Function and firing of the Streptomyces coelicolor contractile injection system requires the membrane protein CisA

  1. Bastien Casu
  2. Joseph W Sallmen
  3. Peter E Haas
  4. Govind Chandra
  5. Pavel Afanasyev
  6. Jingwei Xu
  7. Susan Schlimpert
  8. Martin Pilhofer

  • Curated by eLife

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    eLife Assessment

    This valuable study provides insights into the structure and function of bacterial contractile injection systems that are present in the cytoplasm of many Streptomyces strains. A convincing high-resolution model of the structure of extended forms of the cytoplasmic contractile injection system assembly from Streptomyces coelicolor is presented, with some investigation of the membrane protein CisA in attachment of the extended assembly to the inner face of the cytoplasmic membrane and the firing of the system. The work expands the current understanding of these diverse bacterial nanomachines.

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Abstract

Bacterial contractile injection systems (CIS) are phage tail-like macromolecular complexes that mediate cell-cell interactions by injecting effector proteins into target cells. CIS from Streptomyces coelicolor (CIS Sc ) are localized in the cytoplasm. Under stress, they induce cell death and impact the bacteria’s life cycle. It remains unknown whether CIS Sc require accessory proteins to directly interact with the cytoplasmic membrane and function.Here, we characterize the putative membrane adaptor CisA, a conserved factor in CIS gene clusters across Streptomyces species. We show by cryo-electron tomography imaging and in vivo assays that CIS Sc contraction and function depend on CisA. Using single-particle cryo-electron microscopy, we provide an atomic model of the extended CIS Sc apparatus; however, CisA is not part of the complex. Instead, our findings show that CisA is a membrane protein with a cytoplasmic N-terminus predicted to interact with CIS Sc components, thereby providing a possible mechanism for mediating CIS Sc recruitment to the membrane and subsequent firing.Our work shows that CIS function in multicellular bacteria is distinct from Type 6 Secretion Systems and extracellular CIS, and possibly evolved due to the role CIS Sc play in regulated cell death.

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  1. Version published to 10.7554/elife.104064.1 on eLife
  2. Version published to 10.7554/elife.104064 on eLife
  3. eLife

    eLife Assessment

    This valuable study provides insights into the structure and function of bacterial contractile injection systems that are present in the cytoplasm of many Streptomyces strains. A convincing high-resolution model of the structure of extended forms of the cytoplasmic contractile injection system assembly from Streptomyces coelicolor is presented, with some investigation of the membrane protein CisA in attachment of the extended assembly to the inner face of the cytoplasmic membrane and the firing of the system. The work expands the current understanding of these diverse bacterial nanomachines.

  4. eLife

    Reviewer #1 (Public review):

    Contractile Injection Systems (CIS) are versatile machines that can form pores in membranes or deliver effectors. They can act extra or intracellularly. When intracellular they are positioned to face the exterior of the cell and hence should be anchored to the cell envelope. The authors previously reported the characterization of a CIS in Streptomyces coelicolor, including significant information on the architecture of the apparatus. However, how the tubular structure is attached to the envelope was not investigated. Here they provide a wealth of evidence to demonstrate that a specific gene within the CIS gene cluster, cisA, encodes a membrane protein that anchors the CIS to the envelope. More specifically, they show that:

    - CisA is not required for assembly of the structure but is important for proper contraction and CIS-mediated cell death
    - CisA is associated to the membrane (fluorescence microscopy, cell fractionation) through a transmembrane segment (lacZ-phoA topology fusions in E. coli)
    - Structural prediction of interaction between CisA and a CIS baseplate component
    - In addition they provide a high-resolution model structure of the >750-polypeptide Streptomyces CIS in its extended conformation, revealing new details of this fascinating machine, notably in the baseplate and cap complexes.

    All the experiments are well controlled including trans-complemented of all tested phenotypes.

    One important information we miss is the oligomeric state of CisA.

    While it would have been great to test the interaction between CisA and Cis11, to perform cryo-electron microscopy assays of detergent-extracted CIS structures to maintain the interaction with CisA, I believe that the toxicity of CisA upon overexpression or upon expression in E. coli render these studies difficult and will require a significant amount of time and optimization to be performed. It is worth mentioning that this study is of significant novelty in the CIS field because, except for Type VI secretion systems, very few membrane proteins or complexes responsible for CIS attachment have been identified and studied.

  5. eLife

    Reviewer #2 (Public review):

    Summary:

    The overall question that is addressed in this study is how the S. coelicolor contractile injection system (CISSc) works and affects both cell viability and differentiation, which it has been implicated to do in previous work from this group and others. The CISSc system has been enigmatic in the sense that it is free-floating in the cytoplasm in an extended form and is seen in contracted conformation (i.e. after having been triggered) mainly in dead and partially lysed cells, suggesting involvement in some kind of regulated cell death. So, how do the structure and function of the CISSc system compare to those of related CIS from other bacteria, does it interact with the cytoplasmic membrane, how does it do that, and is the membrane interaction involved in the suggested role in stress-induced, regulated cell death? The authors address these questions by investigating the role of a membrane protein, CisA, that is encoded by a gene in the CIS gene cluster in S. coelicolor. Further, they analyse the structure of the assembled CISSc, purified from the cytoplasm of S. coelicolor, using single-particle cryo-electron microscopy.

    Strengths:

    The beautiful visualisation of the CIS system both by cryo-electron tomography of intact bacterial cells and by single-particle electron microscopy of purified CIS assemblies are clearly the strengths of the paper, both in terms of methods and results. Further, the paper provides genetic evidence that the membrane protein CisA is required for the contraction of the CISSc assemblies that are seen in partially lysed or ghost cells of the wild type. The conclusion that CisA is a transmembrane protein and the inferred membrane topology are well supported by experimental data. The cryo-EM data suggest that CisA is not a stable part of the extended form of the CISSc assemblies. These findings raise the question of what CisA does.

    Weaknesses:

    The investigations of the role of CisA in function, membrane interaction, and triggering of contraction of CIS assemblies, are important parts of the paper and are highlighted in the title. However, the experimental data provided to answer these questions appear partially incomplete and not as conclusive as one would expect.

    The stress-induced loss of viability is only monitored with one method: an in vivo assay where cytoplasmic sfGFP signal is compared to FM5-95 membrane stain. Addition of a sublethal level of nisin lead to loss of sfGFP signal in individual hyphae in the WT, but not in the cisA mutant (similarly to what was previously reported for a CIS-negative mutant). Technically, this experiment and the example images that are shown give rise to some concern. Only individual hyphal fragments are shown that do not look like healthy and growing S. coelicolor hyphae. Under the stated growth conditions, S. coelicolor strains would normally have grown as dense hyphal pellets. It is therefore surprising that only these unbranched hyphal fragments are shown in Fig. 4ab. Further, S. coelicolor would likely be in a stationary phase when grown 48 h in the rich medium that is stated, giving rise to concern about the physiological state of the hyphae that were used for the viability assay. It would be valuable to know whether actively growing mycelium is affected in the same way by the nisin treatment, and also whether the cell death effect could be detected by other methods.

    The model presented in Fig. 5 suggests that stress leads to a CisA-dependent attachment of CIS assemblies to the cytoplasmic membrane, and then triggering of contraction, leading to cell death. This model makes testable predictions that have not been challenged experimentally. Given that sublethal doses of nisin seem to trigger cell death, there appear to be possibilities to monitor whether activation of the system (via CisA?) indeed leads to at least temporally increased interaction of CIS with the membrane. Further, would not the model predict that stress leads to an increased number of contracted CIS assemblies in the cytoplasm? No clear difference in length of the isolated assemblies if Fig. S7 is seen between untreated and nisin-exposed cells, and also no difference between assemblies from WT and cisA mutant hyphae.

    The interaction of CisA with the CIS assembly is critical for the model but is only supported by Alphafold modelling, predicting interaction between cytoplasmic parts of CisA and Cis11 protein in the baseplate wedge. An experimental demonstration of this interaction would have strengthened the conclusions.

    The cisA mutant showed a similarly accelerated sporulation as was previously reported for CIS-negative strains, which supports the conclusion that CisA is required for function of CISSc. But the results do not add any new insights into how CIS/CisA affects the progression of the developmental life cycle and whether this effect has anything to do with the regulated cell death that is caused by CIS. The same applies to the effect on secondary metabolite production, with no further mechanistic insights added, except reporting similar effects of CIS and CisA inactivations.

    Concluding remarks:
    The work will be of interest to anyone interested in contractile injection systems, T6SS, or similar machineries, as well for people working on the biology of streptomycetes. There is also a potential impact of the work in the understanding of how such molecular machineries could have been co-opted during evolution to become a mechanism for regulated cell death. However, this latter aspect remains still poorly understood. Even though this paper adds excellent new structural insights and identifies a putative membrane anchor, it remains elusive how the Streptomyces CIS may lead to cell death. It is also unclear what the advantage would be to trigger death of hyphal compartments in response to stress, as well as how such cell death may impact (or accelerate) the developmental progression. Finally, it is inescapable to wonder whether the Streptomyces CIS could have any role in protection against phage infection.

  6. eLife

    Reviewer #3 (Public review):

    Summary:

    In this work, Casu et al. have reported the characterization of a previously uncharacterized membrane protein CisA encoded in a non-canonical contractile injection system of Streptomyces coelicolor, CISSc, which is a cytosolic CISs significantly distinct from both intracellular membrane-anchored T6SSs and extracellular CISs. The authors have presented the first high-resolution structure of extended CISSc structure. It revealed important structural insights in this conformational state. To further explore how CISSc interacted with cytoplasmic membrane, they further set out to investigate CisA that was previously hypothesized to be the membrane adaptor. However, the structure revealed that it was not associated with CISSc. Using fluorescence microscope and cell fractionation assay, the authors verified that CisA is indeed a membrane-associated protein. They further determined experimentally that CisA had a cytosolic N-terminal domain and a periplasmic C-terminus. The functional analysis of cisA mutant revealed that it is not required for CISSc assembly but is essential for the contraction, as a result, the deletion significantly affects CISSc-mediated cell death upon stress, timely differentiation, as well as secondary metabolite production. Although the work did not resolve the mechanistic detail how CisA interacts with CISSc structure, it provides solid data and a strong foundation for future investigation toward understanding the mechanism of CISSc contraction, and potentially, the relation between the membrane association of CISSc, the sheath contraction and the cell death.

    Strengths:

    The paper is well-structured, and the conclusion of the study is supported by solid data and careful data interpretation was presented. The authors provided strong evidence on (1) the high-resolution structure of extended CISSc determined by cryo-EM, and the subsequent comparison with known eCIS structures, which sheds light on both its similarity and different features from other subtypes of eCISs in detail; (2) the topological features of CisA using fluorescence microscopic analysis, cell fractionation and PhoA-LacZα reporter assays, (3) functions of CisA in CISSc-mediated cell death and secondary metabolite production, likely via the regulation of sheath contraction.

    Weaknesses:

    The data presented are not sufficient to provide mechanistic details of CisA-mediated CISSc contraction, as authors are not able to experimentally demonstrate the direct interaction between CisA with baseplate complex of CISSc (hypothesized to be via Cis11 by structural modeling), since they could not express cisA in E. coli due to its potential toxicity. Therefore, there is a lack of biochemical analysis of direct interaction between CisA and baseplate wedge. In addition, there is no direct evidence showing that CisA is responsible for tethering CISSc to the membrane upon stress, and the spatial and temporal relation between membrane association and contraction remains unclear. Further investigation will be needed to address these questions in future.

    Discussion:

    Overall, the work provides a valuable contribution to our understanding on the structure of a much less understood subtype of CISs, which is unique compared to both membrane-anchored T6SSs and host-membrane targeting eCISs. Importantly, the work serves as a good foundation to further investigate how the sheath contraction works here. The work contributes to expanding our understanding of the diverse CIS superfamilies.

  7. eLife

    Author response:

    We thank the editor and the three reviewers for the positive assessment and constructive feedback on how to improve our manuscript. We greatly appreciate that our work is considered valuable to the field, the recognition of the high-resolution model we presented, and the comments on our investigation of CisA’s role in the attachment and firing mechanism of the extended assembly. It is truly gratifying to know that our study contributes to expanding the current understanding of the biology of Streptomyces and the role of these functionally diverse and fascinating bacterial nanomachines.

    We have provided specific responses to each reviewer's comments below. In summary, we intend to address the following requested revisions:

    We will expand our bioinformatic analysis of CisA and provide additional information on the oligomeric state of CisA. We will also modify the text, figures, and figure legends to improve the clarity of our work and experimental procedures.

    Some reviewer comments would require additional experimental work, some of which would involve extensive optimization of experimental conditions. Because both lead postdoctoral researchers involved in this work have now left the lab, we currently do not have the capability to perform additional experimental work.

    Reviewer #1 (Public review):

    Contractile Injection Systems (CIS) are versatile machines that can form pores in membranes or deliver effectors. They can act extra or intracellularly. When intracellular they are positioned to face the exterior of the cell and hence should be anchored to the cell envelope. The authors previously reported the characterization of a CIS in Streptomyces coelicolor, including significant information on the architecture of the apparatus. However, how the tubular structure is attached to the envelope was not investigated. Here they provide a wealth of evidence to demonstrate that a specific gene within the CIS gene cluster, cisA, encodes a membrane protein that anchors the CIS to the envelope. More specifically, they show that:

    - CisA is not required for assembly of the structure but is important for proper contraction and CIS-mediated cell death

    - CisA is associated to the membrane (fluorescence microscopy, cell fractionation) through a transmembrane segment (lacZ-phoA topology fusions in E. coli)

    - Structural prediction of interaction between CisA and a CIS baseplate component
    - In addition they provide a high-resolution model structure of the >750-polypeptide Streptomyces CIS in its extended conformation, revealing new details of this fascinating machine, notably in the baseplate and cap complexes.

    All the experiments are well controlled including trans-complemented of all tested phenotypes.

    One important information we miss is the oligomeric state of CisA.

    While it would have been great to test the interaction between CisA and Cis11, to perform cryo-electron microscopy assays of detergent-extracted CIS structures to maintain the interaction with CisA, I believe that the toxicity of CisA upon overexpression or upon expression in E. coli render these studies difficult and will require a significant amount of time and optimization to be performed. It is worth mentioning that this study is of significant novelty in the CIS field because, except for Type VI secretion systems, very few membrane proteins or complexes responsible for CIS attachment have been identified and studied.

    We thank this reviewer for their highly supportive and positive comments on our manuscript. We are grateful for this reviewer’s recognition of the novelty of our study, particularly in the context of membrane proteins and complexes involved in CIS attachment.

    We agree that further experimental evidence on the direct interaction between CisA and Cis11 would have strengthened our model of CisA function. However, as noted by this reviewer, this additional work is technically challenging and currently beyond the scope of this study.

    We thank Reviewer #1 for suggesting discussing the potential oligomeric state of CisA. We will perform additional AlphaFold modelling of CisA and discuss the result of this analysis in the revised manuscript.

    Reviewer #2 (Public review):

    Summary:

    The overall question that is addressed in this study is how the S. coelicolor contractile injection system (CISSc) works and affects both cell viability and differentiation, which it has been implicated to do in previous work from this group and others. The CISSc system has been enigmatic in the sense that it is free-floating in the cytoplasm in an extended form and is seen in contracted conformation (i.e. after having been triggered) mainly in dead and partially lysed cells, suggesting involvement in some kind of regulated cell death. So, how do the structure and function of the CISSc system compare to those of related CIS from other bacteria, does it interact with the cytoplasmic membrane, how does it do that, and is the membrane interaction involved in the suggested role in stress-induced, regulated cell death? The authors address these questions by investigating the role of a membrane protein, CisA, that is encoded by a gene in the CIS gene cluster in S. coelicolor. Further, they analyse the structure of the assembled CISSc, purified from the cytoplasm of S. coelicolor, using single-particle cryo-electron microscopy.

    Strengths:

    The beautiful visualisation of the CIS system both by cryo-electron tomography of intact bacterial cells and by single-particle electron microscopy of purified CIS assemblies are clearly the strengths of the paper, both in terms of methods and results. Further, the paper provides genetic evidence that the membrane protein CisA is required for the contraction of the CISSc assemblies that are seen in partially lysed or ghost cells of the wild type. The conclusion that CisA is a transmembrane protein and the inferred membrane topology are well supported by experimental data. The cryo-EM data suggest that CisA is not a stable part of the extended form of the CISSc assemblies. These findings raise the question of what CisA does.

    We thank Reviewer #2 for the overall positive evaluation of our manuscript and the constructive criticism.

    Weaknesses:

    The investigations of the role of CisA in function, membrane interaction, and triggering of contraction of CIS assemblies, are important parts of the paper and are highlighted in the title. However, the experimental data provided to answer these questions appear partially incomplete and not as conclusive as one would expect.

    We acknowledge that some aspects of our work have not been fully answered. We believe that providing additional experimental data is currently beyond the scope of this study. To improve this study, we will modify the text and clarify experimental procedures and figures where possible in the revised version of our manuscript.

    The stress-induced loss of viability is only monitored with one method: an in vivo assay where cytoplasmic sfGFP signal is compared to FM5-95 membrane stain. Addition of a sublethal level of nisin lead to loss of sfGFP signal in individual hyphae in the WT, but not in the cisA mutant (similarly to what was previously reported for a CIS-negative mutant). Technically, this experiment and the example images that are shown give rise to some concern. Only individual hyphal fragments are shown that do not look like healthy and growing S. coelicolor hyphae. Under the stated growth conditions, S. coelicolor strains would normally have grown as dense hyphal pellets. It is therefore surprising that only these unbranched hyphal fragments are shown in Fig. 4ab.

    We thank Reviewer #2 for their thoughtful criticism regarding our stress-induced viability assay and the data presented in Figure 4. We acknowledge the importance of ensuring that the presented images should reflect the physiological state of S. coelicolor under the stated growth conditions and recognize that hyphal fragments shown in Figure 4 do not fully capture the typical morphology of S. coelicolor. As pointed out by this reviewer, S. coelicolor grows in large hyphal clumps when cultured in liquid media, making the quantification of fluorescence intensities in hyphae expressing cytoplasmic GFP and stained with the membrane dye FM5-95 particularly challenging. To improve the image analysis and quantification of GFP and FM5-95-fluorescent intensities across the three S. coelicolor strains (wildtype, cisA deletion mutant and the complemented cisA mutant), we vortexed the cell samples briefly before imaging to break up hyphal clumps, increasing hyphal fragments. The hyphae shown in our images were selected as representative examples across three biological replicates.

    Further, S. coelicolor would likely be in a stationary phase when grown 48 h in the rich medium that is stated, giving rise to concern about the physiological state of the hyphae that were used for the viability assay. It would be valuable to know whether actively growing mycelium is affected in the same way by the nisin treatment, and also whether the cell death effect could be detected by other methods.

    The reasoning behind growing S. coelicolor for 48 h before performing the fluorescence-based viability assay was that we (DOI: 10.1038/s41564-023-01341-x ) and others (e.g.: DOI: 10.1038/s41467-023-37087-7 ) previously showed that the levels of CIS particles peak at the transition from vegetative to reproductive/stationary growth, thus indicating that CIS activity is highest during this growth stage. The obtained results in this manuscript are in agreement with our previous study, in which we showed a similar effect on the viability of wildtype versus cis-deficient S. coelicolor strains (DOI: 10.1038/s41564-023-01341-x ) using nisin, the protonophore CCCP and UV light, and supported by biological replicate experiments and appropriate controls. Furthermore, our results are in agreement with the findings reported in a complementary study by Vladimirov et al. (DOI: 10.1038/s41467-023-37087-7 ) that used a different approach (SYTO9/PI staining of hyphal pellets) to demonstrate that CIS-deficient mutants exhibit decreased hyphal death. We agree that it would be interesting to test if actively growing hyphae respond differently to nisin treatment, and such experiments will be considered in future work.

    Taken together, we believe that the results obtained from our fluorescence-based viability assay are consistent with data reported by others and provide strong experimental evidence that functional CIS mediate hyphal cell death.

    The model presented in Fig. 5 suggests that stress leads to a CisA-dependent attachment of CIS assemblies to the cytoplasmic membrane, and then triggering of contraction, leading to cell death. This model makes testable predictions that have not been challenged experimentally. Given that sublethal doses of nisin seem to trigger cell death, there appear to be possibilities to monitor whether activation of the system (via CisA?) indeed leads to at least temporally increased interaction of CIS with the membrane.

    We thank this reviewer for their suggestions on how to test our model further. In the meantime, we have performed co-immunoprecipitation experiments using S. coelicolor cells that produced CisA-FLAG as bait and were treated with a sub-lethal nisin concentration for 0/15/45 min. Mass spectrometry analysis of co-eluted peptides did not show the presence of CIS-associated peptides. While we cannot exclude the possibility that our experimental assay requires further optimization to successfully demonstrate a CisA-CIS interaction (e.g. optimization of the use of detergents to improve the solubilization of CisA from Streptomyces membrane, which is currently not an established method), an alternative and equally valid hypothesis is that the interaction between CIS particles and CisA is transient and therefore difficult to capture. We would like to mention that we did detect CisA peptides in crude purifications of CIS particles from nisin-stressed cells (Supplementary Table 2, manuscript: line 265/266), supporting our model that CisA associates with CIS particles in vivo.

    Further, would not the model predict that stress leads to an increased number of contracted CIS assemblies in the cytoplasm? No clear difference in length of the isolated assemblies if Fig. S7 is seen between untreated and nisin-exposed cells, and also no difference between assemblies from WT and cisA mutant hyphae.

    The reviewer is correct that there is no clear difference in length in the isolated CIS particles shown in Figure S7. This is in line with our results, which show that CisA is not required for the correct assembly of CIS particles and their ability to contract in the presence and absence of nisin treatment. The purpose of Figure S7 was to support this statement. We would like to note that the particles shown in Figure S7 were purified from cell lysates using a crude sheath preparation protocol, during which CIS particles generally contract irrespective of the presence or absence of CisA. Thus, we cannot comment on whether there is an increased number of contracted CIS assemblies in the cytoplasm of nisin-exposed cells. To answer this point, we would need to acquire additional cryo-electron tomograms (cyroET) of the different strains treated with nisin. We appreciate this reviewer's suggestions. However, cryoET is an extremely time and labour-intensive task, and given that we currently don’t know the exact dynamics of the CIS-CisA interaction following exogenous stress, we believe this experiment is beyond the scope of this work.

    The interaction of CisA with the CIS assembly is critical for the model but is only supported by Alphafold modelling, predicting interaction between cytoplasmic parts of CisA and Cis11 protein in the baseplate wedge. An experimental demonstration of this interaction would have strengthened the conclusions.

    We agree that direct experimental evidence of this interaction would have further strengthened the conclusions of our study, and we have extensively tried to provide additional experimental evidence. Unfortunately, due to the toxicity of CisA expression in E. coli and the transient nature of the interaction under our experimental conditions, we were unable to pursue direct biochemical or biophysical validation methods, such as co-purification or bacterial two-hybrid assays. While these challenges limited our ability to experimentally confirm the interaction, the AlphaFold predictions provided a valuable hypothesis and mechanistic insight into the role of CisA.

    The cisA mutant showed a similarly accelerated sporulation as was previously reported for CIS-negative strains, which supports the conclusion that CisA is required for function of CISSc. But the results do not add any new insights into how CIS/CisA affects the progression of the developmental life cycle and whether this effect has anything to do with the regulated cell death that is caused by CIS. The same applies to the effect on secondary metabolite production, with no further mechanistic insights added, except reporting similar effects of CIS and CisA inactivations.

    We thank this reviewer for their thoughtful feedback and for highlighting the connections between CisA, CIS function, and their effects on the developmental life cycle and secondary metabolite production in S. coelicolor. The main focus of this study was to provide further insight into how CIS contraction and firing are mediated in Streptomyces, and we used the analysis of accelerated sporulation and secondary metabolite production to assess the functionality of CIS in the presence or absence of CisA.

    We agree that we still don’t fully understand the nature of the signals that trigger CIS contraction, but we do know that the production of CIS assemblies seems to be an integral part of the Streptomyces multicellular life cycle as demonstrated in two independent previous studies (DOI: 10.1038/s41564-023-01341-x and DOI: 10.1038/s41467-023-37087-7 ). We propose that the assembly and firing of Streptomyces CIS particles could present a molecular mechanism to sacrifice only a part of the mycelium to either prevent the spread of local cellular damage or to provide additional nutrients for the rest of the mycelium and delay the terminal differentiation into spores and affect the production of secondary metabolites.

    We recognize the importance of understanding the regulation and mechanistic details underpinning the proposed CIS-mediated regulated cell death model. This will be further explored in future studies.

    Concluding remarks:

    The work will be of interest to anyone interested in contractile injection systems, T6SS, or similar machineries, as well for people working on the biology of streptomycetes. There is also a potential impact of the work in the understanding of how such molecular machineries could have been co-opted during evolution to become a mechanism for regulated cell death. However, this latter aspect remains still poorly understood. Even though this paper adds excellent new structural insights and identifies a putative membrane anchor, it remains elusive how the Streptomyces CIS may lead to cell death. It is also unclear what the advantage would be to trigger death of hyphal compartments in response to stress, as well as how such cell death may impact (or accelerate) the developmental progression. Finally, it is inescapable to wonder whether the Streptomyces CIS could have any role in protection against phage infection.

    We thank Reviewer #2 for their supportive assessment of our work. In the revised manuscript, we will briefly discuss the impact of functional CIS assemblies on Streptomyces development. We previously tested if Streptomyces could defend against phages but have not found any experimental evidence to support this idea. The analysis of phage defense mechanisms is an underdeveloped area in Streptomyces research, partly due to the currently limited availability of a diverse phage panel.

    Reviewer #3 (Public review):

    Summary:

    In this work, Casu et al. have reported the characterization of a previously uncharacterized membrane protein CisA encoded in a non-canonical contractile injection system of Streptomyces coelicolor, CISSc, which is a cytosolic CISs significantly distinct from both intracellular membrane-anchored T6SSs and extracellular CISs. The authors have presented the first high-resolution structure of extended CISSc structure. It revealed important structural insights in this conformational state. To further explore how CISSc interacted with cytoplasmic membrane, they further set out to investigate CisA that was previously hypothesized to be the membrane adaptor. However, the structure revealed that it was not associated with CISSc. Using fluorescence microscope and cell fractionation assay, the authors verified that CisA is indeed a membrane-associated protein. They further determined experimentally that CisA had a cytosolic N-terminal domain and a periplasmic C-terminus. The functional analysis of cisA mutant revealed that it is not required for CISSc assembly but is essential for the contraction, as a result, the deletion significantly affects CISSc-mediated cell death upon stress, timely differentiation, as well as secondary metabolite production. Although the work did not resolve the mechanistic detail how CisA interacts with CISSc structure, it provides solid data and a strong foundation for future investigation toward understanding the mechanism of CISSc contraction, and potentially, the relation between the membrane association of CISSc, the sheath contraction and the cell death.

    Strengths:

    The paper is well-structured, and the conclusion of the study is supported by solid data and careful data interpretation was presented. The authors provided strong evidence on (1) the high-resolution structure of extended CISSc determined by cryo-EM, and the subsequent comparison with known eCIS structures, which sheds light on both its similarity and different features from other subtypes of eCISs in detail; (2) the topological features of CisA using fluorescence microscopic analysis, cell fractionation and PhoA-LacZα reporter assays, (3) functions of CisA in CISSc-mediated cell death and secondary metabolite production, likely via the regulation of sheath contraction.

    Weaknesses:

    The data presented are not sufficient to provide mechanistic details of CisA-mediated CISSc contraction, as authors are not able to experimentally demonstrate the direct interaction between CisA with baseplate complex of CISSc (hypothesized to be via Cis11 by structural modeling), since they could not express cisA in E. coli due to its potential toxicity. Therefore, there is a lack of biochemical analysis of direct interaction between CisA and baseplate wedge. In addition, there is no direct evidence showing that CisA is responsible for tethering CISSc to the membrane upon stress, and the spatial and temporal relation between membrane association and contraction remains unclear. Further investigation will be needed to address these questions in future.

    We thank Reviewer #3 for the supportive evaluation and constructive criticism of our study in the public and non-public review. We appreciate your recognition of the technical limitations of experimentally demonstrating a direct interaction between CisA and CIS baseplate complex, and we agree that further investigations in the future will hopefully provide a full mechanistic understanding of the spatiotemporal interaction of CisA and CIS particular and the subsequent CIS firing.

    To further improve the manuscript, we will revise the text and clarify figures and figure legends as suggested in the non-public review.

    Discussion:

    Overall, the work provides a valuable contribution to our understanding on the structure of a much less understood subtype of CISs, which is unique compared to both membrane-anchored T6SSs and host-membrane targeting eCISs. Importantly, the work serves as a good foundation to further investigate how the sheath contraction works here. The work contributes to expanding our understanding of the diverse CIS superfamilies.

    Thank you.

  8. Version published to 10.1101/2024.06.25.600559v2 on bioRxiv
  9. Version published to 10.1101/2024.06.25.600559v1 on bioRxiv