Transport and hydrolysis of peptides by microorganisms

Microcins in Enterobacteriaceae: Peptide Antimicrobials in the Eco-Active Intestinal Chemosphere

Microcins are low-molecular-weight, ribosomally produced, highly stable, bacterial-inhibitory molecules involved in competitive, and amensalistic interactions between Enterobacteriaceae in the intestine. These interactions take place in a highly complex chemical landscape, the intestinal eco-active chemosphere, composed of chemical substances that positively or negatively influence bacterial growth, including those originated from nutrient uptake, and those produced by the action of the human or animal host and the intestinal microbiome. The contribution of bacteria results from their effect on the host generated molecules, on food and digested food, and organic substances from microbial origin, including from bacterial degradation. Here, we comprehensively review the main chemical substances present in the human intestinal chemosphere, particularly of those having inhibitory effects on microorganisms. With this background, and focusing on Enterobacteriaceae, the most relevant human pathogens from the intestinal microbiota, the microcin’s history and classification, mechanisms of action, and mechanisms involved in microcin’s immunity (in microcin producers) and resistance (non-producers) are reviewed. Products from the chemosphere likely modulate the ecological effects of microcin activity. Several cross-resistance mechanisms are shared by microcins, colicins, bacteriophages, and some conventional antibiotics, which are expected to produce cross-effects. Double-microcin-producing strains (such as microcins MccM and MccH47) have been successfully used for decades in the control of pathogenic gut organisms. Microcins are associated with successful gut colonization, facilitating translocation and invasion, leading to bacteremia, and urinary tract infections. In fact, Escherichia coli strains from the more invasive phylogroups (e.g., B2) are frequently microcinogenic. A publicly accessible APD3 database http://aps.unmc.edu/AP/ shows particular genes encoding microcins in 34.1% of E. coli strains (mostly MccV, MccM, MccH47, and MccI47), and much less in Shigella and Salmonella (<2%). Some 4.65% of Klebsiella pneumoniae are microcinogenic (mostly with MccE492), and even less in Enterobacter or Citrobacter (mostly MccS). The high frequency and variety of microcins in some Enterobacteriaceae indicate key ecological functions, a notion supported by their dominance in the intestinal microbiota of biosynthetic gene clusters involved in the synthesis of post-translationally modified peptide microcins.

Mutant Variants of the Substrate-Binding Protein DppA from Escherichia coli Enhance Growth on Nonstandard γ-Glutamyl Amide-Containing Peptides

The import of nonnatural molecules is a recurring problem in fundamental and applied aspects of microbiology. The dipeptide permease (Dpp) of Escherichia coli is an ABC-type multicomponent transporter system located in the cytoplasmic membrane, which is capable of transporting a wide range of di- and tripeptides with structurally and chemically diverse amino acid side chains into the cell. Given this low degree of specificity, Dpp was previously used as an entry gate to deliver natural and nonnatural cargo molecules into the cell by attaching them to amino acid side chains of peptides, in particular, the γ-carboxyl group of glutamate residues. However, the binding affinity of the substrate-binding protein dipeptide permease A (DppA), which is responsible for the initial binding of peptides in the periplasmic space, is significantly higher for peptides consisting of standard amino acids than for peptides containing side-chain modifications. Here, we used adaptive laboratory evolution to identify strains that utilize dipeptides containing γ-substituted glutamate residues more efficiently and linked this phenotype to different mutations in DppA. In vitro characterization of these mutants by thermal denaturation midpoint shift assays and isothermal titration calorimetry revealed significantly higher binding affinities of these variants toward peptides containing γ-glutamyl amides, presumably resulting in improved uptake and therefore faster growth in media supplemented with these nonstandard peptides.IMPORTANCE Fundamental and synthetic biology frequently suffer from insufficient delivery of unnatural building blocks or substrates for metabolic pathways into bacterial cells. The use of peptide-based transport vectors represents an established strategy to enable the uptake of such molecules as a cargo. We expand the scope of peptide-based uptake and characterize in detail the obtained DppA mutant variants. Furthermore, we highlight the potential of adaptive laboratory evolution to identify beneficial insertion mutations that are unlikely to be identified with existing directed evolution strategies.

Screening of an Escherichia coli promoter library for a phenylalanine biosensor

In recent years, the application of transcription factor-based biosensors for the engineering of microbial production strains opened up new opportunities for industrial biotechnology. However, the design of synthetic regulatory circuits depends on the selection of suitable transcription factor-promoter pairs to convert the concentration of effector molecules into a measureable output. Here, we present an efficient strategy to screen promoter libraries for appropriate parts for biosensor design. To this end, we pooled the strains of the Alon library containing about 2000 different Escherichia coli promoter-gfpmut2 fusions, and enriched galactose- and L-phenylalanine-responsive promoters by toggled rounds of positive and negative selection using fluorescence-activated cell sorting (FACS). For both effectors, responsive promoters were isolated and verified by cultivation in microtiter plates. The promoter of mtr, encoding an L-tryptophan-specific transporter, was identified as suitable part for the construction of an L-phenylalanine biosensor. In the following, we performed a comparative analysis of different biosensor constructs based on the mtr promoter. The obtained data revealed a strong influence of the biosensor architecture on the performance characteristics. For proof-of-principle, the mtr sensor was applied in a FACS high-throughput screening of an E. coli MG1655 mutant library for the isolation of L-phenylalanine producers. These results emphasize the developed screening approach as a convenient strategy for the identification of effector-responsive promoters for the design of novel biosensors.

Pathway for uptake and degradation of X-prolyl tripeptides in Streptococcus mutans VA-29R and Streptococcus sanguis ATCC 10556

The growth of Streptococcus mutans and Streptococcus sanguis in the oral environment requires that these micro-organisms be able to degrade salivary proteins and to assimilate the resulting peptides as an amino nitrogen source. Our research is aimed at the definition of the proteolytic enzyme systems in these oral streptococci which allow them to utilize such substrates. In the present work, the nature of the hydrolytic activity expressed by S. mutans VA-29R and S. sanguis ATCC 10556 against X-Pro4-nitroanilide and X-Pro-Y tripeptide substrates was investigated. This activity was predominantly associated with a cytoplasmic dipeptidyl peptidase which preferentially catalyzes the release of an N-terminal dipeptide from substrates in which proline is the penultimate residue. These streptococci also possess a second cytoplasmic peptidase, pepD, which catalyzes the hydrolysis of X-Pro dipeptides. We found that Gly-Pro-Ala or Ala-Pro-Gly were transported into the bacterial cells only when an energy source such as glucose was present. Peptide uptake was time-dependent, and selective exodus of peptide-derived amino acids from the bacterial cells occurred during peptide uptake. Results from these studies provide evidence that S. mutans VA-29R and S. sanguis ATCC 10556 possess a pathway for the complete degradation of X-Pro tripeptides. Transport of the peptides into cells prior to hydrolysis provides an efficient way by which all amino acids of a peptide may be obtained at an energy expense equivalent to that associated with the transport of just one amino acid. In light of the abundance of proline in salivary polypeptides, this degradative pathway could be an important component in the proteolytic pathway for salivary polypeptide utilization in these oral streptococci.

Studies on the subcellular localization of protease and arylaminopeptidase activities in Streptococcus sanguis ATCC 10556

Intact cells of Streptococcus sanguis ATCC 10556 possessed arylaminopeptidases exhibiting activity toward the nitroanilide (NA) derivatives of leucine, alanine, methionine, arginine, or lysine. Weak hydrolytic activity was observed in assays with the NA derivatives of valine, proline, glycine, or glutamic acid. Subcellular localization studies revealed that arylaminopeptidase activities were located in both the cell membrane and cytoplasm. Arylaminopeptidases exhibiting activity toward the leucine, alanine, or methionine NA substrates appeared to be more predominantly associated with the membrane, whereas enzymes exhibiting activity toward arginyl-NA or lysyl-NA were more prevalently located in the cytoplasm. Several results from this study suggest that the membrane-assocaited arginyl and lysyl arylaminopeptidases were located in such a way that their expression was restricted in the intact cell. The addition of 0.5 mol/L NaCl to protoplast preparations derived from mutanolysin-treated cells resulted in an almost complete solubilization of membrane-associated arylaminopeptidase activities. These observations support the conclusion that the association of arylaminopeptidases with the cell membrane may involve hydrophobic or electrostatic interactions, or both. S. sanguis ATCC 10556 also possessed at least one caseinolytic endopeptidase activity. This activity is most likely located near the membrane surface, as no association with the cell wall was evident. The location of membrane-associated endopeptidase and arylaminopeptidase activities, together with intracellular peptidases, is suggested to provide an efficient mechanism for the hydrolysis and subsequent utilization of polypeptide and oligopeptide substrates as sources of amino acids for growth by this microorganism.

Sodium-dependent transport of neutral amino acids by whole cells and membrane vesicles of Streptococcus bovis, a ruminal bacterium

Streptococcus bovis JB1 cells were able to transport serine, threonine, or alanine, but only when they were incubated in sodium buffers. If glucose-energized cells were washed in potassium phosphate and suspended in potassium phosphate buffer, there was no detectable uptake. Cells deenergized with 2-deoxyglucose and incubated in sodium phosphate buffer were still able to transport serine, and this result indicated that the chemical sodium gradient was capable of driving transport. However, when the deenergized cells were treated with valinomycin and diluted into sodium phosphate to create both an artificial membrane potential and a chemical sodium gradient, rates of serine uptake were fivefold greater than in cells having only a sodium gradient. If deenergized cells were preloaded with sodium (no membrane potential or sodium gradient), there was little serine transport. Nigericin and monensin, ionophores capable of reversing sodium gradients across membranes, strongly inhibited sodium-dependent uptake of the three amino acids. Membrane vesicles loaded with potassium and diluted into either lithium or choline chloride were unable to transport serine, but rapid uptake was evident if sodium chloride was added to the assay mixture. Serine transport had an extremely poor affinity for sodium, and more than 30 mM was needed for half-maximal rates of uptake. Serine transport was inhibited by an excess of threonine, but an excess of alanine had little effect. Results indicated that S. bovis had separate sodium symport systems for serine or threonine and alanine, and either the membrane potential or chemical sodium gradient could drive uptake.

THE BIOLOGY OF MYCORRHIZA IN THE RICACEAE: IX. PEPTIDES AS NITROGEN SOURCES FOR THE ERICOID ENDOPHYTE AND FOR MYCORRHIZAL AND NON-MYCORRHIZAL PLANTS

The ericoid mycorrhizal endophyte Hymenoscyphus ericae (Read) Korf &Kernan was grown both in pure culture and in mycorrhizal association with the host plant Vaccinium corymbosum L. on media containing peptides of differing chain length as sole nitrogen sources. The ability to utilize the peptide nitrogen was assessed in terms of growth of the fungus and of growth and nitrogen content of the plants. The tripeptide, glutathione, and alanine units of 1-6 amino acid residues in length were all readily utilized by the endophyte, though assimilation was less rapid in the case of the longer chain lengths. Mycorrhizal seedlings showed significantly higher yields and had higher nitrogen contents than non-mycorrhizal seedlings in almost all cases. The physiological and ecological implications of these results are discussed.

THE BIOLOGY OF MYCORRHIZA IN THE ERICACEAE: X. THE UTILIZATION OF PROTEINS AND THE PRODUCTION OF PROTEOLYTIC ENZYMES BY THE MYCORRHIZAL ENDOPHYTE AND BY MYCORRHIZAL PLANTS

The ability of the ericoid mycorrhizal endophyte to utilize a range of proteins as substrates for growth is assessed in liquid culture and in mycorrhizal association with host plants. Some aspects of proteolytic enzyme production are also investigated. The fungus readily utilizes the soluble protein bovine serum albumin (BSA) as sole nitrogen and carbon source, and produces lower yields on less soluble plant and animal proteins. Maximum yields of endophyte on all substrates were obtained in the pH range 3 to 5. Infection provides a significant enhancement of plant growth on agar over this pH range on most of the proteins. Yields and nitrogen contents of mycorrhizal plants grown on cellulose sheets with BSA as sole N source were significantly higher than those of the uninfected controls, which were unable to use protein. Using a chromogenic substrate it was shown that the pH optimum for enzyme activity is comparable with that for utilization of protein in pure culture and in mycorrhizal association. Non-mycorrhizal plants produced negligible proteolytic activity. The significance of these observations is discussed in relation to the nutrition of both host and fungus in the natural environment, and the broader ecological implications of the results are assessed.