A family of small intrinsically disordered proteins involved in flagellum-dependent motility in salmonella enterica

Tamiko Oguri, Youjeong Kwon, Jerry K.K. Woo, Gerd Prehna, Hyun Lee, Miaoran Ning, Kyoung Jae Won, Jiyoung Lee, Sally Mei, Yixin Shi, Hyunyoung Jeong, Hyunwoo Lee

Research output: Contribution to journalArticle

Abstract

By screening a collection of Salmonella mutants deleted for genes encoding small proteins of 60 amino acids, we identified three paralogous small genes (ymdF, STM14_1829, and yciG) required for wild-type flagellum-dependent swimming and swarming motility. The ymdF, STM14_1829, and yciG genes encode small proteins of 55, 60, and 60 amino acid residues, respectively. A bioinformatics analysis predicted that these small proteins are intrinsically disordered proteins, and circular dichroism analysis of purified recombinant proteins confirmed that all three proteins are unstructured in solution. A mutant deleted for STM14_1829 showed the most severe motility defect, indicating that among the three paralogs, STM14_1829 is a key protein required for wild-type motility. We determined that relative to the wild type, the expression of the flagellin protein FliC is lower in the ΔSTM14_1829 mutant due to the downregulation of the flhDC operon encoding the FlhDC master regulator. By comparing the gene expression profiles between the wild-type and ΔSTM14_1829 strains via RNA sequencing, we found that the gene encoding the response regulator PhoP is upregulated in the ΔSTM14_1829 mutant, suggesting the indirect repression of the flhDC operon by the activated PhoP. Homologs of STM14_1829 are conserved in a wide range of bacteria, including Escherichia coli and Pseudomonas aeruginosa. We showed that the inactivation of STM14_1829 homologs in E. coli and P. aeruginosa also alters motility, suggesting that this family of small intrinsically disordered proteins may play a role in the cellular pathway(s) that affects motility. IMPORTANCE This study reports the identification of a novel family of small intrinsically disordered proteins that are conserved in a wide range of flagellated and nonflagellated bacteria. Although this study identifies the role of these small proteins in the scope of flagellum-dependent motility in Salmonella, they likely play larger roles in a more conserved cellular pathway(s) that indirectly affects flagellum expression in the case of motile bacteria. Small intrinsically disordered proteins have not been well characterized in prokaryotes, and the results of our study provide a basis for their detailed functional characterization.

Original languageEnglish (US)
Article numbere00415-18
JournalJournal of Bacteriology
Volume201
Issue number2
DOIs
StatePublished - Jan 1 2019

Fingerprint

Intrinsically Disordered Proteins
Salmonella enterica
Flagella
Proteins
Operon
Bacteria
Salmonella
Pseudomonas aeruginosa
Genes
Escherichia coli
RNA Sequence Analysis
Flagellin
Amino Acids
Circular Dichroism
Computational Biology
Transcriptome
Recombinant Proteins
Down-Regulation

Keywords

  • Flagella
  • Intrinsically disordered proteins
  • Motility
  • PhoP
  • Salmonella
  • Small proteins

ASJC Scopus subject areas

  • Microbiology
  • Molecular Biology

Cite this

A family of small intrinsically disordered proteins involved in flagellum-dependent motility in salmonella enterica. / Oguri, Tamiko; Kwon, Youjeong; Woo, Jerry K.K.; Prehna, Gerd; Lee, Hyun; Ning, Miaoran; Won, Kyoung Jae; Lee, Jiyoung; Mei, Sally; Shi, Yixin; Jeong, Hyunyoung; Lee, Hyunwoo.

In: Journal of Bacteriology, Vol. 201, No. 2, e00415-18, 01.01.2019.

Research output: Contribution to journalArticle

Oguri, T, Kwon, Y, Woo, JKK, Prehna, G, Lee, H, Ning, M, Won, KJ, Lee, J, Mei, S, Shi, Y, Jeong, H & Lee, H 2019, 'A family of small intrinsically disordered proteins involved in flagellum-dependent motility in salmonella enterica', Journal of Bacteriology, vol. 201, no. 2, e00415-18. https://doi.org/10.1128/JB.00415-18
Oguri, Tamiko ; Kwon, Youjeong ; Woo, Jerry K.K. ; Prehna, Gerd ; Lee, Hyun ; Ning, Miaoran ; Won, Kyoung Jae ; Lee, Jiyoung ; Mei, Sally ; Shi, Yixin ; Jeong, Hyunyoung ; Lee, Hyunwoo. / A family of small intrinsically disordered proteins involved in flagellum-dependent motility in salmonella enterica. In: Journal of Bacteriology. 2019 ; Vol. 201, No. 2.
@article{922243c6fead4cb3aaa37aec38cee542,
title = "A family of small intrinsically disordered proteins involved in flagellum-dependent motility in salmonella enterica",
abstract = "By screening a collection of Salmonella mutants deleted for genes encoding small proteins of 60 amino acids, we identified three paralogous small genes (ymdF, STM14_1829, and yciG) required for wild-type flagellum-dependent swimming and swarming motility. The ymdF, STM14_1829, and yciG genes encode small proteins of 55, 60, and 60 amino acid residues, respectively. A bioinformatics analysis predicted that these small proteins are intrinsically disordered proteins, and circular dichroism analysis of purified recombinant proteins confirmed that all three proteins are unstructured in solution. A mutant deleted for STM14_1829 showed the most severe motility defect, indicating that among the three paralogs, STM14_1829 is a key protein required for wild-type motility. We determined that relative to the wild type, the expression of the flagellin protein FliC is lower in the ΔSTM14_1829 mutant due to the downregulation of the flhDC operon encoding the FlhDC master regulator. By comparing the gene expression profiles between the wild-type and ΔSTM14_1829 strains via RNA sequencing, we found that the gene encoding the response regulator PhoP is upregulated in the ΔSTM14_1829 mutant, suggesting the indirect repression of the flhDC operon by the activated PhoP. Homologs of STM14_1829 are conserved in a wide range of bacteria, including Escherichia coli and Pseudomonas aeruginosa. We showed that the inactivation of STM14_1829 homologs in E. coli and P. aeruginosa also alters motility, suggesting that this family of small intrinsically disordered proteins may play a role in the cellular pathway(s) that affects motility. IMPORTANCE This study reports the identification of a novel family of small intrinsically disordered proteins that are conserved in a wide range of flagellated and nonflagellated bacteria. Although this study identifies the role of these small proteins in the scope of flagellum-dependent motility in Salmonella, they likely play larger roles in a more conserved cellular pathway(s) that indirectly affects flagellum expression in the case of motile bacteria. Small intrinsically disordered proteins have not been well characterized in prokaryotes, and the results of our study provide a basis for their detailed functional characterization.",
keywords = "Flagella, Intrinsically disordered proteins, Motility, PhoP, Salmonella, Small proteins",
author = "Tamiko Oguri and Youjeong Kwon and Woo, {Jerry K.K.} and Gerd Prehna and Hyun Lee and Miaoran Ning and Won, {Kyoung Jae} and Jiyoung Lee and Sally Mei and Yixin Shi and Hyunyoung Jeong and Hyunwoo Lee",
year = "2019",
month = "1",
day = "1",
doi = "10.1128/JB.00415-18",
language = "English (US)",
volume = "201",
journal = "Journal of Bacteriology",
issn = "0021-9193",
publisher = "American Society for Microbiology",
number = "2",

}

TY - JOUR

T1 - A family of small intrinsically disordered proteins involved in flagellum-dependent motility in salmonella enterica

AU - Oguri, Tamiko

AU - Kwon, Youjeong

AU - Woo, Jerry K.K.

AU - Prehna, Gerd

AU - Lee, Hyun

AU - Ning, Miaoran

AU - Won, Kyoung Jae

AU - Lee, Jiyoung

AU - Mei, Sally

AU - Shi, Yixin

AU - Jeong, Hyunyoung

AU - Lee, Hyunwoo

PY - 2019/1/1

Y1 - 2019/1/1

N2 - By screening a collection of Salmonella mutants deleted for genes encoding small proteins of 60 amino acids, we identified three paralogous small genes (ymdF, STM14_1829, and yciG) required for wild-type flagellum-dependent swimming and swarming motility. The ymdF, STM14_1829, and yciG genes encode small proteins of 55, 60, and 60 amino acid residues, respectively. A bioinformatics analysis predicted that these small proteins are intrinsically disordered proteins, and circular dichroism analysis of purified recombinant proteins confirmed that all three proteins are unstructured in solution. A mutant deleted for STM14_1829 showed the most severe motility defect, indicating that among the three paralogs, STM14_1829 is a key protein required for wild-type motility. We determined that relative to the wild type, the expression of the flagellin protein FliC is lower in the ΔSTM14_1829 mutant due to the downregulation of the flhDC operon encoding the FlhDC master regulator. By comparing the gene expression profiles between the wild-type and ΔSTM14_1829 strains via RNA sequencing, we found that the gene encoding the response regulator PhoP is upregulated in the ΔSTM14_1829 mutant, suggesting the indirect repression of the flhDC operon by the activated PhoP. Homologs of STM14_1829 are conserved in a wide range of bacteria, including Escherichia coli and Pseudomonas aeruginosa. We showed that the inactivation of STM14_1829 homologs in E. coli and P. aeruginosa also alters motility, suggesting that this family of small intrinsically disordered proteins may play a role in the cellular pathway(s) that affects motility. IMPORTANCE This study reports the identification of a novel family of small intrinsically disordered proteins that are conserved in a wide range of flagellated and nonflagellated bacteria. Although this study identifies the role of these small proteins in the scope of flagellum-dependent motility in Salmonella, they likely play larger roles in a more conserved cellular pathway(s) that indirectly affects flagellum expression in the case of motile bacteria. Small intrinsically disordered proteins have not been well characterized in prokaryotes, and the results of our study provide a basis for their detailed functional characterization.

AB - By screening a collection of Salmonella mutants deleted for genes encoding small proteins of 60 amino acids, we identified three paralogous small genes (ymdF, STM14_1829, and yciG) required for wild-type flagellum-dependent swimming and swarming motility. The ymdF, STM14_1829, and yciG genes encode small proteins of 55, 60, and 60 amino acid residues, respectively. A bioinformatics analysis predicted that these small proteins are intrinsically disordered proteins, and circular dichroism analysis of purified recombinant proteins confirmed that all three proteins are unstructured in solution. A mutant deleted for STM14_1829 showed the most severe motility defect, indicating that among the three paralogs, STM14_1829 is a key protein required for wild-type motility. We determined that relative to the wild type, the expression of the flagellin protein FliC is lower in the ΔSTM14_1829 mutant due to the downregulation of the flhDC operon encoding the FlhDC master regulator. By comparing the gene expression profiles between the wild-type and ΔSTM14_1829 strains via RNA sequencing, we found that the gene encoding the response regulator PhoP is upregulated in the ΔSTM14_1829 mutant, suggesting the indirect repression of the flhDC operon by the activated PhoP. Homologs of STM14_1829 are conserved in a wide range of bacteria, including Escherichia coli and Pseudomonas aeruginosa. We showed that the inactivation of STM14_1829 homologs in E. coli and P. aeruginosa also alters motility, suggesting that this family of small intrinsically disordered proteins may play a role in the cellular pathway(s) that affects motility. IMPORTANCE This study reports the identification of a novel family of small intrinsically disordered proteins that are conserved in a wide range of flagellated and nonflagellated bacteria. Although this study identifies the role of these small proteins in the scope of flagellum-dependent motility in Salmonella, they likely play larger roles in a more conserved cellular pathway(s) that indirectly affects flagellum expression in the case of motile bacteria. Small intrinsically disordered proteins have not been well characterized in prokaryotes, and the results of our study provide a basis for their detailed functional characterization.

KW - Flagella

KW - Intrinsically disordered proteins

KW - Motility

KW - PhoP

KW - Salmonella

KW - Small proteins

UR - http://www.scopus.com/inward/record.url?scp=85060178875&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85060178875&partnerID=8YFLogxK

U2 - 10.1128/JB.00415-18

DO - 10.1128/JB.00415-18

M3 - Article

VL - 201

JO - Journal of Bacteriology

JF - Journal of Bacteriology

SN - 0021-9193

IS - 2

M1 - e00415-18

ER -