Relevant bibliographies by topics / LytM-domain

Academic literature on the topic 'LytM-domain'

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Published: 9 March 2023
Last updated: 10 March 2023

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Journal articles on the topic "LytM-domain"

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Uehara, Tsuyoshi, Thuy Dinh, and Thomas G. Bernhardt. "LytM-Domain Factors Are Required for Daughter Cell Separation and Rapid Ampicillin-Induced Lysis in Escherichia coli." Journal of Bacteriology 191, no. 16 (June 12, 2009): 5094–107. http://dx.doi.org/10.1128/jb.00505-09.

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ABSTRACT Bacterial cytokinesis is coupled to the localized synthesis of new peptidoglycan (PG) at the division site. This newly generated septal PG is initially shared by the daughter cells. In Escherichia coli and other gram-negative bacteria, it is split shortly after it is made to promote daughter cell separation and allow outer membrane constriction to closely follow that of the inner membrane. We have discovered that the LytM (lysostaphin)-domain containing factors of E. coli (EnvC, NlpD, YgeR, and YebA) are absolutely required for septal PG splitting and daughter cell separation. Mutants lacking all LytM factors form long cell chains with septa containing a layer of unsplit PG. Consistent with these factors playing a direct role in septal PG splitting, both EnvC-mCherry and NlpD-mCherry fusions were found to be specifically recruited to the division site. We also uncovered a role for the LytM-domain factors in the process of β-lactam-induced cell lysis. Compared to wild-type cells, mutants lacking LytM-domain factors were delayed in the onset of cell lysis after treatment with ampicillin. Moreover, rather than lysing from midcell lesions like wild-type cells, LytM− cells appeared to lyse through a gradual loss of cell shape and integrity. Overall, the phenotypes of mutants lacking LytM-domain factors bear a striking resemblance to those of mutants defective for the N-acetylmuramyl-l-alanine amidases: AmiA, AmiB, and AmiC. E. coli thus appears to rely on two distinct sets of putative PG hydrolases to promote proper cell division.
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An, Doo Ri, Hyoun Sook Kim, Jieun Kim, Ha Na Im, Hye Jin Yoon, Ji Young Yoon, Jun Young Jang, et al. "Structure of Csd3 fromHelicobacter pylori, a cell shape-determining metallopeptidase." Acta Crystallographica Section D Biological Crystallography 71, no. 3 (February 26, 2015): 675–86. http://dx.doi.org/10.1107/s1399004715000152.

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Helicobacter pyloriis associated with various gastrointestinal diseases such as gastritis, ulcers and gastric cancer. Its colonization of the human gastric mucosa requires high motility, which depends on its helical cell shape. Seven cell shape-determining genes (csd1,csd2,csd3/hdpA,ccmA,csd4,csd5andcsd6) have been identified inH. pylori. Their proteins play key roles in determining the cell shape through modifications of the cell-wall peptidoglycan by the alteration of cross-linking or by the trimming of peptidoglycan muropeptides. Among them, Csd3 (also known as HdpA) is a bifunctional enzyme. Its D,D-endopeptidase activity cleaves the D-Ala4-mDAP3peptide bond between cross-linked muramyl tetrapeptides and pentapeptides. It is also a D,D-carboxypeptidase that cleaves off the terminal D-Ala5from the muramyl pentapeptide. Here, the crystal structure of this protein has been determined, revealing the organization of its three domains in a latent and inactive state. The N-terminal domain 1 and the core of domain 2 share the same fold despite a very low level of sequence identity, and their surface-charge distributions are different. The C-terminal LytM domain contains the catalytic site with a Zn2+ion, like the similar domains of other M23 metallopeptidases. Domain 1 occludes the active site of the LytM domain. The core of domain 2 is held against the LytM domain by the C-terminal tail region that protrudes from the LytM domain.
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Sabala, Izabela, Ing-Marie Jonsson, Andrej Tarkowski, and Matthias Bochtler. "Anti-staphylococcal activities of lysostaphin and LytM catalytic domain." BMC Microbiology 12, no. 1 (2012): 97. http://dx.doi.org/10.1186/1471-2180-12-97.

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Jagielska, Elzbieta, Olga Chojnacka, and Izabela Sabała. "LytM Fusion with SH3b-Like Domain Expands Its Activity to Physiological Conditions." Microbial Drug Resistance 22, no. 6 (September 2016): 461–69. http://dx.doi.org/10.1089/mdr.2016.0053.

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Sexton, Danielle L., Francesca A. Herlihey, Ashley S. Brott, David A. Crisante, Evan Shepherdson, Anthony J. Clarke, and Marie A. Elliot. "Roles of LysM and LytM domains in resuscitation-promoting factor (Rpf) activity and Rpf-mediated peptidoglycan cleavage and dormant spore reactivation." Journal of Biological Chemistry 295, no. 27 (May 20, 2020): 9171–82. http://dx.doi.org/10.1074/jbc.ra120.013994.

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Bacterial dormancy can take many forms, including formation of Bacillus endospores, Streptomyces exospores, and metabolically latent Mycobacterium cells. In the actinobacteria, including the streptomycetes and mycobacteria, the rapid resuscitation from a dormant state requires the activities of a family of cell-wall lytic enzymes called resuscitation-promoting factors (Rpfs). Whether Rpf activity promotes resuscitation by generating peptidoglycan fragments (muropeptides) that function as signaling molecules for spore germination or by simply remodeling the dormant cell wall has been the subject of much debate. Here, to address this question, we used mutagenesis and peptidoglycan binding and cleavage assays to first gain broader insight into the biochemical function of diverse Rpf enzymes. We show that their LysM and LytM domains enhance Rpf enzyme activity; their LytM domain and, in some cases their LysM domain, also promoted peptidoglycan binding. We further demonstrate that the Rpfs function as endo-acting lytic transglycosylases, cleaving within the peptidoglycan backbone. We also found that unlike in other systems, Rpf activity in the streptomycetes is not correlated with peptidoglycan-responsive Ser/Thr kinases for cell signaling, and the germination of rpf mutant strains could not be stimulated by the addition of known germinants. Collectively, these results suggest that in Streptomyces, Rpfs have a structural rather than signaling function during spore germination, and that in the actinobacteria, any signaling function associated with spore resuscitation requires the activity of additional yet to be identified enzymes.
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Osipovitch, Daniel C., and Karl E. Griswold. "Fusion with a cell wall binding domain renders autolysin LytM a potent anti-Staphylococcus aureus agent." FEMS Microbiology Letters 362, no. 2 (December 8, 2014): 1–7. http://dx.doi.org/10.1093/femsle/fnu035.

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Meisner, J., and C. P. Moran. "A LytM Domain Dictates the Localization of Proteins to the Mother Cell-Forespore Interface during Bacterial Endospore Formation." Journal of Bacteriology 193, no. 3 (November 19, 2010): 591–98. http://dx.doi.org/10.1128/jb.01270-10.

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Peters, Nick T., Cécile Morlot, Desirée C. Yang, Tsuyoshi Uehara, Thierry Vernet, and Thomas G. Bernhardt. "Structure-function analysis of the LytM domain of EnvC, an activator of cell wall remodelling at theEscherichia colidivision site." Molecular Microbiology 89, no. 4 (July 23, 2013): 690–701. http://dx.doi.org/10.1111/mmi.12304.

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Cook, Jonathan, Tyler C. Baverstock, Martin B. L. McAndrew, Phillip J. Stansfeld, David I. Roper, and Allister Crow. "Insights into bacterial cell division from a structure of EnvC bound to the FtsX periplasmic domain." Proceedings of the National Academy of Sciences 117, no. 45 (October 23, 2020): 28355–65. http://dx.doi.org/10.1073/pnas.2017134117.

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FtsEX is a bacterial ABC transporter that regulates the activity of periplasmic peptidoglycan amidases via its interaction with the murein hydrolase activator, EnvC. InEscherichia coli, FtsEX is required to separate daughter cells after cell division and for viability in low-osmolarity media. Both the ATPase activity of FtsEX and its periplasmic interaction with EnvC are required for amidase activation, but the process itself is poorly understood. Here we present the 2.1 Å structure of the FtsX periplasmic domain in complex with its periplasmic partner, EnvC. The EnvC-FtsX periplasmic domain complex has a 1-to-2 stoichiometry with two distinct FtsX-binding sites located within an antiparallel coiled coil domain of EnvC. Residues involved in amidase activation map to a previously identified groove in the EnvC LytM domain that is here found to be occluded by a “restraining arm” suggesting a self-inhibition mechanism. Mutational analysis, combined with bacterial two-hybrid screens and in vivo functional assays, verifies the FtsEX residues required for EnvC binding and experimentally test a proposed mechanism for amidase activation. We also define a predicted link between FtsEX and integrity of the outer membrane. Both the ATPase activity of FtsEX and its periplasmic interaction with EnvC are required for resistance to membrane-attacking antibiotics and detergents to whichE. coliwould usually be considered intrinsically resistant. These structural and functional data provide compelling mechanistic insight into FtsEX-mediated regulation of EnvC and its downstream control of periplasmic peptidoglycan amidases.
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An, Doo Ri, and Se Won Suh. "Crystal structure of the Csd3 protein from Helicobacter pylori." Acta Crystallographica Section A Foundations and Advances 70, a1 (August 5, 2014): C1630. http://dx.doi.org/10.1107/s2053273314083697.

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The helical cell shape of Helicobacter pylori facilitates the penetration of thick gastric mucus and promotes virulence. The peptidoglycan plays a structural role in the bacterial cell wall and its controlled modification is essential for determining the helical shape. Several H. pylori genes were identified to contribute to its helical cell shape through alterations in peptidoglycan crosslinking and trimming of the peptide (Sycuro et al., 2010; Sycuro et al., 2012). One of them is the hp0506 gene that encodes a putative periplasmic peptidase belonging to the M23-family of zinc-metallopeptidase (Sycuro et al., 2010). The HP0506 protein carries out not only a D,D-endopeptidase activity but also a D,D-carboxypeptidase activity. Hence, it has been named Helicobacter D,D-peptidase A (HdpA) and cell shape determinant 3 (Csd3). Csd3 is the first enzyme belonging to the M23-peptidase family that can perform the D,D-carboxypeptidation to regulate the cell shape (Mathilde et al., 2010). To gain structural and functional insights at the molecular level, we have determined the crystal structure of Csd3 at 2.1 Å resolution by using the Pt SAD data. H. pylori Csd3 consists of three domains including a LytM domain, which contains the highly conserved active site motif among the M23 metallopeptidase family. An anomalous scattering experiment with Zn2+ confirmed the metal-binding site in the active site. The Zn2+ ion is tetrahedrally coordinated and a catalytic water for peptide hydrolysis is absent in the active site of Csd3. Furthermore, domain 1 blocks the active site, thus prohibiting the substrate peptide binding. Our mass analysis shows that the full-length Csd3 is inactive as the D,D-carboxypeptidase. These results suggest that proteolytic processing may be necessary for the activation of Csd3.
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Dissertations / Theses on the topic "LytM-domain"

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GURNANI, SERRANO CARLOS KARAN. "ROLE OF PEPTIDOGLYCAN REMODELING IN OVERCOMING LPS BIOGENESIS DEFECTS IN ESCHERICHIA COLI." Doctoral thesis, Università degli Studi di Milano, 2021. http://hdl.handle.net/2434/783882.

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The three layered Gram-negative bacteria envelope consists of an inner membrane (IM), the periplasm‐containing peptidoglycan (PG), and an asymmetric outer membrane (OM) decorated with lipopolysaccharide (LPS) in the outer leaflet. Growth and assembly of cell envelope is orchestrated by action of dedicated protein machineries which span the entire envelope and whose coordinated activity guarantees proper envelope stiffness. Defects in biogenesis in any of these layers compromise the whole cell integrity and lead to cell death. In this thesis we show that Escherichia coli remodels the PG structure by increasing the level of 3-3 crosslinks produced by LD – Transpeptidases (LDTs), to avoid cell lysis when the LPS transport to the OM is disrupted. E. coli codes for six LDTs (LdtA-F): LdtA, LdtB, and LdtC covalently attach Lpp to PG while LdtD and LdtE introduce 3-3crosslinks. LdtF has no LD-Transpeptidase (LD-Tpase) activity but enhances the enzymatic activity of LdtD and LdtE. Our data outlines a major contribution of LdtD in PG remodelling and suggest that LdtD works in concert with the PG synthase PBP1B, its activator LpoB and the DD-CPase PBP6a to form a dedicated PG repair machine that runs a PG remodeling program to counteract damages to the OM. We also show that the lysis phenotype and morphological defects seen in mutants with an impaired LPS transport and lacking ldtF, are rescued and suppressed, respectively, by the loss of YgeR an uncharacterized lipoprotein predicted to be OM anchored. YgeR belongs to the family of LytM-domain factors which are hydrolases or hydrolase regulators implicated in PG remodeling/turnover. Important PG hydrolases are amidases which promote PG septal splitting and daughter cell separation. Our biochemical data reveal that YgeR is an amidase regulator able to activate AmiA, AmiB and AmiC the three amidases encoded by E. coli. We also show that YgeR binds purified PG and physically interacts with the amidase AmiC. Our biochemical analyses are complemented by in vivo data showing that YgeR preferentially activates AmiC and that it does it through its LytM domain. Altogether, our results point out an unexplored protective role of the 3-3 crosslinks in PG to overcome severe OM biogenesis defects and propose YgeR as a novel amidase activator whose action seems required upon envelope stress.
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Shaku, Tube Moagi. "Characterization of LYTM domain containing proteins in mycobacterium smegmatis." Thesis, 2017. http://hdl.handle.net/10539/23164.

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A dissertation submitted to the Faculty of Health Science, University of the Witwatersrand, Johannesburg, in fulfillment of the requirements for the degree of Master of Science in Medicine. 2017
Mycobacterium tuberculosis assembles a complex cell wall consisting of mycolic acids, arabinogalactan and peptidoglycan layers. The peptidoglycan is important for structural maintenance and osmotic protection of the cell. Beta-lactam antibiotics, such as penicillin, perturb biogenesis of cross-linked peptidoglycan by inhibition of penicillin-binding proteins and cause cell death. As a result, penicillin-binding proteins have been extensively used in antimicrobial development. However, penicillin insensitive enzymes involved in peptidoglycan biogenesis such as amidases, transglycosylases and endopeptidases remain to be exploited for anti-TB drug development, a field that urgently requires new drugs in light of the rapid emergence of drug resistant strains. In this study, we functionally characterize a novel class of LytM domain containing peptidoglycan endopeptidases (also known as M23 peptidases) in mycobacteria. Bio-informatics tools were used to identify LytM domain-containing homologues in Mycobacterium smegmatis, designated MepB1-MepB4. These were deleted using standard allelic exchange mutagenesis and recombination techniques and the resulting mutants were assessed for cell wall related defects. We found that mycobacterial LytM endopeptidases have important roles in bacterial growth as demonstrated by delayed cell growth kinetics in a ΔmepB1 deletion mutant. We noted no growth defects in ΔmepB2 and ΔmepB3 single deletion mutants but observed defective cell division in a ΔmepB2 ΔmepB3 double deletion mutant. In this double mutant, spatial localization of new cell wall biosynthesis revealed the inability to degrade the septal bridge joining two daughter cells, pointing to a critical role for these enzymes in cell separation. MepB1 is sequestered from the peptidoglycan by cytosolic localization and its absence causes a septal and polar buldging phenotype. To further investigate the biological roles of these putative peptidoglycan endopeptidases, protein interaction studies were conducted using the bacterial two-hybrid mycobacterial protein fragment complementation assay. This analysis identified FtsX, a key cell division protein, as an interacting partner for both MepB2 and MepB3, thus identifying these proteins as novel components of the mycobacterial divisome. Collectively, these observations provide the first insight into a new group of potential drug targets for tuberculosis disease and notably enhance the overall understanding of peptidoglycan turnover, which is of general revelevance in bacterial pathogens.
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