Genome-Wide Computational Prediction and Analysis of Noncoding RNAs in Oleidesulfovibrio alaskensis G20
Round 1
Reviewer 1 Report
Comments and Suggestions for AuthorsGenome Wide Computational Prediction and Analysis of Noncoding RNAs in 2 Oleidesulfovibrio alaskensis G20
Ram Nageena Singh and Rajesh K. Sani
General comments.
The authors present a genomic analysis of Oleidesulfovibrio alaskensis G20 (OA G20) using three putatively different approaches to identify noncoding RNAs (ncRNAs) that have regulatory roles in cellular metabolism. They are particularly interested in the regulation of biofilm formation in OA G20. The identified ncRNAs are presented in the results section where the authors enumerate all identified ncRNAs from each method. In the discussion the authors again list the identified ncRNAs that are probably, based on sequence analysis, regulatory elements.
Regulatory small RNAs are certainly an interesting topic and focusing on an economically important sulfate reducing bug like OA G20 is logical and might be of interest to the field. There are, however, some confusing aspects of the study. The authors make the claim that they are using three different approaches to screening the OA G20 genome. In the first approach the authors download and analyze the genome of NC_007519.1 using the online search available through the Rfam server. In the second method the authors select the genome of OA G20 (CP000112.1) from the Rfam server and the ncRNAs previously identified by Rfam were used for "further" analysis. This could be confusing to the reader inasmuch as NC_007519.1 and CP000112.1 appear to be identical. Moreover why these approaches would yield different results is not clear and why the authors selected these two apparently identical methods is not made clear. Table 1, in which the tools used for screening are identified, indicate that the first method includes cmsscan and infernal while the second method does not. Moreover there was a substantial difference in the number of ncRNAs detected, 34 versus 93 for the first and second methods respectively. Why is there such a substantial difference in these two methods given that the genomes are the same and the Rfam server is used in both cases? It would appear that all the hard work has already been done by Rfam and that the first method provided little in the way of additional data. There is not a clear statement in the text regarding how many ncRNAs were detected using their third approach using Proksee but reviewing supplemental Table 2 suggests that the third approach was not as sensitive as approaches 1 and 2. In their analysis the authors go through all the ncRNA riboswitches that were detected in each approach, hence there is a considerable amount of repetition in the results section. A more logical approach would be to quantify the number of riboswitches using each method of detection and then systematically describe those ncRNA riboswitches common to all 3 or to two approaches and those that are unique to a single detection method. There was no critical discussion on the possible reasons for the differences seen in the three difference approaches and which the authors feel is preferred. Why eukaryotic and archaeal rRNAs were found in the first method but not the second or third methods is mysterious. In addition to the repetition found in the results section, the discussion is too long. Their interest is in the detection of riboswitches in OA G20 and how these regulatory elements might impact biofilms. It would be helpful to the reader if the authors clearly identified riboswitches that they could logically posit had a role in biofilms.
There are also a considerable number of awkward sentences, incomplete sentences, missing articles, incorrect tense and confounding syntax. I am sure that I have not detected all of the grammatical problems. The paper should be carefully re-proofed before resubmission. Reorganizing and reducing repetition would considerably enhance the manuscript.
Specific comments.
L17 Incomplete sentence
L33-34 This sentence is a bit confusing. Needs to be recast
L41 "stochastic variations" Needs a better description. Do you mean variations in abundance?
L76 Sentence not clear. Needs revising.
L103-104 Poorly phrased.
L120 "splitfasta" Reference needed
L175. Why do you find eukaryotic and archaeal rRNAs? Please explain presence of these rRNAs.
L192 Re. SAM riboswitches, reference?
L193-194 Sentence should be revised.
L196-197 Remove italics.
L198 Change to "applying the second approach"
L219 enrichment? Be more concise. Eg. This approach resulted in the identification of more ncRNAs such as FMN riboswitch, c-di-GMP-I riboswitch, P10, STnc490, sX4, 6S and Bacterial small SRP than the first approach.
L221. Again, I would not consider this an enrichment, it would appear to be a refined analysis leading to more sensitivity in identification.
Table 3. I note the complimentary tables in the supplemental but some type of summary table in whch the reader can easily compare the identifications common to all three techniques as well as those that are unique to a method.
L213 The number of riboswitches identified was the same as in the second approach.
L236-245 Should this detail be here or in the discussion? I note that details for other RNAs appear in the discussion.
L332-343 The section that discusses the proposed secondary structures of the RNAs is quite tedious. If the authors feel that this section is absolutely necessary then OK. However I urge the authors to somehow condense or provide a better synthesis to avoid the tedium that could be conveyed admirably by figures.
L350-360 Much of this is a repeat of the intro.
L361 This is not clear. Should be recast. UTR has not been defined yet.
L388 of the gene metE which encodes for...
L389 and is involved in...
L362-363 Poorly structured sentence
L370-374 Importantly, how do you posit these TPP riboswitches integrate into the metabolism of OA G20. Be specific here, if thiamine phosphate binds to the TPP riboswitch, what are the consequences regarding expression.
L397 D. haf Font size
L388-392 Similar to my comment on the TPP switch, how do you perceive these cobalamine switches regulating metabolism in OA G20?
L427. Be concise. "Only one SAM-riboswitch was identified in the genome of OA G20...""
L428-430 Poorly structured sentence. Needs to be recast.
L471-475 This is of interest and requires somewhat more explanation. You note that there is only one c-di-GMP-I riboswitch in OA G20 yet there are 13 copies of norR genes. How do you perceive this regulatory scheme? What is the genome positions of the 13 copies?
L529-531 This sentence is particularly confusing. Requires recasting.
L519-520 The lead up to this sentence could be shortened considerably given the uninformative conclusion.
L507-508 rather vague
L586-589 Awkward sentence. Needs to be recast.
Comments on the Quality of English LanguageSee above
Author Response
Thanks for the review and critical suggestion of our manuscript. We have revised the manuscript as per the suggestions to improve it.
Pls see the attachment.
Author Response File: 
Author Response.pdf
Reviewer 2 Report
Comments and Suggestions for AuthorsIn this study, the authors identify ncRNAs in the genome of a model SRB, Oleidesulfovibrio alaskensis G20 (OA G20), which could play key roles in the regulation of metabolic pathways and transport etc. The manuscript was acceptable after revision. The major weak points are that conventional prediction and analysis methods were used and the novelty was not obvious. The specific comments are as follows:
(1) The genome location of all the ncRNAs discussed in section 4 are better given.
(2) In the introduction section (lines 106-107), the aim of this study was to identify the ncRNAs related with biofilm formation. While the ncRNAs investigated were not limited to biofilm formation. Actually, the mechanism of biofilm formation as well as its regulation were not clear enough.
(3) There are many type errors, uneven font styles and sizes etc.
Comments on the Quality of English LanguageThe English was acceptable.
Author Response
Please see the attachment.
Author Response File: Author Response.pdf
Round 2
Reviewer 1 Report
Comments and Suggestions for AuthorsThe authors have addressed all of my comments from the review. From my perspective, the paper is ready for publication.
