A compilation of histidine kinase genes in the genome of a tissue macerating <i>Pectobacterium brasiliense</i> isolated from potato in South Africa

Sarah Oluwatobi Otun; Khayalethu Ntushelo

doi:10.12688/f1000research.139906.2

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Data Note

Revised

A compilation of histidine kinase genes in the genome of a tissue macerating Pectobacterium brasiliense isolated from potato in South Africa

[version 2; peer review: 1 approved]

Sarah Oluwatobi Otun ¹, Khayalethu Ntushelo²

PUBLISHED 17 Jun 2024

Author details Author details

¹ Molecular and Cell Biology, University of the Witwatersrand Johannesburg, Johannesburg, Gauteng, 2000, South Africa
² Department of Agriculture and Animal Health, University of South Africa, Pretoria, Gauteng, South Africa

Sarah Oluwatobi Otun
Roles: Data Curation, Methodology, Writing – Original Draft Preparation

Khayalethu Ntushelo
Roles: Conceptualization, Supervision, Writing – Review & Editing

OPEN PEER REVIEW

REVIEWER STATUS

This article is included in the Genomics and Genetics gateway.

Abstract

Background

A compilation of kinase genes of Pectobacterium brasilense is presented. The genes were mined from a complete genome sequence of strain BD163 isolated from potato in Tshwane, South Africa. This work is an effort to collate knowledge on P. brasiliense which has become a worldwide pathogen of potatoes and other vegetables such as tomato. Histidine kinases of P. brasiliense can be targets of bacterial control agents to limit the growth, spread and pathogenicity of P. brasiliense.

Methods

The whole genome sequence of strain BD163 of P. brasiliense deposited on www.ncbi.nlm.nih.gov was downloaded, and individual kinase genes were searched and listed with their properties, namely, locus tag, protein accession number and annotation.

Conclusions

This is the only compilation of histidine kinase genes for P. brasiliense.

Keywords

Pectobcterium brasiliense, Histidine Kinase, Genome, Plant pathogen, Potato disease

Corresponding author: Sarah Oluwatobi Otun

Competing interests: No competing interests were disclosed.

Grant information: The author(s) declared that no grants were involved in supporting this work.

Copyright: © 2024 Otun SO and Ntushelo K. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

How to cite: Otun SO and Ntushelo K. A compilation of histidine kinase genes in the genome of a tissue macerating Pectobacterium brasiliense isolated from potato in South Africa [version 2; peer review: 1 approved]. F1000Research 2024, 13:364 (https://doi.org/10.12688/f1000research.139906.2) First published: 23 Apr 2024, 13:364 (https://doi.org/10.12688/f1000research.139906.1) Latest published: 17 Jun 2024, 13:364 (https://doi.org/10.12688/f1000research.139906.2)

Revised Amendments from Version 1

Major Differences Between Current and Previous Versions:
In this revised version of our manuscript, we have incorporated several significant updates based on the valuable feedback from the reviewers. Firstly, we have expanded the introduction to include detailed information on using histidine kinase inhibitors as a potential control strategy for bacterial infections. This addition highlights the role of histidine kinase inhibitors in altering the expression of virulence factors and the bacteria's ability to adapt to the host environment, thereby offering a promising strategy to control bacterial infections. Relevant references have been added to support this concept, including works by Bem et al. (2015) and Espinasse et al. (2023).
Another significant update is the revision of the schematic representation of histidine kinase in Figure 1. We've made these changes to enhance clarity and aid in understanding the phosphate transfer process. Specifically, we've replaced the letter "A" with "D" in the legend to maintain consistency, and we've clarified the description to accurately reflect the phosphate transfer process from the histidine kinase to the response regulator (RR).
Additionally, we have updated the table title to summarise histidine kinase genes. The new title, "Putative Genes Related to Histidine Kinase Characteristics in the Genome of Pectobacterium brasiliense Strain BD163", more accurately describes the content of the table. This revision ensures that the reader can understand the table's content at a glance.
These revisions aim to enhance the manuscript's overall clarity, depth, and scientific accuracy by addressing the insightful comments and suggestions provided by the reviewers.

See the authors' detailed response to the review by Iris Yedidia

Introduction

Histidine kinases are enzymes that catalyse phosphorylation reactions involving histidine (Figure 1) (Catlett et al., 2003). These kinases are essential for signal transduction and bacterial adaptability to new environments, and they are and widely distributed in bacteria. The function performed by histidine kinases is critical to the function of an organism, and therefore targeting histidine kinases in Pectobacterium brasiliense to limit its growth, spread, and pathogenicity may help reduce its impact as a plant pathogen. Pectobcterium brasiliense is a crops-tissue-macerating pathogen of different crops, and it has gained prominence with recent reports from multiple hosts in Taiwan, China and Korea (Li et al., 2023; Park et al., 2022; Song et al., 2023). Similar to other bacteria, P. brasilense gains entry into the plant through natural openings or wounds. It spreads throughout the intercellular spaces, and upon close contact with target plant cells, it releases a barrage of tissue macerating effectors to disrupt cells and after that survives on the oozing sap. The outside appearance of affected tissues is discoloured, and as the disease worsens, the plant weakens and eventually succumbs to infection. If not interrupted by disease control agents, P. brasiliense may cause unprecedented damage to individual plants and the plants close to the initially infected plant. With the discouraged use of antibiotics ways to control P. brasiliense are limited and therefore new drug targets are necessary. Histidine kinases inhibitors are widely employed as agents in drug design and development. Inhibition of bacterial virulence and pathogenicity was the demonstrated previously using HKs inhibitors (Bem et al., 2015) by changing the expression of virulence factors and the ability of bacteria to adapt to the host environment (Espinasse et al., 2023). Before efforts to design kinase targets in P. brasiliense, it is necessary to first compile all histidine kinases in P. brasiliense. This present work aimed to list all histidine kinases present in P. brasiliense to enable future efforts for design, formulation and testing of histidine kinase inhibitors. We created a list of histidine kinase genes of P. brasilense, strain BD163, whose complete genome sequence is published by Rauwane et al. (2023).

Figure 1. Schematic representation of histidine kinase function of phosphorelay signalling (modified from Catlett et al. (2003).

Phosphorylation of a histidine (H) residue is triggered by an external stimulus and detected by the sensor domain. The effector domain is activated when phosphate is transferred to a conserved aspartic acid residue (D) in the RR receiver domain. This leads to an action such as transcriptional activation or a MAP kinase (MAPK) cascade.

Methods

The genome sequence of strain BD163 of P. brasiliense, BioProject no. PRJNA798891, with raw reads under accession no. JAKNTB000000000, BioSample number SAMN25132833, and GenBank assembly accession number GCA_022172285.1 were downloaded, and individual histidine kinase genes were searched using the standard search function. To create the histidine kinase gene catalogue, the genes were listed with their characteristics: locus tag, protein accession number and annotation (Table 1).

Table 1. Putative genes related to Histidine kinase characteristics in the genome of Pectobacterium brasiliense strain BD163.

Putative gene	Go;Function	Locus tag	NCBI protein accession no	Annotation
23508..24944		L2164_00050	MCG5047093.1	HAMP domain-containing histidine kinase
baeS	phosphorelay sensor kinase activity	L2164_00435	MCG5047166.1	two-component system sensor histidine kinase BaeS
narQ	phosphorelay sensor kinase activity	L2164_03380	MCG5047733.1	nitrate/nitrite two-component system sensor histidine kinase NarQ
rstB	phosphorelay sensor kinase activity	L2164_03965	MCG5047848.1	two-component system sensor histidine kinase RstB
narX	phosphorelay sensor kinase activity	L2164_04035	MCG5047862.1	nitrate/nitrite two-component system sensor histidine kinase NarX
1260325..1262070		L2164_05855	MCG5048221.1	sensor histidine kinase
PhoQ	phosphorelay sensor kinase activity	L2164_05920	MCG5048234.1	two-component system sensor histidine kinase PhoQ
1409731..1411326		L2164_06490	MCG5048346.1	sensor histidine kinase
306488..307987		L2164_08980	MCG5048828.1	HAMP domain-containing histidine kinase
nlpE		L2164_10325	MCG5049091.1	envelope stress response activation lipoprotein
phoR	phosphorelay sensor kinase activity	L2164_10570	MCG5049139.1	phosphate regulon sensor histidine kinase PhoR
rcsC	phosphorelay sensor kinase activity activity	L2164_11025	MCG5049229.1	two-component system sensor histidine kinase RcsC
barA	phosphorelay sensor kinase activity	L2164_11380	MCG5049299.1	two-component sensor histidine kinase BarA
cpxA	phosphorelay sensor kinase activity	L2164_13880	MCG5049786.1	envelope stress sensor histidine kinase CpxA
155127..156755		L2164_14300	MCG5049869.1	sensor histidine kinase
qseC	phosphorelay sensor kinase activity	L2164_14870	MCG5049983.1	two-component system sensor histidine kinase QseC
kdpD	phosphorelay sensor kinase activity	L2164_15625	MCG5050129.1	two-component system sensor histidine kinase KdpD
97813..99531		L2164_16490	MCG5050288.1	sensor histidine kinase
envZ	phosphorelay sensor kinase activity	L2164_16770	MCG5050344.1	two-component system sensor histidine kinase EnvZ
pmrB		L2164_17085	MCG5050406.1	two-component system sensor histidine kinase PmrB
arcB	phosphorelay sensor kinase activity	L2164_19470	MCG5050877.1	aerobic respiration two-component sensor histidine kinase ArcB

Dataset validation

To validate the histidine kinase gene repertoire of P. brasiliense, a comparative analysis was conducted by comparing the identified histidine kinase genes from strain BD163 with other available Pectobacterium genomes in the NCBI database. This analysis aimed to explore the conservation and diversity of histidine kinase genes within the genus Pectobacterium. The histidine kinase genes of three Pectobacterium strains (Pectobacterium carotovorum NX18131, Pectobacterium atrosepticum PB72, and Pectobacterium parmentieri IFB5626) were compared as part of a genome comparison study. The histidine kinase genes were found following the procedures outlined in the methods section. Based on the comparison results, it was found that similar to BD163, strains of P. carotovorum NX18131 and P. atrosepticum PB72 each contained 24 histidine kinase genes, whereas strain IFB5626 of P. parmentieri had just 20. These values show histidine kinase gene frequency differences among Pectobacterium species.

Data availability

References

Bem AE, Velikova N, Pellicer MT, et al.: Bacterial histidine kinases as novel antibacterial drug targets. ACS Chem. Biol. 2015; 10(1): 213–224. Publisher Full Text
Catlett NL, Yoder OC, Turgeon BG: Whole-Genome Analysis of Two-Component Signal Transduction Genes in Fungal Pathogens. Eukaryot. Cell. 2003; 2(6): 1151–1161. PubMed Abstract | Publisher Full Text | Free Full Text
Espinasse A, Goswami M, Yang J, et al.: Targeting multidrug resistant Staphylococcus infections with bacterial histidine kinase inhibitors. Chem. Sci. 2023; 14(19): 5028–5037. PubMed Abstract | Publisher Full Text | Free Full Text
Li N-P, Tang W-Q, Lee S, et al.: First Report of Pectobacterium carotovorum and Pectobacterium brasiliense Causing Bacterial Soft Rot of Bok Choy in Taiwan. Plant Dis. 2023. PubMed Abstract | Publisher Full Text
Park K-T, Hong S-M, Back C-G, et al.: First Report of Pectobacterium brasiliense Causing Soft Rot on Graft Cactus in Korea. Res. Plant Dis. 2022; 28(3): 172–178. Publisher Full Text
Rauwane ME, Mchunu NP, Pierneef R, et al.: Draft Genome Sequence of Pectobacterium brasiliense Isolated from Potato in South Africa. Microbiol. Resour. Announc. 2023; 12(4): e0076322. PubMed Abstract | Publisher Full Text | Free Full Text
Song Z, Yang C, Zeng R, et al.: First Report of Pectobacterium brasiliense Causing Soft Rot on Conophytum luiseae in China. Plant Dis. 2023; 107(1): 211. Publisher Full Text

Comments on this article Comments (0)

Version 2

VERSION 2 PUBLISHED 23 Apr 2024

Author details Author details

Sarah Oluwatobi Otun
Roles: Data Curation, Methodology, Writing – Original Draft Preparation

Khayalethu Ntushelo
Roles: Conceptualization, Supervision, Writing – Review & Editing

Competing interests

No competing interests were disclosed.

Grant information

The author(s) declared that no grants were involved in supporting this work.

Article Versions (2)

version 2

Revised

Published: 17 Jun 2024, 13:364

https://doi.org/10.12688/f1000research.139906.2

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Published: 23 Apr 2024, 13:364

https://doi.org/10.12688/f1000research.139906.1

© 2024 Otun SO and Ntushelo K. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Otun SO and Ntushelo K. A compilation of histidine kinase genes in the genome of a tissue macerating Pectobacterium brasiliense isolated from potato in South Africa [version 2; peer review: 1 approved]. F1000Research 2024, 13:364 (https://doi.org/10.12688/f1000research.139906.2)

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Reviewer Report 01 Jul 2024

Iris Yedidia, Agricultural Research Organization, Rishon Lezion, Israel

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https://doi.org/10.5256/f1000research.167303.r291976

I have gone through the revision made by the authors (Dr. Sarah Oluwatobi Otun) and it ... Continue reading

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Reviewer Report 29 May 2024

Iris Yedidia, Agricultural Research Organization, Rishon Lezion, Israel

Approved with Reservations

https://doi.org/10.5256/f1000research.153222.r271244

Reviewer 1 for: "A compilation of histidine kinase genes in the genome of a tissue macerating Pectobacterium brasiliense isolated from potato in South Africa"
By: Sarah Oluwatobi Otun and Khayalethu Ntushelo.
The paper describes a compilation of genomic data regarding histidine kinase genes in the genome of P. brasiliense BD 163, isolated from potatoes in South Africa. It is a data note and therefore it is not a regular review process. I am adding my comments regarding mainly the way of presenting the data and the introduction, and not the analysis process.

Introduction:

Since the paper deals with data analysis of histidine kinase, I suggest adding a bit of information on the concept of using histidine kinase inhibitors as a potential control strategy. I included two sentences from the draft (in italics) where I think that the explanation should be added:

Histidine kinases inhibitors are widely employed as agents in drug design and development. Inhibition of bacterial virulence and pathogenicity was demonstrated previously using HKs inhibitors, by changing the expression of virulence factors and the ability of bacteria to adapt to the host environment. Before efforts to design kinase targets in P. brasiliense, it is necessary to first compile all histidine kinases in P. brasiliense.

2. I also suggest to add a reference or two that are relevant to the concept of HKs inhibition as a tool to reduce virulence and infection.
Here is short list of references:
[1] Bem AE, et. al., 2015 (Ref 3)
[2] Qin, Z, et. al., 2008 (Ref 1)
[3] Espinasse A, et. al., 2023 (Ref 4)
[4] Gotoh, Y, et. al., 2010 (Ref 2)

3. In the Schematic representation of histidine kinase presented as Figure 1: The letter A in the scheme doesn’t stand for anything in the legend. Shouldn't it be replaced with (D)? moreover, in the description the phosphate is transferred to RR receiver, while in reality it is transferred to the effector (A). Did I misunderstand it or it should be clarified?

4. Table: Genes related to Histidine kinase characteristics in the genome of Pectobacterium brasiliense strain BD163. I suggest changing it to: Genes or putative genes related to histidine kinase….etc.

Is the rationale for creating the dataset(s) clearly described?

Yes
Are the protocols appropriate and is the work technically sound?

Yes
Are sufficient details of methods and materials provided to allow replication by others?

Yes
Are the datasets clearly presented in a useable and accessible format?

Partly

References

1. Qin Z, Zhang J, Xu B, Chen L, et al.: Structure-based discovery of inhibitors of the YycG histidine kinase: new chemical leads to combat Staphylococcus epidermidis infections.BMC Microbiol. 2006; 6: 96 PubMed Abstract | Publisher Full Text
2. Gotoh Y, Eguchi Y, Watanabe T, Okamoto S, et al.: Two-component signal transduction as potential drug targets in pathogenic bacteria.Curr Opin Microbiol. 2010; 13 (2): 232-9 PubMed Abstract | Publisher Full Text
3. Bem AE, Velikova N, Pellicer MT, Baarlen Pv, et al.: Bacterial histidine kinases as novel antibacterial drug targets.ACS Chem Biol. 2015; 10 (1): 213-24 PubMed Abstract | Publisher Full Text
4. Espinasse A, Goswami M, Yang J, Vorasin O, et al.: Targeting multidrug resistant Staphylococcus infections with bacterial histidine kinase inhibitors.Chem Sci. 2023; 14 (19): 5028-5037 PubMed Abstract | Publisher Full Text

Competing Interests: No competing interests were disclosed.

Reviewer Expertise: Plant pathology, Plant microbe interaction, bacterial virulence,

I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard, however I have significant reservations, as outlined above.

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Author Response 17 Jun 2024

Dr Sarah, Molecular and Cell Biology, University of the Witwatersrand Johannesburg, Johannesburg, 2000, South Africa

17 Jun 2024

Author Response
Dear Editor,
We hope this message finds you well. We sincerely thank reviewer 1 for his detailed and constructive feedback on our manuscript, "A compilation of histidine kinase genes in ... Continue reading
Dear Editor,
We hope this message finds you well. We sincerely thank reviewer 1 for his detailed and constructive feedback on our manuscript, "A compilation of histidine kinase genes in the genome of a tissue macerating Pectobacterium brasiliense isolated from potato in South Africa." We have carefully considered each comment and made the necessary revisions to enhance the clarity and quality of our work.
Response to Reviewer Comments:

Comment: "Since the paper deals with data analysis of histidine kinase, I suggest adding a bit of information on the concept of using histidine kinase inhibitors as a potential control strategy. I included two sentences from the draft (in italics) where I think that the explanation should be added:
Histidine kinases inhibitors are widely employed as agents in drug design and development. Inhibition of bacterial virulence and pathogenicity was demonstrated previously using HKs inhibitors, by changing the expression of virulence factors and the ability of bacteria to adapt to the host environment. Before efforts to design kinase targets in P. brasiliense, it is necessary to first compile all histidine kinases in P. brasiliense."

Response: We appreciate this valuable suggestion. We have added the following information to the Introduction section to provide a clearer understanding of the concept:

"Histidine kinase inhibitors are widely employed as agents in drug design and development. Inhibition of bacterial virulence and pathogenicity was demonstrated previously using HK inhibitors, altering the expression of virulence factors and the bacteria's ability to adapt to the host environment. This approach offers a promising strategy to control bacterial infections by targeting key regulatory pathways."

Comment: "I also suggest to add a reference or two that are relevant to the concept of HKs inhibition as a tool to reduce virulence and infection."

Response: We have added the following references to support the concept of histidine kinase inhibition:

Bem AE, et al., 2015

Espinasse A, et al., 2023

Comment: "In the Schematic representation of histidine kinase presented as Figure 1: The letter A in the scheme doesn’t stand for anything in the legend. Shouldn't it be replaced with (D)? Moreover, in the description the phosphate is transferred to RR receiver, while in reality it is transferred to the effector (A). Did I misunderstand it or it should be clarified?"

Response: Thank you for pointing out these discrepancies. We have revised the legend of Figure 1 to replace the letter "A" with "D" to maintain consistency. Additionally, we clarified the description to accurately reflect the phosphate transfer process: "The phosphate group is transferred from the histidine kinase to the response regulator (RR), which then affects the effector."

Comment: "Table: Genes related to Histidine kinase characteristics in the genome of Pectobacterium brasiliense strain BD163. I suggest changing it to: Genes or putative genes related to histidine kinase….etc."

Response: We agree with the suggestion. The table's title has been changed from "Genes” to Putative Genes Related to Histidine Kinase Characteristics in the Genome of Pectobacterium brasiliense Strain BD163."

Revised Manuscript: We have submitted a clean version of the manuscript without comments or tracked changes, per your requirements. Additionally, we have uploaded a version with yellow highlights to 'Track Changes' for easy identification of the revisions made.
Dear Editor,
We hope this message finds you well. We sincerely thank reviewer 1 for his detailed and constructive feedback on our manuscript, "A compilation of histidine kinase genes in the genome of a tissue macerating Pectobacterium brasiliense isolated from potato in South Africa." We have carefully considered each comment and made the necessary revisions to enhance the clarity and quality of our work.
Response to Reviewer Comments:

Comment: "Since the paper deals with data analysis of histidine kinase, I suggest adding a bit of information on the concept of using histidine kinase inhibitors as a potential control strategy. I included two sentences from the draft (in italics) where I think that the explanation should be added:
Histidine kinases inhibitors are widely employed as agents in drug design and development. Inhibition of bacterial virulence and pathogenicity was demonstrated previously using HKs inhibitors, by changing the expression of virulence factors and the ability of bacteria to adapt to the host environment. Before efforts to design kinase targets in P. brasiliense, it is necessary to first compile all histidine kinases in P. brasiliense."

Response: We appreciate this valuable suggestion. We have added the following information to the Introduction section to provide a clearer understanding of the concept:

"Histidine kinase inhibitors are widely employed as agents in drug design and development. Inhibition of bacterial virulence and pathogenicity was demonstrated previously using HK inhibitors, altering the expression of virulence factors and the bacteria's ability to adapt to the host environment. This approach offers a promising strategy to control bacterial infections by targeting key regulatory pathways."

Comment: "I also suggest to add a reference or two that are relevant to the concept of HKs inhibition as a tool to reduce virulence and infection."

Response: We have added the following references to support the concept of histidine kinase inhibition:

Bem AE, et al., 2015

Espinasse A, et al., 2023

Comment: "In the Schematic representation of histidine kinase presented as Figure 1: The letter A in the scheme doesn’t stand for anything in the legend. Shouldn't it be replaced with (D)? Moreover, in the description the phosphate is transferred to RR receiver, while in reality it is transferred to the effector (A). Did I misunderstand it or it should be clarified?"

Response: Thank you for pointing out these discrepancies. We have revised the legend of Figure 1 to replace the letter "A" with "D" to maintain consistency. Additionally, we clarified the description to accurately reflect the phosphate transfer process: "The phosphate group is transferred from the histidine kinase to the response regulator (RR), which then affects the effector."

Comment: "Table: Genes related to Histidine kinase characteristics in the genome of Pectobacterium brasiliense strain BD163. I suggest changing it to: Genes or putative genes related to histidine kinase….etc."

Response: We agree with the suggestion. The table's title has been changed from "Genes” to Putative Genes Related to Histidine Kinase Characteristics in the Genome of Pectobacterium brasiliense Strain BD163."

Revised Manuscript: We have submitted a clean version of the manuscript without comments or tracked changes, per your requirements. Additionally, we have uploaded a version with yellow highlights to 'Track Changes' for easy identification of the revisions made.
Competing Interests: The authors declare that there are no competing interests. Close
Report a concern
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COMMENTS ON THIS REPORT

Author Response 17 Jun 2024

Dr Sarah, Molecular and Cell Biology, University of the Witwatersrand Johannesburg, Johannesburg, 2000, South Africa

17 Jun 2024

Author Response
Dear Editor,
We hope this message finds you well. We sincerely thank reviewer 1 for his detailed and constructive feedback on our manuscript, "A compilation of histidine kinase genes in ... Continue reading
Dear Editor,
We hope this message finds you well. We sincerely thank reviewer 1 for his detailed and constructive feedback on our manuscript, "A compilation of histidine kinase genes in the genome of a tissue macerating Pectobacterium brasiliense isolated from potato in South Africa." We have carefully considered each comment and made the necessary revisions to enhance the clarity and quality of our work.
Response to Reviewer Comments:

Comment: "Since the paper deals with data analysis of histidine kinase, I suggest adding a bit of information on the concept of using histidine kinase inhibitors as a potential control strategy. I included two sentences from the draft (in italics) where I think that the explanation should be added:
Histidine kinases inhibitors are widely employed as agents in drug design and development. Inhibition of bacterial virulence and pathogenicity was demonstrated previously using HKs inhibitors, by changing the expression of virulence factors and the ability of bacteria to adapt to the host environment. Before efforts to design kinase targets in P. brasiliense, it is necessary to first compile all histidine kinases in P. brasiliense."

Response: We appreciate this valuable suggestion. We have added the following information to the Introduction section to provide a clearer understanding of the concept:

"Histidine kinase inhibitors are widely employed as agents in drug design and development. Inhibition of bacterial virulence and pathogenicity was demonstrated previously using HK inhibitors, altering the expression of virulence factors and the bacteria's ability to adapt to the host environment. This approach offers a promising strategy to control bacterial infections by targeting key regulatory pathways."

Comment: "I also suggest to add a reference or two that are relevant to the concept of HKs inhibition as a tool to reduce virulence and infection."

Response: We have added the following references to support the concept of histidine kinase inhibition:

Bem AE, et al., 2015

Espinasse A, et al., 2023

Comment: "In the Schematic representation of histidine kinase presented as Figure 1: The letter A in the scheme doesn’t stand for anything in the legend. Shouldn't it be replaced with (D)? Moreover, in the description the phosphate is transferred to RR receiver, while in reality it is transferred to the effector (A). Did I misunderstand it or it should be clarified?"

Response: Thank you for pointing out these discrepancies. We have revised the legend of Figure 1 to replace the letter "A" with "D" to maintain consistency. Additionally, we clarified the description to accurately reflect the phosphate transfer process: "The phosphate group is transferred from the histidine kinase to the response regulator (RR), which then affects the effector."

Comment: "Table: Genes related to Histidine kinase characteristics in the genome of Pectobacterium brasiliense strain BD163. I suggest changing it to: Genes or putative genes related to histidine kinase….etc."

Response: We agree with the suggestion. The table's title has been changed from "Genes” to Putative Genes Related to Histidine Kinase Characteristics in the Genome of Pectobacterium brasiliense Strain BD163."

Revised Manuscript: We have submitted a clean version of the manuscript without comments or tracked changes, per your requirements. Additionally, we have uploaded a version with yellow highlights to 'Track Changes' for easy identification of the revisions made.
Dear Editor,
We hope this message finds you well. We sincerely thank reviewer 1 for his detailed and constructive feedback on our manuscript, "A compilation of histidine kinase genes in the genome of a tissue macerating Pectobacterium brasiliense isolated from potato in South Africa." We have carefully considered each comment and made the necessary revisions to enhance the clarity and quality of our work.
Response to Reviewer Comments:

Comment: "Since the paper deals with data analysis of histidine kinase, I suggest adding a bit of information on the concept of using histidine kinase inhibitors as a potential control strategy. I included two sentences from the draft (in italics) where I think that the explanation should be added:
Histidine kinases inhibitors are widely employed as agents in drug design and development. Inhibition of bacterial virulence and pathogenicity was demonstrated previously using HKs inhibitors, by changing the expression of virulence factors and the ability of bacteria to adapt to the host environment. Before efforts to design kinase targets in P. brasiliense, it is necessary to first compile all histidine kinases in P. brasiliense."

Response: We appreciate this valuable suggestion. We have added the following information to the Introduction section to provide a clearer understanding of the concept:

"Histidine kinase inhibitors are widely employed as agents in drug design and development. Inhibition of bacterial virulence and pathogenicity was demonstrated previously using HK inhibitors, altering the expression of virulence factors and the bacteria's ability to adapt to the host environment. This approach offers a promising strategy to control bacterial infections by targeting key regulatory pathways."

Comment: "I also suggest to add a reference or two that are relevant to the concept of HKs inhibition as a tool to reduce virulence and infection."

Response: We have added the following references to support the concept of histidine kinase inhibition:

Bem AE, et al., 2015

Espinasse A, et al., 2023

Comment: "In the Schematic representation of histidine kinase presented as Figure 1: The letter A in the scheme doesn’t stand for anything in the legend. Shouldn't it be replaced with (D)? Moreover, in the description the phosphate is transferred to RR receiver, while in reality it is transferred to the effector (A). Did I misunderstand it or it should be clarified?"

Response: Thank you for pointing out these discrepancies. We have revised the legend of Figure 1 to replace the letter "A" with "D" to maintain consistency. Additionally, we clarified the description to accurately reflect the phosphate transfer process: "The phosphate group is transferred from the histidine kinase to the response regulator (RR), which then affects the effector."

Comment: "Table: Genes related to Histidine kinase characteristics in the genome of Pectobacterium brasiliense strain BD163. I suggest changing it to: Genes or putative genes related to histidine kinase….etc."

Response: We agree with the suggestion. The table's title has been changed from "Genes” to Putative Genes Related to Histidine Kinase Characteristics in the Genome of Pectobacterium brasiliense Strain BD163."

Revised Manuscript: We have submitted a clean version of the manuscript without comments or tracked changes, per your requirements. Additionally, we have uploaded a version with yellow highlights to 'Track Changes' for easy identification of the revisions made.
Competing Interests: The authors declare that there are no competing interests. Close
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Iris Yedidia, Agricultural Research Organization, Rishon Lezion, Israel

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I have gone through the revision made by the authors (Dr. Sarah Oluwatobi Otun) and it looks fine on my side.
I have no further comments and the paper is now acceptable.
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Reviewer Report

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29 May 2024 | for Version 1

Iris Yedidia, Agricultural Research Organization, Rishon Lezion, Israel

6 Views Cite this report Responses(1)

Approved With Reservations

Since the paper deals with data analysis of histidine kinase, I suggest adding a bit of information on the concept of using histidine kinase inhibitors as a potential control strategy. I included two sentences from the draft (in italics) where I think that the explanation should be added:

Is the rationale for creating the dataset(s) clearly described?

Yes
Are the protocols appropriate and is the work technically sound?

Yes
Are sufficient details of methods and materials provided to allow replication by others?

Yes
Are the datasets clearly presented in a useable and accessible format?

Partly

References

Competing Interests

No competing interests were disclosed.

Reviewer Expertise

Plant pathology, Plant microbe interaction, bacterial virulence,

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Responses (1)

Author Response

17 Jun 2024

Dr Sarah, Molecular and Cell Biology, University of the Witwatersrand Johannesburg, Johannesburg, 2000, South Africa

Dear Editor,
We hope this message finds you well. We sincerely thank reviewer 1 for his detailed and constructive feedback on our manuscript, "A compilation of histidine kinase genes in the genome of a tissue macerating Pectobacterium brasiliense isolated from potato in South Africa." We have carefully considered each comment and made the necessary revisions to enhance the clarity and quality of our work.
Response to Reviewer Comments:

Comment: "Since the paper deals with data analysis of histidine kinase, I suggest adding a bit of information on the concept of using histidine kinase inhibitors as a potential control strategy. I included two sentences from the draft (in italics) where I think that the explanation should be added:
Histidine kinases inhibitors are widely employed as agents in drug design and development. Inhibition of bacterial virulence and pathogenicity was demonstrated previously using HKs inhibitors, by changing the expression of virulence factors and the ability of bacteria to adapt to the host environment. Before efforts to design kinase targets in P. brasiliense, it is necessary to first compile all histidine kinases in P. brasiliense."
- Response: We appreciate this valuable suggestion. We have added the following information to the Introduction section to provide a clearer understanding of the concept:

"Histidine kinase inhibitors are widely employed as agents in drug design and development. Inhibition of bacterial virulence and pathogenicity was demonstrated previously using HK inhibitors, altering the expression of virulence factors and the bacteria's ability to adapt to the host environment. This approach offers a promising strategy to control bacterial infections by targeting key regulatory pathways."

Comment: "I also suggest to add a reference or two that are relevant to the concept of HKs inhibition as a tool to reduce virulence and infection."
- Response: We have added the following references to support the concept of histidine kinase inhibition:
  - Bem AE, et al., 2015
  - Espinasse A, et al., 2023
Comment: "In the Schematic representation of histidine kinase presented as Figure 1: The letter A in the scheme doesn’t stand for anything in the legend. Shouldn't it be replaced with (D)? Moreover, in the description the phosphate is transferred to RR receiver, while in reality it is transferred to the effector (A). Did I misunderstand it or it should be clarified?"
- Response: Thank you for pointing out these discrepancies. We have revised the legend of Figure 1 to replace the letter "A" with "D" to maintain consistency. Additionally, we clarified the description to accurately reflect the phosphate transfer process: "The phosphate group is transferred from the histidine kinase to the response regulator (RR), which then affects the effector."
Comment: "Table: Genes related to Histidine kinase characteristics in the genome of Pectobacterium brasiliense strain BD163. I suggest changing it to: Genes or putative genes related to histidine kinase….etc."
- Response: We agree with the suggestion. The table's title has been changed from "Genes” to Putative Genes Related to Histidine Kinase Characteristics in the Genome of Pectobacterium brasiliense Strain BD163."

Revised Manuscript: We have submitted a clean version of the manuscript without comments or tracked changes, per your requirements. Additionally, we have uploaded a version with yellow highlights to 'Track Changes' for easy identification of the revisions made.

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Competing Interests

The authors declare that there are no competing interests.

Alongside their report, reviewers assign a status to the article:

Approved - the paper is scientifically sound in its current form and only minor, if any, improvements are suggested

Approved with reservations - A number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.

Not approved - fundamental flaws in the paper seriously undermine the findings and conclusions

[1] Bem AE, Velikova N, Pellicer MT, et al.: Bacterial histidine kinases as novel antibacterial drug targets. ACS Chem. Biol. 2015; 10(1): 213–224. Publisher Full Text

[2] Catlett NL, Yoder OC, Turgeon BG: Whole-Genome Analysis of Two-Component Signal Transduction Genes in Fungal Pathogens. Eukaryot. Cell. 2003; 2(6): 1151–1161. PubMed Abstract | Publisher Full Text | Free Full Text

[3] Espinasse A, Goswami M, Yang J, et al.: Targeting multidrug resistant Staphylococcus infections with bacterial histidine kinase inhibitors. Chem. Sci. 2023; 14(19): 5028–5037. PubMed Abstract | Publisher Full Text | Free Full Text

[4] Li N-P, Tang W-Q, Lee S, et al.: First Report of Pectobacterium carotovorum and Pectobacterium brasiliense Causing Bacterial Soft Rot of Bok Choy in Taiwan. Plant Dis. 2023. PubMed Abstract | Publisher Full Text

[5] Park K-T, Hong S-M, Back C-G, et al.: First Report of Pectobacterium brasiliense Causing Soft Rot on Graft Cactus in Korea. Res. Plant Dis. 2022; 28(3): 172–178. Publisher Full Text

[6] Rauwane ME, Mchunu NP, Pierneef R, et al.: Draft Genome Sequence of Pectobacterium brasiliense Isolated from Potato in South Africa. Microbiol. Resour. Announc. 2023; 12(4): e0076322. PubMed Abstract | Publisher Full Text | Free Full Text

[7] Song Z, Yang C, Zeng R, et al.: First Report of Pectobacterium brasiliense Causing Soft Rot on Conophytum luiseae in China. Plant Dis. 2023; 107(1): 211. Publisher Full Text

A compilation of histidine kinase genes in the genome of a tissue macerating Pectobacterium brasiliense isolated from potato in South Africa

Abstract

Background

Methods

Conclusions

Keywords

Revised Amendments from Version 1

Introduction

Figure 1. Schematic representation of histidine kinase function of phosphorelay signalling (modified from Catlett et al. (2003).

Methods

Table 1. Putative genes related to Histidine kinase characteristics in the genome of Pectobacterium brasiliense strain BD163.

Dataset validation

Data availability

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