The final lipid-linked precursor for peptidoglycan synthesis, lipid II, is made by the glycosyltransferase MurG in the inner leaflet of the plasma membrane. Lipid II is then flipped to the outer leaflet by MurJ where its disaccharide-pentapeptide cargo is inserted into the existing cell wall by membrane-bound transglycosylases and transpeptidases (Zhao et al., 2017). Early in vitro work in Staphylococcus aureus and Escherichia coli indicated that a fluid microenvironment might stimulate the activities of MurG and the upstream, lipid I synthase MraY (Norris and Manners, 1993). More recent in vivo data has localized Bacillus subtilis MurG to regions of increased fluidity (RIFs, Müller et al., 2016; Strahl et al., 2014), one of three classes of membrane domains that have been described in bacteria to date. In mycobacteria, intracellular membrane domains (IMD, formerly called PMf, Morita et al., 2005) can be separated from the conventional plasma membrane (PM-CW, for plasma membrane associated with cell wall) by sucrose density gradient fractionation. The proteome and lipidome of IMD are distinct from those of the PM-CW (Hayashi et al., 2016; Morita et al., 2005). Reanalysis of our proteomics data (Hayashi et al., 2016) suggested that Mycobacterium smegmatis MurG is enriched in the IMD while sequentially acting transglycosylases and transpeptidases associate with the PM-CW. While PM-CW-resident proteins distribute along the perimeter of live mycobacteria, IMD-resident proteins are enriched toward sites of polar cell elongation with additional presence along the sidewalls (Hayashi et al., 2016; Hayashi et al., 2018). We also noted that the polar enrichment of MurG-RFP resembles that of the validated IMD marker mCherry-GlfT2 or GlfT2-GFP (Hayashi et al., 2016; Meniche et al., 2014), but that nascent peptidoglycan at the mycobacterial poles primarily abuts rather than colocalizes with mCherry-GlfT2 (Hayashi et al., 2018). These observations suggested a model where lipid II synthesis is segregated from subsequent steps of cell wall assembly (Figure 1A).

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To test this model, we first expressed a functional MurG-Dendra2 fusion in M. smegmatis (Figure 1—figure supplements 1 and 2) and assayed its distribution in membrane fractions that had been separated by a sucrose density gradient (Figure 1B). MurG-Dendra2, a peripheral membrane protein, was enriched in both the cytoplasmic and IMD membrane fractions (Figure 1C, top; Figure 1—figure supplements 3A and 4). In intact cells, polar enrichment of MurG-Dendra2 was coincident with that of the IMD marker mCherry-GlfT2 (Figure 1—figure supplement 5). This spatial relationship was similar to that previously observed for other MurG and GlfT2 fluorescent fusion proteins (Hayashi et al., 2016; Hayashi et al., 2018; Meniche et al., 2014).

Enzymes from the penicillin-binding proteins (PBPs) and shape, elongation, division, and sporulation (SEDS) families integrate the disaccharide-pentapeptide from lipid II into peptidoglycan (Zhao et al., 2017). While our proteomics did not detect many polytopic membrane proteins, including SEDS proteins, our PM-CW dataset was enriched for all known PBPs (Hayashi et al., 2016). Fluorescent derivatives of β-lactam antibiotics, such as Bocillin-FL, bind to PBPs and report transpeptidase-active enzymes. We incubated subcellular fractions from wild-type M. smegmatis with Bocillin-FL and identified fluorescent proteins in the PM-CW (Figure 1C, bottom; Figure 1—figure supplements 3B and 4). As expected for PBPs, the signal from these bands was diminished by pre-treatment with ampicillin (Figure 1—figure supplement 6). We focused on characterizing PonA1, an essential bifunctional transglycosylase/transpeptidase in M. smegmatis (Hett et al., 2010; Kieser et al., 2015; Baranowski et al., 2018). Depletion of PonA1 (Hett et al., 2010) resulted in the loss of the higher molecular band (Figure 1—figure supplement 6), confirming this protein is present and active in the PM-CW (Figure 1C, bottom). We next expressed a functional PonA1-mRFP fusion in M. smegmatis (Figure 1—figure supplement 2 and Figure 2—figure supplement 1; Kieser et al., 2015; Baranowski et al., 2018). Although we detected potential breakdown products of the fusion protein by anti-RFP immunoblot (Figure 2—figure supplement 1), we found that it, like native PonA1, was active in the PM-CW and distributed along the sidewall in a manner similar to the functional PM-CW marker PimE-GFP (Figure 2—figure supplements 1 and 2, Hayashi et al., 2016). Coexpression of MurG-Dendra2 and PonA1-mRFP confirmed that the proteins have different subcellular localization (Figure 2A). Together, our data show that MurG and PonA1 occupy membrane compartments that are biochemically and likely spatially distinct.

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The association of MurG with the IMD and of PonA1 with the PM-CW implies that the IMD is the site of lipid II synthesis, while the PM-CW is where peptidoglycan assembly takes place. We refined an in vitro d-amino acid exchange assay to detect lipid-linked peptidoglycan precursors from membrane fractions (Figure 2B, García-Heredia et al., 2018; Qiao et al., 2014). In wild-type cells, we detected biotinylated molecules in both the IMD and PM-CW (Figure 2C; Figure 1—figure supplement 3B). We hypothesized that the labeled species comprise precursors in both the inner and outer leaflets of the plasma membrane. We and others have shown that depletion of MurJ results in accumulation of biotinylated precursors (García-Heredia et al., 2018; Qiao et al., 2017). By performing the d-amino acid exchange reaction on membrane fractions obtained from MurJ-depleted M. smegmatis (Figure 2—figure supplement 3A), we found that precursors accumulate in the IMD (Figure 2C; Figure 1—figure supplement 3C; Figure 2—figure supplement 3B). These results suggest that lipid II is made in the IMD and transferred to the PM-CW in a MurJ-dependent manner.

Based on our biochemical data, we hypothesized that lipid II incorporation into the cell wall is laterally segregated from its synthesis. We previously showed that alkynyl and azido d-amino acid dipeptides (Liechti et al., 2014) incorporate into lipid-linked peptidoglycan precursors in M. smegmatis (García-Heredia et al., 2018) and that metabolic labeling with alkynyl dipeptide (alkDADA or EDA-DA, Liechti et al., 2014) is most intense in regions adjacent to the IMD marker mCherry-GlfT2 (Hayashi et al., 2018). We labeled MurG-Dendra2-expressing M. smegmatis with alkDADA and detected the presence of the alkyne by copper-catalyzed azide-alkyne cycloaddition (CuAAC, García-Heredia et al., 2018). To distinguish extracellular alkynes present in periplasmic lipid II and newly polymerized cell wall from alkynes originating from cytoplasmic lipid II, we selected picolyl azide-Cy3 as our label because of its poor membrane permeability (Figure 2B, Yang and Hinner, 2015). Using this optimized protocol, we observed nascent peptidoglycan deposition at the polar tip, whereas MurG-Dendra2 was proximal to this site (Figure 2D). Our data suggest that lipid II synthesis is laterally partitioned from the subsequent steps of peptidoglycan assembly. MurJ depletion reduced and delocalized alkDADA-derived fluorescence (Figure 2—figure supplement 3C), consistent with a gatekeeper role for the flippase in both lateral membrane compartmentalization and flipping across the inner membrane.

Next, we wanted to understand the significance of membrane architecture for cell wall synthesis. We perturbed the membrane with benzyl alcohol, a compound that preferentially inserts into disordered membrane regions in vitro (Muddana et al., 2012) and has been used to fluidize membranes from mammalian and bacterial cells (Friedlander et al., 1987; Ingram, 1976; Konopásek et al., 2000; Nagy et al., 2007; Strahl et al., 2014; Zielińska et al., 2020). In B. subtilis, benzyl alcohol disrupts RIFs (Müller et al., 2016). In M. smegmatis, we found that benzyl alcohol reduced the cellular material associated with the IMD (Figure 3A, Figure 3—figure supplement 1, Figure 1—figure supplement 3D) and altered the distribution of FM4-64, a non-specific lipophilic dye (Figure 3—figure supplement 2), and of plasma membrane glycolipids (Figure 3—figure supplement 3). However, the fluidizer did not alter labeling by N-AlkTMM or O-AlkTMM (Figure 3—figure supplement 4), probes that, respectively, mark the noncovalent and covalent lipids of the outer ‘myco’ membrane (Foley et al., 2016). These observations suggest that benzyl alcohol primarily affects the plasma membrane in M. smegmatis. MurG-Dendra2 was also less enriched in the IMD fraction following benzyl alcohol treatment (Figure 1C, top; Figure 1—figure supplements 3E and 4) and, in live cells, at the poles (Figure 2A). By contrast, benzyl alcohol produced subtle changes in the subcellular distribution of active PBPs (Figure 1C, bottom; Figure 1—figure supplements 3D and 4), although PonA1 shifted toward the poles in live cells (Figure 2A). Disruption of plasma membrane architecture was accompanied by dampening and delocalization of peptidoglycan assembly (Figure 3B, Figure 3—figure supplement 5) as well as a reduction in lipid precursor synthesis (Figure 3C) and halt in polar elongation (Figure 3—figure supplement 4). The effects of benzyl alcohol were reversible, as indicated by colony-forming units and prompt recovery of peptidoglycan synthesis (Figure 3—figure supplement 6). Dibucaine, a compound that preferentially disrupts ordered membrane regions in vitro (Kinoshita et al., 2019) and can fluidize membranes from eukaryotic cells (Kim et al., 1997), also delocalized IMD-resident proteins (Figure 3—figure supplement 7) and delocalized and reduced peptidoglycan synthesis (Figure 3B, Figure 3—figure supplement 5).

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Our data suggest that membrane architecture contributes to peptidoglycan synthesis and cell growth in M. smegmatis. While we cannot rule out pleiotropic effects of chemical fluidizers on membrane potential or membrane protein activity, we note that benzyl alcohol decreases peptidoglycan precursor accumulation (Figure 3C), rather than increasing it as occurs with protonophore treatment (Rubino et al., 2018) or MurJ depletion (Figure 2C; García-Heredia et al., 2018; Qiao et al., 2017); MurG and PonA1 are retained in the membrane upon benzyl alcohol treatment (Figure 1C, Figure 1—figure supplement 4); and at least a subset of membrane-bound PBPs remain competent for Bocillin-FL binding (Figure 1C, Figure 1—figure supplement 4). Moreover, benzyl alcohol and dibucaine delocalize nascent peptidoglycan from the poles to the sidewall (Figure 3B), an effect that cannot be explained by diminished synthesis alone. In the case of benzyl alcohol, redistribution of new cell wall occurs within minutes (Figure 3B, Figure 3—figure supplement 5), consistent with rapid fluidization (Konopásek et al., 2000; Yano et al., 2016), and likely prior to changes in gene expression. Nevertheless, it is possible that chemical fluidizers directly disrupt the activity of cell wall synthesis proteins in addition to altering the milieu in which these proteins function.

The impacts of benzyl alcohol and dibucaine on MurG-Dendra2 localization were subtly different (compare Figure 2A to Figure 3—figure supplement 7) as was the time frame for disruption of cell wall synthesis by these chemicals (Figure 3B, Figure 3—figure supplement 5). In model membranes, benzyl alcohol promotes phase separation by further fluidizing disordered regions (Muddana et al., 2012), while dibucaine disrupts phase separation by fluidizing ordered regions (Kinoshita et al., 2019). In more-complex cellular membranes, the effects of these compounds may be influenced by the presence of pre-existing mechanisms that establish and maintain membrane organization. For example, the architecture of eukaryotic membranes is influenced by transient links, or pinning, to the cytoskeleton (Fujimoto and Parmryd, 2016; Liu et al., 2015). In B. subtilis and E. coli, actin homologs like MreB direct peptidoglycan synthesis along the lateral cell surface (Daniel and Errington, 2003; Iwai et al., 2002; Shi et al., 2018; Zhao et al., 2017). They also organize the membrane into domains of increased (Oswald et al., 2016; Strahl et al., 2014) and decreased fluidity (Wagner et al., 2020). Global reductions in membrane fluidity interfere with the assembly and motion of B. subtilis MreB (Zielińska et al., 2020; Gohrbandt et al., 2019; Kurita et al., 2020), potentially indicating a feedback loop between the physical state of the membrane and MreB-directed cell wall elongation. We found that benzyl alcohol delocalized or dampened cell wall assembly in rod-shaped bacteria with divergent envelope composition and modes of growth (Figure 3D,E). Peptidoglycan synthesis was less affected by benzyl alcohol in coccoid species, which lack MreB or obvious RIFs (Wenzel et al., 2018), and in rounded, A22-treated E. coli, in which MreB assembly is inhibited (Figure 3E). Thus, membrane organization likely contributes to effective, directional cell wall synthesis in rod-shaped bacteria.

Mycobacteria lack MreB. How, then, is the IMD partitioned away from the rest of the plasma membrane? In these organisms, the essential tropomyosin-like protein DivIVA (Wag31) concentrates cell wall assembly at the poles (Jani et al., 2010; Kang et al., 2008; Melzer et al., 2018). DivIVA depletion results in deformation and rounding of mycobacterial cells (Kang et al., 2008; Meniche et al., 2014; Nguyen et al., 2007). Given the similarities in DivIVA and MreB function, we hypothesized that DivIVA creates and/or maintains the IMD. We used M. smegmatis expressing DivIVA-eGFP-ID in which DivIVA is fused to both eGFP and an inducible degradation tag (Meniche et al., 2014) to deplete DivIVA. Depletion of the protein reduced the amount of IMD-associated cellular material (Figure 4A, Figure 3—figure supplement 1, Figure 1—figure supplement 3F–G), altered the distribution of plasma membrane glycolipids (Figure 3—figure supplement 3), and delocalized the IMD marker mCherry-GlfT2 from the poles (Figure 4B).

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DivIVA phosphorylation regulates MraY and/or MurG activity via an indirect, unknown mechanism (Jani et al., 2010). Consistent with these data, we found that depletion of the protein reduced both lipid-linked peptidoglycan precursor abundance and alkDADA incorporation (Figure 3C). Membrane disruption by benzyl alcohol did not delocalize DivIVA from the polar tips (Figure 3—figure supplement 8), and the suppressive effects of benzyl alcohol and DivIVA depletion on precursor abundance and cell wall synthesis were not additive (Figure 3C), suggesting that the perturbations act on the same pathway. Unlike DivIVA depletion (Figure 4B), benzyl alcohol does not change M. smegmatis shape (Figure 2A). Therefore, while we cannot exclude the possibility that spherical morphology in DivIVA-depleted cells indirectly impacts membrane partitioning – for example by mislocalization of curvature-sensing proteins or by altering the spacing between the membrane and cell wall – our results are most consistent with a model in which DivIVA organizes the mycobacterial membrane for optimal cell wall synthesis.

As lipid II both generates and homes to disordered regions of model membranes (Ganchev et al., 2006; Jia et al., 2011; Valtersson et al., 1985), the effect of DivIVA on precursors suggests that concentrated peptidoglycan synthesis is a cause or a consequence (or both) of IMD/PM-CW partitioning. In other organisms, lipid II production is required for MreB rotation (Domínguez-Escobar et al., 2011; Garner et al., 2011; van Teeffelen et al., 2011), to recruit MreB to the plasma membrane (Schirner et al., 2015), and for normal membrane staining by a lipophilic fluorescent dye (Muchová et al., 2011), so the precursor might also play an indirect role in compartmentalizing the mycobacterial membrane via its influence on DivIVA. However, we previously found that the IMD is biochemically intact after 8 hr of treatment with d-cycloserine (Hayashi et al., 2018), an antibiotic that we have shown to block M. smegmatis peptidoglycan precursor synthesis within 1 hr (García-Heredia et al., 2018). IMD-resident proteins delocalize, but not until 6 hr of treatment. The persistence of IMD-resident proteins and the time frame of delocalization indicate that concentrated lipid II synthesis is more likely a consequence, rather than a cause, of mycobacterial membrane compartmentalization.

Our data supported a model in which DivIVA is necessary to maintain membrane partitioning, which in turn supports efficient synthesis of peptidoglycan precursors and their precise incorporation into the cell wall. However, we noted that eukaryotic membrane architecture can also be influenced by transient interactions with external structures like extracellular matrix and cellulose (Fujimoto and Parmryd, 2016; Liu et al., 2015). Furthermore, biophysical modeling suggests that osmotic pinning of the plasma membrane against the bacterial cell wall can induce microphase separation (Mukhopadhyay et al., 2008). In mycobacteria, co-fractionation of the plasma membrane and cell wall (i.e. PM-CW) upon mechanical cell lysis implies that they are physically connected (Morita et al., 2005). We wondered whether the peptidoglycan polymer itself might contribute to the membrane partitioning that organizes its synthesis. In B. subtilis, for example, enzymatic removal of the cell wall delocalizes membrane staining by a lipophilic fluorescent dye (Muchová et al., 2011) and enhances the mobility of membrane domain-associated flotillin proteins (Wagner et al., 2020). To test this hypothesis in M. smegmatis, we spheroplasted bacteria that expressed MurG-Dendra2 or DivIVA-eGFP-ID and mCherry-GlfT2. All fusions were functional (Figure 1—figure supplement 1, Hayashi et al., 2016; Meniche et al., 2014). Fractionated lysates from spheroplasted mycobacteria had more diffuse distribution of cellular material and indistinct separation of the IMD and PM-CW fractions (Figure 4A, Figure 3—figure supplement 1). Consistent with the macroscopic appearance of the fractionated lysate, MurG-Dendra2 was distributed throughout the gradient (Figure 4—figure supplement 1; Figure 1—figure supplement 3H). MurG-Dendra2 and the IMD marker mCherry-GlfT2 were also diffusely distributed around the periphery of spheroplasted cells while DivIVA, likely a PM-CW-associated protein (Hayashi et al., 2016), remained in foci (Figure 4C,D). These experiments suggest that an intact cell wall and DivIVA promote membrane compartmentalization in M. smegmatis (Figure 4E, arrows 1 and 3).

While peptidoglycan biogenesis is well known to vertically span the inner and outer leaflets of the plasma membrane, here we demonstrate in M. smegmatis that it is also horizontally partitioned (Figure 4E, arrow 2). Partitioning of the mycobacterial membrane by DivIVA and the cell wall follows similar logic to that of eukaryotic membranes, which can be compartmentalized by pinning to cytoplasmic structures such as the actin cytoskeleton and to external structures such as the extracellular matrix and cellulose (Fujimoto and Parmryd, 2016; Liu et al., 2015), and of model lipid bilayers, which can be phase separated by adhesive forces (Gordon et al., 2008; Mukhopadhyay et al., 2008). In mycobacteria, the membrane regions that promote cell wall synthesis are likely segregated by the end product of the pathway (Figure 4E, arrow 3). The conservation of the cell wall synthesis machinery and elongation-promoting cytoskeletal proteins among phylogenetically distant species predicts that our findings will generally apply to bacilli beyond our mycobacterial model. For rod-shaped species, our model is that the membrane-cell wall axis is a self-organizing system in which directed cell wall synthesis organizes the plasma membrane, and an organized plasma membrane in turn makes cell wall elongation more efficient and precise.

All of the source data used in this study is deposited in Open Science Framework (https://osf.io.10.17605/OSF.IO/FM794) and available for all public.

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Author details

1. Alam García-Heredia

   Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, United States

   Contribution

   Conceptualization, Resources, Data curation, Formal analysis, Supervision, Validation, Investigation, Visualization, Methodology, Writing - original draft, Writing - review and editing

   Competing interests

   No competing interests declared

   "This ORCID iD identifies the author of this article:" 0000-0002-9573-4087

2. Takehiro Kado

   Department of Microbiology, University of Massachusetts, Amherst, United States

   Contribution

   Resources, Data curation, Formal analysis, Validation, Investigation, Methodology, Writing - review and editing

   Competing interests

   No competing interests declared

3. Caralyn E Sein

   Department of Microbiology, University of Massachusetts, Amherst, United States

   Contribution

   Data curation, Formal analysis, Validation, Investigation, Methodology, Writing - review and editing

   Competing interests

   No competing interests declared

4. Julia Puffal

   Department of Microbiology, University of Massachusetts, Amherst, United States

   Present address

   Department of Biochemistry and Molecular Biology, Rutgers University, Robert Wood Johnson Medical School, Piscataway, United States

   Contribution

   Resources, Data curation, Formal analysis, Validation, Investigation, Methodology, Writing - review and editing

   Competing interests

   No competing interests declared

   "This ORCID iD identifies the author of this article:" 0000-0003-3066-5225

5. Sarah H Osman

   Department of Microbiology, University of Massachusetts, Amherst, United States

   Contribution

   Data curation, Formal analysis, Validation, Investigation, Methodology, Writing - review and editing

   Competing interests

   No competing interests declared

6. Julius Judd

   Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, United States

   Present address

   Department of Molecular Biology and Genetics, Cornell University, Ithaca, United States

   Contribution

   Resources, Validation, Methodology, Writing - review and editing

   Competing interests

   No competing interests declared

   "This ORCID iD identifies the author of this article:" 0000-0002-4602-0205

7. Todd A Gray

   1. Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, United States
   2. Department of Biomedical Sciences, University at Albany, Albany, United States

   Contribution

   Resources, Validation, Visualization, Methodology, Writing - review and editing

   Competing interests

   No competing interests declared

8. Yasu S Morita

   1. Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, United States
   2. Department of Microbiology, University of Massachusetts, Amherst, United States

   Contribution

   Conceptualization, Resources, Data curation, Formal analysis, Supervision, Funding acquisition, Validation, Investigation, Visualization, Methodology, Project administration, Writing - review and editing

   For correspondence

   ymorita@microbio.umass.edu

   Competing interests

   No competing interests declared

   "This ORCID iD identifies the author of this article:" 0000-0002-4514-9242

9. M Sloan Siegrist

   1. Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, United States
   2. Department of Microbiology, University of Massachusetts, Amherst, United States

   Contribution

   Conceptualization, Resources, Data curation, Formal analysis, Supervision, Funding acquisition, Validation, Visualization, Methodology, Writing - original draft, Project administration, Writing - review and editing

   For correspondence

   siegrist@gmail.com

   Competing interests

   No competing interests declared

   "This ORCID iD identifies the author of this article:" 0000-0002-8232-3246

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