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Comparison of transcriptional profiles of Treponema pallidum during experimental infection of rabbits and in vitro culture: Highly similar, yet different

De Lay, Bridget D. ; Cameron, Todd A. ; De Lay, Nicholas R. ; [et al.]

Public Library of Science (PLoS) ; 2021

In: PLOS Pathogens Vol. 17, No. 9 ( 2021-9-27), p. e1009949-

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In: PLOS Pathogens, Public Library of Science (PLoS), Vol. 17, No. 9 ( 2021-9-27), p. e1009949-

Abstract: Treponema pallidum ssp. pallidum , the causative agent of syphilis, can now be cultured continuously in vitro utilizing a tissue culture system, and the multiplication rates are similar to those obtained in experimental infection of rabbits. In this study, the RNA transcript profiles of the T . pallidum Nichols during in vitro culture and rabbit infection were compared to examine whether gene expression patterns differed in these two environments. To this end, RNA preparations were converted to cDNA and subjected to RNA-seq using high throughput Illumina sequencing; reverse transcriptase quantitative PCR was also performed on selected genes for validation of results. The transcript profiles in the in vivo and in vitro environments were remarkably similar, exhibiting a high degree of concordance overall. However, transcript levels of 94 genes (9%) out of the 1,063 predicted genes in the T . pallidum genome were significantly different during rabbit infection versus in vitro culture, varying by up to 8-fold in the two environments. Genes that exhibited significantly higher transcript levels during rabbit infection included those encoding multiple ribosomal proteins, several prominent membrane proteins, glycolysis-associated enzymes, replication initiator DnaA, rubredoxin, thioredoxin, two putative regulatory proteins, and proteins associated with solute transport. In vitro cultured T . pallidum had higher transcript levels of DNA repair proteins, cofactor synthesis enzymes, and several hypothetical proteins. The overall concordance of the transcript profiles may indicate that these environments are highly similar in terms of their effects on T . pallidum physiology and growth, and may also reflect a relatively low level of transcriptional regulation in this reduced genome organism.

Type of Medium: Online Resource

ISSN: 1553-7374

URL: Article

DOI: 10.1371/journal.ppat.1009949

DOI: 10.1371/journal.ppat.1009949.g001

DOI: 10.1371/journal.ppat.1009949.g002

DOI: 10.1371/journal.ppat.1009949.g003

DOI: 10.1371/journal.ppat.1009949.g004

DOI: 10.1371/journal.ppat.1009949.g005

DOI: 10.1371/journal.ppat.1009949.g006

DOI: 10.1371/journal.ppat.1009949.t001

DOI: 10.1371/journal.ppat.1009949.t002

DOI: 10.1371/journal.ppat.1009949.t003

DOI: 10.1371/journal.ppat.1009949.t004

DOI: 10.1371/journal.ppat.1009949.t005

DOI: 10.1371/journal.ppat.1009949.s001

DOI: 10.1371/journal.ppat.1009949.s002

DOI: 10.1371/journal.ppat.1009949.s003

Language: English

Publisher: Public Library of Science (PLoS)

Publication Date: 2021

detail.hit.zdb_id: 2205412-1

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The Phosphorolytic Exoribonucleases Polynucleotide Phosphorylase and RNase PH Stabilize sRNAs and Facilitate Regulation of Their mRNA Targets

Cameron, Todd A. ; De Lay, Nicholas R. ; Gourse, R. L.

American Society for Microbiology ; 2016

In: Journal of Bacteriology Vol. 198, No. 24 ( 2016-12-15), p. 3309-3317

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In: Journal of Bacteriology, American Society for Microbiology, Vol. 198, No. 24 ( 2016-12-15), p. 3309-3317

Abstract: Gene regulation by base pairing between small noncoding RNAs (sRNAs) and their mRNA targets is an important mechanism that allows bacteria to maintain homeostasis and respond to dynamic environments. In Gram-negative bacteria, sRNA pairing and regulation are mediated by several RNA-binding proteins, including the sRNA chaperone Hfq and polynucleotide phosphorylase (PNPase). PNPase and its homolog RNase PH together represent the two 3′ to 5′ phosphorolytic exoribonucleases found in Escherichia coli ; however, the role of RNase PH in sRNA regulation has not yet been explored and reported. Here, we have examined in detail how PNPase and RNase PH interact to support sRNA stability, activity, and base pairing in exponential and stationary growth conditions. Our results indicate that these proteins facilitate the stability and regulatory function of the sRNAs RyhB, CyaR, and MicA during exponential growth. PNPase further appears to contribute to pairing between RyhB and its mRNA targets. During stationary growth, each sRNA responded differently to the absence or presence of PNPase and RNase PH. Finally, our results suggest that PNPase and RNase PH stabilize only Hfq-bound sRNAs. Taken together, these results confirm and extend previous findings that PNPase participates in sRNA regulation and reveal that RNase PH serves a similar, albeit more limited, role as well. These proteins may, therefore, act to protect sRNAs from spurious degradation while also facilitating regulatory pairing with their targets. IMPORTANCE In many bacteria, Hfq-dependent base-pairing sRNAs facilitate rapid changes in gene expression that are critical for maintaining homeostasis and responding to stress and environmental changes. While a role for Hfq in this process was identified more than 2 decades ago, the identity and function of the other proteins required for Hfq-dependent regulation by sRNAs have not been resolved. Here, we demonstrate that PNPase and RNase PH, the two phosphorolytic RNases in E. coli , stabilize sRNAs against premature degradation and, in the case of PNPase, also accelerate regulation by sRNA-mRNA pairings for certain sRNAs. These findings are the first to demonstrate that RNase PH influences and supports sRNA regulation and suggest shared and distinct roles for these phosphorolytic RNases in this process.

Type of Medium: Online Resource

ISSN: 0021-9193 , 1098-5530

URL: Article

DOI: 10.1128/JB.00624-16

Language: English

Publisher: American Society for Microbiology

Publication Date: 2016

detail.hit.zdb_id: 1481988-0

SSG: 12

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S1 Domain RNA-Binding Protein CvfD Is a New Posttranscriptional Regulator That Mediates Cold Sensitivity, Phosphate Transport, and Virulence in Streptococcus pneumoniae D39

Sinha, Dhriti ; Zheng, Jiaqi J. ; Tsui, Ho-Ching Tiffany ; [et al.]

American Society for Microbiology ; 2020

In: Journal of Bacteriology Vol. 202, No. 18 ( 2020-08-25)

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In: Journal of Bacteriology, American Society for Microbiology, Vol. 202, No. 18 ( 2020-08-25)

Abstract: Posttranscriptional gene regulation often involves RNA-binding proteins that modulate mRNA translation and/or stability either directly through protein-RNA interactions or indirectly by facilitating the annealing of small regulatory RNAs (sRNAs). The human pathogen Streptococcus pneumoniae D39 (pneumococcus) does not encode homologs to RNA-binding proteins known to be involved in promoting sRNA stability and function, such as Hfq or ProQ, even though it contains genes for at least 112 sRNAs. However, the pneumococcal genome contains genes for other RNA-binding proteins, including at least six S1 domain proteins: ribosomal protein S1 ( rpsA ), polynucleotide phosphorylase ( pnpA ), RNase R ( rnr ), and three proteins with unknown functions. Here, we characterize the function of one of these conserved, yet uncharacterized, S1 domain proteins, SPD_1366, which we have renamed CvfD ( c onserved v irulence f actor D ), since loss of the protein results in attenuation of virulence in a murine pneumonia model. We report that deletion of cvfD impacts the expression of 144 transcripts, including the pst1 operon, encoding phosphate transport system 1 in S. pneumoniae . We further show that CvfD posttranscriptionally regulates the PhoU2 master regulator of the pneumococcal dual-phosphate transport system by binding phoU2 mRNA and impacting PhoU2 translation. CvfD not only controls expression of phosphate transporter genes but also functions as a pleiotropic regulator that impacts cold sensitivity and the expression of sRNAs and genes involved in diverse cellular functions, including manganese uptake and zinc efflux. Together, our data show that CvfD exerts a broad impact on pneumococcal physiology and virulence, partly by posttranscriptional gene regulation. IMPORTANCE Recent advances have led to the identification of numerous sRNAs in the major human respiratory pathogen S. pneumoniae . However, little is known about the functions of most sRNAs or RNA-binding proteins involved in RNA biology in pneumococcus. In this paper, we characterize the phenotypes and one target of the S1 domain RNA-binding protein CvfD, a homolog of general stress protein 13 identified, but not extensively characterized, in other Firmicutes species. Pneumococcal CvfD is a broadly pleiotropic regulator, whose absence results in misregulation of divalent cation homeostasis, reduced translation of the PhoU2 master regulator of phosphate uptake, altered metabolism and sRNA amounts, cold sensitivity, and attenuation of virulence. These findings underscore the critical roles of RNA biology in pneumococcal physiology and virulence.

Type of Medium: Online Resource

ISSN: 0021-9193 , 1098-5530

URL: Article

DOI: 10.1128/JB.00245-20

Language: English

Publisher: American Society for Microbiology

Publication Date: 2020

detail.hit.zdb_id: 1481988-0

SSG: 12

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Polynucleotide phosphorylase: Not merely an RNase but a pivotal post-transcriptional regulator

Cameron, Todd A. ; Matz, Lisa M. ; De Lay, Nicholas R. ; [et al.]

Public Library of Science (PLoS) ; 2018

In: PLOS Genetics Vol. 14, No. 10 ( 2018-10-11), p. e1007654-

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In: PLOS Genetics, Public Library of Science (PLoS), Vol. 14, No. 10 ( 2018-10-11), p. e1007654-

Type of Medium: Online Resource

ISSN: 1553-7404

URL: Article

DOI: 10.1371/journal.pgen.1007654

DOI: 10.1371/journal.pgen.1007654.g001

DOI: 10.1371/journal.pgen.1007654.g002

DOI: 10.1371/journal.pgen.1007654.t001

Language: English

Publisher: Public Library of Science (PLoS)

Publication Date: 2018

detail.hit.zdb_id: 2186725-2

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A cooperative PNPase-Hfq-RNA carrier complex facilitates bacterial riboregulation

Dendooven, Tom ; Sinha, Dhriti ; Roeselová, Alzbeta ; [et al.]

Elsevier BV ; 2021

In: Molecular Cell Vol. 81, No. 14 ( 2021-07), p. 2901-2913.e5

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In: Molecular Cell, Elsevier BV, Vol. 81, No. 14 ( 2021-07), p. 2901-2913.e5

Type of Medium: Online Resource

ISSN: 1097-2765

URL: Article

DOI: 10.1016/j.molcel.2021.05.032

Language: English

Publisher: Elsevier BV

Publication Date: 2021

detail.hit.zdb_id: 2001948-8

SSG: 12

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In vivo functional analyses of the type II acyl carrier proteins of fatty acid biosynthesis. VOLUME 282 (2007) PAGES 20319-20328

De Lay, Nicholas R. ; Cronan, John E.

Elsevier BV ; 2009

In: Journal of Biological Chemistry Vol. 284, No. 7 ( 2009-02), p. 4748-

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In: Journal of Biological Chemistry, Elsevier BV, Vol. 284, No. 7 ( 2009-02), p. 4748-

Type of Medium: Online Resource

ISSN: 0021-9258

URL: Article

DOI: 10.1016/S0021-9258(20)71077-X

Language: English

Publisher: Elsevier BV

Publication Date: 2009

detail.hit.zdb_id: 2141744-1

detail.hit.zdb_id: 1474604-9

SSG: 12

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Target recognition by RNase E RNA-binding domain AR2 drives sRNA decay in the absence of PNPase

Sinha, Dhriti ; De Lay, Nicholas R.

Proceedings of the National Academy of Sciences ; 2022

In: Proceedings of the National Academy of Sciences Vol. 119, No. 48 ( 2022-11-29)

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In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 119, No. 48 ( 2022-11-29)

Abstract: The C-terminal domain (CTD) of the major endoribonuclease RNase E not only serves as a scaffold for the central RNA decay machinery in gram-negative bacteria but also mediates coupled degradation of small regulatory RNAs (sRNAs) and their cognate target transcripts following RNA chaperone Hfq–facilitated sRNA–mRNA base pairing. Despite the crucial role of RNase E CTD in sRNA-dependent gene regulation, the contribution of particular residues within this domain in recruiting sRNAs and mRNAs upon base pairing remains unknown. We have previously shown that in Escherichia coli , the highly conserved 3′-5′-exoribonuclease polynucleotide phosphorylase (PNPase) paradoxically stabilizes sRNAs by limiting access of RNase E to Hfq-bound sRNAs and by degrading target mRNA fragments that would otherwise promote sRNA decay. Here, we report that in the absence of PNPase, the RNA-binding region AR2 in the CTD is required for RNase E to initiate degradation of the Hfq-dependent sRNAs CyaR and RyhB. Additionally, we show that introducing mutations in either hfq that disrupts target mRNA binding to Hfq or the AR2 coding region of rne impairs RNase E binding to sRNAs. Altogether, our data support a model where sRNAs are recruited via bound mRNA targets to RNase E by its AR2 domain after Hfq catalyzes sRNA–mRNA pairing. These results also support our conclusion that in a PNPase-deficient strain, more rapid decay of sRNAs occurs due to accelerated pairing with mRNA targets as a consequence of their accumulation. Our findings provide insights into the mechanisms by which sRNAs and mRNAs are regulated by RNase E.

Type of Medium: Online Resource

ISSN: 0027-8424 , 1091-6490

URL: Article

DOI: 10.1073/pnas.2208022119

RVK:

TA 1000

RVK:

WA 15000

Language: English

Publisher: Proceedings of the National Academy of Sciences

Publication Date: 2022

detail.hit.zdb_id: 209104-5

detail.hit.zdb_id: 1461794-8

SSG: 11

SSG: 12

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Gene-Specific Random Mutagenesis of Escherichia coli In Vivo: Isolation of Temperature-Sensitive Mutations in the Acyl Carrier Protein of Fatty Acid Synthesis

De Lay, Nicholas R. ; Cronan, John E.

American Society for Microbiology ; 2006

In: Journal of Bacteriology Vol. 188, No. 1 ( 2006-01), p. 287-296

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In: Journal of Bacteriology, American Society for Microbiology, Vol. 188, No. 1 ( 2006-01), p. 287-296

Abstract: Acyl carrier proteins (ACPs) are very small acidic proteins that play a key role in fatty acid and complex lipid synthesis. Moreover, recent data indicate that the acyl carrier protein of Escherichia coli has a large protein interaction network that extends beyond lipid synthesis. Despite extensive efforts over many years, no temperature-sensitive mutants with mutations in the structural gene ( acpP ) that encodes ACP have been isolated. We report the isolation of three such mutants by a new approach that utilizes error-prone PCR mutagenesis, overlap extension PCR, and phage λ Red-mediated homologous recombination and that should be generally applicable. These mutants plus other experiments demonstrate that ACP function is essential for the growth of E. coli . Each of the mutants was efficiently modified with the phosphopantetheinyl moiety essential for the function of ACP in lipid synthesis, and thus lack of function at the nonpermissive temperature cannot be attributed to a lack of prosthetic group attachment. All of the mutant proteins were largely stable at the nonpermissive temperature except the A68T/N73D mutant protein. Fatty acid synthesis in strains that carried the D38V or A68T/N73D mutations was inhibited upon a shift to the nonpermissive temperature and in the latter case declined to a small percentage of the rate of the wild-type strain.

Type of Medium: Online Resource

ISSN: 0021-9193 , 1098-5530

URL: Article

DOI: 10.1128/JB.188.1.287-296.2006

Language: English

Publisher: American Society for Microbiology

Publication Date: 2006

detail.hit.zdb_id: 1481988-0

SSG: 12

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A genome rearrangement has orphaned the Escherichia coli K-12 AcpT phosphopantetheinyl transferase from its cognate Escherichia coli O157:H7 substrates : E. coli AcpT

De Lay, Nicholas R. ; Cronan, John E.

Wiley ; 2006

In: Molecular Microbiology Vol. 61, No. 1 ( 2006-07), p. 232-242

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In: Molecular Microbiology, Wiley, Vol. 61, No. 1 ( 2006-07), p. 232-242

Type of Medium: Online Resource

ISSN: 0950-382X

URL: Issue

URL: Article

DOI: 10.1111/mmi.2006.61.issue-1

DOI: 10.1111/j.1365-2958.2006.05222.x

Language: English

Publisher: Wiley

Publication Date: 2006

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In Vivo Functional Analyses of the Type II Acyl Carrier Proteins of Fatty Acid Biosynthesis

De Lay, Nicholas R. ; Cronan, John E.

Elsevier BV ; 2007

In: Journal of Biological Chemistry Vol. 282, No. 28 ( 2007-07), p. 20319-20328

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In: Journal of Biological Chemistry, Elsevier BV, Vol. 282, No. 28 ( 2007-07), p. 20319-20328

Type of Medium: Online Resource

ISSN: 0021-9258

URL: Article

DOI: 10.1074/jbc.M703789200

Language: English

Publisher: Elsevier BV

Publication Date: 2007

detail.hit.zdb_id: 2141744-1

detail.hit.zdb_id: 1474604-9

SSG: 12

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