1
|
Drabinska J, Steczkiewicz K, Kujawa M, Kraszewska E. Searching for Biological Function of the Mysterious PA2504 Protein from Pseudomonas aeruginosa. Int J Mol Sci 2021; 22:ijms22189833. [PMID: 34575996 PMCID: PMC8466066 DOI: 10.3390/ijms22189833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 09/08/2021] [Accepted: 09/09/2021] [Indexed: 11/16/2022] Open
Abstract
For nearly half of the proteome of an important pathogen, Pseudomonas aeruginosa, the function has not yet been recognised. Here, we characterise one such mysterious protein PA2504, originally isolated by us as a sole partner of the RppH RNA hydrolase involved in transcription regulation of multiple genes. This study aims at elucidating details of PA2504 function and discussing its implications for bacterial biology. We show that PA2504 forms homodimers and is evenly distributed in the cytoplasm of bacterial cells. Molecular modelling identified the presence of a Tudor-like domain in PA2504. Transcriptomic analysis of a ΔPA2504 mutant showed that 42 transcripts, mainly coding for proteins involved in sulphur metabolism, were affected by the lack of PA2504. In vivo crosslinking of cellular proteins in the exponential and stationary phase of growth revealed several polypeptides that bound to PA2504 exclusively in the stationary phase. Mass spectrometry analysis identified them as the 30S ribosomal protein S4, the translation elongation factor TufA, and the global response regulator GacA. These results indicate that PA2504 may function as a tether for several important cellular factors.
Collapse
|
2
|
Forrest S, Welch M. Arming the troops: Post-translational modification of extracellular bacterial proteins. Sci Prog 2020; 103:36850420964317. [PMID: 33148128 PMCID: PMC10450907 DOI: 10.1177/0036850420964317] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Protein secretion is almost universally employed by bacteria. Some proteins are retained on the cell surface, whereas others are released into the extracellular milieu, often playing a key role in virulence. In this review, we discuss the diverse types and potential functions of post-translational modifications (PTMs) occurring to extracellular bacterial proteins.
Collapse
Affiliation(s)
- Suzanne Forrest
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Martin Welch
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| |
Collapse
|
3
|
White JT, Cato T, Deramchi N, Gabunilas J, Roy KR, Wang C, Chanfreau GF, Clarke SG. Protein Methylation and Translation: Role of Lysine Modification on the Function of Yeast Elongation Factor 1A. Biochemistry 2019; 58:4997-5010. [PMID: 31738538 DOI: 10.1021/acs.biochem.9b00818] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To date, 12 protein lysine methyltransferases that modify translational elongation factors and ribosomal proteins (Efm1-7 and Rkm 1-5) have been identified in the yeast Saccharomyces cerevisiae. Of these 12, five (Efm1 and Efm4-7) appear to be specific to elongation factor 1A (EF1A), the protein responsible for bringing aminoacyl-tRNAs to the ribosome. In S. cerevisiae, the functional implications of lysine methylation in translation are mostly unknown. In this work, we assessed the physiological impact of disrupting EF1A methylation in a strain where four of the most conserved methylated lysine sites are mutated to arginine residues and in strains lacking either four or five of the Efm lysine methyltransferases specific to EF1A. We found that loss of EF1A methylation was not lethal but resulted in reduced growth rates, particularly under caffeine and rapamycin stress conditions, suggesting EF1A interacts with the TORC1 pathway, as well as altered sensitivities to ribosomal inhibitors. We also detected reduced cellular levels of the EF1A protein, which surprisingly was not reflected in its stability in vivo. We present evidence that these Efm methyltransferases appear to be largely devoted to the modification of EF1A, finding no evidence of the methylation of other substrates in the yeast cell. This work starts to illuminate why one protein can need five different methyltransferases for its functions and highlights the resilience of yeast to alterations in their posttranslational modifications.
Collapse
Affiliation(s)
- Jonelle T White
- Department of Chemistry and Biochemistry and Molecular Biology Institute , University of California, Los Angeles , Los Angeles , California 90095 , United States
| | - Tieranee Cato
- Department of Chemistry and Biochemistry and Molecular Biology Institute , University of California, Los Angeles , Los Angeles , California 90095 , United States
| | - Neil Deramchi
- Department of Chemistry and Biochemistry and Molecular Biology Institute , University of California, Los Angeles , Los Angeles , California 90095 , United States
| | - Jason Gabunilas
- Department of Chemistry and Biochemistry and Molecular Biology Institute , University of California, Los Angeles , Los Angeles , California 90095 , United States
| | - Kevin R Roy
- Department of Chemistry and Biochemistry and Molecular Biology Institute , University of California, Los Angeles , Los Angeles , California 90095 , United States
| | - Charles Wang
- Department of Chemistry and Biochemistry and Molecular Biology Institute , University of California, Los Angeles , Los Angeles , California 90095 , United States
| | - Guillaume F Chanfreau
- Department of Chemistry and Biochemistry and Molecular Biology Institute , University of California, Los Angeles , Los Angeles , California 90095 , United States
| | - Steven G Clarke
- Department of Chemistry and Biochemistry and Molecular Biology Institute , University of California, Los Angeles , Los Angeles , California 90095 , United States
| |
Collapse
|
4
|
Kuiper EG, Dey D, LaMore PA, Owings JP, Prezioso SM, Goldberg JB, Conn GL. Substrate recognition by the Pseudomonas aeruginosa EF-Tu-modifying methyltransferase EftM. J Biol Chem 2019; 294:20109-20121. [PMID: 31753919 DOI: 10.1074/jbc.ra119.011213] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 11/20/2019] [Indexed: 01/09/2023] Open
Abstract
The opportunistic bacterial pathogen Pseudomonas aeruginosa is a leading cause of serious infections in individuals with cystic fibrosis, compromised immune systems, or severe burns. P. aeruginosa adhesion to host epithelial cells is enhanced by surface-exposed translation elongation factor EF-Tu carrying a Lys-5 trimethylation, incorporated by the methyltransferase EftM. Thus, the EF-Tu modification by EftM may represent a target to prevent P. aeruginosa infections in vulnerable individuals. Here, we extend our understanding of EftM activity by defining the molecular mechanism by which it recognizes EF-Tu. Acting on the observation that EftM can bind to EF-Tu lacking its N-terminal peptide (encompassing the Lys-5 target site), we generated an EftM homology model and used it in protein/protein docking studies to predict EftM/EF-Tu interactions. Using site-directed mutagenesis of residues in both proteins, coupled with binding and methyltransferase activity assays, we experimentally validated the predicted protein/protein interface. We also show that EftM cannot methylate the isolated N-terminal EF-Tu peptide and that binding-induced conformational changes in EftM are likely needed to enable placement of the first 5-6 amino acids of EF-Tu into a conserved peptide-binding channel in EftM. In this channel, a group of residues that are highly conserved in EftM proteins position the N-terminal sequence to facilitate Lys-5 modification. Our findings reveal that EftM employs molecular strategies for substrate recognition common among both class I (Rossmann fold) and class II (SET domain) methyltransferases and pave the way for studies seeking a deeper understanding of EftM's mechanism of action on EF-Tu.
Collapse
Affiliation(s)
- Emily G Kuiper
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322.,Graduate Program in Biochemistry, Cell and Developmental Biology (BCDB), Graduate Division of Biological and Biomedical Sciences (GDBBS), Emory University, Atlanta, Georgia 30322
| | - Debayan Dey
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322
| | - Paige A LaMore
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322
| | - Joshua P Owings
- Department of Pediatrics, Division of Pulmonology, Allergy/Immunology, Cystic Fibrosis and Sleep, and Emory Children's Center for Cystic Fibrosis Research, Emory University and Children's Healthcare of Atlanta, Atlanta, Georgia 30322
| | - Samantha M Prezioso
- Department of Pediatrics, Division of Pulmonology, Allergy/Immunology, Cystic Fibrosis and Sleep, and Emory Children's Center for Cystic Fibrosis Research, Emory University and Children's Healthcare of Atlanta, Atlanta, Georgia 30322.,Graduate Program in Microbiology and Molecular Genetics (MMG), Graduate Division of Biological and Biomedical Sciences (GDBBS), Emory University, Atlanta, Georgia 30322
| | - Joanna B Goldberg
- Department of Pediatrics, Division of Pulmonology, Allergy/Immunology, Cystic Fibrosis and Sleep, and Emory Children's Center for Cystic Fibrosis Research, Emory University and Children's Healthcare of Atlanta, Atlanta, Georgia 30322.,Graduate Program in Microbiology and Molecular Genetics (MMG), Graduate Division of Biological and Biomedical Sciences (GDBBS), Emory University, Atlanta, Georgia 30322.,Emory Antibiotic Resistance Center (ARC), Emory University School of Medicine, Atlanta, Georgia 30322
| | - Graeme L Conn
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322 .,Graduate Program in Biochemistry, Cell and Developmental Biology (BCDB), Graduate Division of Biological and Biomedical Sciences (GDBBS), Emory University, Atlanta, Georgia 30322.,Emory Antibiotic Resistance Center (ARC), Emory University School of Medicine, Atlanta, Georgia 30322
| |
Collapse
|