1
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Lakey B, Alberge F, Donohue TJ. Insights into Alphaproteobacterial regulators of cell envelope remodeling. Curr Opin Microbiol 2024; 81:102538. [PMID: 39232444 DOI: 10.1016/j.mib.2024.102538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2024] [Revised: 08/13/2024] [Accepted: 08/14/2024] [Indexed: 09/06/2024]
Abstract
The cell envelope is at the center of many processes essential for bacterial lifestyles. In addition to giving bacteria shape and delineating it from the environment, it contains macromolecules important for energy transduction, cell division, protection against toxins, biofilm formation, or virulence. Hence, many systems coordinate different processes within the cell envelope to ensure function and integrity. Two-component systems have been identified as crucial regulators of cell envelope functions over the last few years. In this review, we summarize the new information obtained on the regulation of cell envelope biosynthesis and homeostasis in α-proteobacteria, as well as newly identified targets that coordinate the processes in the cell envelope.
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Affiliation(s)
- Bryan Lakey
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - François Alberge
- CEA, CNRS, Aix-Marseille Université, Institut de Biosciences et Biotechnologies d'Aix-Marseille, UMR 7265, CEA Cadarache, Saint Paul-lez Durance, France
| | - Timothy J Donohue
- Department of Bacteriology, Wisconsin Energy Institute, University of Wisconsin Madison, Madison, WI, USA.
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2
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Sommerfield AG, Wang M, Mamana J, Darwin AJ. In vivo and in vitro analyses of the role of the Prc protease in inducing mucoidy in Pseudomonas aeruginosa. J Bacteriol 2024:e0022224. [PMID: 39287400 DOI: 10.1128/jb.00222-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Accepted: 08/20/2024] [Indexed: 09/19/2024] Open
Abstract
In Pseudomonas aeruginosa, alginate biosynthesis gene expression is inhibited by the transmembrane anti-sigma factor MucA, which sequesters the AlgU sigma factor. Cell envelope stress initiates cleavage of the MucA periplasmic domain by site-1 protease AlgW, followed by further MucA degradation to release AlgU. However, after colonizing the lungs of people with cystic fibrosis, P. aeruginosa converts to a mucoid form that produces alginate constitutively. Mucoid isolates often have mucA mutations, with the most common being mucA22, which truncates the periplasmic domain. MucA22 is degraded constitutively, and genetic studies suggested that the Prc protease is responsible. Some studies also suggested that Prc contributes to induction in strains with wild-type MucA, whereas others suggested the opposite. However, missing from all previous studies is a demonstration that Prc cleaves any protein directly, which leaves open the possibility that the effect of a prc null mutation is indirect. To address the ambiguities and shortfalls, we reevaluated the roles of AlgW and Prc as MucA and MucA22 site-1 proteases. In vivo analyses using three different assays and two different inducing conditions all suggested that AlgW is the only site-1 protease for wild-type MucA in any condition. In contrast, genetics suggested that AlgW or Prc act as MucA22 site-1 proteases in inducing conditions, whereas Prc is the only MucA22 site-1 protease in non-inducing conditions. For the first time, we also show that Prc is unable to degrade the periplasmic domain of wild-type MucA but does degrade the mutated periplasmic domain of MucA22 directly. IMPORTANCE After colonizing the lungs of individuals with cystic fibrosis, Pseudomonas aeruginosa undergoes mutagenic conversion to a mucoid form, worsening the prognosis. Most mucoid isolates have a truncated negative regulatory protein MucA, which leads to constitutive production of the extracellular polysaccharide alginate. The protease Prc has been implicated, but not shown, to degrade the most common MucA variant, MucA22, to trigger alginate production. This work provides the first demonstration that the molecular mechanism of Prc involvement is direct degradation of the MucA22 periplasmic domain and perhaps other truncated MucA variants as well. MucA truncation and degradation by Prc might be the predominant mechanism of mucoid conversion in cystic fibrosis infections, suggesting that Prc activity could be a useful therapeutic target.
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Affiliation(s)
- Alexis G Sommerfield
- Department of Microbiology, NYU Grossman School of Medicine, New York, New York, USA
| | - Michelle Wang
- Department of Microbiology, NYU Grossman School of Medicine, New York, New York, USA
| | - Julia Mamana
- Department of Microbiology, NYU Grossman School of Medicine, New York, New York, USA
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3
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Lyu Z, Yang X, Yahashiri A, Ha S, McCausland JW, Chen X, Britton BM, Weiss DS, Xiao J. E. coli FtsN coordinates synthesis and degradation of septal peptidoglycan by partitioning between a synthesis track and a denuded glycan track. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.13.594014. [PMID: 39253420 PMCID: PMC11383011 DOI: 10.1101/2024.05.13.594014] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/11/2024]
Abstract
The E. coli cell division protein FtsN was proposed to coordinate septal peptidoglycan (sPG) synthesis and degradation to ensure robust cell wall constriction without lethal lesions. Although the precise mechanism remains unclear, previous work highlights the importance of two FtsN domains: the E domain, which interacts with and activates the sPG synthesis complex FtsWIQLB, and the SPOR domain, which binds to denuded glycan (dnG) strands, key intermediates in sPG degradation. Here, we used single-molecule tracking of FtsN and FtsW (a proxy for the sPG synthesis complex FtsWIQLB) to investigate how FtsN coordinates the two opposing processes. We observed dynamic behaviors indicating that FtsN's SPOR domain binds to dnGs cooperatively, which both sequesters the sPG synthesis complex on dnG (termed as the dnG-track) and protects dnGs from degradation by lytic transglycosylases (LTs). The release of the SPOR domain from dnGs leads to activating the sPG synthesis complex on the sPG-track and simultaneously exposing those same dnGs to degradation. Furthermore, FtsN's SPOR domain self-interacts and facilitates the formation of a multimeric sPG synthesis complex on both tracks. The cooperative self-interaction of the SPOR domain creates a sensitive switch to regulate the partitioning of FtsN between the dnG- and sPG-tracks, thereby controlling the balance between sequestered and active populations of the sPG synthesis complex. As such, FtsN coordinates sPG synthesis and degradation in space and time.
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4
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Ma Y, Pirolo M, Jana B, Mebus VH, Guardabassi L. The intrinsic macrolide resistome of Escherichia coli. Antimicrob Agents Chemother 2024; 68:e0045224. [PMID: 38940570 PMCID: PMC11304742 DOI: 10.1128/aac.00452-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 05/16/2024] [Indexed: 06/29/2024] Open
Abstract
Intrinsic resistance to macrolides in Gram-negative bacteria is primarily attributed to the low permeability of the outer membrane, though the underlying genetic and molecular mechanisms remain to be fully elucidated. Here, we used transposon directed insertion-site sequencing (TraDIS) to identify chromosomal non-essential genes involved in Escherichia coli intrinsic resistance to a macrolide antibiotic, tilmicosin. We constructed two highly saturated transposon mutant libraries of >290,000 and >390,000 unique Tn5 insertions in a clinical enterotoxigenic strain (ETEC5621) and in a laboratory strain (K-12 MG1655), respectively. TraDIS analysis identified genes required for growth of ETEC5621 and MG1655 under 1/8 MIC (n = 15 and 16, respectively) and 1/4 MIC (n = 38 and 32, respectively) of tilmicosin. For both strains, 23 genes related to lipopolysaccharide biosynthesis, outer membrane assembly, the Tol-Pal system, efflux pump, and peptidoglycan metabolism were enriched in the presence of the antibiotic. Individual deletion of genes (n = 10) in the wild-type strains led to a 64- to 2-fold reduction in MICs of tilmicosin, erythromycin, and azithromycin, validating the results of the TraDIS analysis. Notably, deletion of surA or waaG, which impairs the outer membrane, led to the most significant decreases in MICs of all three macrolides in ETEC5621. Our findings contribute to a genome-wide understanding of intrinsic macrolide resistance in E. coli, shedding new light on the potential role of the peptidoglycan layer. They also provide an in vitro proof of concept that E. coli can be sensitized to macrolides by targeting proteins maintaining the outer membrane such as SurA and WaaG.
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Affiliation(s)
- Yibing Ma
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Mattia Pirolo
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Bimal Jana
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Viktor Hundtofte Mebus
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Luca Guardabassi
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
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5
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Son JE, Park SH, Choi U, Lee CR. Lytic transglycosylase repertoire diversity enables intrinsic antibiotic resistance and daughter cell separation in Escherichia coli under acidic stress. Antimicrob Agents Chemother 2024; 68:e0037224. [PMID: 38884456 PMCID: PMC11232391 DOI: 10.1128/aac.00372-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Accepted: 05/21/2024] [Indexed: 06/18/2024] Open
Abstract
Peptidoglycan (PG) is an important architectural element that imparts physical toughness and rigidity to the bacterial envelope. It is also a dynamic structure that undergoes continuous turnover or autolysis. Escherichia coli possesses redundant PG degradation enzymes responsible for PG turnover; however, the advantage afforded by the existence of numerous PG degradation enzymes remains incompletely understood. In this study, we elucidated the physiological roles of MltE and MltC, members of the lytic transglycosylase (LTG) family that catalyze the cleavage of glycosidic bonds between disaccharide subunits within PG strands. MltE and MltC are acidic LTGs that exhibit increased enzymatic activity and protein levels under acidic pH conditions, respectively, and deletion of these two LTGs results in a pronounced growth defect at acidic pH. Furthermore, inactivation of these two LTGs induces increased susceptibility at acidic pH against various antibiotics, particularly vancomycin, which seems to be partially caused by elevated membrane permeability. Intriguingly, inactivation of these LTGs induces a chaining morphology, indicative of daughter cell separation defects, only under acidic pH conditions. Simultaneous deletion of PG amidases, known contributors to daughter cell separation, exacerbates the chaining phenotype at acidic pH. This suggests that the two LTGs may participate in the cleavage of glycan strands between daughter cells under acidic pH conditions. Collectively, our findings highlight the role of LTG repertoire diversity in facilitating bacterial survival and antibiotic resistance under stressful conditions.
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Affiliation(s)
- Ji Eun Son
- Department of Biological Sciences, Myongji University, Yongin, Gyeonggido, Republic of Korea
| | - Si Hyoung Park
- Department of Biological Sciences, Myongji University, Yongin, Gyeonggido, Republic of Korea
| | - Umji Choi
- Department of Biological Sciences, Myongji University, Yongin, Gyeonggido, Republic of Korea
| | - Chang-Ro Lee
- Department of Biological Sciences, Myongji University, Yongin, Gyeonggido, Republic of Korea
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6
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Karimullina E, Guo Y, Khan HM, Emde T, Quade B, Leo RD, Otwinowski Z, Tieleman Peter D, Borek D, Savchenko A. Structural architecture of TolQ-TolR inner membrane protein complex from opportunistic pathogen Acinetobacter baumannii. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.19.599759. [PMID: 38948712 PMCID: PMC11212960 DOI: 10.1101/2024.06.19.599759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Gram-negative bacteria harness the proton motive force (PMF) within their inner membrane (IM) to uphold the integrity of their cell envelope, an indispensable aspect for both division and survival. The IM TolQ-TolR complex is the essential part of the Tol-Pal system, serving as a conduit for PMF energy transfer to the outer membrane. Here we present cryo-EM reconstructions of Acinetobacter baumannii TolQ in apo and TolR- bound forms at atomic resolution. The apo TolQ configuration manifests as a symmetric pentameric pore, featuring a trans-membrane funnel leading towards a cytoplasmic chamber. In contrast, the TolQ-TolR complex assumes a proton non-permeable stance, characterized by the TolQ pentamer's flexure to accommodate the TolR dimer, where two protomers undergo a translation-based relationship. Our structure-guided analysis and simulations support the rotor-stator mechanism of action, wherein the rotation of the TolQ pentamer harmonizes with the TolR protomers' interplay. These findings broaden our mechanistic comprehension of molecular stator units empowering critical functions within the Gram-negative bacterial cell envelope. Teaser Apo TolQ and TolQ-TolR structures depict structural rearrangements required for cell envelope organization in bacterial cell division.
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7
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Amstutz J, Krol E, Verhaeghe A, De Bolle X, Becker A, Brown PJ. Getting to the point: unipolar growth of Hyphomicrobiales. Curr Opin Microbiol 2024; 79:102470. [PMID: 38569420 DOI: 10.1016/j.mib.2024.102470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 03/15/2024] [Accepted: 03/17/2024] [Indexed: 04/05/2024]
Abstract
The governing principles and suites of genes for lateral elongation or incorporation of new cell wall material along the length of a rod-shaped cell are well described. In contrast, relatively little is known about unipolar elongation or incorporation of peptidoglycan at one end of the rod. Recent work in three related model systems of unipolar growth (Agrobacterium tumefaciens, Brucella abortus, and Sinorhizobium meliloti) has clearly established that unipolar growth in the Hyphomicrobiales order relies on a set of genes distinct from the canonical elongasome. Polar incorporation of envelope components relies on homologous proteins shared by the Hyphomicrobiales, reviewed here. Ongoing and future work will reveal how unipolar growth is integrated into the alphaproteobacterial cell cycle and coordinated with other processes such as chromosome segregation and cell division.
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Affiliation(s)
- Jennifer Amstutz
- Division of Biological Sciences, University of Missouri-Columbia, Columbia, Missouri, USA
| | - Elizaveta Krol
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, D-35032 Marburg, Germany; Department of Biology, Philipps-Universität Marburg, D-35032 Marburg, Germany
| | - Audrey Verhaeghe
- Research Unit in Biology of Microorganisms (URBM), Narilis, University of Namur (UNamur), 61 rue de Bruxelles, 5000 Namur, Belgium
| | - Xavier De Bolle
- Research Unit in Biology of Microorganisms (URBM), Narilis, University of Namur (UNamur), 61 rue de Bruxelles, 5000 Namur, Belgium.
| | - Anke Becker
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, D-35032 Marburg, Germany; Department of Biology, Philipps-Universität Marburg, D-35032 Marburg, Germany.
| | - Pamela Jb Brown
- Division of Biological Sciences, University of Missouri-Columbia, Columbia, Missouri, USA.
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8
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Sommerfield AG, Wang M, Mamana J, Darwin AJ. In vivo and in vitro analysis of the role of the Prc protease in inducing mucoidy in Pseudomonas aeruginosa. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.28.596254. [PMID: 38854061 PMCID: PMC11160602 DOI: 10.1101/2024.05.28.596254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
In Pseudomonas aeruginosa, alginate biosynthesis gene expression is inhibited by the transmembrane anti-sigma factor MucA, which sequesters the AlgU sigma factor. Cell envelope stress initiates cleavage of the MucA periplasmic domain by site-1 protease AlgW, followed by further MucA degradation to release AlgU. However, after colonizing the lungs of people with cystic fibrosis, P. aeruginosa converts to a mucoid form that produces alginate constitutively. Mucoid isolates often have mucA mutations, with the most common being mucA22 , which truncates the periplasmic domain. MucA22 is degraded constitutively, and genetic studies suggested that the Prc protease is responsible. Some studies also suggested that Prc contributes to induction in strains with wild type MucA, whereas others suggested the opposite. However, missing from all previous studies is a demonstration that Prc cleaves any protein directly, which leaves open the possibility that the effect of a prc null mutation is indirect. To address the ambiguities and shortfalls, we reevaluated the roles of AlgW and Prc as MucA and MucA22 site-1 proteases. In vivo analyses using three different assays, and two different inducing conditions, all suggested that AlgW is the only site-1 protease for wild type MucA in any condition. In contrast, genetics suggested that AlgW or Prc act as MucA22 site-1 proteases in inducing conditions, whereas Prc is the only MucA22 site-1 protease in non-inducing conditions. For the first time, we also show that Prc is unable to degrade the periplasmic domain of wild type MucA, but does degrade the mutated periplasmic domain of MucA22 directly. IMPORTANCE After colonizing the lungs of individuals with cystic fibrosis, P. aeruginosa undergoes mutagenic conversion to a mucoid form, worsening the prognosis. Most mucoid isolates have a truncated negative regulatory protein MucA, which leads to constitutive production of the extracellular polysaccharide alginate. The protease Prc has been implicated, but not shown, to degrade the most common MucA variant, MucA22, to trigger alginate production. This work provides the first demonstration that the molecular mechanism of Prc involvement is direct degradation of the MucA22 periplasmic domain, and perhaps other truncated MucA variants as well. MucA truncation and degradation by Prc might be the predominant mechanism of mucoid conversion in cystic fibrosis infections, suggesting that Prc activity could be a useful therapeutic target.
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9
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Kelly S, Tham JL, McKeever K, Dillon E, O'Connell D, Scholz D, Simpson JC, O'Connor K, Narancic T, Cagney G. Comprehensive Proteomics Analysis of Polyhydroxyalkanoate (PHA) Biology in Pseudomonas putida KT2440: The Outer Membrane Lipoprotein OprL is a Newly Identified Phasin. Mol Cell Proteomics 2024; 23:100765. [PMID: 38608840 PMCID: PMC11103573 DOI: 10.1016/j.mcpro.2024.100765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 03/01/2024] [Accepted: 03/23/2024] [Indexed: 04/14/2024] Open
Abstract
Pseudomonas putida KT2440 is an important bioplastic-producing industrial microorganism capable of synthesizing the polymeric carbon-rich storage material, polyhydroxyalkanoate (PHA). PHA is sequestered in discrete PHA granules, or carbonosomes, and accumulates under conditions of stress, for example, low levels of available nitrogen. The pha locus responsible for PHA metabolism encodes both anabolic and catabolic enzymes, a transcription factor, and carbonosome-localized proteins termed phasins. The functions of phasins are incompletely understood but genetic disruption of their function causes PHA-related phenotypes. To improve our understanding of these proteins, we investigated the PHA pathways of P.putida KT2440 using three types of experiments. First, we profiled cells grown in nitrogen-limited and nitrogen-excess media using global expression proteomics, identifying sets of proteins found to coordinately increase or decrease within clustered pathways. Next, we analyzed the protein composition of isolated carbonosomes, identifying two new putative components. We carried out physical interaction screens focused on PHA-related proteins, generating a protein-protein network comprising 434 connected proteins. Finally, we confirmed that the outer membrane protein OprL (the Pal component of the Pal-Tol system) localizes to the carbonosome and shows a PHA-related phenotype and therefore is a novel phasin. The combined datasets represent a valuable overview of the protein components of the PHA system in P.putida highlighting the complex nature of regulatory interactions responsive to nutrient stress.
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Affiliation(s)
- Siobhan Kelly
- BiOrbic - Bioeconomy Research Centre, University College Dublin, Belfield, Dublin, Ireland; UCD Conway Institute, University College Dublin, Belfield, Dublin, Ireland; School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin, Ireland
| | - Jia-Lynn Tham
- BiOrbic - Bioeconomy Research Centre, University College Dublin, Belfield, Dublin, Ireland; UCD Conway Institute, University College Dublin, Belfield, Dublin, Ireland; School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin, Ireland
| | - Kate McKeever
- BiOrbic - Bioeconomy Research Centre, University College Dublin, Belfield, Dublin, Ireland; UCD Conway Institute, University College Dublin, Belfield, Dublin, Ireland; School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin, Ireland
| | - Eugene Dillon
- UCD Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - David O'Connell
- BiOrbic - Bioeconomy Research Centre, University College Dublin, Belfield, Dublin, Ireland; UCD Conway Institute, University College Dublin, Belfield, Dublin, Ireland; School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin, Ireland
| | - Dimitri Scholz
- UCD Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Jeremy C Simpson
- UCD Conway Institute, University College Dublin, Belfield, Dublin, Ireland; UCD Earth Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Kevin O'Connor
- BiOrbic - Bioeconomy Research Centre, University College Dublin, Belfield, Dublin, Ireland; School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin, Ireland; UCD School of Biology and Environmental Science, University College Dublin, Belfield, Dublin, Ireland
| | - Tanja Narancic
- BiOrbic - Bioeconomy Research Centre, University College Dublin, Belfield, Dublin, Ireland; School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin, Ireland.
| | - Gerard Cagney
- BiOrbic - Bioeconomy Research Centre, University College Dublin, Belfield, Dublin, Ireland; UCD Conway Institute, University College Dublin, Belfield, Dublin, Ireland; School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin, Ireland.
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10
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Poulsen BE, Warrier T, Barkho S, Bagnall J, Romano KP, White T, Yu X, Kawate T, Nguyen PH, Raines K, Ferrara K, Golas A, Fitzgerald M, Boeszoermenyi A, Kaushik V, Serrano-Wu M, Shoresh N, Hung DT. "Multiplexed screen identifies a Pseudomonas aeruginosa -specific small molecule targeting the outer membrane protein OprH and its interaction with LPS". BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.16.585348. [PMID: 38559044 PMCID: PMC10980007 DOI: 10.1101/2024.03.16.585348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The surge of antimicrobial resistance threatens efficacy of current antibiotics, particularly against Pseudomonas aeruginosa , a highly resistant gram-negative pathogen. The asymmetric outer membrane (OM) of P. aeruginosa combined with its array of efflux pumps provide a barrier to xenobiotic accumulation, thus making antibiotic discovery challenging. We adapted PROSPECT 1 , a target-based, whole-cell screening strategy, to discover small molecule probes that kill P. aeruginosa mutants depleted for essential proteins localized at the OM. We identified BRD1401, a small molecule that has specific activity against a P. aeruginosa mutant depleted for the essential lipoprotein, OprL. Genetic and chemical biological studies identified that BRD1401 acts by targeting the OM β-barrel protein OprH to disrupt its interaction with LPS and increase membrane fluidity. Studies with BRD1401 also revealed an interaction between OprL and OprH, directly linking the OM with peptidoglycan. Thus, a whole-cell, multiplexed screen can identify species-specific chemical probes to reveal novel pathogen biology.
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11
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Kaul M, Meher SK, Nallamotu KC, Reddy M. Glycan strand cleavage by a lytic transglycosylase, MltD contributes to the expansion of peptidoglycan in Escherichia coli. PLoS Genet 2024; 20:e1011161. [PMID: 38422114 DOI: 10.1371/journal.pgen.1011161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 03/12/2024] [Accepted: 01/31/2024] [Indexed: 03/02/2024] Open
Abstract
Peptidoglycan (PG) is a protective sac-like exoskeleton present in most bacterial cell walls. It is a large, covalently crosslinked mesh-like polymer made up of many glycan strands cross-bridged to each other by short peptide chains. Because PG forms a continuous mesh around the bacterial cytoplasmic membrane, opening the mesh is critical to generate space for the incorporation of new material during its expansion. In Escherichia coli, the 'space-making activity' is known to be achieved by cleavage of crosslinks between the glycan strands by a set of redundant PG endopeptidases whose absence leads to rapid lysis and cell death. Here, we demonstrate a hitherto unknown role of glycan strand cleavage in cell wall expansion in E. coli. We find that overexpression of a membrane-bound lytic transglycosylase, MltD that cuts the glycan polymers of the PG sacculus rescues the cell lysis caused by the absence of essential crosslink-specific endopeptidases, MepS, MepM and MepH. We find that cellular MltD levels are stringently controlled by two independent regulatory pathways; at the step of post-translational stability by a periplasmic adaptor-protease complex, NlpI-Prc, and post-transcriptionally by RpoS, a stationary-phase specific sigma factor. Further detailed genetic and biochemical analysis implicated a role for MltD in cleaving the nascent uncrosslinked glycan strands generated during the expansion of PG. Overall, our results show that the combined activity of PG endopeptidases and lytic transglycosylases is necessary for successful expansion of the cell wall during growth of a bacterium.
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Affiliation(s)
- Moneca Kaul
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Suraj Kumar Meher
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Krishna Chaitanya Nallamotu
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Manjula Reddy
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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12
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Govers SK, Campos M, Tyagi B, Laloux G, Jacobs-Wagner C. Apparent simplicity and emergent robustness in the control of the Escherichia coli cell cycle. Cell Syst 2024; 15:19-36.e5. [PMID: 38157847 DOI: 10.1016/j.cels.2023.12.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 06/15/2023] [Accepted: 12/01/2023] [Indexed: 01/03/2024]
Abstract
To examine how bacteria achieve robust cell proliferation across diverse conditions, we developed a method that quantifies 77 cell morphological, cell cycle, and growth phenotypes of a fluorescently labeled Escherichia coli strain and >800 gene deletion derivatives under multiple nutrient conditions. This approach revealed extensive phenotypic plasticity and deviating mutant phenotypes were often nutrient dependent. From this broad phenotypic landscape emerged simple and robust unifying rules (laws) that connect DNA replication initiation, nucleoid segregation, FtsZ ring formation, and cell constriction to specific aspects of cell size (volume, length, or added length) at the population level. Furthermore, completion of cell division followed the initiation of cell constriction after a constant time delay across strains and nutrient conditions, identifying cell constriction as a key control point for cell size determination. Our work provides a population-level description of the governing principles by which E. coli integrates cell cycle processes and growth rate with cell size to achieve its robust proliferative capability. A record of this paper's transparent peer review process is included in the supplemental information.
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Affiliation(s)
- Sander K Govers
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA; de Duve Institute, UCLouvain, Brussels, Belgium; Department of Biology, KU Leuven, Leuven, Belgium
| | - Manuel Campos
- Centre de Biologie Intégrative de Toulouse, Laboratoire de Microbiologie et Génétique Moléculaires, Université de Toulouse, Toulouse, France
| | - Bhavyaa Tyagi
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA 94305, USA
| | | | - Christine Jacobs-Wagner
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA 94305, USA; Sarafan Chemistry, Engineering Medicine for Human Health Institute, Stanford University, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford School of Medicine, Stanford, CA 94305, USA.
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13
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Cook D, Flannigan MD, Chariker JH, Hare JM. DNA damage response coregulator ddrR affects many cellular pathways and processes in Acinetobacter baumannii 17978. Front Cell Infect Microbiol 2024; 13:1324091. [PMID: 38274737 PMCID: PMC10808703 DOI: 10.3389/fcimb.2023.1324091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 12/20/2023] [Indexed: 01/27/2024] Open
Abstract
Introduction Acinetobacter baumannii strain 17978 is an opportunistic pathogen possessing a DNA damage response (DDR) in which multiple error-prone polymerase genes are co-repressed by a UmuD homolog, UmuDAb, and the small Acinetobacter-specific protein DdrR. Additionally, these regulators coactivate nine other genes. We identified the DNA damage-inducible transcriptome for wildtype, umuDAb, and recA strains, and later established the ddrR DDR transcriptome. However, the ATCC 17978 reference genome had several assembly errors and lacked the 44 kb virulence locus, AbaAL44, that is present in the strain 17978 UN. Methods For this project, we combined our earlier single-end read RNAseq data with the ddrR paired-end reads and aligned these data to the improved 17978 UN genome assembly that resembled our laboratory strain, 17978 JH. Results New DESeq2 analyses verified previous differentially expressed genes (DEGs) but also found 339 genes in 17978 JH that were not annotated or physically present in the older genome assembly. Sixty-three were differentially expressed after DNA damage, and 182 had differential basal expression when comparing umuDAb, ddrR, or recA strains to wildtype, with 94 genes' expression unchanged. This work identified and characterized the 55 gene DNA damage-repressible transcriptome, 98% of which required either umuDAb or ddrR for repression. Two-thirds of these DEGs required both regulators. We also identified 110 genes repressed only in the ddrR strain, ~50% of which were due to increased basal expression levels. Basal gene expression in the ddrR mutant was further dysregulated independent of the DDR. Over 800 genes were upregulated, and over 1200 genes were downregulated compared to wildtype expression. Half of A. baumannii's essential genes were upregulated in the ddrR strain, including cell division genes, and two-thirds of these were downregulated in the umuDAb strain. Discussion The ddrR mutant upregulated genes enriched in translation, RNA metabolism, protein metabolism, AA/FA/cell-structure synthesis, and transport, while downregulating genes enriched in quorum sensing, biofilm production, secretion systems, pilus production, cell adhesion, and aromatics and chlorine degradation. Our data underscore the need for accurate and appropriately matched genome assemblies and indicate that ddrR affects approximately 60% of the genome, rendering it a potential target for Acinetobacter baumannii infection treatment.
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Affiliation(s)
- Deborah Cook
- Department of Biology and Chemistry, Morehead State University, Morehead, KY, United States
| | - Mollee D. Flannigan
- Department of Biology and Chemistry, Morehead State University, Morehead, KY, United States
| | - Julia H. Chariker
- Kentucky IDeA Networks of Biomedical Research Excellence (KY INBRE) Bioinformatics Core, University of Louisville, Louisville, KY, United States
| | - Janelle M. Hare
- Department of Biology and Chemistry, Morehead State University, Morehead, KY, United States
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14
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Ferrarini MG, Vallier A, Vincent-Monégat C, Dell'Aglio E, Gillet B, Hughes S, Hurtado O, Condemine G, Zaidman-Rémy A, Rebollo R, Parisot N, Heddi A. Coordination of host and endosymbiont gene expression governs endosymbiont growth and elimination in the cereal weevil Sitophilus spp. MICROBIOME 2023; 11:274. [PMID: 38087390 PMCID: PMC10717185 DOI: 10.1186/s40168-023-01714-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 10/30/2023] [Indexed: 12/18/2023]
Abstract
BACKGROUND Insects living in nutritionally poor environments often establish long-term relationships with intracellular bacteria that supplement their diets and improve their adaptive and invasive powers. Even though these symbiotic associations have been extensively studied on physiological, ecological, and evolutionary levels, few studies have focused on the molecular dialogue between host and endosymbionts to identify genes and pathways involved in endosymbiosis control and dynamics throughout host development. RESULTS We simultaneously analyzed host and endosymbiont gene expression during the life cycle of the cereal weevil Sitophilus oryzae, from larval stages to adults, with a particular emphasis on emerging adults where the endosymbiont Sodalis pierantonius experiences a contrasted growth-climax-elimination dynamics. We unraveled a constant arms race in which different biological functions are intertwined and coregulated across both partners. These include immunity, metabolism, metal control, apoptosis, and bacterial stress response. CONCLUSIONS The study of these tightly regulated functions, which are at the center of symbiotic regulations, provides evidence on how hosts and bacteria finely tune their gene expression and respond to different physiological challenges constrained by insect development in a nutritionally limited ecological niche. Video Abstract.
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Affiliation(s)
- Mariana Galvão Ferrarini
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621, Villeurbanne, France
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622, Villeurbanne, France
| | - Agnès Vallier
- Univ Lyon, INRAE, INSA Lyon, BF2I, UMR 203, 69621, Villeurbanne, France
| | | | - Elisa Dell'Aglio
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621, Villeurbanne, France
| | - Benjamin Gillet
- Institut de Génomique Fonctionnelle de Lyon (IGFL), CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Université de Lyon, Lyon, France
| | - Sandrine Hughes
- Institut de Génomique Fonctionnelle de Lyon (IGFL), CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Université de Lyon, Lyon, France
| | - Ophélie Hurtado
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621, Villeurbanne, France
| | - Guy Condemine
- Univ Lyon, Université Lyon 1, INSA de Lyon, CNRS UMR 5240 Microbiologie Adaptation et Pathogénie, Villeurbanne, France
| | - Anna Zaidman-Rémy
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621, Villeurbanne, France
- Institut universitaire de France (IUF), Paris, France
| | - Rita Rebollo
- Univ Lyon, INRAE, INSA Lyon, BF2I, UMR 203, 69621, Villeurbanne, France
| | - Nicolas Parisot
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621, Villeurbanne, France.
| | - Abdelaziz Heddi
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621, Villeurbanne, France.
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15
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Liu X, den Blaauwen T. NlpI-Prc Proteolytic Complex Mediates Peptidoglycan Synthesis and Degradation via Regulation of Hydrolases and Synthases in Escherichia coli. Int J Mol Sci 2023; 24:16355. [PMID: 38003545 PMCID: PMC10671308 DOI: 10.3390/ijms242216355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/09/2023] [Accepted: 11/13/2023] [Indexed: 11/26/2023] Open
Abstract
Balancing peptidoglycan (PG) synthesis and degradation with precision is essential for bacterial growth, yet our comprehension of this intricate process remains limited. The NlpI-Prc proteolytic complex plays a crucial but poorly understood role in the regulation of multiple enzymes involved in PG metabolism. In this paper, through fluorescent D-amino acid 7-hydroxycoumarincarbonylamino-D-alanine (HADA) labeling and immunolabeling assays, we have demonstrated that the NlpI-Prc complex regulates the activity of PG transpeptidases and subcellular localization of PBP3 under certain growth conditions. PBP7 (a PG hydrolase) and MltD (a lytic transglycosylase) were confirmed to be negatively regulated by the NlpI-Prc complex by an in vivo degradation assay. The endopeptidases, MepS, MepM, and MepH, have consistently been demonstrated as redundantly essential "space makers" for nascent PG insertion. However, we observed that the absence of NlpI-Prc complex can alleviate the lethality of the mepS mepM mepH mutant. A function of PG lytic transglycosylases MltA and MltD as "space makers" was proposed through multiple gene deletions. These findings unveil novel roles for NlpI-Prc in the regulation of both PG synthesis and degradation, shedding light on the previously undiscovered function of lytic transglycosylases as "space makers" in PG expansion.
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Affiliation(s)
| | - Tanneke den Blaauwen
- Bacterial Cell Biology and Physiology, Swammerdam Institute for Life Science, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
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16
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Ge F, Guo R, Liang Y, Chen Y, Shao H, Sung YY, Mok WJ, Wong LL, McMinn A, Wang M. Characterization and genomic analysis of Stutzerimonas stutzeri phage vB_PstS_ZQG1, representing a novel viral genus. Virus Res 2023; 336:199226. [PMID: 37739268 PMCID: PMC10520572 DOI: 10.1016/j.virusres.2023.199226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 09/11/2023] [Accepted: 09/19/2023] [Indexed: 09/24/2023]
Abstract
Stutzerimonas stutzeri is an opportunistic pathogenic bacterium belonging to the Gammaproteobacteria, exhibiting wide distribution in the environment and playing significant ecological roles such as nitrogen fixation or pollutant degradation. Despite its ecological importance, only two S. stutzeri phages have been isolated to date. Here, a novel S. stutzeri phage, vB_PstS_ZQG1, was isolated from the surface seawater of Qingdao, China. Transmission electron microscopy analysis indicates that vB_PstS_ZQG1 has a morphology characterized by a long non-contractile tail. The genomic sequence of vB_PstS_ZQG1 contains a linear, double-strand 61,790-bp with the G+C content of 53.24% and encodes 90 putative open reading frames. Two auxiliary metabolic genes encoding TolA protein and nucleotide pyrophosphohydrolase were identified, which are likely involved in host adaptation and phage reproduction. Phylogenetic and comparative genomic analyses demonstrated that vB_PstS_ZQG1 exhibits low similarity with previously isolated phages or uncultured viruses (average nucleotide identity values range from 21.7 to 29.4), suggesting that it represents a novel viral genus by itself, here named as Fuevirus. Biogeographic analysis showed that vB_PstS_ZQG1 was only detected in epipelagic and mesopelagic zone with low abundance. In summary, our findings of the phage vB_PstS_ZQG1 will provide helpful insights for further research on the interactions between S. stutzeri phages and their hosts, and contribute to discovering unknown viral sequences in the metagenomic database.
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Affiliation(s)
- Fuyue Ge
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MoE Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Ruizhe Guo
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MoE Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Yantao Liang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MoE Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China; UMT-OUC Joint Centre for Marine Studies, Qingdao, China.
| | - Ying Chen
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MoE Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Hongbing Shao
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MoE Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China; UMT-OUC Joint Centre for Marine Studies, Qingdao, China
| | - Yeong Yik Sung
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China; Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala Terengganu, Malaysia
| | - Wen Jye Mok
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China; Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala Terengganu, Malaysia
| | - Li Lian Wong
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China; Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala Terengganu, Malaysia
| | - Andrew McMinn
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MoE Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China; Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, Australia
| | - Min Wang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MoE Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China; UMT-OUC Joint Centre for Marine Studies, Qingdao, China; Haide College, Ocean University of China, Qingdao, China; The Affiliated Hospital of Qingdao University, Qingdao, China.
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17
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Sen O, Hinks J, Lin Q, Lin Q, Kjelleberg S, Rice SA, Seviour T. Escherichia coli displays a conserved membrane proteomic response to a range of alcohols. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:147. [PMID: 37789404 PMCID: PMC10546733 DOI: 10.1186/s13068-023-02401-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 09/18/2023] [Indexed: 10/05/2023]
Abstract
BACKGROUND Alcohol is a good and environment-friendly fuel that can be microbially produced, capable of eliminating many of the limitations of the present-day fossil fuels. However, the inherent toxic nature of alcohols to the microbial cells leads to end-product inhibition that limits large-scale alcohol production by fermentation. Fundamental knowledge about the stress responses of microorganisms to alcohols would greatly facilitate to improve the microbial alcohol tolerance. The current study elucidates and compares the changes in the membrane proteome of Escherichia coli in response to a range of alcohols. RESULTS Although alcohol toxicity increased exponentially with alcohol chain length (2-6 carbon), similar stress responses were observed in the inner and outer membrane proteome of E. coli in the presence of 2-, 4- and 6-carbon alcohols at the MIC50. This pertains to: (1) increased levels of inner membrane transporters for uptake of energy-producing metabolites, (2) reduced levels of non-essential proteins, associated with anaerobic, carbon starvation and osmotic stress, for energy conservation, (3) increased levels of murein degrading enzymes (MltA, EmtA, MliC and DigH) promoting cell elongation and 4) reduced levels of most outer membrane β-barrel proteins (LptD, FadL, LamB, TolC and BamA). Major outer membrane β-barrel protein OmpC, which is known to contribute to ethanol tolerance and membrane integrity, was notably reduced by alcohol stress. While LPS is important for OmpC trimerisation, LPS release by EDTA did not lower OmpC levels. This suggests that LPS release, which is reported under alcohol stress, does not contribute to the reduced levels of OmpC in the presence of alcohol. CONCLUSIONS Since alcohol primarily targets the integrity of the membrane, maintenance of outer membrane OmpC levels in the presence of alcohol might help in the survival of E. coli to higher alcohol concentrations. The study provides important information about the membrane protein responses of E. coli to a range of alcohols, which can be used to develop targeted strategies for increased microbial alcohol tolerance and hence bioalcohol production.
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Affiliation(s)
- Oishi Sen
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Jamie Hinks
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Qifeng Lin
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, Singapore
| | - Qingsong Lin
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, Singapore
| | - Staffan Kjelleberg
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, 2052, Australia
| | - Scott A Rice
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- The Australian Institute for Microbiology and Immunology, University of Technology Sydney, Sydney, 2007, Australia
- CSIRO, Agriculture and Food, Westmead and Microbiomes for One Systems Health, Sydney, Australia
| | - Thomas Seviour
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore.
- WATEC Aarhus University Centre for Water Technology, Universitetsbyen 36, Bldg 1783, 8000, Aarhus, Denmark.
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18
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Fordjour E, Bai Z, Li S, Li S, Sackey I, Yang Y, Liu CL. Improved Membrane Permeability via Hypervesiculation for In Situ Recovery of Lycopene in Escherichia coli. ACS Synth Biol 2023; 12:2725-2739. [PMID: 37607052 DOI: 10.1021/acssynbio.3c00306] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Lycopene biosynthesis is frequently hampered by downstream processing hugely due to its inability to be secreted out from the producing chassis. Engineering cell factories can resolve this issue by secreting this hydrophobic compound. A highly permeable E. coli strain was developed for a better release rate of lycopene. Specifically, the heterologous mevalonate pathway and crtEBI genes from Corynebacterium glutamicum were overexpressed in Escherichia coli BL21 (DE3) for lycopene synthesis. To ensure in situ lycopene production, murein lipoprotein, lipoprotein NlpI, inner membrane permease protein, and membrane-anchored protein in TolA-TolQ-TolR were deleted for improved membrane permeability. The final strain, LYC-8, produced 438.44 ± 8.11 and 136.94 ± 1.94 mg/L of extracellular and intracellular lycopene in fed-batch fermentation. Both proteomics and lipidomics analyses of secreted outer membrane vesicles were perfect indicators of hypervesiculation. Changes in the ratio of saturated fatty acids, unsaturated fatty acids, and cyclopropane fatty acids coupled with the branching and acyl chain lengths altered the membrane fatty acid composition. This ensured membrane fluidity and permeability for in situ lycopene release. The combinatorial deletion of these genes altered the cellular morphology. The structural and morphological changes in cell shape, size, and length were associated with changes in the mechanical strength of the cell envelope. The enhanced lycopene production and secretion mediated by improved membrane permeability established a cell lysis-free system for an efficient releasing rate and downstream processing, demonstrating the importance of vesicle-associated membrane permeability in efficient lycopene production.
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Affiliation(s)
- Eric Fordjour
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- National Engineering Research Center of Cereal Fermentation, and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China
- Jiangsu Provincial Research Centre for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, China
| | - Zhonghu Bai
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- National Engineering Research Center of Cereal Fermentation, and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China
- Jiangsu Provincial Research Centre for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, China
| | - Sihan Li
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- National Engineering Research Center of Cereal Fermentation, and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China
- Jiangsu Provincial Research Centre for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, China
| | - Shijie Li
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- National Engineering Research Center of Cereal Fermentation, and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China
- Jiangsu Provincial Research Centre for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, China
| | - Isaac Sackey
- Department of Biological Sciences, Faculty of Biosciences, University for Development Studies, P.O. Box TL1350, NT-0272-1946 Tamale, Ghana
| | - Yankun Yang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- National Engineering Research Center of Cereal Fermentation, and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China
- Jiangsu Provincial Research Centre for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, China
| | - Chun-Li Liu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- National Engineering Research Center of Cereal Fermentation, and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China
- Jiangsu Provincial Research Centre for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, China
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19
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Alberge F, Lakey BD, Schaub RE, Dohnalkova AC, Lemmer KC, Dillard JP, Noguera DR, Donohue TJ. A previously uncharacterized divisome-associated lipoprotein, DalA, is needed for normal cell division in Rhodobacterales. mBio 2023; 14:e0120323. [PMID: 37389444 PMCID: PMC10470522 DOI: 10.1128/mbio.01203-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 05/23/2023] [Indexed: 07/01/2023] Open
Abstract
The bacterial cell envelope is a key subcellular compartment with important roles in antibiotic resistance, nutrient acquisition, and cell morphology. We seek to gain a better understanding of proteins that contribute to the function of the cell envelope in Alphaproteobacteria. Using Rhodobacter sphaeroides, we show that a previously uncharacterized protein, RSP_1200, is an outer membrane (OM) lipoprotein that non-covalently binds peptidoglycan (PG). Using a fluorescently tagged version of this protein, we find that RSP_1200 undergoes a dynamic repositioning during the cell cycle and is enriched at the septum during cell division. We show that the position of RSP_1200 mirrors the location of FtsZ rings, leading us to propose that RSP_1200 is a newly identified component of the R. sphaeroides' divisome. Additional support for this hypothesis includes the co-precipitation of RSP_1200 with FtsZ, the Pal protein, and several predicted PG L,D-transpeptidases. We also find that a ∆RSP_1200 mutation leads to defects in cell division, sensitivity to PG-active antibiotics, and results in the formation of OM protrusions at the septum during cell division. Based on these results, we propose to name RSP_1200 DalA (for division-associated lipoprotein A) and postulate that DalA serves as a scaffold to position or modulate the activity of PG transpeptidases that are needed to form envelope invaginations during cell division. We find that DalA homologs are present in members of the Rhodobacterales order within Alphaproteobacteria. Therefore, we propose that further analysis of this and related proteins will increase our understanding of the macromolecular machinery and proteins that participate in cell division in Gram-negative bacteria. IMPORTANCE Multi-protein complexes of the bacterial cell envelope orchestrate key processes like growth, division, biofilm formation, antimicrobial resistance, and production of valuable compounds. The subunits of these protein complexes are well studied in some bacteria, and differences in their composition and function are linked to variations in cell envelope composition, shape, and proliferation. However, some envelope protein complex subunits have no known homologs across the bacterial phylogeny. We find that Rhodobacter sphaeroides RSP_1200 is a newly identified lipoprotein (DalA) and that loss of this protein causes defects in cell division and changes the sensitivity to compounds, affecting cell envelope synthesis and function. We find that DalA forms a complex with proteins needed for cell division, binds the cell envelope polymer peptidoglycan, and colocalizes with enzymes involved in the assembly of this macromolecule. The analysis of DalA provides new information on the cell division machinery in this and possibly other Alphaproteobacteria.
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Affiliation(s)
- François Alberge
- />Wisconsin Energy Institute, Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Bryan D. Lakey
- />Wisconsin Energy Institute, Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Ryan E. Schaub
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Alice C. Dohnalkova
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
| | | | - Joseph P. Dillard
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Daniel R. Noguera
- />Wisconsin Energy Institute, Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Timothy J. Donohue
- />Wisconsin Energy Institute, Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
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20
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Lakey BD, Alberge F, Parrell D, Wright ER, Noguera DR, Donohue TJ. The role of CenKR in the coordination of Rhodobacter sphaeroides cell elongation and division. mBio 2023; 14:e0063123. [PMID: 37283520 PMCID: PMC10470753 DOI: 10.1128/mbio.00631-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 03/24/2023] [Indexed: 06/08/2023] Open
Abstract
Cell elongation and division are essential aspects of the bacterial life cycle that must be coordinated for viability and replication. The impact of misregulation of these processes is not well understood as these systems are often not amenable to traditional genetic manipulation. Recently, we reported on the CenKR two-component system (TCS) in the Gram-negative bacterium Rhodobacter sphaeroides that is genetically tractable, widely conserved in α-proteobacteria, and directly regulates the expression of components crucial for cell elongation and division, including genes encoding subunit of the Tol-Pal complex. In this work, we show that overexpression of cenK results in cell filamentation and chaining. Using cryo-electron microscopy (cryo-EM) and cryo-electron tomography (cryo-ET), we generated high-resolution two-dimensional (2D) images and three-dimensional (3D) volumes of the cell envelope and division septum of wild-type cells and a cenK overexpression strain finding that these morphological changes stem from defects in outer membrane (OM) and peptidoglycan (PG) constriction. By monitoring the localization of Pal, PG biosynthesis, and the bacterial cytoskeletal proteins MreB and FtsZ, we developed a model for how increased CenKR activity leads to changes in cell elongation and division. This model predicts that increased CenKR activity decreases the mobility of Pal, delaying OM constriction, and ultimately disrupting the midcell positioning of MreB and FtsZ and interfering with the spatial regulation of PG synthesis and remodeling. IMPORTANCE By coordinating cell elongation and division, bacteria maintain their shape, support critical envelope functions, and orchestrate division. Regulatory and assembly systems have been implicated in these processes in some well-studied Gram-negative bacteria. However, we lack information on these processes and their conservation across the bacterial phylogeny. In R. sphaeroides and other α-proteobacteria, CenKR is an essential two-component system (TCS) that regulates the expression of genes known or predicted to function in cell envelope biosynthesis, elongation, and/or division. Here, we leverage unique features of CenKR to understand how increasing its activity impacts cell elongation/division and use antibiotics to identify how modulating the activity of this TCS leads to changes in cell morphology. Our results provide new insight into how CenKR activity controls the structure and function of the bacterial envelope, the localization of cell elongation and division machinery, and cellular processes in organisms with importance in health, host-microbe interactions, and biotechnology.
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Affiliation(s)
- Bryan D. Lakey
- Wisconsin Energy Institute, Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - François Alberge
- Wisconsin Energy Institute, Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Daniel Parrell
- Wisconsin Energy Institute, Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Elizabeth R. Wright
- Wisconsin Energy Institute, Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Cryo-Electron Microscopy Research Center,Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Daniel R. Noguera
- Wisconsin Energy Institute, Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Timothy J. Donohue
- Wisconsin Energy Institute, Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
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21
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Weaver A, Taguchi A, Dörr T. Masters of Misdirection: Peptidoglycan Glycosidases in Bacterial Growth. J Bacteriol 2023; 205:e0042822. [PMID: 36757204 PMCID: PMC10029718 DOI: 10.1128/jb.00428-22] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023] Open
Abstract
The dynamic composition of the peptidoglycan cell wall has been the subject of intense research for decades, yet how bacteria coordinate the synthesis of new peptidoglycan with the turnover and remodeling of existing peptidoglycan remains elusive. Diversity and redundancy within peptidoglycan synthases and peptidoglycan autolysins, enzymes that degrade peptidoglycan, have often made it challenging to assign physiological roles to individual enzymes and determine how those activities are regulated. For these reasons, peptidoglycan glycosidases, which cleave within the glycan strands of peptidoglycan, have proven veritable masters of misdirection over the years. Unlike many of the broadly conserved peptidoglycan synthetic complexes, diverse bacteria can employ unrelated glycosidases to achieve the same physiological outcome. Additionally, although the mechanisms of action for many individual enzymes have been characterized, apparent conserved homologs in other organisms can exhibit an entirely different biochemistry. This flexibility has been recently demonstrated in the context of three functions critical to vegetative growth: (i) release of newly synthesized peptidoglycan strands from their membrane anchors, (ii) processing of peptidoglycan turned over during cell wall expansion, and (iii) removal of peptidoglycan fragments that interfere with daughter cell separation during cell division. Finally, the regulation of glycosidase activity during these cell processes may be a cumulation of many factors, including protein-protein interactions, intrinsic substrate preferences, substrate availability, and subcellular localization. Understanding the true scope of peptidoglycan glycosidase activity will require the exploration of enzymes from diverse organisms with equally diverse growth and division strategies.
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Affiliation(s)
- Anna Weaver
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Atsushi Taguchi
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, Ibaraki, Osaka, Japan
| | - Tobias Dörr
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, USA
- Department of Microbiology, Cornell University, Ithaca, New York, USA
- Cornell Institute of Host-Microbe Interactions and Disease, Cornell University, Ithaca, New York, USA
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22
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Izrael Živković L, Hüttmann N, Susevski V, Medić A, Beškoski V, Berezovski MV, Minić Z, Živković L, Karadžić I. A comprehensive proteomics analysis of the response of Pseudomonas aeruginosa to nanoceria cytotoxicity. Nanotoxicology 2023; 17:20-41. [PMID: 36861958 DOI: 10.1080/17435390.2023.2180451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Abstract
The increased commercial use and spread of nanoceria raises concerns about the risks associated with its effects on living organisms. Although Pseudomonas aeruginosa may be ubiquitous in nature, it is largely found in locations closely linked with human activity. P. aeruginosa san ai was used as a model organism for a deeper understanding of the interaction between biomolecules of the bacteria with this intriguing nanomaterial. A comprehensive proteomics approach along with analysis of altered respiration and production of targeted/specific secondary metabolites was conducted to study the response of P. aeruginosa san ai to nanoceria. Quantitative proteomics found that proteins associated with redox homeostasis, biosynthesis of amino acids, and lipid catabolism were upregulated. Proteins from outer cellular structures were downregulated, including transporters responsible for peptides, sugars, amino acids and polyamines, and the crucial TolB protein of the Tol-Pal system, required for the structural formation of the outer membrane layer. In accordance with the altered redox homeostasis proteins, an increased amount of pyocyanin, a key redox shuttle, and the upregulation of the siderophore, pyoverdine, responsible for iron homeostasis, were found. Production of extracellular molecules, e.g. pyocyanin, pyoverdine, exopolysaccharides, lipase, and alkaline protease, was significantly increased in P. aeruginosa san ai exposed to nanoceria. Overall, nanoceria at sublethal concentrations induces profound metabolic changes in P. aeruginosa san ai and provokes increased secretion of extracellular virulence factors, revealing the powerful influence this nanomaterial has on the vital functions of the microorganism.
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Affiliation(s)
| | - Nico Hüttmann
- John L. Holmes Mass Spectrometry Facility, University of Ottawa, Ottawa, Ontario, Canada
| | - Vanessa Susevski
- John L. Holmes Mass Spectrometry Facility, University of Ottawa, Ottawa, Ontario, Canada
| | - Ana Medić
- Department of Chemistry, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Vladimir Beškoski
- Department of Biochemistry, Faculty of Chemistry, University of Belgrade, Belgrade, Serbia
| | - Maxim V Berezovski
- John L. Holmes Mass Spectrometry Facility, University of Ottawa, Ottawa, Ontario, Canada
| | - Zoran Minić
- John L. Holmes Mass Spectrometry Facility, University of Ottawa, Ottawa, Ontario, Canada
| | - Ljiljana Živković
- The Vinča Institute of Nuclear Sciences, University of Belgrade, Belgrade, Serbia
| | - Ivanka Karadžić
- Department of Chemistry, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
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23
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Hussein M, Jasim R, Gocol H, Baker M, Thombare VJ, Ziogas J, Purohit A, Rao GG, Li J, Velkov T. Comparative Proteomics of Outer Membrane Vesicles from Polymyxin-Susceptible and Extremely Drug-Resistant Klebsiella pneumoniae. mSphere 2023; 8:e0053722. [PMID: 36622250 PMCID: PMC9942579 DOI: 10.1128/msphere.00537-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 12/06/2022] [Indexed: 01/10/2023] Open
Abstract
Outer membrane vesicles (OMVs) secreted by Gram-negative bacteria serve as transporters for the delivery of cargo such as virulence and antibiotic resistance factors. OMVs play a key role in the defense against membrane-targeting antibiotics such as the polymyxin B. Herein, we conducted comparative proteomics of OMVs from paired Klebsiella pneumoniae ATCC 700721 polymyxin-susceptible (polymyxin B MIC = 0.5 mg/L) and an extremely resistant (polymyxin B MIC ≥128 mg/L), following exposure to 2 mg/L of polymyxin B. Comparative profiling of the OMV subproteome of each strain revealed proteins from multiple perturbed pathways, particularly in the polymyxin-susceptible strain, including outer membrane assembly (lipopolysaccharide, O-antigen, and peptidoglycan biosynthesis), cationic antimicrobial peptide resistance, β-lactam resistance, and quorum sensing. In the polymyxin-susceptible strain, polymyxin B treatment reduced the expression of OMV proteins in the pathways related to adhesion, virulence, and the cell envelope stress responses, whereas, in the polymyxin-resistant strain, the proteins involved in LPS biosynthesis, RNA degradation, and nucleotide excision repair were significantly overexpressed in response to polymyxin B treatment. Intriguingly, the key polymyxin resistance enzymes 4-amino-4-deoxy-l-arabinose transferase and the PhoPQ two-component protein kinase were significantly downregulated in the OMVs of the polymyxin-susceptible strain. Additionally, a significant reduction in class A β-lactamase proteins was observed following polymyxin B treatment in the OMVs of both strains, particularly the OMVs of the polymyxin-susceptible strain. These findings shed new light on the OMV subproteome of extremely polymyxin resistant K. pneumoniae, which putatively may serve as active decoys to make the outer membrane more impervious to polymyxin attack. IMPORTANCE OMVs can help bacteria to fight antibiotics not only by spreading antibiotic resistance genes but also by acting as protective armor against antibiotics. By employing proteomics, we found that OMVs have a potential role in shielding K. pneumoniae and acting as decoys to polymyxin attack, through declining the export of proteins (e.g., 4-amino-4-deoxy-l-arabinose transferase) involved in polymyxin resistance. Furthermore, polymyxin B treatment of both strains leads to shedding of the OMVs with perturbed proteins involved in outer membrane remodeling (e.g., LPS biosynthesis) as well as pathogenic potential of K. pneumoniae (e.g., quorum sensing). The problematic extended spectrum beta-lactamases SHV and TEM were significantly reduced in both strains, suggesting that polymyxin B may act as a potentiator to sensitize the bacterium to β-lactam antibiotics. This study highlights the importance of OMVs as "molecular mules" for the intercellular transmission and delivery of resistance and cellular repair factors in the bacterial response to polymyxins.
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Affiliation(s)
- Maytham Hussein
- Monash Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Raad Jasim
- Department of Pharmacology, College of Pharmacy, University of Babylon, Iraq
| | - Hakan Gocol
- Department of Biochemistry and Pharmacology, School of Biomedical Sciences, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Mark Baker
- Discipline of Biological Sciences, Priority Research Centre in Reproductive Biology, Faculty of Science and IT, University of Newcastle, Callaghan, New South Wales, Australia
| | - Varsha J. Thombare
- Monash Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - James Ziogas
- Department of Biochemistry and Pharmacology, School of Biomedical Sciences, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Aayush Purohit
- Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Gauri G. Rao
- Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Jian Li
- Monash Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Tony Velkov
- Monash Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, Victoria, Australia
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24
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Sheng Q, Zhang MY, Liu SM, Chen ZW, Yang PL, Zhang HS, Liu MY, Li K, Zhao LS, Liu NH, Liu LN, Chen XL, Hobbs JK, Foster SJ, Zhang YZ, Su HN. In situ visualization of Braun's lipoprotein on E. coli sacculi. SCIENCE ADVANCES 2023; 9:eadd8659. [PMID: 36662863 PMCID: PMC9858504 DOI: 10.1126/sciadv.add8659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 12/20/2022] [Indexed: 06/17/2023]
Abstract
Braun's lipoprotein (Lpp) plays a major role in stabilizing the integrity of the cell envelope in Escherichia coli, as it provides a covalent cross-link between the outer membrane and the peptidoglycan layer. An important challenge in elucidating the physiological role of Lpp lies in attaining a detailed understanding of its distribution on the peptidoglycan layer. Here, using atomic force microscopy, we visualized Lpp directly on peptidoglycan sacculi. Lpp is homogeneously distributed over the outer surface of the sacculus at a high density. However, it is absent at the constriction site during cell division, revealing its role in the cell division process with Pal, another cell envelope-associated protein. Collectively, we have established a framework to elucidate the distribution of Lpp and other peptidoglycan-bound proteins via a direct imaging modality.
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Affiliation(s)
- Qi Sheng
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
- College of Marine Life Sciences and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, China
| | - Meng-Yao Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Si-Min Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Zhuo-Wei Chen
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Pei-Ling Yang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Hong-Su Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Meng-Yun Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Kang Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Long-Sheng Zhao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Ning-Hua Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Lu-Ning Liu
- College of Marine Life Sciences and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, China
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Jamie K. Hobbs
- The Florey Institute for Host-Pathogen Interactions, University of Sheffield, Sheffield, UK
- Department of Physics and Astronomy, University of Sheffield, Sheffield, UK
| | - Simon J. Foster
- The Florey Institute for Host-Pathogen Interactions, University of Sheffield, Sheffield, UK
- School of Biosciences, University of Sheffield, Sheffield, UK
| | - Yu-Zhong Zhang
- College of Marine Life Sciences and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Hai-Nan Su
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
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25
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Hubloher JJ, Van der Sande L, Schaudinn C, Müller V, Averhoff B. The Tol-Pal system of Acinetobacter baumannii is important for cell morphology, antibiotic resistance and virulence. Int Microbiol 2023:10.1007/s10123-022-00319-9. [PMID: 36648597 PMCID: PMC10397113 DOI: 10.1007/s10123-022-00319-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 12/27/2022] [Accepted: 12/30/2022] [Indexed: 01/18/2023]
Abstract
Acinetobacter baumannii is an opportunistic human pathogen that has become a global threat to healthcare institutions. This Gram-negative bacterium is one of the most successful human pathogens worldwide and responsible for hospital-acquired infections. This is due to its outstanding potential to adapt to very different environments, to persist in the human host and most important, its ability to develop multidrug resistance. Our combined approach of genomic and phenotypic analyses led to the identification of the envelope spanning Tol-Pal system in A. baumannii. We found that the deletion of the tolQ, tolR, tolA, tolB, and pal genes affects cell morphology and increases antibiotic sensitivity, such as the ∆tol-pal mutant exhibits a significantly increased gentamicin and bacitracin sensitivity. Furthermore, Galleria mellonella caterpillar killing assays revealed that the ∆tol-pal mutant exhibits a decreased killing phenotype. Taken together, our findings suggest that the Tol-Pal system is important for cell morphology, antibiotic resistance, and virulence of A. baumannii.
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Affiliation(s)
- Josephine Joy Hubloher
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Goethe-University Frankfurt Am Main, Max-Von-Laue-Str. 9, 60438, Frankfurt, Germany
| | - Lisa Van der Sande
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Goethe-University Frankfurt Am Main, Max-Von-Laue-Str. 9, 60438, Frankfurt, Germany
| | - Christoph Schaudinn
- Advanced Light and Electron Microscopy ZBS4, Robert-Koch-Institut, Berlin, Germany
| | - Volker Müller
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Goethe-University Frankfurt Am Main, Max-Von-Laue-Str. 9, 60438, Frankfurt, Germany
| | - Beate Averhoff
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Goethe-University Frankfurt Am Main, Max-Von-Laue-Str. 9, 60438, Frankfurt, Germany.
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26
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Schoelmerich MC, Sachdeva R, West-Roberts J, Waldburger L, Banfield JF. Tandem repeats in giant archaeal Borg elements undergo rapid evolution and create new intrinsically disordered regions in proteins. PLoS Biol 2023; 21:e3001980. [PMID: 36701369 PMCID: PMC9879509 DOI: 10.1371/journal.pbio.3001980] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 12/23/2022] [Indexed: 01/27/2023] Open
Abstract
Borgs are huge, linear extrachromosomal elements associated with anaerobic methane-oxidizing archaea. Striking features of Borg genomes are pervasive tandem direct repeat (TR) regions. Here, we present six new Borg genomes and investigate the characteristics of TRs in all ten complete Borg genomes. We find that TR regions are rapidly evolving, recently formed, arise independently, and are virtually absent in host Methanoperedens genomes. Flanking partial repeats and A-enriched character constrain the TR formation mechanism. TRs can be in intergenic regions, where they might serve as regulatory RNAs, or in open reading frames (ORFs). TRs in ORFs are under very strong selective pressure, leading to perfect amino acid TRs (aaTRs) that are commonly intrinsically disordered regions. Proteins with aaTRs are often extracellular or membrane proteins, and functionally similar or homologous proteins often have aaTRs composed of the same amino acids. We propose that Borg aaTR-proteins functionally diversify Methanoperedens and all TRs are crucial for specific Borg-host associations and possibly cospeciation.
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Affiliation(s)
| | - Rohan Sachdeva
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
- Earth and Planetary Science, University of California, Berkeley, California, United States of America
| | - Jacob West-Roberts
- Earth and Planetary Science, University of California, Berkeley, California, United States of America
| | - Lucas Waldburger
- Bioengineering, University of California, Berkeley, California, United States of America
| | - Jillian F. Banfield
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
- Earth and Planetary Science, University of California, Berkeley, California, United States of America
- Environmental Science, Policy and Management, University of California, Berkeley, California, United States of America
- Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
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27
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Castillo-Romero KF, Santacruz A, González-Valdez J. Production and purification of bacterial membrane vesicles for biotechnology applications: Challenges and opportunities. Electrophoresis 2023; 44:107-124. [PMID: 36398478 DOI: 10.1002/elps.202200133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 10/17/2022] [Accepted: 11/06/2022] [Indexed: 11/19/2022]
Abstract
Bacterial membrane vesicles (BMVs) are bi-layered nanostructures derived from Gram-negative and Gram-positive bacteria. Among other pathophysiological roles, BMVs are critical messengers in intercellular communication. As a result, BMVs are emerging as a promising technology for the development of numerous therapeutic applications. Despite the remarkable progress in unveiling BMV biology and functions in recent years, their successful isolation and purification have been limited. Several challenges related to vesicle purity, yield, and scalability severely hamper the further development of BMVs for biotechnology and clinical applications. This review focuses on the current technologies and methodologies used in BMV production and purification, such as ultracentrifugation, density-gradient centrifugation, size-exclusion chromatography, ultrafiltration, and precipitation. We also discuss the current challenges related to BMV isolation, large-scale production, storage, and stability that limit their application. More importantly, the present work explains the most recent strategies proposed for overcoming those challenges. Finally, we summarize the ongoing applications of BMVs in the biotechnological field.
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Affiliation(s)
- Keshia F Castillo-Romero
- School of Engineering and Science, Tecnologico de Monterrey, Av. Eugenio Garza Sada 2501 Sur, Monterrey, Nuevo León, Mexico
| | - Arlette Santacruz
- School of Engineering and Science, Tecnologico de Monterrey, Av. Eugenio Garza Sada 2501 Sur, Monterrey, Nuevo León, Mexico
| | - José González-Valdez
- School of Engineering and Science, Tecnologico de Monterrey, Av. Eugenio Garza Sada 2501 Sur, Monterrey, Nuevo León, Mexico
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28
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Abstract
This review focuses on nonlytic outer membrane vesicles (OMVs), a subtype of bacterial extracellular vesicles (BEVs) produced by Gram-negative organisms focusing on the mechanisms of their biogenesis, cargo, and function. Throughout, we highlight issues concerning the characterization of OMVs and distinguishing them from other types of BEVs. We also highlight the shortcomings of commonly used methodologies for the study of BEVs that impact the interpretation of their functionality and suggest solutions to standardize protocols for OMV studies.
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Affiliation(s)
| | - Simon R. Carding
- Quadram Institute Bioscience, Norwich, United Kingdom
- Norwich Medical School, University of East Anglia, Norwich, United Kingdom
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29
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Antibacterial Effects of ZnO Nanodisks: Shape Effect of the Nanostructure on the Lethality in Escherichia coli. Appl Biochem Biotechnol 2022; 195:3067-3095. [PMID: 36520354 DOI: 10.1007/s12010-022-04265-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/08/2022] [Indexed: 12/23/2022]
Abstract
The role of the shape of the nanostructure on the antibacterial effects of ZnO nanodisks has been investigated by detailed mass spectrometry-based proteomics along with other spectroscopic and microscopic studies on E. coli. The primary interaction study of the E. coli cells in the presence of ZnO nanodisks showed rigorous cell surface damage disrupting the cell wall/membrane components detected by microscopic and ATR-FTIR studies. Protein profiling of whole-cell extracts in the presence and absence of ZnO nanodisks identified several proteins that are upregulated and downregulated under the stress of the nanodisks. This suggests that the bacterial response to the primary stress leads to a secondary impact of ZnO nanodisk toxicity via regulation of the expression of specific proteins. Results showed that the ZnO nanodisks lead to the over-expression of peptidyl-dipeptidase Dcp, Transketolase-1, etc., which are important to maintaining the osmotic balance in the cell. The abrupt change in osmotic pressure leads to mechanical injury to the membrane, and nutritional starvation conditions, which is revealed from the expression of the key proteins involved in membrane-protein assembly, maintaining membrane integrity, cell division processes, etc. Thus, indicating a deleterious effect of ZnO nanodisk on the protective layer of E. coli. ZnO nanodisks seem to primarily affect the protective membrane layer, inducing cell death via the development of osmotic shock conditions, as one of the possible reasons for cell death. These results unravel a unique behavior of the disk-shaped ZnO nanostructure in executing lethality in E. coli, which has not been reported for other known shapes or morphologies of ZnO nanoforms.
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30
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In vitro studies of the protein-interaction network of cell-wall lytic transglycosylase RlpA of Pseudomonas aeruginosa. Commun Biol 2022; 5:1314. [PMID: 36451021 PMCID: PMC9712689 DOI: 10.1038/s42003-022-04230-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 11/07/2022] [Indexed: 12/03/2022] Open
Abstract
The protein networks of cell-wall-biosynthesis assemblies are largely unknown. A key class of enzymes in these assemblies is the lytic transglycosylases (LTs), of which eleven exist in P. aeruginosa. We have undertaken a pulldown strategy in conjunction with mass-spectrometry-based proteomics to identify the putative binding partners for the eleven LTs of P. aeruginosa. A total of 71 putative binding partners were identified for the eleven LTs. A systematic assessment of the binding partners of the rare lipoprotein A (RlpA), one of the pseudomonal LTs, was made. This 37-kDa lipoprotein is involved in bacterial daughter-cell separation by an unknown process. RlpA participates in both the multi-protein and multi-enzyme divisome and elongasome assemblies. We reveal an extensive protein-interaction network for RlpA involving at least 19 proteins. Their kinetic parameters for interaction with RlpA were assessed by microscale thermophoresis, surface-plasmon resonance, and isothermal-titration calorimetry. Notable RlpA binding partners include PBP1b, PBP4, and SltB1. Elucidation of the protein-interaction networks for each of the LTs, and specifically for RlpA, opens opportunities for the study of their roles in the complex protein assemblies intimately involved with the cell wall as a structural edifice critical for bacterial survival.
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31
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An in silico reverse vaccinology study of Brachyspira pilosicoli, the causative organism of intestinal spirochaetosis, to identify putative vaccine candidates. Process Biochem 2022. [DOI: 10.1016/j.procbio.2022.08.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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32
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Molecular Characteristics and Quantitative Proteomic Analysis of Klebsiella pneumoniae Strains with Carbapenem and Colistin Resistance. Antibiotics (Basel) 2022; 11:antibiotics11101341. [PMID: 36289999 PMCID: PMC9598126 DOI: 10.3390/antibiotics11101341] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 09/27/2022] [Accepted: 09/29/2022] [Indexed: 12/05/2022] Open
Abstract
Carbapenem-resistant Klebsiella pneumoniae (CRKP) are usually multidrug resistant (MDR) and cause serious therapeutic problems. Colistin is a critical last-resort therapeutic option for MDR bacterial infections. However, increasing colistin use has led to the emergence of extensively drug-resistant (XDR) strains, raising a significant challenge for healthcare. In order to gain insight into the antibiotic resistance mechanisms of CRKP and identify potential drug targets, we compared the molecular characteristics and the proteomes among drug-sensitive (DS), MDR, and XDR K. pneumoniae strains. All drug-resistant isolates belonged to ST11, harboring blaKPC and hypervirulent genes. None of the plasmid-encoded mcr genes were detected in the colistin-resistant XDR strains. Through a tandem mass tag (TMT)-labeled proteomic technique, a total of 3531 proteins were identified in the current study. Compared to the DS strains, there were 247 differentially expressed proteins (DEPs) in the MDR strains and 346 DEPs in the XDR strains, respectively. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that a majority of the DEPs were involved in various metabolic pathways, which were beneficial to the evolution of drug resistance in K. pneumoniae. In addition, a total of 67 DEPs were identified between the MDR and XDR strains. KEGG enrichment and protein-protein interaction network analysis showed their participation in cationic antimicrobial peptide resistance and two-component systems. In conclusion, our results highlight the emergence of colistin-resistant and hypervirulent CRKP, which is a noticeable superbug. The DEPs identified in our study are of great significance for the exploration of effective control strategies against infections of CRKP.
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33
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Zhang E, Zhang J, Zhao R, Lu Y, Yin X, Lan X, Luo Z. Role of MicroRNA-Like RNAs in the Regulation of Spore Morphological Differences in the Entomopathogenic Fungus Metarhizium acridum. Pol J Microbiol 2022; 71:309-324. [PMID: 36185022 PMCID: PMC9608168 DOI: 10.33073/pjm-2022-028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 07/01/2022] [Indexed: 11/24/2022] Open
Abstract
Metarhizium acridum is an important microbial pesticide. Conidia (CO) and blastospores (BS) are two types of spores that occur in different patterns in the M. acridum life cycle and exhibit significant differences in cell morphology, structure, and activity. It may suggest that the fungus has a complex gene regulation mechanism. While previous studies on the differences between CO and BS have mainly focused on cell structure and application, little is known regarding the differences between CO and BS in fungi on the transcriptome levels. MicroRNAs (miRNAs) are small noncoding RNAs crucial to gene regulation and cell function. Understanding the miRNA-like RNAs (milRNA) and mRNA expression profiles related to cell growth and cellular morphological changes would elucidate the roles of miRNAs in spore morphological differences. In this study, 4,646 differentially expressed genes (DEGs) were identified and mainly classified in the GO terms cell, cell part, biological process, and catalytic activity. The KEGG annotation suggested that they were enriched in amino acid biosynthesis, carbohydrate metabolism, ribosome, and oxidative phosphorylation and might be involved in cell activity and structure. There were 113 differentially expressed milRNAs (DEMs), targeting 493 DEGs. Target gene functional analysis revealed that the target genes were mainly enriched in RNA transport, purine metabolism, and the cell cycle. In addition, we identified essential genes from milRNA-mRNA pairs that might participate in cell budding growth and cell membrane and wall integrity, including adenosine deaminase, glycosyl hydrolase, and G-patch domain protein (dno-miR-328-3p), WD repeat-containing protein pop1 (age-miR-127), and GPI-anchored wall transfer protein (cgr-miR-598). MilRNAs might therefore play a crucial role in cell growth and cellular morphological changes as transcriptional and post-transcriptional regulators.
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Affiliation(s)
- Erhao Zhang
- Food Science College, Tibet Agriculture and Animal Husbandry University, Nyingchi, China
| | - Jie Zhang
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, China
| | - Rundong Zhao
- Food Science College, Tibet Agriculture and Animal Husbandry University, Nyingchi, China
| | - Yazhou Lu
- Food Science College, Tibet Agriculture and Animal Husbandry University, Nyingchi, China
| | - Xiu Yin
- Food Science College, Tibet Agriculture and Animal Husbandry University, Nyingchi, China
| | - Xiaozhong Lan
- Food Science College, Tibet Agriculture and Animal Husbandry University, Nyingchi, China, E-mail:
| | - Zhang Luo
- Food Science College, Tibet Agriculture and Animal Husbandry University, Nyingchi, China, E-mail:
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A Defect in Lipoprotein Modification by Lgt Leads to Abnormal Morphology and Cell Death in Escherichia coli That Is Independent of Major Lipoprotein Lpp. J Bacteriol 2022; 204:e0016422. [PMID: 35938851 PMCID: PMC9487459 DOI: 10.1128/jb.00164-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Lgt is an essential enzyme in proteobacteria and therefore a potential target for novel antibiotics. The effect of Lgt depletion on growth, morphology, and viability was studied in Escherichia coli to assess whether absence of Lgt leads to cell death. Two Lgt depletion strains were used in which lgt was under the control of an arabinose-inducible promoter that allowed regulation of Lgt protein levels. Reduced levels of Lgt led to severe growth and morphological defects that could be restored by expressing lgt in trans, demonstrating that only Lgt is responsible for the distorted phenotypes. In the absence of major lipoprotein Lpp, growth defects were partially restored when low levels of Lgt were still present; however, lgt could not be deleted in the absence of Lpp. Our results demonstrate that Lpp is not the main cause of cell death under conditions of Lgt depletion and that other lipoproteins are important in cell envelope biogenesis and cell viability. Specific inhibitors of Lgt are thus promising for the development of novel antibiotics. IMPORTANCE Incomplete maturation and envelope mislocalization of lipoproteins, through inhibition or mutations in lipoprotein modification enzymes or transport to the outer membrane, are lethal in proteobacteria. Resistance to small-molecule inhibition or the appearance of suppressor mutations is often directly correlated with the presence of abundant outer membrane lipoprotein Lpp. Our results show that Lgt, the first enzyme of the lipoprotein modification pathway, is still required for growth and viability in the absence of Lpp and thus is necessary for the function of other essential lipoproteins in the cell envelope. This adds credence to the hypothesis that Lgt is essential in proteobacteria and an attractive target for the development of novel antibiotics.
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Roba A, Carlier E, Godessart P, Naili C, De Bolle X. A histidine auxotroph mutant is defective for cell separation and allows the identification of crucial factors for cell division in Brucella abortus. Mol Microbiol 2022; 118:145-154. [PMID: 35748337 DOI: 10.1111/mmi.14956] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 06/20/2022] [Accepted: 06/21/2022] [Indexed: 11/29/2022]
Abstract
The pathogenic bacterium Brucella abortus invades and multiplies inside host cells. To grow inside host cells, B. abortus requires a functional histidine biosynthesis pathway. Here, we show that a B. abortus histidine auxotroph mutant also displays an unexpected chaining phenotype. The intensity of this phenotype varies according to the culture medium and is exacerbated inside host cells. Chains of bacteria consist of contiguous peptidoglycan, and likely result from the defective cleavage of peptidoglycan at septa. Genetic suppression of the chaining phenotype unearthed two essential genes with a role in B. abortus cell division, dipM and cdlP. Loss of function of dipM and cdlP generates swelling at the division site. While DipM is strictly localized at the division site, CdlP is localized at the growth pole and the division site. Altogether, the unexpected chaining phenotype of a hisB mutant allowed the discovery of new crucial actors in cell division in B. abortus.
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Affiliation(s)
- Agnès Roba
- Research Unit in Biology of Microorganisms, Narilis, University of Namur, Namur, Belgium
| | - Elodie Carlier
- Research Unit in Biology of Microorganisms, Narilis, University of Namur, Namur, Belgium
| | - Pierre Godessart
- Research Unit in Biology of Microorganisms, Narilis, University of Namur, Namur, Belgium
| | - Cerine Naili
- Research Unit in Biology of Microorganisms, Narilis, University of Namur, Namur, Belgium
| | - Xavier De Bolle
- Research Unit in Biology of Microorganisms, Narilis, University of Namur, Namur, Belgium
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36
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The Ankyrin Repeat Protein RARP-1 Is a Periplasmic Factor That Supports Rickettsia parkeri Growth and Host Cell Invasion. J Bacteriol 2022; 204:e0018222. [PMID: 35727033 DOI: 10.1128/jb.00182-22] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Rickettsia spp. are obligate intracellular bacterial pathogens that have evolved a variety of strategies to exploit their host cell niche. However, the bacterial factors that contribute to this intracellular lifestyle are poorly understood. Here, we show that the conserved ankyrin repeat protein RARP-1 supports Rickettsia parkeri infection. Specifically, RARP-1 promotes efficient host cell entry and growth within the host cytoplasm, but it is not necessary for cell-to-cell spread or evasion of host autophagy. We further demonstrate that RARP-1 is not secreted into the host cytoplasm by R. parkeri. Instead, RARP-1 resides in the periplasm, and we identify several binding partners that are predicted to work in concert with RARP-1 during infection. Altogether, our data reveal that RARP-1 plays a critical role in the rickettsial life cycle. IMPORTANCE Rickettsia spp. are obligate intracellular bacterial pathogens that pose a growing threat to human health. Nevertheless, their strict reliance on a host cell niche has hindered investigation of the molecular mechanisms driving rickettsial infection. This study yields much-needed insight into the Rickettsia ankyrin repeat protein RARP-1, which is conserved across the genus but has not yet been functionally characterized. Earlier work had suggested that RARP-1 is secreted into the host cytoplasm. However, the results from this work demonstrate that R. parkeri RARP-1 resides in the periplasm and is important both for invasion of host cells and for growth in the host cell cytoplasm. These results reveal RARP-1 as a novel regulator of the rickettsial life cycle.
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Krishnan N, Kubiatowicz LJ, Holay M, Zhou J, Fang RH, Zhang L. Bacterial membrane vesicles for vaccine applications. Adv Drug Deliv Rev 2022; 185:114294. [PMID: 35436569 DOI: 10.1016/j.addr.2022.114294] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 03/13/2022] [Accepted: 04/10/2022] [Indexed: 12/11/2022]
Abstract
Vaccines have been highly successful in the management of many diseases. However, there are still numerous illnesses, both infectious and noncommunicable, for which there are no clinically approved vaccine formulations. While there are unique difficulties that must be overcome in the case of each specific disease, there are also a number of common challenges that have to be addressed for effective vaccine development. In recent years, bacterial membrane vesicles (BMVs) have received increased attention as a potent and versatile vaccine platform. BMVs are inherently immunostimulatory and are able to activate both innate and adaptive immune responses. Additionally, BMVs can be readily taken up and processed by immune cells due to their nanoscale size. Finally, BMVs can be modified in a variety of ways, including by genetic engineering, cargo loading, and nanoparticle coating, in order to create multifunctional platforms that can be leveraged against different diseases. Here, an overview of the interactions between BMVs and immune cells is provided, followed by discussion on the applications of BMV vaccine nanotechnology against bacterial infections, viral infections, and cancers.
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Affiliation(s)
- Nishta Krishnan
- Department of NanoEngineering, Chemical Engineering Program, and Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA
| | - Luke J Kubiatowicz
- Department of NanoEngineering, Chemical Engineering Program, and Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA
| | - Maya Holay
- Department of NanoEngineering, Chemical Engineering Program, and Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA
| | - Jiarong Zhou
- Department of NanoEngineering, Chemical Engineering Program, and Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA
| | - Ronnie H Fang
- Department of NanoEngineering, Chemical Engineering Program, and Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA.
| | - Liangfang Zhang
- Department of NanoEngineering, Chemical Engineering Program, and Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA.
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Lakey BD, Myers KS, Alberge F, Mettert EL, Kiley PJ, Noguera DR, Donohue TJ. The essential Rhodobacter sphaeroides CenKR two-component system regulates cell division and envelope biosynthesis. PLoS Genet 2022; 18:e1010270. [PMID: 35767559 PMCID: PMC9275681 DOI: 10.1371/journal.pgen.1010270] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 07/12/2022] [Accepted: 05/20/2022] [Indexed: 12/13/2022] Open
Abstract
Bacterial two-component systems (TCSs) often function through the detection of an extracytoplasmic stimulus and the transduction of a signal by a transmembrane sensory histidine kinase. This kinase then initiates a series of reversible phosphorylation modifications to regulate the activity of a cognate, cytoplasmic response regulator as a transcription factor. Several TCSs have been implicated in the regulation of cell cycle dynamics, cell envelope integrity, or cell wall development in Escherichia coli and other well-studied Gram-negative model organisms. However, many α-proteobacteria lack homologs to these regulators, so an understanding of how α-proteobacteria orchestrate extracytoplasmic events is lacking. In this work we identify an essential TCS, CenKR (Cell envelope Kinase and Regulator), in the α-proteobacterium Rhodobacter sphaeroides and show that modulation of its activity results in major morphological changes. Using genetic and biochemical approaches, we dissect the requirements for the phosphotransfer event between CenK and CenR, use this information to manipulate the activity of this TCS in vivo, and identify genes that are directly and indirectly controlled by CenKR in Rb. sphaeroides. Combining ChIP-seq and RNA-seq, we show that the CenKR TCS plays a direct role in maintenance of the cell envelope, regulates the expression of subunits of the Tol-Pal outer membrane division complex, and indirectly modulates the expression of peptidoglycan biosynthetic genes. CenKR represents the first TCS reported to directly control the expression of Tol-Pal machinery genes in Gram-negative bacteria, and we predict that homologs of this TCS serve a similar function in other closely related organisms. We propose that Rb. sphaeroides genes of unknown function that are directly regulated by CenKR play unknown roles in cell envelope biosynthesis, assembly, and/or remodeling in this and other α-proteobacteria.
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Affiliation(s)
- Bryan D. Lakey
- Wisconsin Energy Institute, Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Kevin S. Myers
- Wisconsin Energy Institute, Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - François Alberge
- Wisconsin Energy Institute, Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Erin L. Mettert
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Patricia J. Kiley
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Daniel R. Noguera
- Wisconsin Energy Institute, Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Timothy J. Donohue
- Wisconsin Energy Institute, Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
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Chaouche AA, Houot L, Duché D, Iobbi-Nivol C, Giudici-Orticoni MT, Fons M, Méjean V. The Tol-Pal system of Escherichia coli plays an unexpected role in the import of the oxyanions chromate and phosphate. Res Microbiol 2022; 173:103967. [PMID: 35660524 DOI: 10.1016/j.resmic.2022.103967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 05/23/2022] [Accepted: 05/24/2022] [Indexed: 10/18/2022]
Abstract
Chromate is a toxic metal that enters bacteria by using oxyanion importers. Here, we show that each mutant of the Tol-Pal system of Escherichia coli exhibited increased chromate resistance. This system, which spans the cell envelope, plays a major role in envelope integrity and septation. The ΔtolQR mutant accumulated three-fold less chromate than the wild-type. Addition of phosphate but not sulfate to rich medium drastically reduced chromate toxicity and import in the wild-type strain. Furthermore, the intracellular concentration of free inorganic phosphate was significantly reduced for the ΔtolR mutant in comparison to the wild-type strain. Moreover, extracellular labelled phosphate was significantly less incorporated into the ΔtolR mutant. Finally, two distinct TolQR mutant complexes, specifically affected in Tol-Pal energization without affecting the TolQRA complex structure, did not complement the ΔtolQR mutant for inorganic phosphate accumulation. We thus propose that, while the Pst system is well known to import inorganic phosphate, the Tol-Pal system participates to phosphate uptake in particular at medium to high extracellular phosphate concentrations. Since mutations disabling the Tol-Pal system lead to pleiotropic effects, chromate resistance and reduced inorganic phosphate import could occur from an indirect effect of mutations in components of the Tol-Pal system.
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Affiliation(s)
- Amine Ali Chaouche
- Aix Marseille Univ, CNRS, BIP UMR 7281, IMM, IM2B, 31 Chemin Joseph Aiguier, CS70071, 13402, Marseille Cedex 09, France.
| | - Laetitia Houot
- Aix Marseille Univ, CNRS, LISM UMR 7255, IMM, IM2B, 31 Chemin Joseph Aiguier, CS70071, 13402, Marseille Cedex 09, France.
| | - Denis Duché
- Aix Marseille Univ, CNRS, LISM UMR 7255, IMM, IM2B, 31 Chemin Joseph Aiguier, CS70071, 13402, Marseille Cedex 09, France.
| | - Chantal Iobbi-Nivol
- Aix Marseille Univ, CNRS, BIP UMR 7281, IMM, IM2B, 31 Chemin Joseph Aiguier, CS70071, 13402, Marseille Cedex 09, France.
| | - Marie-Thérèse Giudici-Orticoni
- Aix Marseille Univ, CNRS, BIP UMR 7281, IMM, IM2B, 31 Chemin Joseph Aiguier, CS70071, 13402, Marseille Cedex 09, France.
| | - Michel Fons
- Aix Marseille Univ, CNRS, BIP UMR 7281, IMM, IM2B, 31 Chemin Joseph Aiguier, CS70071, 13402, Marseille Cedex 09, France.
| | - Vincent Méjean
- Aix Marseille Univ, CNRS, BIP UMR 7281, IMM, IM2B, 31 Chemin Joseph Aiguier, CS70071, 13402, Marseille Cedex 09, France
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40
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Park S, Cho H. The Tol-Pal System Plays an Important Role in Maintaining Cell Integrity During Elongation in Escherichia coli. Front Microbiol 2022; 13:891926. [PMID: 35592005 PMCID: PMC9111525 DOI: 10.3389/fmicb.2022.891926] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 04/07/2022] [Indexed: 11/13/2022] Open
Abstract
The Tol-Pal system is a transenvelope complex widely conserved among Gram-negative bacteria. It is recruited to the septal ring during cytokinesis, and its inactivation causes pleiotropic phenotypes mainly associated with the division process. From our genetic screen to identify factors required for delaying lysis upon treatment of beta lactams, we discovered that the tol-pal mutant shares similar defects with mutants of the major class A PBP system (PBP1b-LpoB) in terms of lysis prevention. Further phenotypic analyses revealed that the Tol-Pal system plays an important role in maintaining cell integrity not only during septation, but also during cell elongation. Simultaneous inactivation of the Tol-Pal system and the PBP1b-LpoB system leads to lysis during cell elongation as well as during division. Moreover, production of the Lpo activator-bypass PBP1b, but not wild-type PBP1b, partially suppressed the Tol-Pal defect in maintaining cell integrity upon treatment of mecillinam specific for the Rod system, suggesting that the Tol-Pal system is likely to be involved in the activation of aPBP by Lpo factors. Overall, our results indicate that the Tol-Pal system plays an important role in maintaining cell wall integrity during elongation in addition to its multifaceted roles during cytokinesis.
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Affiliation(s)
- Sohee Park
- Department of Biological Sciences, College of Natural Sciences, Sungkyunkwan University, Suwon, South Korea
| | - Hongbaek Cho
- Department of Biological Sciences, College of Natural Sciences, Sungkyunkwan University, Suwon, South Korea
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41
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Sommerfield AG, Darwin AJ. Bacterial Carboxyl-Terminal Processing Proteases Play Critical Roles in the Cell Envelope and Beyond. J Bacteriol 2022; 204:e0062821. [PMID: 35293777 PMCID: PMC9017358 DOI: 10.1128/jb.00628-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Proteolysis is essential throughout life, and as more proteases are characterized, our understanding of the roles they play continues to expand. Among other things, proteases are critical for protein turnover and quality control, the activation or inactivation of some enzymes, and they are integral components of signal transduction pathways. This review focuses on a family of proteases in bacteria known as the carboxyl-terminal processing proteases, or CTPs. Members of this family occur in all domains of life. In bacteria, CTPs have emerged as important enzymes that have been implicated in critical processes including regulation, stress response, peptidoglycan remodeling, and virulence. Here, we provide an overview of the roles that CTPs play in diverse bacterial species, and some of the underlying mechanisms. We also describe the structures of some bacterial CTPs, and their adaptor proteins, which have revealed striking differences in arrangements and mechanisms of action. Finally, we discuss what little is known about the distinguishing features of CTP substrates and cleavage sites, and speculate about how CTP activities might be regulated in the bacterial cell. Compared with many other proteases, the study of bacterial CTPs is still in its infancy, but it has now become clear that they affect fundamental processes in many different species. This is a protease family with broad significance, and one that holds the promise of more high impact discoveries to come.
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Affiliation(s)
- Alexis G. Sommerfield
- Department of Microbiology, NYU Grossman School of Medicine, New York, New York, USA
| | - Andrew J. Darwin
- Department of Microbiology, NYU Grossman School of Medicine, New York, New York, USA
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42
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Jeon WJ, Cho H. A Cell Wall Hydrolase MepH Is Negatively Regulated by Proteolysis Involving Prc and NlpI in Escherichia coli. Front Microbiol 2022; 13:878049. [PMID: 35418955 PMCID: PMC8996183 DOI: 10.3389/fmicb.2022.878049] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 03/04/2022] [Indexed: 11/13/2022] Open
Abstract
Cell wall assembly of Gram-negative bacteria requires DD-endopeptidase activity that cleaves peptidoglycan (PG) crosslinks in addition to PG synthetic activity, and the activity of DD-endopeptidases needs to be tightly regulated to maintain cell wall integrity during PG expansion. Among the major DD-endopeptidases functioning for PG assembly in Escherichia coli, MepS and MepM have been shown to be negatively controlled by the periplasmic protease Prc. In this study, we performed a genetic selection using the synthetic lethality between the mepS and mepM mutations in rich medium to uncover regulatory mechanisms controlling the activity of DD-endopeptidases other than MepS and MepM. This selection revealed mutations in prc and nlpI as suppressors. Gene deletion analyses revealed that MepH is required for suppression of the MepS— MepM— growth defect by the prc or nlpI mutation. We also discovered that MepH is directly degraded by Prc and that this degradation is further promoted by NlpI. Thus, our study showed that all three DD-endopeptidases which play major roles in PG assembly of E. coli under normal physiological conditions are controlled by a common periplasmic protease.
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Affiliation(s)
- Wook-Jong Jeon
- Department of Biological Sciences, College of Natural Sciences, Sungkyunkwan University, Suwon, South Korea
| | - Hongbaek Cho
- Department of Biological Sciences, College of Natural Sciences, Sungkyunkwan University, Suwon, South Korea
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43
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Yeow J, Chng SS. Of zones, bridges and chaperones - phospholipid transport in bacterial outer membrane assembly and homeostasis. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35384832 DOI: 10.1099/mic.0.001177] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The outer membrane (OM) is a formidable permeability barrier that protects Gram-negative bacteria from detergents and antibiotics. It possesses exquisite lipid asymmetry, requiring the placement and retention of lipopolysaccharides (LPS) in the outer leaflet, and phospholipids (PLs) in the inner leaflet. To establish OM lipid asymmetry, LPS are transported from the inner membrane (IM) directly to the outer leaflet of the OM. In contrast, mechanisms for PL trafficking across the cell envelope are much less understood. In this review, we summarize and discuss recent advances in our understanding of PL transport, making parallel comparisons to well-established pathways for OM lipoprotein (Lol) and LPS (Lpt). Insights into putative PL transport systems highlight possible connections back to the 'Bayer bridges', adhesion zones between the IM and the OM that had been observed more than 50 years ago, and proposed as passages for export of OM components, including LPS and PLs.
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Affiliation(s)
- Jiang Yeow
- Department of Chemistry, National University of Singapore, Singapore 117543, Singapore
| | - Shu-Sin Chng
- Department of Chemistry, National University of Singapore, Singapore 117543, Singapore
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44
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Webby MN, Williams-Jones DP, Press C, Kleanthous C. Force-Generation by the Trans-Envelope Tol-Pal System. Front Microbiol 2022; 13:852176. [PMID: 35308353 PMCID: PMC8928145 DOI: 10.3389/fmicb.2022.852176] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 01/26/2022] [Indexed: 11/13/2022] Open
Abstract
The Tol-Pal system spans the cell envelope of Gram-negative bacteria, transducing the potential energy of the proton motive force (PMF) into dissociation of the TolB-Pal complex at the outer membrane (OM), freeing the lipoprotein Pal to bind the cell wall. The primary physiological role of Tol-Pal is to maintain OM integrity during cell division through accumulation of Pal molecules at division septa. How the protein complex couples the PMF at the inner membrane into work at the OM is unknown. The effectiveness of this trans-envelope energy transduction system is underscored by the fact that bacteriocins and bacteriophages co-opt Tol-Pal as part of their import/infection mechanisms. Mechanistic understanding of this process has been hindered by a lack of structural data for the inner membrane TolQ-TolR stator, of its complexes with peptidoglycan (PG) and TolA, and of how these elements combined power events at the OM. Recent studies on the homologous stators of Ton and Mot provide a starting point for understanding how Tol-Pal works. Here, we combine ab initio protein modeling with previous structural data on sub-complexes of Tol-Pal as well as mutagenesis, crosslinking, co-conservation analysis and functional data. Through this composite pooling of in silico, in vitro, and in vivo data, we propose a mechanism for force generation in which PMF-driven rotary motion within the stator drives conformational transitions within a long TolA helical hairpin domain, enabling it to reach the TolB-Pal complex at the OM.
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Affiliation(s)
| | | | | | - Colin Kleanthous
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
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45
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Extracellular vesicles from phytobacteria: Properties, functions and uses. Biotechnol Adv 2022; 58:107934. [DOI: 10.1016/j.biotechadv.2022.107934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 02/25/2022] [Accepted: 02/26/2022] [Indexed: 11/20/2022]
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46
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de Jonge EF, van Boxtel R, Balhuizen MD, Haagsman HP, Tommassen J. Pal depletion results in hypervesiculation and affects cell morphology and outer-membrane lipid asymmetry in bordetellae. Res Microbiol 2022; 173:103937. [DOI: 10.1016/j.resmic.2022.103937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 02/18/2022] [Accepted: 02/21/2022] [Indexed: 10/18/2022]
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47
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Glycan-mediated molecular interactions in bacterial pathogenesis. Trends Microbiol 2022; 30:254-267. [PMID: 34274195 PMCID: PMC8758796 DOI: 10.1016/j.tim.2021.06.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 06/10/2021] [Accepted: 06/22/2021] [Indexed: 02/06/2023]
Abstract
Glycans are expressed on the surface of nearly all host and bacterial cells. Not surprisingly, glycan-mediated molecular interactions play a vital role in bacterial pathogenesis and host responses against pathogens. Glycan-mediated host-pathogen interactions can benefit the pathogen, host, or both. Here, we discuss (i) bacterial glycans that play a critical role in bacterial colonization and/or immune evasion, (ii) host glycans that are utilized by bacteria for pathogenesis, and (iii) bacterial and host glycans involved in immune responses against pathogens. We further discuss (iv) opportunities and challenges for transforming these research findings into more effective antibacterial strategies, and (v) technological advances in glycoscience that have helped to accelerate progress in research. These studies collectively offer valuable insights into new perspectives on antibacterial strategies that may effectively tackle the drug-resistant pathogens that are rapidly spreading globally.
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Was the Last Bacterial Common Ancestor a Monoderm after All? Genes (Basel) 2022; 13:genes13020376. [PMID: 35205421 PMCID: PMC8871954 DOI: 10.3390/genes13020376] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/09/2022] [Accepted: 02/15/2022] [Indexed: 12/20/2022] Open
Abstract
The very nature of the last bacterial common ancestor (LBCA), in particular the characteristics of its cell wall, is a critical issue to understand the evolution of life on earth. Although knowledge of the relationships between bacterial phyla has made progress with the advent of phylogenomics, many questions remain, including on the appearance or disappearance of the outer membrane of diderm bacteria (also called Gram-negative bacteria). The phylogenetic transition between monoderm (Gram-positive bacteria) and diderm bacteria, and the associated peptidoglycan expansion or reduction, requires clarification. Herein, using a phylogenomic tree of cultivated and characterized bacteria as an evolutionary framework and a literature review of their cell-wall characteristics, we used Bayesian ancestral state reconstruction to infer the cell-wall architecture of the LBCA. With the same phylogenomic tree, we further revisited the evolution of the division and cell-wall synthesis (dcw) gene cluster using homology- and model-based methods. Finally, extensive similarity searches were carried out to determine the phylogenetic distribution of the genes involved with the biosynthesis of the outer membrane in diderm bacteria. Quite unexpectedly, our analyses suggest that all cultivated and characterized bacteria might have evolved from a common ancestor with a monoderm cell-wall architecture. If true, this would indicate that the appearance of the outer membrane was not a unique event and that selective forces have led to the repeated adoption of such an architecture. Due to the lack of phenotypic information, our methodology cannot be applied to all extant bacteria. Consequently, our conclusion might change once enough information is made available to allow the use of an even more diverse organism selection.
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BACCELLI P, RACHEDI R, SERRANO B, PETITI M, BERNARD C, HOUOT L, DUCHE D. Timing of TolA and TolQ recruitment at the septum depends on the functionality of the Tol-Pal system. J Mol Biol 2022; 434:167519. [DOI: 10.1016/j.jmb.2022.167519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 02/11/2022] [Accepted: 02/24/2022] [Indexed: 10/19/2022]
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Weaver AI, Alvarez L, Rosch KM, Ahmed A, Wang GS, van Nieuwenhze MS, Cava F, Dörr T. Lytic transglycosylases mitigate periplasmic crowding by degrading soluble cell wall turnover products. eLife 2022; 11:e73178. [PMID: 35073258 PMCID: PMC8820737 DOI: 10.7554/elife.73178] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 01/23/2022] [Indexed: 11/25/2022] Open
Abstract
The peptidoglycan cell wall is a predominant structure of bacteria, determining cell shape and supporting survival in diverse conditions. Peptidoglycan is dynamic and requires regulated synthesis of new material, remodeling, and turnover - or autolysis - of old material. Despite exploitation of peptidoglycan synthesis as an antibiotic target, we lack a fundamental understanding of how peptidoglycan synthesis and autolysis intersect to maintain the cell wall. Here, we uncover a critical physiological role for a widely misunderstood class of autolytic enzymes, lytic transglycosylases (LTGs). We demonstrate that LTG activity is essential to survival by contributing to periplasmic processes upstream and independent of peptidoglycan recycling. Defects accumulate in Vibrio cholerae LTG mutants due to generally inadequate LTG activity, rather than absence of specific enzymes, and essential LTG activities are likely independent of protein-protein interactions, as heterologous expression of a non-native LTG rescues growth of a conditional LTG-null mutant. Lastly, we demonstrate that soluble, uncrosslinked, endopeptidase-dependent peptidoglycan chains, also detected in the wild-type, are enriched in LTG mutants, and that LTG mutants are hypersusceptible to the production of diverse periplasmic polymers. Collectively, our results suggest that LTGs prevent toxic crowding of the periplasm with synthesis-derived peptidoglycan polymers and, contrary to prevailing models, that this autolytic function can be temporally separate from peptidoglycan synthesis.
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Affiliation(s)
- Anna Isabell Weaver
- Weill Institute for Cell and Molecular Biology, Cornell UniversityIthacaUnited States
- Department of Microbiology, Cornell UniversityIthacaUnited States
| | - Laura Alvarez
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Department of Molecular Biology, Umeå UniversityUmeåSweden
| | - Kelly M Rosch
- Weill Institute for Cell and Molecular Biology, Cornell UniversityIthacaUnited States
| | - Asraa Ahmed
- Weill Institute for Cell and Molecular Biology, Cornell UniversityIthacaUnited States
- Cornell Institute of Host-Microbe Interactions and Disease, Cornell UniversityIthacaUnited States
| | - Garrett Sean Wang
- Weill Institute for Cell and Molecular Biology, Cornell UniversityIthacaUnited States
| | - Michael S van Nieuwenhze
- Department of Molecular and Cellular Biochemistry, Indiana UniversityBloomingtonSweden
- Department of Chemistry, Indiana UniversityBloomingtonUnited States
| | - Felipe Cava
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Department of Molecular Biology, Umeå UniversityUmeåSweden
| | - Tobias Dörr
- Weill Institute for Cell and Molecular Biology, Cornell UniversityIthacaUnited States
- Department of Microbiology, Cornell UniversityIthacaUnited States
- Cornell Institute of Host-Microbe Interactions and Disease, Cornell UniversityIthacaUnited States
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