gly, Ser, and Gln, as well as authentic hydrophobic residues. Intravenous injection of DPP7 into mice orally administered glucose caused declines in plasma glucagon-like peptide-1 and insulin, accompanied by increased blood glucose levels. A newly developed coupled enzyme reaction system that uses synthetic fluorogenic peptides revealed that the P1′ and P2′ residues of substrates significantly elevated kcat values, providing an expanded substrate preference. This activity enhancement was most effective toward the substrates with nonfavorable but nonrepulsive P1 residues in DPP7. Enhancement of kcat by prime-side residues was also observed in DPP11 but not DPP4 and DPP5. Based on this expanded substrate specificity, we demonstrate that a combination of DPPs enables proteolytic liberation of all types of N-terminal dipeptides and ensures P. gingivalis growth and pathogenicity.

136 Beef as a Functional Food for Improving Human Nutrition and Health

Beef is an abundant source of all proteinogenic amino acids (AAs; in both adequate amounts and balanced ratios) and physiologically essential nonproteinogenic AAs (taurine and β-alanine). The content and bioavailabilities of proteinogenic AAs in beef are greater than those in plant-sourced foods. Taurine (a potent anti-oxidant) is essential for the integrity and functions of tissues, including eyes, heart, and skeletal muscle, whereas β-alanine is required for the production of antioxidative and neuromodulatory dipeptides. Furthermore, beef contains a large amount of creatine (essential for energy metabolism in tissues, particularly brain and skeletal muscle), anti-oxidative dipeptides (carnosine and anserine), and 4-hydroxyproline (an anti-inflammatory nutrient that maintains intestinal integrity and inhibits colitis). There are myths that plants provide all nutrients that are available in animal-sourced foods. However, taurine, vitamin B12, creatine, carnosine, and anserine are absent from plants, whereas β-alanine and 4-hydroxyproline are low or negligible in plants. Like other animal-sourced foods, beef plays an important role in the optimum growth of children and the prevention of anemia in humans, as well as maintaining muscle mass, delaying ageing, and mitigating sarcopenia in adults, while meeting the high demands of exercising individuals for high-quality protein. Some epidemiological studies raised concern that the consumption of red meat might increase risks for chronic diseases in humans, including obesity, type 2 diabetes mellitus, cardiovascular disease, kidney disease, and cancers. However, findings from many epidemiological and clinical studies do not support these claims. Beef-derived AAs and other nutrients enhance the metabolism (e.g., nitric-oxide and glutathione syntheses) and the functions of monocytes, macrophages, lymphocytes, and other cells of the immune system, thereby helping the human host to kill pathogenic bacteria, fungi, parasites, and viruses. The latter include severe acute respiratory syndrome coronavirus (SARS-CoV) and SARS-CoV-2 (COVID-19). Therefore, beef is a functional food for optimizing human growth, development, and health.

Incorporation of alternative amino acids into cyanophycin by different cyanophycin synthetases heterologously expressed in Corynebacterium glutamicum

Cyanophycin (multi-l-arginyl-poly-l-aspartic acid; also known as cyanophycin grana peptide [CGP]) is a biopolymer that could be used in various fields, for example, as a potential precursor for the synthesis of polyaspartic acid or for the production of CGP-derived dipeptides. To extend the applications of this polymer, it is therefore of interest to synthesize CGP with different compositions. A recent re-evaluation of the CGP synthesis in C. glutamicum has shown that C. glutamicum is a potentially interesting microorganism for CGP synthesis with a high content of alternative amino acids. This study shows that the amount of alternative amino acids can be increased by using mutants of C. glutamicum with altered amino acid biosynthesis. With the DM1729 mutant, the lysine content in the polymer could be increased up to 33.5 mol%. Furthermore, an ornithine content of up to 12.6 mol% was achieved with ORN2(Pgdh4). How much water-soluble or insoluble CGP is synthesized is strongly related to the used cyanophycin synthetase. CphADh synthesizes soluble CGP exclusively. However, soluble CGP could also be isolated from cells expressing CphA6308Δ1 or CphA6308Δ1_C595S in addition to insoluble CGP in all examined strains. The point mutation in CphA6308Δ1_C595S partially resulted in a higher lysine content. In addition, the CGP content could be increased to 36% of the cell dry weight under optimizing growth conditions in C. glutamicum ATCC13032. All known alternative major amino acids for CGP synthesis (lysine, ornithine, citrulline, and glutamic acid) could be incorporated into CGP in C. glutamicum.

Revision of the genus Aciculosporium (Clavicipitaceae) with a description of a new species on wavyleaf basketgrass, and proline-containing cyclic dipeptide production by A. take.

The genus Aciculosporium (Clavicipitaceae, Hypocreales, Ascomycota)was established in 1908 for A. take , which is the causal fungus of witches' broom of bamboo. Although the original description was valid at that time, a type specimen for A. take has not been designated. To standardize the use of this genus and species name, a neotypification and reference specimen of A. take are proposed. Multilocus phylogenetic analyses based on DNA sequences from 28S rDNA, TEF, Tub2, Mcm7, and RPB2 revealed that A.sasicola is from a different lineage to A. take, and other specimens from wavyleaf basket grass (Oplismenus undulatifolius) represent a distinct species proposed here as Aciculosporium oplismeni sp. nov. Chemical analysis using mass spectrometry and nuclear magnetic resonance spectroscopy showed that A. take produces four proline-containing cyclic dipeptides, which are moieties of ergot alkaloids. However, ergot alkaloids, lolines, peramine, indole-diterpenes, and lolitrem were not detected in the culture solvent. This study offers clarification of the lineage and morphology of this genus.

Toward Molecular Cooperation by De Novo Peptides.

Theoretical models of the chemical origins of life depend on self-replication or autocatalysis, processes that arise from molecular interactions, recruitment, and cooperation. Such models often lack details about the molecules and reactions involved, giving little guidance to those seeking to detect signs of interaction, recruitment, or cooperation in the laboratory. Here, we develop minimal mathematical models of reactions involving specific chemical entities: amino acids and their condensation reactions to form de novo peptides. Reactions between two amino acids form a dipeptide product, which enriches linearly in time; subsequent recruitment of such products to form longer peptides exhibit super-linear growth. Such recruitment can be reciprocated: a peptide contributes to and benefits from the formation of one or more other peptides; in this manner, peptides can cooperate and thereby exhibit autocatalytic or exponential growth. We have started to test these predictions by quantitative analysis of de novo peptide synthesis conducted by wet-dry cycling of a five-amino acid mixture over 21days. Using high-performance liquid chromatography, we tracked abundance changes for >60 unique peptide species. Some species were highly transient, with the emergence of up to 17 new species and the extinction of nine species between samplings, while other species persisted across many cycles. Of the persisting species, most exhibited super-linear growth, a sign of recruitment anticipated by our models. This work shows how mathematical modeling and quantitative analysis of kinetic data can guide the search for prebiotic chemistries that have the potential to cooperate and replicate.

Dipeptidyl‐peptidases: Key enzymes producing entry forms of extracellular proteins in asaccharolytic periodontopathic bacterium Porphyromonas gingivalis

Porphyromonas gingivalis, a pathogen of chronic periodontitis, is an asaccharolytic microorganism that solely utilizes nutritional amino acids as its energy source and cellular constituents. The bacterium is considered to incorporate proteinaceous nutrients mainly as dipeptides, thus exopeptidases that produce dipeptides from polypeptides are critical for survival and proliferation. We present here an overview of dipeptide production by P. gingivalis mediated by dipeptidyl‐peptidases (DPPs), e.g., DPP4, DPP5, DPP7, and DPP11, serine exopeptidases localized in periplasm, which release dipeptides from the N‐terminus of polypeptides. Additionally, two other exopeptidases, acylpeptidyl‐oligopeptidase (AOP) and prolyl tripeptidyl‐peptidase A (PTP‐A), which liberate N‐terminal acylated di‐/tri‐peptides and tripeptides with Pro at the third position, respectively, provide polypeptides in an acceptable form for DPPs. Hence, a large fraction of dipeptides is produced from nutritional polypeptides by DPPs with differential specificities in combination with AOP and PTP‐A. The resultant dipeptides are then incorporated across the inner membrane mainly via a proton‐dependent oligopeptide transporter (POT), a member of the major facilitator superfamily. Recent studies also indicate that DPP4 and DPP7 directly link between periodontal and systemic diseases, such as type 2 diabetes mellitus and coagulation abnormality, respectively. Therefore, these dipeptide‐producing and incorporation molecules are considered to be potent targets for prevention and treatment of periodontal and related systemic diseases.

Biological potential of Bacillus subtilis V26 for the control of Fusarium wilt and tuber dry rot on potato caused by Fusarium species and the promotion of plant growth

Fusariosis of potato caused by the Fusarium spp. is one of the most destructive soil-borne diseases throughout the world. This study aimed to investigate the growth-promoting and biocontrol potential of Bacillus subtilis V26 against the causal agents of Fusarium wilt and Fusarium dry rot diseases on potato. Characterization of plant growth promoting traits was assessed in vitro. The strain V26 was able to fix nitrogen, to produce indole-3-acetic acid, siderophore, hydrolytic enzymes and to solubilize inorganic phosphate. The PCR detection of ituC, fenA, fenB, fenD, srfAA, bmy, mnlA, bae and bac genes coding for iturin, fengycin, surfactin, bacyllomicin, macrolactin, bacillaene and bacilysin indicated a potential for lipopeptides, polyketides and dipeptide production, respectively by the strain V26. In vitro antagonism test showed that this strain can effectively inhibit F. oxysporum, F. solani, F. gramineaurum and F. sambucinum growth by 54.7 to 85.3% as compared to the untreated control, in a dual method. Antifungal activity was demonstrated against the dry rot potato tubers caused by Fusarium species. The preventive application of V26 significantly decreased the Fusarium dry rot disease severity at 42.8–63.8%, after 21 days of fungi inoculation. After 15 days of seedling emergence, plants were irrigated with V26 spore suspensions (108 CFU/mL), prior infection by Fusaium species, Fusarium wilt severity were reduced by 54.8 to 60.8% and plant growth parameters were improved, compared to the untreated ones, 60 days post-inoculation. Therefore, this strain could be a promising candidate to be developed as commercial biofertilizer and biocontrol formulation in sustainable agriculture.