Gene Regulatory Mechanism of Mycobacterium Tuberculosis during Dormancy

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

The primary focus of this research is to understand the gene regulatory network of Mycobacterium tuberculosis (Mtb) during its dormant state. The study is devoted to study the intricate mechanisms that govern dormancy, particularly emphasizing the regulation of lipid and energy metabolism, the DosR regulon, Wbl family proteins, toxin-antitoxin (TA) systems, sigma factors, and the MprAB two-component system. By elucidating these regulatory pathways, the research aims to provide insights into the persistence of latent tuberculosis infection (LTBI) and explore potential avenues for developing more effective vaccines and therapeutic strategies.

This paper presents several significant and original contributions to the field of tuberculosis research:

-Detailed Analysis of Regulatory Mechanisms: The review provides a comprehensive analysis of the various regulatory mechanisms that enable Mtb to enter and maintain a dormant state. This includes an in-depth examination of the roles of DosR, Wbl family proteins, TA systems, sigma factors, and the MprAB system. This detailed overview fills a critical gap in the understanding of Mtb dormancy.

-Focus on Lipid and Energy Metabolism: The study highlights the importance of lipid and energy metabolism in Mtb dormancy. It discusses how Mtb utilizes host cholesterol and fatty acids, synthesizing triacylglycerol (TAG) to store energy and sustain dormancy. The identification of key enzymes and pathways, such as the glyoxylate shunt and gluconeogenesis, is particularly noteworthy.

-Morphological Changes During Dormancy: The paper outlines the morphological changes that Mtb undergoes during dormancy, such as thickening of the cell wall and alterations in cell volume and metabolic rate. This aspect of the study provides valuable insights into the physical adaptations of Mtb in response to environmental stresses.

Potential Drug and Vaccine Targets: By identifying critical genes and proteins involved in Mtb dormancy, the study suggests potential targets for new anti-TB drugs and vaccines. The focus on the DosR regulon, for example, highlights its role in regulating genes essential for Mtb's adaptation to hypoxia and other stress conditions, making it a promising target for therapeutic intervention.

-Specific Gap Addressed: The review addresses a significant gap in the current understanding of Mtb's dormancy mechanisms. Despite extensive research on active TB, the latent phase of the infection, which affects a substantial portion of the global population, remains poorly understood. This paper aims to bridge this knowledge gap by providing a detailed examination of the genetic and biochemical pathways that support Mtb dormancy.

Compared to existing literature, this review offers a more integrated and comprehensive perspective on the gene regulatory mechanisms of Mtb dormancy. While other studies often focus on isolated aspects of Mtb biology, this review synthesizes information from various sources to present a holistic view of the regulatory networks involved in dormancy. This approach not only enhances the understanding of Mtb persistence but also underscores the interconnectedness of different regulatory pathways.

Added Value to the Subject Area:

-Holistic View: The review consolidates various aspects of Mtb dormancy, providing a unified framework that highlights the interplay between different regulatory mechanisms. This holistic view is essential for developing integrated strategies to combat LTBI.

-Identification of New Targets: By pinpointing specific genes and proteins involved in dormancy, the study offers valuable insights for identifying new drug and vaccine targets. This could lead to the development of more effective interventions to prevent the progression of LTBI to active TB.

While the review offers valuable insights, several methodological improvements and further controls could enhance the robustness and applicability of the findings:

-Experimental Validation: The review relies heavily on existing literature, and while it synthesizes this information effectively, the inclusion of more experimental and novel data (from 2022 and 2023 or 2024) would strengthen the conclusions. Future research should aim to validate the proposed mechanisms through direct experimental studies, such as genetic knock-out models and in vivo experiments. Summarize these data will be a strenght point of the review attracting more citations.

-Comparative Studies: To validate the uniqueness of the dormancy mechanisms in Mtb, comparative studies with other mycobacterial species are necessary. This could help identify conserved and unique regulatory pathways, providing a broader context for the findings. We suggest, in the light of COVID pandemic, to add a paragraph about the exposure of the Healthcare workers (HCWs). They are at a significantly higher risk of acquiring latent tuberculosis infection (LTBI) due to their frequent exposure to patients with active tuberculosis (TB). In particular, we suggest to consult and add as a reference the paper with DOI: 10.3390/epidemiologia4040038.

-Longitudinal Studies: Observing the dynamics of gene expression changes during the transition from active infection to dormancy and subsequent reactivation would provide valuable insights. Longitudinal studies could reveal the temporal regulation of key genes and proteins, offering a more detailed understanding of dormancy mechanisms.

-Advanced Imaging Techniques: exploring studies employing advanced imaging techniques, such as live-cell imaging and electron microscopy, could provide real-time observations of morphological changes in Mtb during dormancy. This would complement the genetic and biochemical data, offering a more comprehensive view of dormancy. Provide more example citing appropriate literature.

-Gene Silencing and Knock-Out Models: Utilizing genetic knock-out models and gene silencing techniques can help confirm the functional roles of specific genes in dormancy. This would provide direct evidence for the involvement of these genes in Mtb persistence. Provide more example citing appropriate literature.

-Proteomic,transcriptomic and metagenomic integration: integrating transcriptomic, metagenomic, and proteomic data would offer a more comprehensive understanding of the regulatory networks. This approach could identify post-transcriptional and post-translational modifications that play critical roles in dormancy. Provide more example citing appropriate literature.

The conclusions drawn in the review are generally consistent with the evidence and arguments presented. The review effectively links the described regulatory mechanisms to their roles in Mtb dormancy and persistence. For example, the discussion on lipid metabolism is well-supported by evidence showing the accumulation of TAG and its role in sustaining Mtb during dormancy. Similarly, the role of the DosR regulon in regulating gene expression under hypoxic conditions is backed by substantial experimental data.

The main questions posed by the study are addressed through a comprehensive review of existing literature. Each regulatory mechanism discussed is supported by relevant studies, providing a coherent narrative that ties together various aspects of Mtb dormancy. However, some sections could benefit from additional experimental evidence to further strengthen the claims.

The references used in the review are in general appropriate and cover a wide range of studies related to Mtb dormancy. They include recent and relevant research articles, reviews, and primary data sources. The extensive reference list reflects a thorough literature review, ensuring that the discussed mechanisms are grounded in current scientific knowledge. However, while the references are comprehensive, including more recent studies from 2022-2023 could further strengthen the review.  The inclusion of more references to experimental studies (some suggestion are at point 4) would enhance the credibility and robustness of the review.

The tables and figures included in the review are well-designed and effectively aid in understanding the complex regulatory networks discussed. The visual aids provide clear and concise summaries of key points, making it easier for readers to grasp the detailed information presented in the text. However, to improve the quality of the data and enhance the overall impact of the figures and tables, the authors could consider the following:

- Providing more detailed legends and explanations for the figures would enhance their clarity and contextual relevance. This would help readers understand the significance of the data presented in each figure.

- Suggest to revise the English in the captions of all the figures, it seems to be written with a different style comparing to the rest of the manuscript.

- Including more graphical representations of data from recent experimental studies would strengthen the visual aids. This could involve elaborating data from the key experiments and studies that support the review's conclusions.

Despite its strengths, the manuscript has several weaknesses that should be addressed:

- Limited Discussion of Controversies: The review does not adequately address existing controversies and differing viewpoints in the field. A more balanced discussion of conflicting evidence would provide a more nuanced understanding of the regulatory mechanisms involved in Mtb dormancy. A suggestion to develop this part is to address the different latency of TB in different working environment and the exposure factors of different class of health workers.

- Insufficient Focus on Clinical Implications: While the review discusses potential drug and vaccine targets, it lacks a detailed discussion on the clinical implications of these findings. Including more information on how the identified targets could be translated into clinical applications would enhance the review's relevance to public health.

- Need for More In-Depth Analysis: Some sections of the review would benefit from a more in-depth analysis of specific regulatory pathways. For instance, the discussion on TA systems could be expanded to include more details on the interactions between different TA modules and their specific roles in dormancy.

Overall, the manuscript is well-written and makes a significant contribution to understanding Mtb dormancy.

Accept with minor revisions.

Comments on the Quality of English Language

Some sentences could be streamlined for clarity. For example, the sentence on page 4, lines 118-124, could be revised for better flow.

Ensure consistency in tense usage and correct minor grammatical errors and typos throughout the manuscript.

Author Response

Please see the attachment.

Author Response File: Author Response.docx

Reviewer 2 Report

Comments and Suggestions for Authors

Dear Editor,

I would like to thank you for your invitation to this peer review of an original review article entitled ”Gene regulatory mechanism of Mycobacterium tuberculosis during dormancy".

In this article, the authors reviewed thе gеnе rеgulatory nеtwork of Mycobactеrium tubеrculosis during dormancy and highlighting thе rolеs of various rеgulatory еlеmеnts such as protеins , lipid mеtabolism and strеss rеsponsе . I have made some minor comments mentioned below.

 

Comments for Authors

Accepted with minor revision

Question # 1: The figures # 1-6 illustration are more clear (OK), However, it would be better to cite the source if you used biorender.com.

Question # 2: In table # 2 line 186: 1733c gene highly expressed instead expresses, Rv3132c (DosS), encodes sensor kinases invovled instead invovling, correct it accordingly.

Question # 3: I think it would be very helpfull for the reader to include an additional workflow chart for your review strategy (lable as figure 1) if possible.

Question # 4: Thе authors should еnsurе that Mycobactеrium tubеrculosis is italicizеd throughout thе еntirе manuscript where used, in additon I would suggest to revise the manuscript with some minor english editing.

Question # 5: In nutshell, this study provides valuable insights in the field of infectious diseases particlularly tuberculosis (LTBI). Further studied are needed to review or experimentally investigate, What influences DosR in dormancy, Sigma factors that interact during dormancy, how WhiB proteins affect virulence and potential target for drugs and vaccine developments?

Good Luck!

Comments on the Quality of English Language

 Minor editing of the English language required

Author Response

Please see the attachment.

Author Response File: Author Response.docx