Emerging knowledge of regulatory roles of d-amino acids in bacteria

Cava, Felipe; Lam, Hubert; Pedro, Miguel A. de; Waldor, Matthew K.

doi:10.1007/s00018-010-0571-8

Cited by 331 publications

(277 citation statements)

References 134 publications

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“…Another challenge that cells may frequently face in the environment is D-amino acids, which many bacteria release into the medium in considerable amounts after transition to the stationary growth phase (40). D-Amino acids were shown to significantly affect peptidoglycan biosynthesis, either by replacing the terminal D-alanine residues of the peptide side chains and thus affecting their recognition by peptidoglycan-modifying enzymes or by directly blocking the substrate-binding site of transpeptidases (41,42). We observed that the C. crescentus wild type was resistant to elevated concentrations of D-alanine.…”

Section: Resultsmentioning

confidence: 99%

Function and Localization Dynamics of Bifunctional Penicillin-Binding Proteins in Caulobacter crescentus

et al. 2014

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The peptidoglycan cell wall of bacteria is a complex macromolecule composed of glycan strands that are cross-linked by short peptide bridges. Its biosynthesis involves a conserved group of enzymes, the bifunctional penicillin-binding proteins (bPBPs), which contain both a transglycosylase and a transpeptidase domain, thus being able to elongate the glycan strands and, at the same time, generate the peptide cross-links. The stalked model bacterium Caulobacter crescentus possesses five bPBP paralogs, named Pbp1A, PbpC, PbpX, PbpY, and PbpZ, whose function is still incompletely understood. In this study, we show that any of these proteins except for PbpZ is sufficient for growth and normal morphogenesis when expressed at native or elevated levels, whereas inactivation of all five paralogs is lethal. Growth analyses indicate a central role of PbpX in the resistance of C. crescentus against the noncanonical amino acid D-alanine. Moreover, we show that PbpX and PbpY localize to the cell division site. Their recruitment to the divisome is dependent on the essential cell division protein FtsN and likely involves interactions with FtsL and the putative peptidoglycan hydrolase DipM. The same interaction pattern is observed for Pbp1A and PbpC, although these proteins do not accumulate at midcell. Our findings demonstrate that the bPBPs of C. crescentus are, to a large extent, redundant and have retained the ability to interact with the peptidoglycan biosynthetic machineries responsible for cell elongation, cytokinesis, and stalk growth. Nevertheless, they may preferentially act in specific peptidoglycan biosynthetic complexes, thereby facilitating the independent regulation of distinct growth processes.

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Section: Resultsmentioning

confidence: 99%

Function and Localization Dynamics of Bifunctional Penicillin-Binding Proteins in Caulobacter crescentus

et al. 2014

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“…D-Amino acids incorporate into the peptide cross bridge of the peptidoglycan component of the cell wall (5,6,11). It was previously shown that D-tyrosine, D-leucine, D-tryptophan, and D-methionine were active in inhibiting biofilm formation by B. subtilis, whereas D isomers of other amino acids, such as D-phenylalanine, were inert in inhibiting biofilm formation (10).…”

Section: Discussionmentioning

confidence: 99%

Inhibitory Effects of d -Amino Acids on Staphylococcus aureus Biofilm Development

et al. 2011

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Most bacteria form matrix-enclosed communities, or biofilms, when growing on surfaces. In clinical settings, biofilms are particularly problematic since they tend to form on indwelling devices and cause persistent infections and sepsis. Biofilmassociated bacteria are much less sensitive to antibiotics, making biofilm-related infections especially difficult to cure (7, 13). Often the only solution for a biofilm-infected catheter is complete replacement, a procedure that can range from uncomfortable and inconvenient to painful, expensive, and life threatening. Consequently, the development of methods to prevent biofilm formation may be just as important for treating hospital-acquired infections as the development of new antibiotics.Bacterial signaling molecules that trigger the dispersal of old biofilms hold promise as possible therapeutic agents. Recent work has demonstrated that D-amino acids may be an exemplary class of such compounds (10, 19). Certain D-amino acids isolated from the supernatants of disassembled Bacillus subtilis biofilms were shown to prevent biofilm formation in fresh cultures by disrupting the connection between an extracellular matrix protein and the cell. Similar inhibitory effects for Staphylococcus aureus and Pseudomonas aeruginosa biofilms suggested that D-amino acids might constitute a general strategy for inhibiting biofilm formation in opportunistic pathogens (10). Genes whose products are involved in biofilm formation are not orthologous across these species, however, and the mechanism of action of D-amino acids against biofilms formed by these dissimilar pathogens remains unknown.Here we describe investigations of the mechanism by which D-amino acids inhibit biofilm formation by S. aureus using fluorescence and confocal scanning laser microscopy. These techniques provide a more detailed picture of biofilm development on surfaces than visual inspection and bulk staining alone. Using dyes for specific components of the biofilm, such as cells, proteins, and polysaccharides, we have found that D-amino acids inhibit biofilm formation in S. aureus in much the same way as in B. subtilis: by preventing protein localization at the cell surface. Since S. aureus employs cell surface-associated proteins to connect neighboring cells in large aggregates (9), D-amino acids could prove effective at preventing mature biofilm development. MATERIALS AND METHODSBacterial growth. Staphylococcus aureus wild-type (WT) strain SC01 (2) was obtained from the Kolter lab collection. Tryptic soy broth (TSB) medium and D and L isomers of proline, tyrosine, phenylalanine, tryptophan, and leucine were obtained from Sigma-Aldrich (Atlanta). Cells were cultured in a shaking LB medium overnight and diluted 1:100 in TSB medium supplemented with NaCl (3%), glucose (0.5%), and the appropriate concentrations of L-or D-amino acids (or lack thereof). Cells were grown for the specified period of time in the bottom of 6-or 12-well polystyrene plates or in 6-well plates with submerged substrates without shaking at 37°C. Plan...

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“…It has long been known that D-amino acids such as D-Ala and D-Glu are structural components of bacterial peptidoglycan, which make the bacterial cell wall resistant to proteases (10). D-amino acid is also an important structural and functional component of diverse bioactive peptides that act as analgesics, antimicrobials, and bactericidal agents among many others (9). More recently, research has begun to reveal important physiological roles of D-amino acids in bacteria and mammals.…”

Section: Discussionmentioning

confidence: 99%

“…D-amino acids also play important structural and physiological roles in diverse life systems. In bacteria, D-amino acids confer cell-wall protease resistance and regulate cell-wall remodeling (9)(10)(11). D-amino acids were also found to be involved in signaling mechanisms in animal nervous systems and plant pollination (12,13).…”

mentioning

confidence: 99%

Discovery of a novel amino acid racemase through exploration of natural variation in Arabidopsis thaliana

Strauch

Svedin

Dilkes

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

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Plants produce diverse low-molecular-weight compounds via specialized metabolism. Discovery of the pathways underlying production of these metabolites is an important challenge for harnessing the huge chemical diversity and catalytic potential in the plant kingdom for human uses, but this effort is often encumbered by the necessity to initially identify compounds of interest or purify a catalyst involved in their synthesis. As an alternative approach, we have performed untargeted metabolite profiling and genome-wide association analysis on 440 natural accessions of Arabidopsis thaliana. This approach allowed us to establish genetic linkages between metabolites and genes. Investigation of one of the metabolitegene associations led to the identification of N-malonyl-D-alloisoleucine, and the discovery of a novel amino acid racemase involved in its biosynthesis. This finding provides, to our knowledge, the first functional characterization of a eukaryotic member of a large and widely conserved phenazine biosynthesis protein PhzF-like protein family. Unlike most of known eukaryotic amino acid racemases, the newly discovered enzyme does not require pyridoxal 5′-phosphate for its activity. This study thus identifies a new D-amino acid racemase gene family and advances our knowledge of plant Damino acid metabolism that is currently largely unexplored. It also demonstrates that exploitation of natural metabolic variation by integrating metabolomics with genome-wide association is a powerful approach for functional genomics study of specialized metabolism.D-amino acid | racemase | genome-wide association | secondary metabolism | natural variation P lants have the ability to create over 200,000 small compounds known as secondary or specialized metabolites (1). These chemically diverse compounds help mediate plant adaptation to their environment and play important roles in plant defense mechanisms, pigmentation, and development. In addition, many of these metabolites are desirable to humans as medicinal and nutritional compounds. Therefore, furthering our understanding of plant specialized metabolism will have profound impacts on various applications from crop improvement to human health.To date, only a small fraction of the chemical and catalytic space in plant specialized metabolism has been explored. Even in the best-studied model plant Arabidopsis thaliana, there are still many uncharacterized metabolites, and the vast majority of genes encoding enzymes implied to be involved in specialized metabolism do not have known associations with any metabolites. Several studies of Arabidopsis natural accessions (individuals collected from wild populations) revealed considerable qualitative and quantitative variation in the accumulation of various compounds such as glucosinolates, terpenoids, and phenylpropanoids (2-4). This extensive metabolite variation can be attributed to genetic variation in genes encoding enzymes and regulatory factors of the pathways involved; quantitative trait locus (QTL) mapping has successfully uncove...

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Emerging knowledge of regulatory roles of d-amino acids in bacteria

Cited by 331 publications

References 134 publications

Function and Localization Dynamics of Bifunctional Penicillin-Binding Proteins in Caulobacter crescentus

Function and Localization Dynamics of Bifunctional Penicillin-Binding Proteins in Caulobacter crescentus

Inhibitory Effects of d -Amino Acids on Staphylococcus aureus Biofilm Development

Discovery of a novel amino acid racemase through exploration of natural variation in Arabidopsis thaliana

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