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1. Binding of Dipeptides to Fatty Acid Membranes Explains Their Colocalization in Protocells but Does Not Select for Them Relative to Unjoined Amino Acids

   Mengjun Xue, Roy A. (July 2021, The journal of physical chemistry)

   null (Ed.)

   Dipeptides, which consist of two amino acids joined by a peptide bond, have been shown to have catalytic functions. This observation leads to fundamental questions relevant to the origin of life. How could peptides have become colocalized with the first protocells? Which structural features would have determined the association of amino acids and peptides with membranes? Could the association of dipeptides with protocell membranes have driven molecular evolution, favoring dipeptides over individual amino acids? Using pulsed-field gradient nuclear magnetic resonance, we find that several prebiotic amino acids and dipeptides bind to prebiotic membranes. For amino acids, the side chains and carboxylate contribute to the interaction. For dipeptides, the extent of binding is generally less than that of the constituent amino acids, implying that other mechanisms would be necessary to drive molecular evolution. Nevertheless, our results are consistent with a scheme in which the building blocks of the biological polymers colocalized with protocells prior to the emergence of RNA and proteins. 

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2. Anaerobic Conversion of Proteinogenic Amino Acids When Methanogenesis Is Inhibited: Carboxylic Acid Production from Single Amino Acids

   https://doi.org/10.3390/fermentation10050237  

   Conrado, Leandro; McCoy, Jacob; Rabinovich, Leo; Davoudimehr, Mona; Stamatopoulou, Panagiota; Scarborough, Matthew (May 2024, Fermentation)

   Proteins are an abundant biopolymer in organic waste feedstocks for biorefining. When degraded, amino acids are released, but their fate in non-methanogenic microbiomes is not well understood. The ability of a microbiome obtained from an anaerobic digester to produce volatile fatty acids from the twenty proteinogenic amino acids was tested using batch experiments. Batch tests were conducted using an initial concentration of each amino acid of 9000 mg COD L−1 along with 9000 mg COD L−1 acetate. Butyrate production was observed from lysine, glutamate, and serine fermentation. Lesser amounts of propionate, iso-butyrate, and iso-valerate were also observed from individual amino acids. Based on 16S rRNA gene amplicon sequencing, Anaerostignum, Intestimonas, Aminipila, and Oscillibacter all likely play a role in the conversion of amino acids to butyrate. The specific roles of other abundant taxa, including Coprothermobacter, Fervidobacterium, Desulfovibrio, and Wolinella, remain unknown, but these genera should be studied for their role in fermentation of amino acids and proteins to VFAs. 

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3. Reaction of Carboxylic Acids and Dehydroalanine Allyl Esters via One‐Pot Sequential Decarboxylative Couplings

   https://doi.org/10.1002/cctc.202500696  

   Londhe, Shrikant_S; Waller, Colin_W; Tunge, Jon_A (June 2025, ChemCatChem)

   Abstract A protocol for the iterative decarboxylative cross‐coupling of carboxylic acids with dehydroalanine (Dha) allyl esters is described. A procedure for decarboxylative Giese addition to dehydroalanine allyl esters that avoids 5‐exo‐trig radical cyclization onto the allyl moiety was developed. This results in complex, substituted alanine allyl esters that are poised for a second decarboxylative coupling. Thus, following the photocatalytic decarboxylative alkylation of Dha, the resulting amino acid allyl esters were subjected to decarboxylative allylation under metallaphotoredox/palladium catalysis. The Giese addition and decarboxylative allylation can be performed in one pot simply by triggering the decarboxylative allylation by addition of a palladium catalyst. These one‐pot decarboxylative couplings leverage temporally controlled carboxylate formation to allow controlled, sequential photoredox activation of the carboxylates. The ability to perform sequential, one‐pot photoredox C─C bond formations obviates the need for isolation of intermediates. The final products of these coupling reactions are densely functionalized homoallylic amines and/or unsymmetric, differentiated 1,3‐diamines, both known for their high synthetic value. 

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4. Exogenous Fatty Acids Remodel Staphylococcus aureus Lipid Composition through Fatty Acid Kinase

   https://doi.org/10.1128/JB.00128-20  

   DeMars, Zachary; Singh, Vineet K.; Bose, Jeffrey L. (June 2020, Journal of Bacteriology)

   Stock, Ann M. (Ed.)

   ABSTRACT Staphylococcus aureus can utilize exogenous fatty acids for phospholipid synthesis. The fatty acid kinase FakA is essential for this utilization by phosphorylating exogenous fatty acids for incorporation into lipids. How FakA impacts the lipid membrane composition is unknown. In this study, we used mass spectrometry to determine the membrane lipid composition and properties of S. aureus in the absence of fakA . We found the fakA mutant to have increased abundance of lipids containing longer acyl chains. Since S. aureus does not synthesize unsaturated fatty acids, we utilized oleic acid (18:1) to track exogenous fatty acid incorporation into lipids. We observed a concentration-dependent incorporation of exogenous fatty acids into the membrane that required FakA. We also tested how FakA and exogenous fatty acids impact membrane-related physiology and identified changes in membrane potential, cellular respiration, and membrane fluidity. To mimic the host environment, we characterized the lipid composition of wild-type and fakA mutant bacteria grown in mouse skin homogenate. We show that wild-type S. aureus can incorporate exogenous unsaturated fatty acids from host tissue, highlighting the importance of FakA in the presence of host skin tissue. In conclusion, FakA is important for maintaining the composition and properties of the phospholipid membrane in the presence of exogenous fatty acids, impacting overall cell physiology. IMPORTANCE Environmental fatty acids can be harvested to supplement endogenous fatty acid synthesis to produce membranes and circumvent fatty acid biosynthesis inhibitors. However, how the inability to use these fatty acids impacts lipids is unclear. Our results reveal lipid composition changes in response to fatty acid addition and when S. aureus is unable to activate fatty acids through FakA. We identify concentration-dependent utilization of oleic acid that, when combined with previous work, provides evidence that fatty acids can serve as a signal to S. aureus . Furthermore, using mouse skin homogenates as a surrogate for in vivo conditions, we showed that S. aureus can incorporate host fatty acids. This study highlights how exogenous fatty acids impact bacterial membrane composition and function. 

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5. Oxidation of Amino Acids by Peracetic Acid: Reaction Kinetics, Pathways and Theoretical Calculations

   https://doi.org/https://doi.org/10.1016/j.wroa.2018.09.002  

   Du, P.; Liu, W.; Cao, H.; Zhao, H.; Huang, C.-H. (January 2018, Water research. X)

   Peracetic acid (PAA) is a sanitizer with increasing use in food, medical and water treatment industries. Amino acids are important components in targeted foods for PAA treatment and ubiquitous in natural waterbodies and wastewater effluents as the primary form of dissolved organic nitrogen. To better understand the possible reactions, this work investigated the reaction kinetics and transformation pathways of selected amino acids towards PAA. Experimental results demonstrated that most amino acids showed sluggish reactivity to PAA except cysteine (CYS), methionine (MET), and histidine (HIS). CYS showed the highest reactivity with a very rapid reaction rate. Reactions of MET and HIS with PAA followed second-order kinetics with rate constants of 4.6 ± 0.2, and 1.8 ± 0.1 M−1s−1 at pH 7, respectively. The reactions were faster at pH 5 and 7 than at pH 9 due to PAA speciation. Low concentrations of H2O2 coexistent with PAA contributed little to the oxidation of amino acids. The primary oxidation products of amino acids with PAA were [O] addition compounds on the reactive sites at thiol, thioether and imidazole groups. Theoretical calculations were applied to predict the reactivity and regioselectivity of PAA electrophilic attacks on amino acids and improved mechanistic understanding. As an oxidative disinfectant, the reaction of PAA with organics to form byproducts is inevitable; however, this study shows that PAA exhibits lower and more selective reactivity towards biomolecules such as amino acids than other common disinfectants, causing less concern of toxic disinfection byproducts. This attribute may allow greater stability and more targeted actions of PAA in various applications. 

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