Journal articles: '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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Nilsen, Trine, Ingolf F. Nes, and Helge Holo. "Enterolysin A, a Cell Wall-Degrading Bacteriocin from Enterococcus faecalis LMG 2333." Applied and Environmental Microbiology 69, no. 5 (May 2003): 2975–84. http://dx.doi.org/10.1128/aem.69.5.2975-2984.2003.

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ABSTRACT A novel antimicrobial protein, designated enterolysin A, was purified from an Enterococcus faecalis LMG 2333 culture. Enterolysin A inhibits growth of selected enterococci, pediococci, lactococci, and lactobacilli. Antimicrobial activity was initially detected only on solid media, but by growing the bacteria in a fermentor under optimized production conditions (MRS broth with 4% [wt/vol] glucose, pH 6.5, and a temperature between 25 and 35°C), the bacteriocin activity was increased to 5,120 bacteriocin units ml−1. Enterolysin A production was regulated by pH, and activity was first detected in the transition between the logarithmic and stationary growth phases. Killing of sensitive bacteria by enterolysin A showed a dose-response behavior, and the bacteriocin has a bacteriolytic mode of action. Enterolysin A was purified, and the primary structure was determined by combined amino acid and DNA sequencing. This bacteriocin is translated as a 343-amino-acid preprotein with an sec-dependent signal peptide of 27 amino acids, which is followed by a sequence corresponding to the N-terminal part of the purified protein. Mature enterolysin A consists of 316 amino acids and has a calculated molecular weight of 34,501, and the theoretical pI is 9.24. The N terminus of enterolysin A is homologous to the catalytic domains of different cell wall-degrading proteins with modular structures. These include lysostaphin, ALE-1, zoocin A, and LytM, which are all endopeptidases belonging to the M37 protease family. The N-terminal part of enterolysin A is linked by a threonine-proline-rich region to a putative C-terminal recognition domain, which shows significant sequence identity to two bacteriophage lysins.

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Figueroa-Cuilan, Wanda M., Amelia M. Randich, Caroline M. Dunn, Gustavo Santiago-Collazo, Andrew Yowell, and Pamela J. B. Brown. "Diversification of LytM Protein Functions in Polar Elongation and Cell Division of Agrobacterium tumefaciens." Frontiers in Microbiology 12 (August 18, 2021). http://dx.doi.org/10.3389/fmicb.2021.729307.

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LytM-domain containing proteins are LAS peptidases (lysostaphin-type enzymes, D-Ala-D-Ala metallopeptidases, and sonic hedgehog) and are known to play diverse roles throughout the bacterial cell cycle through direct or indirect hydrolysis of the bacterial cell wall. A subset of the LytM factors are catalytically inactive but regulate the activity of other cell wall hydrolases and are classically described as cell separation factors NlpD and EnvC. Here, we explore the function of four LytM factors in the alphaproteobacterial plant pathogen Agrobacterium tumefaciens. An LmdC ortholog (Atu1832) and a MepM ortholog (Atu4178) are predicted to be catalytically active. While Atu1832 does not have an obvious function in cell growth or division, Atu4178 is essential for polar growth and likely functions as a space-making endopeptidase that cleaves amide bonds in the peptidoglycan cell wall during elongation. The remaining LytM factors are degenerate EnvC and NlpD orthologs. Absence of these proteins results in striking phenotypes indicative of misregulation of cell division and growth pole establishment. The deletion of an amidase, AmiC, closely phenocopies the deletion of envC suggesting that EnvC might regulate AmiC activity. The NlpD ortholog DipM is unprecedently essential for viability and depletion results in the misregulation of early stages of cell division, contrasting with the canonical view of DipM as a cell separation factor. Finally, we make the surprising observation that absence of AmiC relieves the toxicity induced by dipM overexpression. Together, these results suggest EnvC and DipM may function as regulatory hubs with multiple partners to promote proper cell division and establishment of polarity.

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Wang, Min, Sanne van den Berg, Yaremit Mora Hernández, Aafke Hinke Visser, Elias Vera Murguia, Dennis G. A. M. Koedijk, Channah Bellink, et al. "Differential binding of human and murine IgGs to catalytic and cell wall binding domains of Staphylococcus aureus peptidoglycan hydrolases." Scientific Reports 11, no. 1 (July 5, 2021). http://dx.doi.org/10.1038/s41598-021-93359-6.

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AbstractStaphylococcus aureus is an opportunistic pathogen causing high morbidity and mortality. Since multi-drug resistant S. aureus lineages are nowadays omnipresent, alternative tools for preventive or therapeutic interventions, like immunotherapy, are urgently needed. However, there are currently no vaccines against S. aureus. Surface-exposed and secreted proteins are regarded as potential targets for immunization against S. aureus infections. Yet, many potential staphylococcal antigens of this category do not elicit protective immune responses. To obtain a better understanding of this problem, we compared the binding of serum IgGs from healthy human volunteers, highly S. aureus-colonized patients with the genetic blistering disease epidermolysis bullosa (EB), or immunized mice to the purified S. aureus peptidoglycan hydrolases Sle1, Aly and LytM and their different domains. The results show that the most abundant serum IgGs from humans and immunized mice target the cell wall-binding domain of Sle1, and the catalytic domains of Aly and LytM. Interestingly, in a murine infection model, these particular IgGs were not protective against S. aureus bacteremia. In contrast, relatively less abundant IgGs against the catalytic domain of Sle1 and the N-terminal domains of Aly and LytM were almost exclusively detected in sera from EB patients and healthy volunteers. These latter IgGs may contribute to the protection against staphylococcal infections, as previous studies suggest that serum IgGs protect EB patients against severe S. aureus infection. Together, these observations focus attention on the use of particular protein domains for vaccination to direct potentially protective immune responses towards the most promising epitopes within staphylococcal antigens.

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Ercoli, Giuseppe, Chiara Tani, Alfredo Pezzicoli, Irene Vacca, Manuele Martinelli, Simone Pecetta, Roberto Petracca, et al. "LytM Proteins Play a Crucial Role in Cell Separation, Outer Membrane Composition, and Pathogenesis in Nontypeable Haemophilus influenzae." mBio 6, no. 2 (February 24, 2015). http://dx.doi.org/10.1128/mbio.02575-14.

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ABSTRACTLytM proteins belong to a family of bacterial metalloproteases. In Gram-negative bacteria, LytM factors are mainly reported to have a direct effect on cell division by influencing cleavage and remodeling of peptidoglycan. In this study, mining nontypeableHaemophilus influenzae(NTHI) genomes, three highly conserved open reading frames (ORFs) containing a LytM domain were identified, and the proteins encoded by the ORFs were named YebA, EnvC, and NlpD on the basis of their homology with theEscherichia coliproteins. Immunoblotting and confocal analysis showed that while NTHI NlpD is exposed on the bacterial surface, YebA and EnvC reside in the periplasm. NTHI ΔyebAand ΔnlpDdeletion mutants revealed an aberrant division phenotype characterized by an altered cell architecture and extensive membrane blebbing. The morphology of the ΔenvCdeletion mutant was identical to that of the wild-type strain, but it showed a drastic reduction of periplasmic proteins, including the chaperones HtrA, SurA, and Skp, and an accumulation of β-barrel-containing outer membrane proteins comprising the autotransporters Hap, IgA serine protease, and HMW2A, as observed by proteomic analysis. These data suggest that EnvC may influence the bacterial surface protein repertoire by facilitating the passage of the periplasmic chaperones through the peptidoglycan layer to the close vicinity of the inner face of the outer membrane. This hypothesis was further corroborated by the fact that an NTHIenvCdefective strain had an impaired capacity to adhere to epithelial cells and to form biofilm. Notably, this strain also showed a reduced serum resistance. These results suggest that LytM factors are not only important components of cell division but they may also influence NTHI physiology and pathogenesis by affecting membrane composition.IMPORTANCENontypeableHaemophilus influenzae(NTHI) is an opportunistic pathogen that colonizes the human nasopharynx and can cause serious infections in children (acute otitis media) and adults (chronic obstructive pulmonary disease). Several virulence factors are well studied, but the complete scenario of NTHI pathogenesis is still unclear. We identified and characterized three NTHI LytM factors homologous to the Escherichia coli LytM proteins. Although LytM factors are reported to play a crucial role in the cell division process, in NTHI they are also involved in other bacterial functions. In particular, YebA and NlpD are fundamental for membrane stability: indeed, their absence causes an increased release of outer membrane vesicles (OMVs). On the other hand, our data suggest that EnvC could directly or indirectly affect peptidoglycan permeability and consequently, bacterial periplasmic and outer membrane protein distribution. Interestingly, by modulating the surface composition of virulence determinants, EnvC also has an impact on NTHI pathogenesis.

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Chodisetti, Pavan Kumar, Raj Bahadur, R. N. Amrutha, and Manjula Reddy. "A LytM-Domain Factor, ActS, Functions in Two Distinctive Peptidoglycan Hydrolytic Pathways in E. coli." Frontiers in Microbiology 13 (June 14, 2022). http://dx.doi.org/10.3389/fmicb.2022.913949.

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Bacterial cell wall contains peptidoglycan (PG) to protect the cells from turgor and environmental stress. PG consists of polymeric glycans cross-linked with each other by short peptide chains and forms an elastic mesh-like sacculus around the cytoplasmic membrane. Bacteria encode a plethora of PG hydrolytic enzymes of diverse specificity playing crucial roles in growth, division, or turnover of PG. In Escherichia coli, the cross-link-specific endopeptidases, MepS, -M, and -H, facilitate the enlargement of PG sacculus during cell elongation, whereas LytM-domain factors, EnvC and NlpD activate the division-specific amidases, AmiA, -B, and -C to facilitate the cell separation. In a screen to isolate additional factors involved in PG enlargement, we identified actS (encoding a LytM paralog, formerly ygeR) as its overexpression compensated the loss of elongation-specific endopeptidase, MepS. The overexpression of ActS resulted in the generation of partly denuded glycan strands in PG sacculi, indicating that ActS is either an amidase or an activator of amidase(s). The detailed genetic and biochemical analyses established that ActS is not a PG hydrolase, but an activator of the division-specific amidase, AmiC. However, interestingly, the suppression of the mepS growth defects by actS is not mediated through AmiC. The domain-deletion experiments confirmed the requirement of the N-terminal LysM domain of ActS for the activation of AmiC, but not for the alleviation of growth defects in mepS mutants, indicating that ActS performs two distinctive PG metabolic functions. Altogether our results suggest that in addition to activating the division-specific amidase, AmiC, ActS modulates yet another pathway that remains to be identified.

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Journal articles on the topic 'LytM-domain'

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