Amino acid analogues provide multiple plausible pathways to prebiotic peptides.

Prebiotic peptide synthesis has consistently been a prominent topic within the field of the origin of life. While research predominantly centres on the 20 classical amino acids, the synthesis process encounters significant thermodynamic barriers. Consequently, amino acid analogues are being explored as potential building blocks for prebiotic peptide synthesis. This review delves into the pathway of polypeptide formation, identifying specific amino acid analogues that might have existed on early Earth, potentially participating in peptide synthesis and chemical evolution. Moreover, considering the complexity and variability of the environment on early Earth, we propose the plausibility of coevolution between amino acids and their analogues.

A model for N-to-C direction in prebiotic peptide synthesis.

Drawing inspiration from the initiating amino acid modification in biosynthetic peptides, we have successfully demonstrated a biomimetic mechanism for N-to-C terminal extension in prebiotic peptide synthesis. This achievement was accomplished by using acetylated amino acid amides as the N-terminal substrate for peptide synthesis and amino acid amides as the C-terminal extension, with the reaction carried out in a dry-wet cycle at 80 °C without requiring any activators. This provides a plausible pathway for the formation of prebiotic peptides.

A Practical Method for Amino Acid Analysis by LC-MS Using Precolumn Derivatization with Urea.

Amino acid (AA) analysis is important in biochemistry, food science, and clinical medicine. However, due to intrinsic limitations, AAs usually require derivatization to improve their separation and determination. Here, we present a liquid chromatography-mass spectrometry (LC-MS) method for the derivatization of AAs using the simple agent urea. The reactions proceed quantitatively under a wide range of conditions without any pretreatment steps. Urea-derivatized products (carbamoyl amino acids) of 20 AAs exhibit better separation on reversed-phase columns and increased response in a UV detector compared to underivatized ones. We applied this approach to AA analysis in complex samples using a cell culture media as a model, and it showed potential for the determination of oligopeptides. This fast, simple, and inexpensive method should be useful for AA analysis in complex samples.

Prebiotic chemistry: a review of nucleoside phosphorylation and polymerization.

The phosphorylation of nucleosides and their polymerization are crucial issues concerning the origin of life. The question of how these plausible chemical processes took place in the prebiotic Earth is still perplexing, despite several studies that have attempted to explain these prebiotic processes. The purpose of this article is to review these chemical reactions with respect to chemical evolution in the primeval Earth. Meanwhile, from our perspective, the chiral properties and selection of biomolecules should be considered in the prebiotic chemical origin of life, which may contribute to further research in this field to some extent.

A novel in-situ strategy for enantiomeric discrimination and selective identification of multicomponent carboxylic acids in foods.

Chiral carboxylic acids are ubiquitous in nature and are of pivotal importance in practical applications in the field of food science and pharmaceuticals. Simultaneous enantiomeric analysis of carboxylic acids mixtures is a significant research goal. Herein, we demonstrate a new strategy involving the use of the highly selective chiral derivatizing agent (R)-2-amino-1,1,1-trifluoropropane ((R)-TFPA) for the enantiomeric discrimination and selective identification of carboxylic acids in mixtures, even structurally similar drugs. The key success of this sensing approach lies in the distinguishable 19F NMR signals of diastereoisomers formed via derivatization of the substrates by (R)-TFPA. The utility of this approach was demonstrated by simultaneously differentiating 20 chiral carboxylic acids in a complicated mixture with accurate determination of the enantiomeric excess (ee). Most importantly, our approach can be applied to food analysis, where the diverse carboxylic acids in real samples without separation were unambiguously identified, such as vinegar, yogurt, and grape.

Prebiotic Chemistry: The Role of Trimetaphosphate in Prebiotic Chemical Evolution.

Life's origins have always been a scientific puzzle. Understanding the production of biomolecules is crucial for understanding the evolution of life on Earth. Numerous studies on trimetaphosphate have been conducted in the field of prebiotic chemistry. However, its role in prebiotic chemistry has been documented infrequently in the review literature. The goal of this thesis is to review the role of trimetaphosphate in the early Earth's biomolecule synthesis and phosphorylation. Additionally, various trimetaphosphate-mediated reaction pathways are discussed, as well as the role of trimetaphosphate in prebiotic chemistry. Finally, in our opinion, interactions between biomolecules should be considered in prebiotic synthesis scenarios since this may result in some advances in subsequent research on this subject. The research establishes an essential and opportune foundation for an in-depth examination of the "mystery of life".

trans-4-Fluoro-l-proline: A Sensitive 19F NMR Probe for the Rapid Simultaneous Enantiomeric Analysis of Multicomponent Amines.

Simultaneous enantiomeric analysis is especially important for medicine, food security, and life science. Chiral analysis of multicomponent amine mixtures still faces many challenges. Here, our work demonstrates for the first time that a novel chiral derivatizing agent CDApro based on trans-4-fluoro-l-proline (trans4Fpro) has been successfully used for the rapid simultaneous analysis of 22 chiral nonamino acid (non-AA) amines, multicomponent l/d-AAs, or mirror-image dipeptides in a mixture, as well as amines with chiral centers several carbons remote to the amino group. Furthermore, determination of enantiomeric purity and quantification of chiral amines can be made using CDApro, which serves as a robust and powerful reagent for the differentiation of multicomponent chiral amines.

Palladium-Catalyzed Cascade Difluoroalkylation and Phosphinoylation of 2-Vinyloxy Arylalkynes: Selective Synthesis of Difluoroalkyl-Containing Tetrasubstituted Alkenylphosphine Oxides.

A Pd-catalyzed difluoroalkylation/cyclization/phosphinoylation of 2-vinyloxy arylalkynes with ethyl difluoroiodoacetate and diarylphosphine oxides has been successfully developed. This reaction allows the formation of Csp3-CF2, Csp3-Csp2, and Csp2-P(O) bonds in one step, providing a straightforward route to difluoroalkyl-containing tetrasubstituted alkenylphosphine oxides with complete stereoselectivities under mild conditions.

Cyclic Dipeptides Formation From Linear Dipeptides Under Potentially Prebiotic Earth Conditions.

Cyclic dipeptides (DKPs) are peptide precursors and chiral catalysts in the prebiotic process. This study reports proline-containing DKPs that were spontaneously obtained from linear dipeptides under an aqueous solution. Significantly, the yields of DKPs were affected by the sequence of linear dipeptides and whether the reaction contains trimetaphosphate. These findings provide the possibility that DKPs might play a key role in the origin of life.

An electronic circular dichroism spectroscopy method for the quantification of L- and D-amino acids in enantiomeric mixtures.

Rapid quantitative analysis of single chiral amino acid (aa) was achieved using circular dichroism (CD) with data analysis by standard calibration curve. The absolute concentrations of D- and L-aas in enantiomeric mixtures were determined by CD and achiral liquid chromatography (LC) method. It is worth noting that CD and LC were used independently, not online LC/CD in this study. The errors of the experimental results were less than 10%. The method is also applicable to the quantification of non-aa chiral molecules, such as chiral nucleoside and chiral quinine. With this study, we provide a new method for the chiral quantitative analysis of enantiomeric aas mixtures.

A plausible model correlates prebiotic peptide synthesis with the primordial genetic code.

Aminoacyladenylates (5'-aa-AMPs) are key intermediates in peptide synthesis. Here we report analogs of 5'-aa-AMPs, namely nucleotide amidates (aa-N-NMPs), obtained under Hadean conditions. Significantly, dipeptides were detected from the above reactions and their yields varied with different nucleosides through the formation of different aa-N-NMPs. This model provides both prebiotic peptides and the primordial version of the genetic code through reactions that occurred under potentially prebiotic conditions.

Prebiotic formation of cyclic dipeptides under potentially early Earth conditions.

Cyclic dipeptides, also known as 2,5-diketopiperazines (DKPs), represent the simplest peptides that were first completely characterized. DKPs can catalyze the chiral selection of reactions and are considered as peptide precursors. The origin of biochemical chirality and synthesis of peptides remains abstruse problem believed to be essential precondition to origin of life. Therefore, it is reasonable to believe that the DKPs could have played a key role in the origin of life. How the formation of the DKPs through the condensation of unprotected amino acids in simulated prebiotic conditions has been unclear. Herein, it was found that cyclo-Pro-Pro could be formed directly from unprotected proline in the aqueous solution of trimetaphosphate (P3m) under mild condition with the yield up to 97%. Other amino acids were found to form proline-containing DKPs under the same conditions in spite of lower yield. During the formation process of these DKPs, P3m promotes the formation of linear dipeptides in the first step of the mechanism. The above findings are helpful and significant for understanding the formation of DKPs in the process of chemical evolution of life.

Main group metal-ligand cooperation of N-heterocyclic germylene: an efficient catalyst for hydroboration of carbonyl compounds.

N-heterocyclic ylide-like germylene effectively promotes the hydroboration of aldehydes and ketones under mild conditions with broad substrate tolerance, operational simplicity of procedure and excellent yields. A key intermediate in this catalytic system featuring a bicyclo[2,2,2]octane-like core has been successfully isolated and characterized, suggesting a new type of mechanism that involves the activation mode that mimics that of transition metal catalysts.

Specific interactions of leucine with disaccharides by electrospray ionization mass spectrometry: application to rapid differentiation of disaccharide isomers in combination with statistical analysis.

The identification of carbohydrate isomers, including mono units, linkage positions and anomeric configurations, remains an arduous subject. In this study, the natural amino acid leucine (Leu) was found to specifically interact with cellobiose (Cello) to form a series of potassium adducts as [Cello + Leu + K](+), [Cello + 2Leu + K](+), and [2Cello + Leu + K](+) in the gas phase using mass spectrometry. By using CID-MS/MS, these complexes produced specific fragmentation patterns from the sugar backbone cleavage instead of non-covalent interactions. Moreover, their fragment distributions were dependent on the ratios of Cello-to-Leu in the complexes and the fragmentation pathways of potassium-cationized disaccharides (Dis) were remarkably changed with leucine binding. It should be pointed out that the ternary complex [2Cello + AA + K](+) was unique for leucine among all the twenty natural amino acids. The [2Dis + Leu + K](+) complex produced the most informative fragments by tandem mass spectrometry, which was successfully applied for rapid and efficient discrimination of twelve glucose-containing disaccharide isomers in combination with statistical analyses including PCA and OPLS-DA. The methodology developed here not only provides a novel analytical approach for the differentiation of disaccharide isomers, but also brings new sight towards the interactions of amino acids with disaccharides.

Draft Genome Sequence of the Carrageenan-Degrading Bacterium Cellulophaga sp. Strain KL-A, Isolated from Decaying Marine Algae.

Cellulophaga sp. strain KL-A, isolated from decaying marine algae, is able to degrade iota-carrageenan. Here, we report the draft genome sequence of Cellulophaga sp. strain KL-A.

Diversity and novelty of actinobacteria in Arctic marine sediments.

The actinobacterial diversity of Arctic marine sediments was investigated using culture-dependent and culture-independent approaches. A total of 152 strains were isolated from seven different media; 18 isolates were selected for phylogenetic analysis on the basis of their 16S rRNA gene sequences. Results showed that the 18 isolates belonged to a potential novel genus and 10 known genera including Actinotalea, Arthrobacter, Brachybacterium, Brevibacterium, Kocuria, Kytococcus, Microbacterium, Micrococcus, Mycobacterium, and Pseudonocardia. Subsequently, 172 rDNA clones were selected by restriction fragment length polymorphism analysis from 692 positive clones within four actinobacteria-specific 16S rDNA libraries of Arctic marine sediments, and then these 172 clones were sequenced. In total, 67 phylotypes were clustered in 11 known genera of actinobacteria including Agrococcus, Cellulomonas, Demequina, Iamia, Ilumatobacter, Janibacter, Kocuria, Microbacterium, Phycicoccus, Propionibacterium, and Pseudonocardia, along with other, unidentified actinobacterial clones. Based on the detection of a substantial number of uncultured phylotypes showing low BLAST identities (<95 %), this study confirms that Arctic marine environments harbour highly diverse actinobacterial communities, many of which appear to be novel, uncultured species.

Isolation, characterization, and bioactivity evaluation of 3-((6-methylpyrazin-2-yl)methyl)-1H-indole, a new alkaloid from a deep-sea-derived actinomycete Serinicoccus profundi sp. nov.

One new alkaloid, 3-((6-methylpyrazin-2-yl)methyl)-1H-indole (1) was obtained from the deep-sea actinomycete Serinicoccus profundi sp. nov., along with five known compounds (2-6). Their structures were determined on the basis of detailed analysis of the 1D and 2D NMR as well as MS data. The new indole alkaloid displayed weak antimicrobial activity against Staphylococcus aureus ATCC 25923 with an MIC value of 96 µg/mL. It showed no cytotoxicity on a normal human liver cell line (BEL7402) and a human liver tumor cell line (HL-7702).

Characterization of cathepsin B proteinase (AcCP-2) in eggs and larvae stages of hookworm Ancylostoma caninum.

Cathepsin B proteinase constitutes a large multigenes family in parasitic and non-parasitic nematodes. The localization of cathepsin B proteinases (AcCP-1 and AcCP-2) in adult worm of Ancylostoma caninum has been characterized (Harrop et al., 1995), but the localization and function in eggs and larval stages remained undiscovered. Here we described the expressing of cathepsin B proteinase (AcCP-2) in Escherichia coli, and immuno-localization of cathepsin B proteinase in eggs and larvae stages of A. caninum. A cDNA fragment encoding a cathepsin B proteinase (AcCP-2) was cloned from A. caninum and expressed in E. coli. Gelatin digestion showed that recombinant cathepsin B proteinase (AcCP-2) has protease activity. The protein level of cathepsin B proteinase in larval and adult worm was detected by western blot. The immuno-localization of cathepsin B proteinase in eggs and larval stages was characterized. The expression of cathepsin B proteinase was more abundant in eggs and larvae stages of A. caninum. It implied that cathepsin B proteinase might play roles in the early development of A. caninum.